Bacteroides thetaiotaomicron (DSM 2079, ATCC 29148, NCTC 10582)

Name: Bacteroides thetaiotaomicron (DSM 2079, ATCC 29148, NCTC 10582)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 1599

Type strain

Strain Designation E50 (VPI 5482), VPI-5482

Culture col. no. DSM 2079 ATCC 29148 NCTC 10582 CCUG 10774 CIP 104206 5 more

NCBI tax ID(s) 818

Special Collections DSMZ CCUG JCM CIP

History <- NCTC <- H. Werner, E50 (VPI 5482) ATCC 29148 <-- E. P. Cato VPI 5482 <-- H. Werner E 50.

Links

Bacteroides thetaiotaomicron E50 is an anaerobe bacterium that was isolated from human faeces.

anaerobe genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 39378

ATCC 29148,CIP 104206,NCTC 10582,CCUG 10774,DSM 2079,JCM 5827,VTT E-001738,LMG 28903

@ref 20215

Last LPSN update 2026-02-09 11:18:08

Domain Bacteria

Phylum Bacteroidota

Class Bacteroidia

Order Bacteroidales

Family Bacteroidaceae

Genus Bacteroides

Species Bacteroides thetaiotaomicron

Full scientific name Bacteroides thetaiotaomicron (Distaso 1912) Castellani and Chalmers 1919 (Approved Lists 1980)

Synonyms (2)

"Bacteroides fragilis subsp. thetaiotaomicron"
"Bacillus thetaiotaomicron"

BacDive ID	Other strains from **Bacteroides thetaiotaomicron** (11)	Type strain
1600	B. thetaiotaomicron DSM 2255, ATCC 29741, WAL 2926, CIP 104207, ...
147878	B. thetaiotaomicron CCUG 34419
149779	B. thetaiotaomicron CCUG 38386 A
149982	B. thetaiotaomicron CCUG 38792
151917	B. thetaiotaomicron CCUG 45196
157019	B. thetaiotaomicron CCUG 68684
157023	B. thetaiotaomicron CCUG 68702
157029	B. thetaiotaomicron CCUG 68746
158885	B. thetaiotaomicron H3_25, DSM 108160
158886	B. thetaiotaomicron H5_3, DSM 108161
169208	B. thetaiotaomicron HM-168, 1/1/14, DSM 24846

Morphology

Cell morphology

@ref	Gram stain	Confidence
125438	negative	95.095
125439	negative	93.1

Colony morphology

714

Incubation period1-2 days

Culture and growth conditions

Culture medium

@ref	Name	Medium link	Composition
714	COLUMBIA BLOOD MEDIUM (DSMZ Medium 693)	Medium recipe at MediaDive	Name: COLUMBIA BLOOD MEDIUM (DSMZ Medium 693) Composition: Defibrinated sheep blood 50.0 g/l Columbia agar base
714	CHOPPED MEAT MEDIUM (DSMZ Medium 78)	Medium recipe at MediaDive	Name: CHOPPED MEAT MEDIUM (DSMZ Medium 78) Composition: Ground beef 500.0 g/l Casitone 30.0 g/l Agar 15.0 g/l Ethanol 9.5 g/l (optional) K2HPO4 5.0 g/l Yeast extract 5.0 g/l L-Cysteine HCl 0.5 g/l Haemin 0.005 g/l (optional) Resazurin 0.001 g/l Vitamin K3 0.0005 g/l (optional) Vitamin K1 (optional) NaOH (optional) Distilled water
41048	MEDIUM 20 - for Anaerobic bacteria		Agar (15.000 g);Glucose (5.000 g);Yeast extract (20.000 g);Tryptone (30.000 g);Cysteine hydrochloride (0.500 g);distilled water (1000.000 ml);Hemin solution -M00149 (25.000 ml)
42081	MEDIUM 20 - for Anaerobic bacteria		Agar (15.000 g);Glucose (5.000 g);Yeast extract (20.000 g);Tryptone (30.000 g);Cysteine hydrochloride (0.500 g);distilled water (1000.000 ml);Hemin solution -M00149 (25.000 ml)
714	FASTIDIOUS ANAEROBE BROTH (DSMZ Medium 1203a)	Medium recipe at MediaDive	Name: FASTIDIOUS ANAEROBE BROTH (DSMZ Medium 1203a) Composition: Fastidious Anaerobe Basal Broth 35.4 g/l Distilled water

Culture temp

@ref	Growth	Type	Temperature (°C)
714	positive	growth	37
41048	positive	growth	37
42081	positive	growth	37
45331	positive	growth	37
67770	positive	growth	37

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance
714	anaerobe
45331	anaerobe

Spore formation

@ref	Spore formation	Confidence
125438		90.942
125439		93.5

Observation

67770

Observationquinones: MK-10, MK-11

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
68380	29016 ChEBI	arginine	-	hydrolysis	from API rID32A
68367	17057 ChEBI	cellobiose	+	builds acid from	from API 20A
68367	17634 ChEBI	D-glucose	+	builds acid from	from API 20A
68380	16024 ChEBI	D-mannose	+	fermentation	from API rID32A
68367	16024 ChEBI	D-mannose	+	builds acid from	from API 20A
68367	65327 ChEBI	D-xylose	+	builds acid from	from API 20A
68367	4853 ChEBI	esculin	+	hydrolysis	from API 20A
68367	30849 ChEBI	L-arabinose	+	builds acid from	from API 20A
68380	29985 ChEBI	L-glutamate	+	degradation	from API rID32A
68367	62345 ChEBI	L-rhamnose	+	builds acid from	from API 20A
68367	17716 ChEBI	lactose	+	builds acid from	from API 20A
68367	17306 ChEBI	maltose	+	builds acid from	from API 20A
68367	6731 ChEBI	melezitose	+	builds acid from	from API 20A
68380	17632 ChEBI	nitrate	-	reduction	from API rID32A
68380	16634 ChEBI	raffinose	+	fermentation	from API rID32A
68367	16634 ChEBI	raffinose	+	builds acid from	from API 20A
68367	17992 ChEBI	sucrose	+	builds acid from	from API 20A
68367	27082 ChEBI	trehalose	+	builds acid from	from API 20A
68380	27897 ChEBI	tryptophan	+	energy source	from API rID32A
68367	27897 ChEBI	tryptophan	+	energy source	from API 20A
68380	16199 ChEBI	urea	-	hydrolysis	from API rID32A
68367	16199 ChEBI	urea	-	hydrolysis	from API 20A

Metabolite production

@ref	Chebi-ID	Metabolite	Production
68380	35581 ChEBI	indole		from API rID32A
68367	35581 ChEBI	indole		from API 20A

Metabolite tests

@ref	Chebi-ID	Metabolite	Indole test
68380	35581 ChEBI	indole	+	from API rID32A
68367	35581 ChEBI	indole	+	from API 20A

Enzymes

@ref	Value	Activity	Ec
68380	alanine arylamidase	+	3.4.11.2	from API rID32A
68380	alkaline phosphatase	+	3.1.3.1	from API rID32A
68380	alpha-arabinosidase	+	3.2.1.55	from API rID32A
68380	alpha-fucosidase	+	3.2.1.51	from API rID32A
68380	alpha-galactosidase	+	3.2.1.22	from API rID32A
68380	alpha-glucosidase	+	3.2.1.20	from API rID32A
68380	arginine dihydrolase	-	3.5.3.6	from API rID32A
68380	beta-galactosidase	+	3.2.1.23	from API rID32A
68380	beta-Galactosidase 6-phosphate	-		from API rID32A
68380	beta-glucosidase	+	3.2.1.21	from API rID32A
68367	beta-glucosidase	+	3.2.1.21	from API 20A
68380	beta-glucuronidase	-	3.2.1.31	from API rID32A
68380	glutamate decarboxylase	+	4.1.1.15	from API rID32A
68380	glycin arylamidase	-		from API rID32A
68380	L-arginine arylamidase	+		from API rID32A
68380	leucine arylamidase	+	3.4.11.1	from API rID32A
68380	leucyl glycin arylamidase	+	3.4.11.1	from API rID32A
68380	N-acetyl-beta-glucosaminidase	+	3.2.1.52	from API rID32A
68380	proline-arylamidase	-	3.4.11.5	from API rID32A
68380	pyrrolidonyl arylamidase	-	3.4.19.3	from API rID32A
68380	serine arylamidase	-		from API rID32A
68380	tryptophan deaminase	+	4.1.99.1	from API rID32A
68380	urease	-	3.5.1.5	from API rID32A
68367	urease	-	3.5.1.5	from API 20A

API 20A

@ref	IND	URE	GLU	MAN	LAC	SAC	MAL	SAL	XYL	ARA	GEL	ESC	GLY	CEL	MNE	MLZ	RAF	SOR	RHA	TRE	CAT	Spores presentSPOR	GramGRAM	Morphology coccus="+" rod="-"COCC
714	+	-	+	-	+	+	+	-	+	+	-	+	-	+	+	+	+	-	+	+	not determinedn.d.	not determinedn.d.	not determinedn.d.	not determinedn.d.
714	+	-	+	+	+	+	+	+	+	+	-	+	+/-	+	+	+	+	+/-	+	+	not determinedn.d.	not determinedn.d.	not determinedn.d.	not determinedn.d.
714	+	-	+	-	+	+	+	-	+	+	-	+	-	+	+	+	+	-	+	+	not determinedn.d.	not determinedn.d.	not determinedn.d.	not determinedn.d.
714	+	-	+	-	+	+	+	-	+	+	+	+	-	+	+	+	+	-	+	+	not determinedn.d.	not determinedn.d.	not determinedn.d.	not determinedn.d.

API rID32A

@ref	URE	ADH (Arg)	alpha GAL	beta GAL	beta-Galactosidase 6-phosphatebeta GP	alpha GLU	beta GLU	alpha ARA	beta GUR	beta-N-Acetyl-beta-glucosaminidasebeta NAG	MNE	RAF	GDC	alpha FUC	Reduction of nitrateNIT	IND	PAL	L-arginine arylamidaseArgA	ProA	LGA	Phenylalanine arylamidasePheA	Leucine arylamidaseLeuA	PyrA	Tyrosine arylamidaseTyrA	Alanine arylamidaseAlaA	Glycin arylamidaseGlyA	Histidine arylamidaseHisA	Glutamyl-glutamate arylamidaseGGA	Serine arylamidaseSerA
714	-	-	+	+	-	+	+	+	-	+	+	+	+	+	-	+	+	+	-	+	+/-	+	-	+/-	+	-	+	+/-	-
714	-	-	+	+	-	+	+	+	-	+	+	+	+	+	-	+	+	+	-	+	+/-	+	-	-	+	-	+/-	+/-	-
714	-	-	+	+	-	+	+	+	-	+	+	+	+	+	-	+	+	+	-	+	+/-	+	-	-	+	-	+/-	+/-	-
714	-	-	+	+	-	+	+	+	-	+	+	+	+	+	-	+	+	+	-	+	+/-	+	-	-	+	-	+/-	-	-
714	-	-	+	+	-	+	+	+	-	+	+	+	+	+	-	+	+	+	-	+	+/-	+	-	-	+	-	+/-	+/-	-
714	-	-	+	+	-	+	+	+	-	+	+	+	+	+	-	+	+	+	-	+	-	+	-	-	+	-	+	+	-
714	-	-	+	+	-	+	+	+	-	+	+	+	+	+	-	+	+	+	-	+	-	+	-	-	+	-	-	-	-
714	-	-	+	+	-	+	+	+	-	+	+	+	+	+	-	+	+	+	-	+	-	+	-	-	+	-	-	-	-
714	-	-	+	+	-	+	+	+	-	+	+	+	+	+	-	+	+	+	-	+	-	+	-	-	+	-	-	-	-
714	-	-	+	+	-	+	+	+	-	+	+	+	+	+	-	+	+	+	-	+	-	+	-	-	+	-	-	+	-

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Host	#Human	-
#Host Body Product	#Gastrointestinal tract	#Feces (Stool)

Isolation

@ref	Sample type
714	human faeces
45331	Human feces
67770	Human feces

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
714	2	Risk group (German classification) According to TRBA 466

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
66792	ASM1413175v1 assembly for Bacteroides thetaiotaomicron DSM 2079	complete	GCA_014131755	818.1357	8109328688	818	98.6
66792	ASM2245366v1 assembly for Bacteroides thetaiotaomicron VPI 5482	complete	GCA_022453665	818.1979	8115853185	818	98.52
66792	ASM1106v1 assembly for Bacteroides thetaiotaomicron VPI-5482	complete	GCA_000011065	226186.12	637000026	226186	98.26
66792	ASM295969v1 assembly for Bacteroides thetaiotaomicron VPI-5482	contig	GCA_002959695	818.184	8024209697	818	74.34
124043	ASM1610319v1 assembly for Bacteroides thetaiotaomicron FDAARGOS_912	scaffold	GCA_016103195	818.1393		818	74.29
66792	51334_D01 assembly for Bacteroides thetaiotaomicron NCTC10582	contig	GCA_900445595	818.190	2984892730	818	70.58
66792	ASM2017949v1 assembly for Bacteroides thetaiotaomicron VPI-5482	contig	GCA_020179495	818.1665	8119490510	818	59.39
66792	ASM2853942v1 assembly for Bacteroides thetaiotaomicron DSM 2079	contig	GCA_028539425	818.2441	8119495620	818	58.81
66792	SRR1027507 assembly for Bacteroides thetaiotaomicron VPI-5482	contig	GCA_900227605	226186.70		226186

16S sequences

@ref	Description	Accession	Length	NCBI tax ID
20218	Bacteroides thetaiotaomicron 16S-23S ribosomal RNA intergenic spacer region, partial sequence	AF172710	523	818
20218	Bacteroides thetaiotaomicron strain DSM 2079 16S ribosomal RNA gene, partial sequence	HQ012026	931	818
20218	Bacteroides thetaiotaomicron (ATCC 29148) 16S ribosomal RNA	L16489	1475	818
67770	Bacteroides thetaiotaomicron gene for 16S ribosomal RNA, partial sequence, strain: JCM 5827	AB510710	1461	818
67770	Bacteroides thetaiotaomicron 16S ribosomal RNA gene, partial sequence	M58763	1482	818

GC content

@ref	GC-content (mol%)	Method
714	42.0	thermal denaturation, midpoint method (Tm)
714	42.9	sequence analysis
67770	42	thermal denaturation, midpoint method (Tm)

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Bacteroides thetaiotaomicron DSM 2079
NCBI: GCA_014131755

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	93.50	no
125439	motility	BacteriaNetⓘ	no	63.50	no
125439	gram_stain	BacteriaNetⓘ	negative	93.10	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate anaerobe	83.10	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Bacteroides thetaiotaomicron DSM 2079
NCBI: GCA_014131755.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	95.10	no
125438	anaerobic	anaerobicⓘ	yes	73.74	yes
125438	aerobic	aerobicⓘ	no	86.16	no
125438	spore-forming	spore-formingⓘ	no	90.94	no
125438	thermophilic	thermophileⓘ	no	96.47	yes
125438	flagellated	motile2+ⓘ	no	88.00	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Genetics	Growth stage and interspecies interactions shape the cell biology and cell cycle characteristics of human gut bacteria Bacteroides thetaiotaomicron and Roseburia intestinalis.	Liu B, Sondervorst K, Nesporova K, Faust K, Govers SK.	Commun Biol	10.1038/s42003-025-08949-1	2025
	Distinct in vitro utilization and degradation of porcine gastric mucin glycans by human intestinal bacteria.	de Ram C, Berkhout MD, O Pandeirada C, Vincken JP, Hooiveld GJEJ, Belzer C, Schols HA.	FEMS Microbiol Ecol	10.1093/femsec/fiaf066	2025
	Vitamin B12 analogues from gut microbes and diet differentially impact commensal propionate producers of the human gut.	Kundra P, Greppi A, Duppenthaler M, Pluss S, Pugin B, Lacroix C, Geirnaert A.	Front Nutr	10.3389/fnut.2024.1360199	2024
Phylogeny	Exploring the resilience and stability of a defined human gut microbiota consortium: An isothermal microcalorimetric study.	Kattel A, Aro V, Lahtvee PJ, Kazantseva J, Joers A, Nahku R, Belouah I.	Microbiologyopen	10.1002/mbo3.1430	2024
	Membrane vesicles produced by next-generation probiotics from the gut as innovative tools for human health.	Abraham L, Raise A, Beney L, Lapaquette P, Rieu A.	Gut Microbes	10.1080/19490976.2025.2552344	2025
	Microbially-produced folate forms support the growth of Roseburia intestinalis but not its competitive fitness in fecal batch fermentations.	Kundra P, Geirnaert A, Pugin B, Pluss S, Kariluoto S, Lacroix C, Greppi A.	BMC Microbiol	10.1186/s12866-024-03528-6	2024
	Environmental factors drive bacterial degradation of gastrointestinal mucus.	Arias SL, van Wijngaarden EW, Balint D, Jones J, Crawford CC, Shukla PJ, Silberstein M, Brito IL.	NPJ Biofilms Microbiomes	10.1038/s41522-025-00741-7	2025
	Phylogenetic diversity of core rumen microbiota as described by cryo-ET.	Wimmer BH, Morais S, Zalk R, Mizrahi I, Medalia O.	Microlife	10.1093/femsml/uqad010	2023
	Bacteroides thetaiotaomicron enhances H₂S production in Bilophila wadsworthia.	Davies J, Mayer MJ, Juge N, Narbad A, Sayavedra L.	Gut Microbes	10.1080/19490976.2024.2431644	2024
	The Quantitative Measurement of Peptidoglycan Components Obtained from Acidic Hydrolysis in Gram-Positive and Gram-Negative Bacteria via Hydrophilic Interaction Liquid Chromatography Coupled with Mass Spectrometry.	Pismennoi D, Kattel A, Belouah I, Nahku R, Vilu R, Kobrin EG.	Microorganisms	10.3390/microorganisms11092134	2023
	Identification and characterization of two AA9 lytic polysaccharide monooxygenases isolated from the enzymatic arsenal in Phanerochaete chrysosporium.	Xu X, Chu CE, Li N, Sun XB, Han J, Xu Z, Liu Y, Wang JK, Zhang TT, Wang Q.	Bioresour Bioprocess	10.1186/s40643-025-00950-0	2025
	Modulation of Designed Gut Bacterial Communities by Prebiotics and the Impact of Their Metabolites on Intestinal Cells.	Roupar D, Gonzalez A, Martins JT, Goncalves DA, Teixeira JA, Botelho C, Nobre C.	Foods	10.3390/foods12234216	2023
	Technical versus biological variability in a synthetic human gut community.	van de Velde C, Joseph C, Simoens K, Raes J, Bernaerts K, Faust K.	Gut Microbes	10.1080/19490976.2022.2155019	2023
	A Gnotobiotic Mouse Model with Divergent Equol-Producing Phenotypes: Potential for Determining Microbial-Driven Health Impacts of Soy Isoflavone Daidzein.	Leonard LM, Simpson AMR, Li S, Reddivari L, Cross TL.	Nutrients	10.3390/nu16071079	2024
	Adaptation and Resistance: How Bacteroides thetaiotaomicron Copes with the Bisphenol A Substitute Bisphenol F.	Riesbeck S, Petruschke H, Rolle-Kampczyk U, Schori C, Ahrens CH, Eberlein C, Heipieper HJ, von Bergen M, Jehmlich N.	Microorganisms	10.3390/microorganisms10081610	2022
Genetics	The estrobolome: Estrogen-metabolizing pathways of the gut microbiome and their relation to breast cancer.	Larnder AH, Manges AR, Murphy RA.	Int J Cancer	10.1002/ijc.35427	2025
	Exploring the Probiotic Potential of Bacteroides spp. Within One Health Paradigm.	Tufail MA, Schmitz RA.	Probiotics Antimicrob Proteins	10.1007/s12602-024-10370-9	2025
	Deciphering oxidative stress responses in human gut microbes and fecal microbiota: a cultivation-based approach.	Zund JN, Caflisch M, Mujezinovic D, Pluss S, Lacroix C, Pugin B.	FEMS Microbiol Ecol	10.1093/femsec/fiaf054	2025
	Recovery of Bacteroides thetaiotaomicron ameliorates hepatic steatosis in experimental alcohol-related liver disease.	Sangineto M, Grander C, Grabherr F, Mayr L, Enrich B, Schwarzler J, Dallio M, Bukke VN, Moola A, Moschetta A, Adolph TE, Sabba C, Serviddio G, Tilg H.	Gut Microbes	10.1080/19490976.2022.2089006	2022
Enzymology	Transcriptional delineation of polysaccharide utilization loci in the human gut commensal Segatella copri DSM18205 and co-culture with exemplar Bacteroides species on dietary plant glycans.	Panwar D, Briggs J, Fraser ASC, Stewart WA, Brumer H.	Appl Environ Microbiol	10.1128/aem.01759-24	2025
	The use of a multicellular in vitro model to investigate uptake and migration of bacterial extracellular vesicles derived from the human gut commensal Bacteroides thetaiotaomicron	Modasia A, Jones E, Martel L, Louvel H, Couraud P, Blackshaw L, Carding S.	J Extracell Biol		2023
	Comparative Proteomic Analysis of Fucosylated Glycoproteins Produced by Bacteroides thetaiotaomicron Under Different Polysaccharide Nutrition Conditions.	Tian X, Jiang H, Cai B, Feng H, Wang X, Yu G.	Front Microbiol	10.3389/fmicb.2022.826942	2022
	Characterization of Lactiplantibacillus paraplantarum HK-1 and GABA Synthesis Under Simulated Gastrointestinal Conditions.	Castro-Seriche S, Alvarez-Norambuena J, Linconir-Campos P, Gutierrez-Zamorano C, Ruiz-Garrido A, Jerez-Angulo B, Garcia-Cancino A, Jerez-Morales A.	Foods	10.3390/foods14193345	2025
	Diet-driven differential response of Akkermansia muciniphila modulates pathogen susceptibility.	Wolter M, Grant ET, Boudaud M, Pudlo NA, Pereira GV, Eaton KA, Martens EC, Desai MS.	Mol Syst Biol	10.1038/s44320-024-00036-7	2024
	Simvastatin induces human gut bacterial cell surface genes.	Escalante V, Nayak RR, Noecker C, Babdor J, Spitzer M, Deutschbauer AM, Turnbaugh PJ.	Mol Microbiol	10.1111/mmi.15151	2024
Genetics	Cultivated genome references for protein database construction and high-resolution taxonomic annotation in metaproteomics.	Gao X, Liang H, Hu T, Zou Y, Xiao L.	Microbiol Spectr	10.1128/spectrum.01755-24	2025
	Evaluation of cholesterol transformation abilities and probiotic properties of Bacteroides dorei YGMCC0564.	He Z, Wang T, Zhang S, Shi K, Wang F, Li Y, Lin C, Chen J.	Front Microbiol	10.3389/fmicb.2023.1279996	2023
	Intestinal alpha-Defensins Play a Minor Role in Modulating the Small Intestinal Microbiota Composition as Compared to Diet.	Puertolas-Balint F, Schroeder BO.	Microbiol Spectr	10.1128/spectrum.00567-23	2023
	Dietary fibre directs microbial tryptophan metabolism via metabolic interactions in the gut microbiota.	Sinha AK, Laursen MF, Brinck JE, Rybtke ML, Hjorne AP, Prochazkova N, Pedersen M, Roager HM, Licht TR.	Nat Microbiol	10.1038/s41564-024-01737-3	2024
Enzymology	Products Released from Structurally Different Dextrans by Bacterial and Fungal Dextranases.	Pittrof SL, Kaufhold L, Fischer A, Wefers D.	Foods	10.3390/foods10020244	2021
	Fast quantification of gut bacterial species in cocultures using flow cytometry and supervised classification.	van de Velde CC, Joseph C, Biclot A, Huys GRB, Pinheiro VB, Bernaerts K, Raes J, Faust K.	ISME Commun	10.1038/s43705-022-00123-6	2022
Genetics	Targeted isolation of Methanobrevibacter strains from fecal samples expands the cultivated human archaeome.	Duller S, Vrbancic S, Szydlowski L, Mahnert A, Blohs M, Predl M, Kumpitsch C, Zrim V, Hogenauer C, Kosciolek T, Schmitz RA, Eberhard A, Dragovan M, Schmidberger L, Zurabischvili T, Weinberger V, Moser AM, Kolb D, Pernitsch D, Mohammadzadeh R, Kuhnast T, Rattei T, Moissl-Eichinger C.	Nat Commun	10.1038/s41467-024-52037-7	2024
	Mid-Infrared Photothermal-Fluorescence In Situ Hybridization for Functional Analysis and Genetic Identification of Single Cells.	Bai Y, Guo Z, Pereira FC, Wagner M, Cheng JX.	Anal Chem	10.1021/acs.analchem.2c04474	2023
	Diversification of the Rho transcription termination factor in bacteria.	Moreira SM, Chyou TY, Wade JT, Brown CM.	Nucleic Acids Res	10.1093/nar/gkae582	2024
	Bacteroides thetaiotaomicron Ameliorates Colon Inflammation in Preclinical Models of Crohn's Disease.	Delday M, Mulder I, Logan ET, Grant G.	Inflamm Bowel Dis	10.1093/ibd/izy281	2019
	Bacteroides thetaiotaomicron Fosters the Growth of Butyrate-Producing Anaerostipes caccae in the Presence of Lactose and Total Human Milk Carbohydrates.	Chia LW, Mank M, Blijenberg B, Aalvink S, Bongers RS, Stahl B, Knol J, Belzer C.	Microorganisms	10.3390/microorganisms8101513	2020
Genetics	Systematically investigating and identifying bacteriocins in the human gut microbiome.	Zhang D, Zou Y, Shi Y, Zhang J, Liu J, Wu G, Zhang J, Gao Y, Chen M, Li YX.	Cell Genom	10.1016/j.xgen.2025.100983	2025
Enzymology	H₂ generated by fermentation in the human gut microbiome influences metabolism and competitive fitness of gut butyrate producers.	Campbell A, Gdanetz K, Schmidt AW, Schmidt TM.	Microbiome	10.1186/s40168-023-01565-3	2023
	How microbial glycosyl hydrolase activity in the gut mucosa initiates microbial cross-feeding.	Berkhout MD, Plugge CM, Belzer C.	Glycobiology	10.1093/glycob/cwab105	2022
	Screening for effective cell-penetrating peptides with minimal impact on epithelial cells and gut commensals in vitro.	Gelli HP, Vazquez-Uribe R, Sommer MOA.	Front Pharmacol	10.3389/fphar.2022.1049324	2022
	Impact of changes at the Candida albicans cell surface upon immunogenicity and colonisation in the gastrointestinal tract.	Avelar GM, Dambuza IM, Ricci L, Yuecel R, Mackenzie K, Childers DS, Bain JM, Pradhan A, Larcombe DE, Netea MG, Erwig LP, Brown GD, Duncan SH, Gow NAR, Walker AW, Brown AJP.	Cell Surf	10.1016/j.tcsw.2022.100084	2022
	Independent and Combined Effects of Lactitol, Polydextrose, and Bacteroides thetaiotaomicron on Postprandial Metabolism and Body Weight in Rats Fed a High-Fat Diet.	Olli K, Saarinen MT, Forssten SD, Madetoja M, Herzig KH, Tiihonen K.	Front Nutr	10.3389/fnut.2016.00015	2016
	Bacteroides vulgatus attenuates experimental mice colitis through modulating gut microbiota and immune responses.	Liu L, Xu M, Lan R, Hu D, Li X, Qiao L, Zhang S, Lin X, Yang J, Ren Z, Xu J.	Front Immunol	10.3389/fimmu.2022.1036196	2022
	Cross-feeding interactions between human gut commensals belonging to the Bacteroides and Bifidobacterium genera when grown on dietary glycans.	Fernandez-Julia P, Commane DM, van Sinderen D, Munoz-Munoz J.	Microbiome Res Rep	10.20517/mrr.2021.05	2022
	Opposing diet, microbiome, and metabolite mechanisms regulate inflammatory bowel disease in a genetically susceptible host.	Pereira GV, Boudaud M, Wolter M, Alexander C, De Sciscio A, Grant ET, Trindade BC, Pudlo NA, Singh S, Campbell A, Shan M, Zhang L, Yang Q, Willieme S, Kim K, Denike-Duval T, Fuentes J, Bleich A, Schmidt TM, Kennedy L, Lyssiotis CA, Chen GY, Eaton KA, Desai MS, Martens EC.	Cell Host Microbe	10.1016/j.chom.2024.03.001	2024
	Bacterial microcompartments and energy metabolism drive gut colonization by Bilophila wadsworthia	Sayavedra L, Yasir M, Goldson A, Brion A, Le Gall G, Moreno-Gonzalez M, Altera A, Paxhia M, Warren M, Savva G, Turner A, Beraza N, Narbad A.	Nat Commun		2025
	The Parkinson's disease drug entacapone disrupts gut microbiome homoeostasis via iron sequestration.	Pereira FC, Ge X, Kristensen JM, Kirkegaard RH, Maritsch K, Szamosvari D, Imminger S, Seki D, Shazzad JB, Zhu Y, Decorte M, Hausmann B, Berry D, Wasmund K, Schintlmeister A, Bottcher T, Cheng JX, Wagner M.	Nat Microbiol	10.1038/s41564-024-01853-0	2024
Pathogenicity	Constructing a gnotobiotic mouse model with a synthetic human gut microbiome to study host-microbe cross talk.	Steimle A, De Sciscio A, Neumann M, Grant ET, Pereira GV, Ohno H, Martens EC, Desai MS.	STAR Protoc	10.1016/j.xpro.2021.100607	2021
	Molecular strategies for the utilisation of human milk oligosaccharides by infant gut-associated bacteria.	Kiely LJ, Busca K, Lane JA, van Sinderen D, Hickey RM.	FEMS Microbiol Rev	10.1093/femsre/fuad056	2023
	FiberGrowth Pipeline: A Framework Toward Predicting Fiber-Specific Growth From Human Gut Bacteroidetes Genomes.	Colnet B, Sieber CMK, Perraudeau F, Leclerc M.	Front Microbiol	10.3389/fmicb.2021.632567	2021
Metabolism	A Highly Active Endo-Levanase BT1760 of a Dominant Mammalian Gut Commensal Bacteroides thetaiotaomicron Cleaves Not Only Various Bacterial Levans, but Also Levan of Timothy Grass.	Mardo K, Visnapuu T, Vija H, Aasamets A, Viigand K, Alamae T.	PLoS One	10.1371/journal.pone.0169989	2017
Metabolism	Prebiotic galactooligosaccharides activate mucin and pectic galactan utilization pathways in the human gut symbiont Bacteroides thetaiotaomicron.	Lammerts van Bueren A, Mulder M, Leeuwen SV, Dijkhuizen L.	Sci Rep	10.1038/srep40478	2017
	Propionate-Producing Consortium Restores Antibiotic-Induced Dysbiosis in a Dynamic in vitro Model of the Human Intestinal Microbial Ecosystem.	El Hage R, Hernandez-Sanabria E, Calatayud Arroyo M, Props R, Van de Wiele T.	Front Microbiol	10.3389/fmicb.2019.01206	2019
Proteome	Three alginate lyases provide a new gut Bacteroides ovatus isolate with the ability to grow on alginate.	Ronne ME, Tandrup T, Madsen M, Hunt CJ, Myers PN, Moll JM, Holck J, Brix S, Strube ML, Aachmann FL, Wilkens C, Svensson B.	Appl Environ Microbiol	10.1128/aem.01185-23	2023
Metabolism	Prevalent Human Gut Bacteria Hydrolyse and Metabolise Important Food-Derived Mycotoxins and Masked Mycotoxins.	Daud N, Currie V, Duncan G, Farquharson F, Yoshinari T, Louis P, Gratz S.	Toxins (Basel)	10.3390/toxins12100654	2020
	Assessment of Gram- and Viability-Staining Methods for Quantifying Bacterial Community Dynamics Using Flow Cytometry.	Duquenoy A, Bellais S, Gasc C, Schwintner C, Dore J, Thomas V.	Front Microbiol	10.3389/fmicb.2020.01469	2020
Metabolism	Interactions between Bifidobacterium and Bacteroides species in cofermentations are affected by carbon sources, including exopolysaccharides produced by bifidobacteria.	Rios-Covian D, Arboleya S, Hernandez-Barranco AM, Alvarez-Buylla JR, Ruas-Madiedo P, Gueimonde M, de los Reyes-Gavilan CG.	Appl Environ Microbiol	10.1128/aem.02545-13	2013
	Fermented foods affect the seasonal stability of gut bacteria in an Indian rural population.	Jeyaram K, Lahti L, Tims S, Heilig HGHJ, van Gelder AH, de Vos WM, Smidt H, Zoetendal EG.	Nat Commun	10.1038/s41467-025-56014-6	2025
	Evaluation of the Effects of Different Bacteroides vulgatus Strains against DSS-Induced Colitis.	Li S, Wang C, Zhang C, Luo Y, Cheng Q, Yu L, Sun Z.	J Immunol Res	10.1155/2021/9117805	2021
	Effect of cryopreservation and lyophilization on viability and growth of strict anaerobic human gut microbes.	Bircher L, Geirnaert A, Hammes F, Lacroix C, Schwab C.	Microb Biotechnol	10.1111/1751-7915.13265	2018
Metabolism	Sulfonolipids as novel metabolite markers of Alistipes and Odoribacter affected by high-fat diets.	Walker A, Pfitzner B, Harir M, Schaubeck M, Calasan J, Heinzmann SS, Turaev D, Rattei T, Endesfelder D, Castell WZ, Haller D, Schmid M, Hartmann A, Schmitt-Kopplin P.	Sci Rep	10.1038/s41598-017-10369-z	2017
Pathogenicity	Akkermansia muciniphila strain ATCC BAA-835 does not promote short-term intestinal inflammation in gnotobiotic interleukin-10-deficient mice.	Ring C, Klopfleisch R, Dahlke K, Basic M, Bleich A, Blaut M.	Gut Microbes	10.1080/19490976.2018.1511663	2019
Phylogeny	The Membrane Attack Complex/Perforin Superfamily.	Moreno-Hagelsieb G, Vitug B, Medrano-Soto A, Saier MH.	J Mol Microbiol Biotechnol	10.1159/000481286	2017
	A multi-strategy antimicrobial discovery approach reveals new ways to treat Chlamydia.	Olander M, Rea Vazquez D, Meier K, Singh A, Silva de Sousa A, Puertolas-Balint F, Milivojevic M, Mooij L, Fredlund J, Calpe Bosch E, Rayon Diaz M, Lundgren M, van der Wal K, Zhu S, Mateus A, Schroeder BO, Lohman JR, Sixt BS.	PLoS Biol	10.1371/journal.pbio.3003123	2025
	Human Tumor-Infiltrating MAIT Cells Display Hallmarks of Bacterial Antigen Recognition in Colorectal Cancer.	Li S, Simoni Y, Becht E, Loh CY, Li N, Lachance D, Koo SL, Lim TP, Tan EKW, Mathew R, Nguyen A, Golovato J, Berkson JD, Prlic M, Lee B, Minot SS, Nagarajan N, Dey N, Tan DSW, Tan IB, Newell EW.	Cell Rep Med	10.1016/j.xcrm.2020.100039	2020
	Microbiota-derived 3-IAA influences chemotherapy efficacy in pancreatic cancer.	Tintelnot J, Xu Y, Lesker TR, Schonlein M, Konczalla L, Giannou AD, Pelczar P, Kylies D, Puelles VG, Bielecka AA, Peschka M, Cortesi F, Riecken K, Jung M, Amend L, Broring TS, Trajkovic-Arsic M, Siveke JT, Renne T, Zhang D, Boeck S, Strowig T, Uzunoglu FG, Gungor C, Stein A, Izbicki JR, Bokemeyer C, Sinn M, Kimmelman AC, Huber S, Gagliani N.	Nature	10.1038/s41586-023-05728-y	2023
	Limited Neonatal Carbohydrate-Specific Antibody Repertoire Consecutive to Partial Prenatal Transfer of Maternal Antibodies.	Kappler K, Restin T, Lasanajak Y, Smith DF, Bassler D, Hennet T.	Front Immunol	10.3389/fimmu.2020.573629	2020
	Critical Assessment of MetaProteome Investigation (CAMPI): a multi-laboratory comparison of established workflows.	Van Den Bossche T, Kunath BJ, Schallert K, Schape SS, Abraham PE, Armengaud J, Arntzen MO, Bassignani A, Benndorf D, Fuchs S, Giannone RJ, Griffin TJ, Hagen LH, Halder R, Henry C, Hettich RL, Heyer R, Jagtap P, Jehmlich N, Jensen M, Juste C, Kleiner M, Langella O, Lehmann T, Leith E, May P, Mesuere B, Miotello G, Peters SL, Pible O, Queiros PT, Reichl U, Renard BY, Schiebenhoefer H, Sczyrba A, Tanca A, Trappe K, Trezzi JP, Uzzau S, Verschaffelt P, von Bergen M, Wilmes P, Wolf M, Martens L, Muth T.	Nat Commun	10.1038/s41467-021-27542-8	2021
Metabolism	Methotrexate impacts conserved pathways in diverse human gut bacteria leading to decreased host immune activation.	Nayak RR, Alexander M, Deshpande I, Stapleton-Gray K, Rimal B, Patterson AD, Ubeda C, Scher JU, Turnbaugh PJ.	Cell Host Microbe	10.1016/j.chom.2020.12.008	2021
	Design, Biological Evaluation, and Computer-Aided Analysis of Dihydrothiazepines as Selective Antichlamydial Agents.	de Campos LJ, Seleem MA, Feng J, Pires de Oliveira KM, de Andrade Dos Santos JV, Hayer S, Clayton JB, Kathi S, Fisher DJ, Ouellette SP, Conda-Sheridan M.	J Med Chem	10.1021/acs.jmedchem.2c01894	2023
Metabolism	SIMMER employs similarity algorithms to accurately identify human gut microbiome species and enzymes capable of known chemical transformations.	Bustion AE, Nayak RR, Agrawal A, Turnbaugh PJ, Pollard KS.	Elife	10.7554/elife.82401	2023
Pathogenicity	The Use of Defined Microbial Communities To Model Host-Microbe Interactions in the Human Gut.	Elzinga J, van der Oost J, de Vos WM, Smidt H.	Microbiol Mol Biol Rev	10.1128/mmbr.00054-18	2019
Metabolism	Clostridium ramosum regulates enterochromaffin cell development and serotonin release.	Mandic AD, Woting A, Jaenicke T, Sander A, Sabrowski W, Rolle-Kampcyk U, von Bergen M, Blaut M.	Sci Rep	10.1038/s41598-018-38018-z	2019
	Increased Antibody Response to Fucosylated Oligosaccharides and Fucose-Carrying Bacteroides Species in Crohn's Disease.	Kappler K, Lasanajak Y, Smith DF, Opitz L, Hennet T.	Front Microbiol	10.3389/fmicb.2020.01553	2020
Phylogeny	Pipeline for amplifying and analyzing amplicons of the V1-V3 region of the 16S rRNA gene.	Allen HK, Bayles DO, Looft T, Trachsel J, Bass BE, Alt DP, Bearson SM, Nicholson T, Casey TA.	BMC Res Notes	10.1186/s13104-016-2172-6	2016
Pathogenicity	Inflammatory arthritis disrupts gut resolution mechanisms, promoting barrier breakdown by Porphyromonas gingivalis.	Flak MB, Colas RA, Munoz-Atienza E, Curtis MA, Dalli J, Pitzalis C.	JCI Insight	10.1172/jci.insight.125191	2019
	The role of secretory immunoglobulin A in the natural sensing of commensal bacteria by mouse Peyer's patch dendritic cells.	Rol N, Favre L, Benyacoub J, Corthesy B.	J Biol Chem	10.1074/jbc.m112.405001	2012
	Developing standards for the microbiome field.	Amos GCA, Logan A, Anwar S, Fritzsche M, Mate R, Bleazard T, Rijpkema S.	Microbiome	10.1186/s40168-020-00856-3	2020
Enzymology	Development of a semiquantitative degenerate real-time pcr-based assay for estimation of numbers of butyryl-coenzyme A (CoA) CoA transferase genes in complex bacterial samples.	Louis P, Flint HJ.	Appl Environ Microbiol	10.1128/aem.02561-06	2007
Metabolism	The Activation of Mucosal-Associated Invariant T (MAIT) Cells Is Affected by Microbial Diversity and Riboflavin Utilization in vitro.	Krause JL, Schape SS, Schattenberg F, Muller S, Ackermann G, Rolle-Kampczyk UE, Jehmlich N, Pierzchalski A, von Bergen M, Herberth G.	Front Microbiol	10.3389/fmicb.2020.00755	2020
Pathogenicity	Inhibitory activity spectrum of reuterin produced by Lactobacillus reuteri against intestinal bacteria.	Cleusix V, Lacroix C, Vollenweider S, Duboux M, Le Blay G.	BMC Microbiol	10.1186/1471-2180-7-101	2007
	Association of germ-free mice with a simplified human intestinal microbiota results in a shortened intestine.	Slezak K, Krupova Z, Rabot S, Loh G, Levenez F, Descamps A, Lepage P, Dore J, Bellier S, Blaut M.	Gut Microbes	10.4161/gmic.28203	2014
Genetics	Discovery of novel community-relevant small proteins in a simplified human intestinal microbiome.	Petruschke H, Schori C, Canzler S, Riesbeck S, Poehlein A, Daniel R, Frei D, Segessemann T, Zimmerman J, Marinos G, Kaleta C, Jehmlich N, Ahrens CH, von Bergen M.	Microbiome	10.1186/s40168-020-00981-z	2021
Metabolism	Recognition of gram-positive intestinal bacteria by hybridoma- and colostrum-derived secretory immunoglobulin A is mediated by carbohydrates.	Mathias A, Corthesy B.	J Biol Chem	10.1074/jbc.m110.209015	2011
	A Dietary Fiber-Deprived Gut Microbiota Degrades the Colonic Mucus Barrier and Enhances Pathogen Susceptibility.	Desai MS, Seekatz AM, Koropatkin NM, Kamada N, Hickey CA, Wolter M, Pudlo NA, Kitamoto S, Terrapon N, Muller A, Young VB, Henrissat B, Wilmes P, Stappenbeck TS, Nunez G, Martens EC.	Cell	10.1016/j.cell.2016.10.043	2016
	Preliminary safety evaluation of a new Bacteroides xylanisolvens isolate.	Ulsemer P, Toutounian K, Schmidt J, Karsten U, Goletz S.	Appl Environ Microbiol	10.1128/aem.06641-11	2012
Metabolism	Diastereomer-specific quantification of bioactive hexosylceramides from bacteria and mammals.	von Gerichten J, Schlosser K, Lamprecht D, Morace I, Eckhardt M, Wachten D, Jennemann R, Grone HJ, Mack M, Sandhoff R.	J Lipid Res	10.1194/jlr.d076190	2017
Metabolism	Clostridium ramosum promotes high-fat diet-induced obesity in gnotobiotic mouse models.	Woting A, Pfeiffer N, Loh G, Klaus S, Blaut M.	mBio	10.1128/mbio.01530-14	2014
	Alleviation of high fat diet-induced obesity by oligofructose in gnotobiotic mice is independent of presence of Bifidobacterium longum.	Woting A, Pfeiffer N, Hanske L, Loh G, Klaus S, Blaut M.	Mol Nutr Food Res	10.1002/mnfr.201500249	2015
Phylogeny	Colostrum of healthy Slovenian mothers: microbiota composition and bacteriocin gene prevalence.	Obermajer T, Lipoglavsek L, Tompa G, Treven P, Lorbeg PM, Matijasic BB, Rogelj I.	PLoS One	10.1371/journal.pone.0123324	2014
Enzymology	Gut microbiota in human adults with type 2 diabetes differs from non-diabetic adults.	Larsen N, Vogensen FK, van den Berg FW, Nielsen DS, Andreasen AS, Pedersen BK, Al-Soud WA, Sorensen SJ, Hansen LH, Jakobsen M.	PLoS One	10.1371/journal.pone.0009085	2010
	Commensal Akkermansia muciniphila exacerbates gut inflammation in Salmonella Typhimurium-infected gnotobiotic mice.	Ganesh BP, Klopfleisch R, Loh G, Blaut M.	PLoS One	10.1371/journal.pone.0074963	2013
Enzymology	Bacteriophages active against Bacteroides fragilis in sewage-polluted waters.	Tartera C, Jofre J.	Appl Environ Microbiol	10.1128/aem.53.7.1632-1637.1987	1987
	Commensal gut bacteria employ de-chelatase HmuS to harvest iron from heme.	Kumar Nath A, da Silva RR, Gauvin CC, Akpoto E, Dlakic M, Lawrence CM, DuBois JL.	EMBO J	10.1038/s44318-025-00563-5	2025
	Transcriptional regulatory networks of the human gut symbiont Bacteroides thetaiotaomicron are uncovered using machine learning.	Kim K, Choe D, Kim SC, Yim SS, Jeong KJ, Palsson B, Cho S, Cho BK.	Nucleic Acids Res	10.1093/nar/gkaf1166	2025
	Gut Microbe Fermentation of Moringa oleifera Leaf Extract Increases Measurable Polyphenols and Improves Barrier Function in a Cell Culture Model.	Kable ME, Storms DH, Alkan Z, Muriki M, DeVries D, Waterman C, Lemay DG.	Microbiologyopen	10.1002/mbo3.70068	2025
	Semi-rational engineering of an alpha-L-fucosidase for regioselective synthesis of fucosyl-N-acetylglucosamine disaccharides.	Liu P, Chen X, Cao X, Wang Y, Gao Y, Xu L, Jiang X, Xiao M.	Food Chem (Oxf)	10.1016/j.fochms.2025.100244	2025
	BT1549 coordinates the in vitro IL-10 inducing activity of Bacteroides thetaiotaomicron.	Engelhart MJ, Brock OD, Till JM, Glowacki RWP, Cantwell JW, Clarke DJ, Wesener DA, Ahern PP.	Microbiol Spectr	10.1128/spectrum.01669-24	2025
Proteome	Heme and iron limitation in a GI-tract foundation species leads to a reshuffling of the metalloproteome and a shift toward manganese usage.	Rodrigues da Silva R, Larson J, Bothner B, DuBois JL.	Front Chem	10.3389/fchem.2025.1562189	2025
Pathogenicity	Bacteroides ovatus alleviates dysbiotic microbiota-induced graft-versus-host disease.	Hayase E, Hayase T, Mukherjee A, Stinson SC, Jamal MA, Ortega MR, Sanchez CA, Ahmed SS, Karmouch JL, Chang CC, Flores II, McDaniel LK, Brown AN, El-Himri RK, Chapa VA, Tan L, Tran BQ, Xiao Y, Fan C, Pham D, Halsey TM, Jin Y, Tsai WB, Prasad R, Glover IK, Enkhbayar A, Mohammed A, Schmiester M, King KY, Britton RA, Reddy P, Wong MC, Ajami NJ, Wargo JA, Shelburne S, Okhuysen PC, Liu C, Fowler SW, Conner ME, Katsamakis Z, Smith N, Burgos da Silva M, Ponce DM, Peled JU, van den Brink MRM, Peterson CB, Rondon G, Molldrem JJ, Champlin RE, Shpall EJ, Lorenzi PL, Mehta RS, Martens EC, Alousi AM, Jenq RR.	Cell Host Microbe	10.1016/j.chom.2024.08.004	2024
	MetaPep: A core peptide database for faster human gut metaproteomics database searches.	Sun Z, Ning Z, Cheng K, Duan H, Wu Q, Mayne J, Figeys D.	Comput Struct Biotechnol J	10.1016/j.csbj.2023.08.025	2023
Pathogenicity	Bacteroides and NAFLD: pathophysiology and therapy.	Zhang J, Zhou J, He Z, Li H.	Front Microbiol	10.3389/fmicb.2024.1288856	2024
	Bacteroides thetaiotaomicron and Faecalibacterium prausnitzii served as key components of fecal microbiota transplantation to alleviate colitis.	Xu B, Fu Y, Yin N, Qin W, Huang Z, Xiao W, Huang H, Mei Q, Fan J, Zeng Y, Huang C.	Am J Physiol Gastrointest Liver Physiol	10.1152/ajpgi.00303.2023	2024
Phylogeny	Bacteroides thetaiotaomicron Ameliorates Experimental Allergic Airway Inflammation via Activation of ICOS⁺Tregs and Inhibition of Th2 Response.	Pang W, Jiang Y, Li A, Zhang J, Chen M, Hu L, Li Z, Wang D.	Front Immunol	10.3389/fimmu.2021.620943	2021
Genetics	High-throughput protein characterization by complementation using DNA barcoded fragment libraries.	Biggs BW, Price MN, Lai D, Escobedo J, Fortanel Y, Huang YY, Kim K, Trotter VV, Kuehl JV, Lui LM, Chakraborty R, Deutschbauer AM, Arkin AP.	Mol Syst Biol	10.1038/s44320-024-00068-z	2024
Metabolism	Bacteroides thetaiotaomicron, a Model Gastrointestinal Tract Species, Prefers Heme as an Iron Source, Yields Protoporphyrin IX as a Product, and Acts as a Heme Reservoir.	Mesle MM, Gray CR, Dlakic M, DuBois JL.	Microbiol Spectr	10.1128/spectrum.04815-22	2023
	Analysis of Two SusE-Like Enzymes From Bacteroides thetaiotaomicron Reveals a Potential Degradative Capacity for This Protein Family.	Stevenson J, Ngo M, Brandt A, Weadge JT, Suits MDL.	Front Microbiol	10.3389/fmicb.2021.645765	2021
Genetics	A metagenomics pipeline reveals insertion sequence-driven evolution of the microbiota.	Kirsch JM, Hryckowian AJ, Duerkop BA.	Cell Host Microbe	10.1016/j.chom.2024.03.005	2024
	A critical evaluation of methodological and mechanistic insights on probiotic-derived extracellular vesicles.	Ronacher C, Gonzalez CF, Lorca GL.	Front Nutr	10.3389/fnut.2025.1632232	2025
Pathogenicity	Mucus-degrading Bacteroides link carbapenems to aggravated graft-versus-host disease.	Hayase E, Hayase T, Jamal MA, Miyama T, Chang CC, Ortega MR, Ahmed SS, Karmouch JL, Sanchez CA, Brown AN, El-Himri RK, Flores II, McDaniel LK, Pham D, Halsey T, Frenk AC, Chapa VA, Heckel BE, Jin Y, Tsai WB, Prasad R, Tan L, Veillon L, Ajami NJ, Wargo JA, Galloway-Pena J, Shelburne S, Chemaly RF, Davey L, Glowacki RWP, Liu C, Rondon G, Alousi AM, Molldrem JJ, Champlin RE, Shpall EJ, Valdivia RH, Martens EC, Lorenzi PL, Jenq RR.	Cell	10.1016/j.cell.2022.09.007	2022
	Biglycan regulated colorectal cancer progress by modulating enteric neuron-derived IL-10 and abundance of Bacteroides thetaiotaomicron.	Xu Y, Wang F, Mi K, Wang X, Wang D, Zhao Q, Wang J, Liu Z, Zhang Q, Liu Y, Zhang X, Liu X.	iScience	10.1016/j.isci.2023.107515	2023
	Amidinoquinoxaline N-oxides: synthesis and activity against anaerobic bacteria.	Gruber N, Fernandez-Canigia L, Kilimciler NB, Stipa P, Bisceglia JA, Garcia MB, Gonzalez Maglio DH, Paz ML, Orelli LR.	RSC Adv	10.1039/d3ra01184d	2023
	A GH89 human alpha-N-acetylglucosaminidase (hNAGLU) homologue from gut microbe Bacteroides thetaiotaomicron capable of hydrolyzing heparosan oligosaccharides.	Yang X, Yang X, Yu H, Na L, Ghosh T, McArthur JB, Chou TF, Dickson P, Chen X.	AMB Express	10.1186/s13568-021-01253-1	2021
Pathogenicity	Neonates exposed to HIV but uninfected exhibit an altered gut microbiota and inflammation associated with impaired breast milk antibody function.	Byrne A, Diener C, Brown BP, Maust BS, Feng C, Alinde BL, Gibbons SM, Koch M, Gray CM, Jaspan HB, Nyangahu DD.	Microbiome	10.1186/s40168-024-01973-z	2024
	Microbiota shape the colon epithelium controlling inter-crypt absorptive goblet cells via butyrate-GP R109A signalling.	Dias Nirello V, Araujo N, Carvalho de Assis H, Moreno-Gonzalez M, Ruiz P, Castro PR, Shealy NG, Shelton C, Font Fernandes M, de Oliveira S, Boroni M, Ryffel B, Byndloss MX, Beraza N, Ramirez Vinolo MA, Varga-Weisz P.	Gut Microbes	10.1080/19490976.2025.2573045	2025
	Microbial Features Linked to Medication Strategies in Cardiometabolic Disease Management.	Shearer J, Shah S, Shen-Tu G, Schlicht K, Laudes M, Mu C.	ACS Pharmacol Transl Sci	10.1021/acsptsci.3c00261	2024
	The NQR Complex Regulates the Immunomodulatory Function of Bacteroides thetaiotaomicron.	Engelhart MJ, Glowacki RWP, Till JM, Harding CV, Martens EC, Ahern PP.	J Immunol	10.4049/jimmunol.2200892	2023
Pathogenicity	Quantifying the varying harvest of fermentation products from the human gut microbiota.	Arnoldini M, Sharma R, Moresi C, Chure G, Chabbey J, Slack E, Cremer J.	Cell	10.1016/j.cell.2025.07.005	2025
	Engineering intelligent chassis cells via recombinase-based MEMORY circuits.	Huang BD, Kim D, Yu Y, Wilson CJ.	Nat Commun	10.1038/s41467-024-46755-1	2024
	Fitness advantage of Bacteroides thetaiotaomicron capsular polysaccharide in the mouse gut depends on the resident microbiota.	Hoces D, Greter G, Arnoldini M, Staubli ML, Moresi C, Sintsova A, Berent S, Kolinko I, Bansept F, Woller A, Hafliger J, Martens E, Hardt WD, Sunagawa S, Loverdo C, Slack E.	Elife	10.7554/elife.81212	2023
	Characterizing the mucin-degrading capacity of the human gut microbiota.	Glover JS, Ticer TD, Engevik MA.	Sci Rep	10.1038/s41598-022-11819-z	2022
	Mucin-Degrading Microbes Release Monosaccharides That Chemoattract Clostridioides difficile and Facilitate Colonization of the Human Intestinal Mucus Layer.	Engevik MA, Engevik AC, Engevik KA, Auchtung JM, Chang-Graham AL, Ruan W, Luna RA, Hyser JM, Spinler JK, Versalovic J.	ACS Infect Dis	10.1021/acsinfecdis.0c00634	2021
Genetics	Discovery of antimicrobial peptides in the global microbiome with machine learning.	Santos-Junior CD, Torres MDT, Duan Y, Rodriguez Del Rio A, Schmidt TSB, Chong H, Fullam A, Kuhn M, Zhu C, Houseman A, Somborski J, Vines A, Zhao XM, Bork P, Huerta-Cepas J, de la Fuente-Nunez C, Coelho LP.	Cell	10.1016/j.cell.2024.05.013	2024
Genetics	Large-Scale Analyses of Human Microbiomes Reveal Thousands of Small, Novel Genes.	Sberro H, Fremin BJ, Zlitni S, Edfors F, Greenfield N, Snyder MP, Pavlopoulos GA, Kyrpides NC, Bhatt AS.	Cell	10.1016/j.cell.2019.07.016	2019
Metabolism	Structure-dependent stimulation of gut bacteria by arabinoxylo-oligosaccharides (AXOS): a review.	Leschonski KP, Mortensen MS, Hansen LBS, Krogh KBRM, Kabel MA, Laursen MF.	Gut Microbes	10.1080/19490976.2024.2430419	2024
	Untargeted Metabolomics Sensitively Differentiates Gut Bacterial Species in Single Culture and Co-Culture Systems.	Zhang S, Zhu J.	ACS Omega	10.1021/acsomega.1c07114	2022
	HLA-II immunopeptidome profiling and deep learning reveal features of antigenicity to inform antigen discovery.	Strazar M, Park J, Abelin JG, Taylor HB, Pedersen TK, Plichta DR, Brown EM, Eraslan B, Hung YM, Ortiz K, Clauser KR, Carr SA, Xavier RJ, Graham DB.	Immunity	10.1016/j.immuni.2023.05.009	2023
Metabolism	Metabolic Feedback Inhibition Influences Metabolite Secretion by the Human Gut Symbiont Bacteroides thetaiotaomicron.	Catlett JL, Catazaro J, Cashman M, Carr S, Powers R, Cohen MB, Buan NR.	mSystems	10.1128/msystems.00252-20	2020
	In vitro co-cultures of human gut bacterial species as predicted from co-occurrence network analysis.	Das P, Das P, Ji B, Kovatcheva-Datchary P, Backhed F, Nielsen J.	PLoS One	10.1371/journal.pone.0195161	2018
	Repertoire of Abs primed by bacteria in gnotobiotic mice.	Khasbiullina NR, Shilova NV, Navakouski ME, Nokel AY, Knirel YA, Blixt O, Bovin NV.	Innate Immun	10.1177/1753425918763524	2018
	Bifidobacterium infantis associates with T cell immunity in human infants and is sufficient to enhance antigen-specific T cells in mice.	Nyangahu DD, Happel AU, Wendoh J, Kiravu A, Wang Y, Feng C, Plumlee C, Cohen S, Brown BP, Djukovic D, Ganief T, Gasper M, Raftery D, Blackburn JM, Allbritton NL, Gray CM, Paik J, Urdahl KB, Jaspan HB.	Sci Adv	10.1126/sciadv.ade1370	2023
	Functional genetics of human gut commensal Bacteroides thetaiotaomicron reveals metabolic requirements for growth across environments.	Liu H, Shiver AL, Price MN, Carlson HK, Trotter VV, Chen Y, Escalante V, Ray J, Hern KE, Petzold CJ, Turnbaugh PJ, Huang KC, Arkin AP, Deutschbauer AM.	Cell Rep	10.1016/j.celrep.2021.108789	2021
Pathogenicity	Obesity and the gut microbiota: implications of neuroendocrine and immune signaling.	Romani-Perez M, Liebana-Garcia R, Flor-Duro A, Bonillo-Jimenez D, Bullich-Vilarrubias C, Olivares M, Sanz Y.	FEBS J	10.1111/febs.17249	2025
Metabolism	A Ribose-Scavenging System Confers Colonization Fitness on the Human Gut Symbiont Bacteroides thetaiotaomicron in a Diet-Specific Manner.	Glowacki RWP, Pudlo NA, Tuncil Y, Luis AS, Sajjakulnukit P, Terekhov AI, Lyssiotis CA, Hamaker BR, Martens EC.	Cell Host Microbe	10.1016/j.chom.2019.11.009	2020
	Genetic circuit design automation for the gut resident species Bacteroides thetaiotaomicron.	Taketani M, Zhang J, Zhang S, Triassi AJ, Huang YJ, Griffith LG, Voigt CA.	Nat Biotechnol	10.1038/s41587-020-0468-5	2020
Transcriptome	Simplified Intestinal Microbiota to Study Microbe-Diet-Host Interactions in a Mouse Model.	Kovatcheva-Datchary P, Shoaie S, Lee S, Wahlstrom A, Nookaew I, Hallen A, Perkins R, Nielsen J, Backhed F.	Cell Rep	10.1016/j.celrep.2019.02.090	2019
	A high-fiber diet synergizes with Prevotella copri and exacerbates rheumatoid arthritis.	Jiang L, Shang M, Yu S, Liu Y, Zhang H, Zhou Y, Wang M, Wang T, Li H, Liu Z, Zhang X.	Cell Mol Immunol	10.1038/s41423-022-00934-6	2022
	Microbiota functional activity biosensors for characterizing nutrient metabolism in vivo.	Wesener DA, Beller ZW, Peters SL, Rajabi A, Dimartino G, Giannone RJ, Hettich RL, Gordon JI.	Elife	10.7554/elife.64478	2021
Metabolism	Metabolic Synergy between Human Symbionts Bacteroides and Methanobrevibacter.	Catlett JL, Carr S, Cashman M, Smith MD, Walter M, Sakkaff Z, Kelley C, Pierobon M, Cohen MB, Buan NR.	Microbiol Spectr	10.1128/spectrum.01067-22	2022
	Engineered phage with antibacterial CRISPR-Cas selectively reduce E. coli burden in mice.	Gencay YE, Jasinskyte D, Robert C, Semsey S, Martinez V, Petersen AO, Brunner K, de Santiago Torio A, Salazar A, Turcu IC, Eriksen MK, Koval L, Takos A, Pascal R, Schou TS, Bayer L, Bryde T, Johansen KC, Bak EG, Smrekar F, Doyle TB, Satlin MJ, Gram A, Carvalho J, Jessen L, Hallstrom B, Hink J, Damholt B, Troy A, Grove M, Clube J, Grondahl C, Haaber JK, van der Helm E, Zdravkovic M, Sommer MOA.	Nat Biotechnol	10.1038/s41587-023-01759-y	2024
	¹³C-Stable isotope resolved metabolomics uncovers dynamic biochemical landscape of gut microbiome-host organ communications in mice.	Xiao X, Zhou Y, Li X, Jin J, Durham J, Ye Z, Wang Y, Hennig B, Deng P.	Microbiome	10.1186/s40168-024-01808-x	2024
	Interindividual Variation in Dietary Carbohydrate Metabolism by Gut Bacteria Revealed with Droplet Microfluidic Culture.	Villa MM, Bloom RJ, Silverman JD, Durand HK, Jiang S, Wu A, Dallow EP, Huang S, You L, David LA.	mSystems	10.1128/msystems.00864-19	2020
	Bacterial extracellular vesicles control murine norovirus infection through modulation of antiviral immune responses.	Bhar S, Zhao G, Bartel JD, Sterchele H, Del Mazo A, Emerson LE, Edelmann MJ, Jones MK.	Front Immunol	10.3389/fimmu.2022.909949	2022
Metabolism	Gut Microbiota-Produced Tryptamine Activates an Epithelial G-Protein-Coupled Receptor to Increase Colonic Secretion.	Bhattarai Y, Williams BB, Battaglioli EJ, Whitaker WR, Till L, Grover M, Linden DR, Akiba Y, Kandimalla KK, Zachos NC, Kaunitz JD, Sonnenburg JL, Fischbach MA, Farrugia G, Kashyap PC.	Cell Host Microbe	10.1016/j.chom.2018.05.004	2018
	Granzyme B⁺ CD4 T cells accumulate in the colon during chronic HIV-1 infection.	Dillon SM, Mickens KL, Thompson TA, Cooper EH, Nesladek S, Christians AJ, Castleman M, Guo K, Wood C, Frank DN, Kechris K, Santiago ML, Wilson CC.	Gut Microbes	10.1080/19490976.2022.2045852	2022
Metabolism	Gut microbes impact stroke severity via the trimethylamine N-oxide pathway.	Zhu W, Romano KA, Li L, Buffa JA, Sangwan N, Prakash P, Tittle AN, Li XS, Fu X, Androjna C, DiDonato AJ, Brinson K, Trapp BD, Fischbach MA, Rey FE, Hajjar AM, DiDonato JA, Hazen SL.	Cell Host Microbe	10.1016/j.chom.2021.05.002	2021
	Carbohydrate complexity limits microbial growth and reduces the sensitivity of human gut communities to perturbations.	Ostrem Loss E, Thompson J, Cheung PLK, Qian Y, Venturelli OS.	Nat Ecol Evol	10.1038/s41559-022-01930-9	2023
Metabolism	A selective gut bacterial bile salt hydrolase alters host metabolism.	Yao L, Seaton SC, Ndousse-Fetter S, Adhikari AA, DiBenedetto N, Mina AI, Banks AS, Bry L, Devlin AS.	Elife	10.7554/elife.37182	2018
Genetics	Developing a Bacteroides System for Function-Based Screening of DNA from the Human Gut Microbiome.	Lam KN, Martens EC, Charles TC.	mSystems	10.1128/msystems.00195-17	2018
Enzymology	Separating host and microbiome contributions to drug pharmacokinetics and toxicity.	Zimmermann M, Zimmermann-Kogadeeva M, Wegmann R, Goodman AL.	Science	10.1126/science.aat9931	2019
Metabolism	Colitogenic Bacteroides thetaiotaomicron Antigens Access Host Immune Cells in a Sulfatase-Dependent Manner via Outer Membrane Vesicles.	Hickey CA, Kuhn KA, Donermeyer DL, Porter NT, Jin C, Cameron EA, Jung H, Kaiko GE, Wegorzewska M, Malvin NP, Glowacki RW, Hansson GC, Allen PM, Martens EC, Stappenbeck TS.	Cell Host Microbe	10.1016/j.chom.2015.04.002	2015
	Identification of PGN_1123 as the Gene Encoding Lipid A Deacylase, an Enzyme Required for Toll-Like Receptor 4 Evasion, in Porphyromonas gingivalis.	Jain S, Chang AM, Singh M, McLean JS, Coats SR, Kramer RW, Darveau RP.	J Bacteriol	10.1128/jb.00683-18	2019
	Understanding how commensal obligate anaerobic bacteria regulate immune functions in the large intestine.	Maier E, Anderson RC, Roy NC.	Nutrients	10.3390/nu7010045	2014
Metabolism	Surface Exposure and Packing of Lipoproteins into Outer Membrane Vesicles Are Coupled Processes in Bacteroides.	Valguarnera E, Scott NE, Azimzadeh P, Feldman MF.	mSphere	10.1128/msphere.00559-18	2018
Metabolism	Indoleacrylic Acid Produced by Commensal Peptostreptococcus Species Suppresses Inflammation.	Wlodarska M, Luo C, Kolde R, d'Hennezel E, Annand JW, Heim CE, Krastel P, Schmitt EK, Omar AS, Creasey EA, Garner AL, Mohammadi S, O'Connell DJ, Abubucker S, Arthur TD, Franzosa EA, Huttenhower C, Murphy LO, Haiser HJ, Vlamakis H, Porter JA, Xavier RJ.	Cell Host Microbe	10.1016/j.chom.2017.06.007	2017
Metabolism	The Stringent Response Determines the Ability of a Commensal Bacterium to Survive Starvation and to Persist in the Gut.	Schofield WB, Zimmermann-Kogadeeva M, Zimmermann M, Barry NA, Goodman AL.	Cell Host Microbe	10.1016/j.chom.2018.06.002	2018
Metabolism	Regulated expression of polysaccharide utilization and capsular biosynthesis loci in biofilm and planktonic Bacteroides thetaiotaomicron during growth in chemostats.	TerAvest MA, He Z, Rosenbaum MA, Martens EC, Cotta MA, Gordon JI, Angenent LT.	Biotechnol Bioeng	10.1002/bit.24994	2014
Metabolism	An Oxidative Central Metabolism Enables Salmonella to Utilize Microbiota-Derived Succinate.	Spiga L, Winter MG, Furtado de Carvalho T, Zhu W, Hughes ER, Gillis CC, Behrendt CL, Kim J, Chessa D, Andrews-Polymenis HL, Beiting DP, Santos RL, Hooper LV, Winter SE.	Cell Host Microbe	10.1016/j.chom.2017.07.018	2017
	Programming a Human Commensal Bacterium, Bacteroides thetaiotaomicron, to Sense and Respond to Stimuli in the Murine Gut Microbiota.	Mimee M, Mimee M, Tucker AC, Voigt CA, Lu TK.	Cell Syst	10.1016/j.cels.2015.06.001	2015
Genetics	Gut microbiota dysbiosis is associated with malnutrition and reduced plasma amino acid levels: Lessons from genome-scale metabolic modeling.	Kumar M, Ji B, Babaei P, Das P, Lappa D, Ramakrishnan G, Fox TE, Haque R, Petri WA, Backhed F, Nielsen J.	Metab Eng	10.1016/j.ymben.2018.07.018	2018
Genetics	Inter-individual differences in the gene content of human gut bacterial species.	Zhu A, Sunagawa S, Mende DR, Bork P.	Genome Biol	10.1186/s13059-015-0646-9	2015
	Skin-penetrating nematodes exhibit life-stage-specific interactions with host-associated and environmental bacteria.	Chavez IN, Brown TM, Assie A, Bryant AS, Samuel BS, Hallem EA.	BMC Biol	10.1186/s12915-021-01153-7	2021
	Deep-learning-enabled antibiotic discovery through molecular de-extinction.	Wan F, Torres MDT, Peng J, de la Fuente-Nunez C.	Nat Biomed Eng	10.1038/s41551-024-01201-x	2024
	DNA enrichment and tagmentation method for species-level identification and strain-level differentiation using ON-rep-seq.	Krych L, Castro-Mejia JL, Forero-Junco LM, Moesby DN, Mikkelsen MB, Rasmussen MA, Sykulski M, Nielsen DS.	Commun Biol	10.1038/s42003-019-0617-x	2019
Pathogenicity	In vitro and in vivo activities of HPi1, a selective antimicrobial against Helicobacter pylori.	Gavrish E, Shrestha B, Chen C, Lister I, North EJ, Yang L, Lee RE, Han A, Williams B, Charnuska D, Coleman K, Lewis K, LaFleur MD.	Antimicrob Agents Chemother	10.1128/aac.02573-13	2014
	Large-Scale Molecular Evolutionary Analysis Uncovers a Variety of Polynucleotide Kinase Clp1 Family Proteins in the Three Domains of Life.	Saito M, Sato A, Nagata S, Tamaki S, Tomita M, Suzuki H, Kanai A.	Genome Biol Evol	10.1093/gbe/evz195	2019
Metabolism	1H nuclear magnetic resonance spectroscopy-based studies of the metabolism of food-borne carcinogen 2-amino-3-methylimidazo[4,5-f]quinoline by human intestinal microbiota.	Humblot C, Combourieu B, Vaisanen ML, Furet JP, Delort AM, Rabot S.	Appl Environ Microbiol	10.1128/aem.71.9.5116-5123.2005	2005
	Gut Bacteroides act in a microbial consortium to cause susceptibility to severe malaria.	Mandal RK, Mandal A, Denny JE, Namazii R, John CC, Schmidt NW.	Nat Commun	10.1038/s41467-023-42235-0	2023
Metabolism	Strain-level fitness in the gut microbiome is an emergent property of glycans and a single metabolite.	Park SY, Rao C, Coyte KZ, Kuziel GA, Zhang Y, Huang W, Franzosa EA, Weng JK, Huttenhower C, Rakoff-Nahoum S.	Cell	10.1016/j.cell.2022.01.002	2022
Metabolism	Ruminococcus bromii is a keystone species for the degradation of resistant starch in the human colon.	Ze X, Duncan SH, Louis P, Flint HJ.	ISME J	10.1038/ismej.2012.4	2012
	Improving microbial fitness in the mammalian gut by in vivo temporal functional metagenomics.	Yaung SJ, Deng L, Li N, Braff JL, Church GM, Bry L, Wang HH, Gerber GK.	Mol Syst Biol	10.15252/msb.20145866	2015
Pathogenicity	Intestinal serotonin and fluoxetine exposure modulate bacterial colonization in the gut.	Fung TC, Vuong HE, Luna CDG, Pronovost GN, Aleksandrova AA, Riley NG, Vavilina A, McGinn J, Rendon T, Forrest LR, Hsiao EY.	Nat Microbiol	10.1038/s41564-019-0540-4	2019
Phylogeny	Imaging the in vivo growth patterns of bacteria in human gut Microbiota.	Lin L, Song J, Li J, Zuo X, Wei H, Yang C, Wang W.	Gut Microbes	10.1080/19490976.2021.1960134	2021
	Transcriptional programming in a Bacteroides consortium.	Huang BD, Groseclose TM, Wilson CJ.	Nat Commun	10.1038/s41467-022-31614-8	2022
	Diet-derived metabolites and mucus link the gut microbiome to fever after cytotoxic cancer treatment.	Schwabkey ZI, Wiesnoski DH, Chang CC, Tsai WB, Pham D, Ahmed SS, Hayase T, Ortega Turrubiates MR, El-Himri RK, Sanchez CA, Hayase E, Frenk Oquendo AC, Miyama T, Halsey TM, Heckel BE, Brown AN, Jin Y, Raybaud M, Prasad R, Flores I, McDaniel L, Chapa V, Lorenzi PL, Warmoes MO, Tan L, Swennes AG, Fowler S, Conner M, McHugh K, Graf T, Jensen VB, Peterson CB, Do KA, Zhang L, Shi Y, Wang Y, Galloway-Pena JR, Okhuysen PC, Daniel-MacDougall CR, Shono Y, Burgos da Silva M, Peled JU, van den Brink MRM, Ajami N, Wargo JA, Reddy P, Valdivia RH, Davey L, Rondon G, Srour SA, Mehta RS, Alousi AM, Shpall EJ, Champlin RE, Shelburne SA, Molldrem JJ, Jamal MA, Karmouch JL, Jenq RR.	Sci Transl Med	10.1126/scitranslmed.abo3445	2022
	Microorganisms linked to inflammatory bowel disease-associated dysbiosis differentially impact host physiology in gnotobiotic mice.	Hoffmann TW, Pham HP, Bridonneau C, Aubry C, Lamas B, Martin-Gallausiaux C, Moroldo M, Rainteau D, Lapaque N, Six A, Richard ML, Fargier E, Le Guern ME, Langella P, Sokol H.	ISME J	10.1038/ismej.2015.127	2016
Metabolism	Human norovirus binding to select bacteria representative of the human gut microbiota.	Almand EA, Moore MD, Outlaw J, Jaykus LA.	PLoS One	10.1371/journal.pone.0173124	2017
Metabolism	Reciprocal Prioritization to Dietary Glycans by Gut Bacteria in a Competitive Environment Promotes Stable Coexistence.	Tuncil YE, Xiao Y, Porter NT, Reuhs BL, Martens EC, Hamaker BR.	mBio	10.1128/mbio.01068-17	2017
Metabolism	Multidomain Carbohydrate-binding Proteins Involved in Bacteroides thetaiotaomicron Starch Metabolism.	Cameron EA, Maynard MA, Smith CJ, Smith TJ, Koropatkin NM, Martens EC.	J Biol Chem	10.1074/jbc.m112.397380	2012
Phylogeny	Method for isolation of Bacteroides bacteriophage host strains suitable for tracking sources of fecal pollution in water.	Payan A, Ebdon J, Taylor H, Gantzer C, Ottoson J, Papageorgiou GT, Blanch AR, Lucena F, Jofre J, Muniesa M.	Appl Environ Microbiol	10.1128/aem.71.9.5659-5662.2005	2005
Enzymology	hypD as a marker for [NiFe]-hydrogenases in microbial communities of surface waters.	Beimgraben C, Gutekunst K, Opitz F, Appel J.	Appl Environ Microbiol	10.1128/aem.00690-14	2014
	Long-term temporal analysis of the human fecal microbiota revealed a stable core of dominant bacterial species.	Martinez I, Muller CE, Walter J.	PLoS One	10.1371/journal.pone.0069621	2013
Pathogenicity	Recovery of the Gut Microbiota after Antibiotics Depends on Host Diet, Community Context, and Environmental Reservoirs.	Ng KM, Aranda-Diaz A, Tropini C, Frankel MR, Van Treuren W, O'Loughlin CT, Merrill BD, Yu FB, Pruss KM, Oliveira RA, Higginbottom SK, Neff NF, Fischbach MA, Xavier KB, Sonnenburg JL, Huang KC.	Cell Host Microbe	10.1016/j.chom.2019.10.011	2019
Metabolism	Bacteroides thetaiotaomicron and Faecalibacterium prausnitzii influence the production of mucus glycans and the development of goblet cells in the colonic epithelium of a gnotobiotic model rodent.	Wrzosek L, Miquel S, Noordine ML, Bouet S, Joncquel Chevalier-Curt M, Robert V, Philippe C, Bridonneau C, Cherbuy C, Robbe-Masselot C, Langella P, Thomas M.	BMC Biol	10.1186/1741-7007-11-61	2013
Pathogenicity	Overexpression of the rhamnose catabolism regulatory protein, RhaR: a novel mechanism for metronidazole resistance in Bacteroides thetaiotaomicron.	Patel EH, Paul LV, Casanueva AI, Patrick S, Abratt VR.	J Antimicrob Chemother	10.1093/jac/dkp203	2009
	Insulin-like peptide 5 is a microbially regulated peptide that promotes hepatic glucose production.	Lee YS, De Vadder F, Tremaroli V, Wichmann A, Mithieux G, Backhed F.	Mol Metab	10.1016/j.molmet.2016.01.007	2016
Metabolism	Intramolecular arrangement of sensor and regulator overcomes relaxed specificity in hybrid two-component systems.	Townsend GE, Raghavan V, Zwir I, Groisman EA.	Proc Natl Acad Sci U S A	10.1073/pnas.1212102110	2013
	Multi-omics analyses of the ulcerative colitis gut microbiome link Bacteroides vulgatus proteases with disease severity.	Mills RH, Dulai PS, Vazquez-Baeza Y, Sauceda C, Daniel N, Gerner RR, Batachari LE, Malfavon M, Zhu Q, Weldon K, Humphrey G, Carrillo-Terrazas M, Goldasich LD, Bryant M, Raffatellu M, Quinn RA, Gewirtz AT, Chassaing B, Chu H, Sandborn WJ, Dorrestein PC, Knight R, Gonzalez DJ.	Nat Microbiol	10.1038/s41564-021-01050-3	2022
Metabolism	Symbiotic Human Gut Bacteria with Variable Metabolic Priorities for Host Mucosal Glycans.	Pudlo NA, Urs K, Kumar SS, German JB, Mills DA, Martens EC.	mBio	10.1128/mbio.01282-15	2015
Enzymology	A decrease in iron availability to human gut microbiome reduces the growth of potentially pathogenic gut bacteria; an in vitro colonic fermentation study.	Parmanand BA, Kellingray L, Le Gall G, Basit AW, Fairweather-Tait S, Narbad A.	J Nutr Biochem	10.1016/j.jnutbio.2019.01.010	2019
Metabolism	Respiration of Microbiota-Derived 1,2-propanediol Drives Salmonella Expansion during Colitis.	Faber F, Thiennimitr P, Spiga L, Byndloss MX, Litvak Y, Lawhon S, Andrews-Polymenis HL, Winter SE, Baumler AJ.	PLoS Pathog	10.1371/journal.ppat.1006129	2017
Pathogenicity	Transient Osmotic Perturbation Causes Long-Term Alteration to the Gut Microbiota.	Tropini C, Moss EL, Merrill BD, Ng KM, Higginbottom SK, Casavant EP, Gonzalez CG, Fremin B, Bouley DM, Elias JE, Bhatt AS, Huang KC, Sonnenburg JL.	Cell	10.1016/j.cell.2018.05.008	2018
Metabolism	Dynamic responses of Bacteroides thetaiotaomicron during growth on glycan mixtures.	Rogers TE, Pudlo NA, Koropatkin NM, Bell JS, Moya Balasch M, Jasker K, Martens EC.	Mol Microbiol	10.1111/mmi.12228	2013
Metabolism	Mapping human microbiome drug metabolism by gut bacteria and their genes.	Zimmermann M, Zimmermann-Kogadeeva M, Wegmann R, Goodman AL.	Nature	10.1038/s41586-019-1291-3	2019
Metabolism	A universal trade-off between growth and lag in fluctuating environments.	Basan M, Honda T, Christodoulou D, Horl M, Chang YF, Leoncini E, Mukherjee A, Okano H, Taylor BR, Silverman JM, Sanchez C, Williamson JR, Paulsson J, Hwa T, Sauer U.	Nature	10.1038/s41586-020-2505-4	2020
Metabolism	Gut microbiota-produced succinate promotes C. difficile infection after antibiotic treatment or motility disturbance.	Ferreyra JA, Wu KJ, Hryckowian AJ, Bouley DM, Weimer BC, Sonnenburg JL.	Cell Host Microbe	10.1016/j.chom.2014.11.003	2014
Pathogenicity	Reprofiled anthelmintics abate hypervirulent stationary-phase Clostridium difficile.	Gooyit M, Janda KD.	Sci Rep	10.1038/srep33642	2016
	Deciphering microbial interactions in synthetic human gut microbiome communities.	Venturelli OS, Carr AC, Fisher G, Hsu RH, Lau R, Bowen BP, Hromada S, Northen T, Arkin AP.	Mol Syst Biol	10.15252/msb.20178157	2018
Metabolism	Dps and DpsL Mediate Survival In Vitro and In Vivo during the Prolonged Oxidative Stress Response in Bacteroides fragilis.	Betteken MI, Rocha ER, Smith CJ.	J Bacteriol	10.1128/jb.00342-15	2015
Metabolism	Metabolic, Epigenetic, and Transgenerational Effects of Gut Bacterial Choline Consumption.	Romano KA, Martinez-Del Campo A, Kasahara K, Chittim CL, Vivas EI, Amador-Noguez D, Balskus EP, Rey FE.	Cell Host Microbe	10.1016/j.chom.2017.07.021	2017
	Effect of water flow and chemical environment on microbiota growth and composition in the human colon.	Cremer J, Arnoldini M, Hwa T.	Proc Natl Acad Sci U S A	10.1073/pnas.1619598114	2017
Metabolism	Structural and functional analysis of a glycoside hydrolase family 97 enzyme from Bacteroides thetaiotaomicron.	Kitamura M, Okuyama M, Tanzawa F, Mori H, Kitago Y, Watanabe N, Kimura A, Tanaka I, Yao M.	J Biol Chem	10.1074/jbc.m806115200	2008
Metabolism	Starch catabolism by a prominent human gut symbiont is directed by the recognition of amylose helices.	Koropatkin NM, Martens EC, Gordon JI, Smith TJ.	Structure	10.1016/j.str.2008.03.017	2008
Enzymology	A distinctive 'microbial signature' in celiac pediatric patients.	Schippa S, Iebba V, Barbato M, Di Nardo G, Totino V, Checchi MP, Longhi C, Maiella G, Cucchiara S, Conte MP.	BMC Microbiol	10.1186/1471-2180-10-175	2010
Pathogenicity	Acceptive Immunity: The Role of Fucosylated Glycans in Human Host-Microbiome Interactions.	Kononova S, Litvinova E, Vakhitov T, Skalinskaya M, Sitkin S.	Int J Mol Sci	10.3390/ijms22083854	2021
Pathogenicity	Microbiota-liberated host sugars facilitate post-antibiotic expansion of enteric pathogens.	Ng KM, Ferreyra JA, Higginbottom SK, Lynch JB, Kashyap PC, Gopinath S, Naidu N, Choudhury B, Weimer BC, Monack DM, Sonnenburg JL.	Nature	10.1038/nature12503	2013
Metabolism	A bacterial bile acid metabolite modulates T_reg activity through the nuclear hormone receptor NR4A1.	Li W, Hang S, Fang Y, Bae S, Zhang Y, Zhang M, Wang G, McCurry MD, Bae M, Paik D, Franzosa EA, Rastinejad F, Huttenhower C, Yao L, Devlin AS, Huh JR.	Cell Host Microbe	10.1016/j.chom.2021.07.013	2021
Metabolism	Bile Salts Modulate the Mucin-Activated Type VI Secretion System of Pandemic Vibrio cholerae.	Bachmann V, Kostiuk B, Unterweger D, Diaz-Satizabal L, Ogg S, Pukatzki S.	PLoS Negl Trop Dis	10.1371/journal.pntd.0004031	2015
Metabolism	Recognition of protein-linked glycans as a determinant of peptidase activity.	Noach I, Ficko-Blean E, Pluvinage B, Stuart C, Jenkins ML, Brochu D, Buenbrazo N, Wakarchuk W, Burke JE, Gilbert M, Boraston AB.	Proc Natl Acad Sci U S A	10.1073/pnas.1615141114	2017
	MetaRibo-Seq measures translation in microbiomes.	Fremin BJ, Sberro H, Bhatt AS.	Nat Commun	10.1038/s41467-020-17081-z	2020
Enzymology	PCR detection and quantitation of predominant anaerobic bacteria in human and animal fecal samples.	Wang RF, Cao WW, Cerniglia CE.	Appl Environ Microbiol	10.1128/aem.62.4.1242-1247.1996	1996
Metabolism	Structure of a SusD homologue, BT1043, involved in mucin O-glycan utilization in a prominent human gut symbiont.	Koropatkin N, Martens EC, Gordon JI, Smith TJ.	Biochemistry	10.1021/bi801942a	2009
	Evolution of symbiotic bacteria in the distal human intestine.	Xu J, Mahowald MA, Ley RE, Lozupone CA, Hamady M, Martens EC, Henrissat B, Coutinho PM, Minx P, Latreille P, Cordum H, Van Brunt A, Kim K, Fulton RS, Fulton LA, Clifton SW, Wilson RK, Knight RD, Gordon JI.	PLoS Biol	10.1371/journal.pbio.0050156	2007
Metabolism	Multifunctional nutrient-binding proteins adapt human symbiotic bacteria for glycan competition in the gut by separately promoting enhanced sensing and catalysis.	Cameron EA, Kwiatkowski KJ, Lee BH, Hamaker BR, Koropatkin NM, Martens EC.	mBio	10.1128/mbio.01441-14	2014
	Deciphering interactions between the gut microbiota and the immune system via microbial cultivation and minimal microbiomes.	Clavel T, Gomes-Neto JC, Lagkouvardos I, Ramer-Tait AE.	Immunol Rev	10.1111/imr.12578	2017
	A new Bacteroides conjugative transposon that carries an ermB gene.	Gupta A, Vlamakis H, Shoemaker N, Salyers AA.	Appl Environ Microbiol	10.1128/aem.69.11.6455-6463.2003	2003
	Monitoring of antibiotic-induced alterations in the human intestinal microflora and detection of probiotic strains by use of terminal restriction fragment length polymorphism.	Jernberg C, Sullivan A, Edlund C, Jansson JK.	Appl Environ Microbiol	10.1128/aem.71.1.501-506.2005	2005
Metabolism	Reduction of malachite green to leucomalachite green by intestinal bacteria.	Henderson AL, Schmitt TC, Heinze TM, Cerniglia CE.	Appl Environ Microbiol	10.1128/aem.63.10.4099-4101.1997	1997
	Distribution, detection of enterotoxigenic strains and antimicrobial drug susceptibility patterns of bacteroides fragilis group in diarrheic and non-diarrheic feces from brazilian infants.	Ferreira DP, Silva VL, Guimaraes DA, Coelho CM, Zauli DA, Farias LM, Carvalho MA, Diniz CG.	Braz J Microbiol	10.1590/s1517-83822010000300010	2010
	A low-cost paper-based synthetic biology platform for analyzing gut microbiota and host biomarkers.	Takahashi MK, Tan X, Dy AJ, Braff D, Akana RT, Furuta Y, Donghia N, Ananthakrishnan A, Collins JJ.	Nat Commun	10.1038/s41467-018-05864-4	2018
Pathogenicity	In vitro activities of gatifloxacin, two other quinolones, and five nonquinolone antimicrobials against obligately anaerobic bacteria.	Schaumann R, Ackermann G, Pless B, Claros MC, Rodloff AC.	Antimicrob Agents Chemother	10.1128/aac.43.11.2783	1999
Metabolism	Recurrent neural networks enable design of multifunctional synthetic human gut microbiome dynamics.	Baranwal M, Clark RL, Thompson J, Sun Z, Hero AO, Venturelli OS.	Elife	10.7554/elife.73870	2022
Enzymology	Introduction of the Bacteroides ruminicola xylanase gene into the Bacteroides thetaiotaomicron chromosome for production of xylanase activity.	Whitehead TR, Cotta MA, Hespell RB.	Appl Environ Microbiol	10.1128/aem.57.1.277-282.1991	1991
Metabolism	Human Secretory IgM Emerges from Plasma Cells Clonally Related to Gut Memory B Cells and Targets Highly Diverse Commensals.	Magri G, Comerma L, Pybus M, Sintes J, Llige D, Segura-Garzon D, Bascones S, Yeste A, Grasset EK, Gutzeit C, Uzzan M, Ramanujam M, van Zelm MC, Albero-Gonzalez R, Vazquez I, Iglesias M, Serrano S, Marquez L, Mercade E, Mehandru S, Cerutti A.	Immunity	10.1016/j.immuni.2017.06.013	2017
	Comparing the similarity of different groups of bacteria to the human proteome.	Trost B, Pajon R, Jayaprakash T, Kusalik A.	PLoS One	10.1371/journal.pone.0034007	2012
Phylogeny	Tunable Expression Tools Enable Single-Cell Strain Distinction in the Gut Microbiome.	Whitaker WR, Shepherd ES, Sonnenburg JL.	Cell	10.1016/j.cell.2017.03.041	2017
Metabolism	Species-specific dynamic responses of gut bacteria to a mammalian glycan.	Raghavan V, Groisman EA.	J Bacteriol	10.1128/jb.00010-15	2015
Enzymology	Characterization of a neopullulanase and an alpha-glucosidase from Bacteroides thetaiotaomicron 95-1.	Smith KA, Salyers AA.	J Bacteriol	10.1128/jb.173.9.2962-2968.1991	1991
Metabolism	Genetic evidence that outer membrane binding of starch is required for starch utilization by Bacteroides thetaiotaomicron.	Anderson KL, Salyers AA.	J Bacteriol	10.1128/jb.171.6.3199-3204.1989	1989
Enzymology	Use of randomly cloned DNA fragments for identification of Bacteroides thetaiotaomicron.	Salyers AA, Lynn SP, Gardner JF.	J Bacteriol	10.1128/jb.154.1.287-293.1983	1983
Enzymology	Ruminococcin A, a new lantibiotic produced by a Ruminococcus gnavus strain isolated from human feces.	Dabard J, Bridonneau C, Phillipe C, Anglade P, Molle D, Nardi M, Ladire M, Girardin H, Marcille F, Gomez A, Fons M.	Appl Environ Microbiol	10.1128/aem.67.9.4111-4118.2001	2001
Metabolism	Genomic and metabolic studies of the impact of probiotics on a model gut symbiont and host.	Sonnenburg JL, Chen CT, Gordon JI.	PLoS Biol	10.1371/journal.pbio.0040413	2006
Metabolism	Use of targeted insertional mutagenesis to determine whether chondroitin lyase II is essential for chondroitin sulfate utilization by Bacteroides thetaiotaomicron.	Guthrie EP, Salyers AA.	J Bacteriol	10.1128/jb.166.3.966-971.1986	1986
	Identifying genetic determinants needed to establish a human gut symbiont in its habitat.	Goodman AL, McNulty NP, Zhao Y, Leip D, Mitra RD, Lozupone CA, Knight R, Gordon JI.	Cell Host Microbe	10.1016/j.chom.2009.08.003	2009
Metabolism	Biochemical evidence that starch breakdown by Bacteroides thetaiotaomicron involves outer membrane starch-binding sites and periplasmic starch-degrading enzymes.	Anderson KL, Salyers AA.	J Bacteriol	10.1128/jb.171.6.3192-3198.1989	1989
	In vitro enrofloxacin binding in human fecal slurries.	Ahn Y, Linder SW, Veach BT, Steve Yan S, Haydee Fernandez A, Pineiro SA, Cerniglia CE.	Regul Toxicol Pharmacol	10.1016/j.yrtph.2011.11.013	2012
	Mucin glycan foraging in the human gut microbiome.	Tailford LE, Crost EH, Kavanaugh D, Juge N.	Front Genet	10.3389/fgene.2015.00081	2015
	Honor thy symbionts.	Xu J, Gordon JI.	Proc Natl Acad Sci U S A	10.1073/pnas.1734063100	2003
Metabolism	Cell-associated pullulanase from Bacteroides thetaiotaomicron: cloning, characterization, and insertional mutagenesis to determine role in pullulan utilization.	Smith KA, Salyers AA.	J Bacteriol	10.1128/jb.171.4.2116-2123.1989	1989
Metabolism	Analysis of outer membrane proteins which are associated with growth of Bacteroides thetaiotaomicron on chondroitin sulfate.	Kotarski SF, Linz J, Braun DM, Salyers AA.	J Bacteriol	10.1128/jb.163.3.1080-1086.1985	1985
Metabolism	Virulence meets metabolism: Cra and KdpE gene regulation in enterohemorrhagic Escherichia coli.	Njoroge JW, Nguyen Y, Curtis MM, Moreira CG, Sperandio V.	mBio	10.1128/mbio.00280-12	2012
	Further perspective on the catalytic core and secondary structure of ribonuclease P RNA.	Haas ES, Brown JW, Pitulle C, Pace NR.	Proc Natl Acad Sci U S A	10.1073/pnas.91.7.2527	1994
Metabolism	Mutual Cross-Feeding Interactions between Bifidobacterium longum subsp. longum NCC2705 and Eubacterium rectale ATCC 33656 Explain the Bifidogenic and Butyrogenic Effects of Arabinoxylan Oligosaccharides.	Riviere A, Gagnon M, Weckx S, Roy D, De Vuyst L.	Appl Environ Microbiol	10.1128/aem.02089-15	2015
Metabolism	Digestion of proteoglycan by Bacteroides thetaiotaomicron.	Kuritza AP, Salyers AA.	J Bacteriol	10.1128/jb.153.3.1180-1186.1983	1983
Enzymology	Cloning and expression in Escherichia coli of a gene coding for a chondroitin lyase from Bacteroides thetaiotaomicron.	Guthrie EP, Shoemaker NB, Salyers AA.	J Bacteriol	10.1128/jb.164.2.510-515.1985	1985
Enzymology	Isolation and characterization of two chondroitin lyases from Bacteroides thetaiotaomicron.	Linn S, Chan T, Lipeski L, Salyers AA.	J Bacteriol	10.1128/jb.156.2.859-866.1983	1983
Enzymology	Location and characteristics of enzymes involved in the breakdown of polygalacturonic acid by Bacteroides thetaiotaomicron.	McCarthy RE, Kotarski SF, Salyers AA.	J Bacteriol	10.1128/jb.161.2.493-499.1985	1985
Pathogenicity	In vitro model of colonization resistance by the enteric microbiota: effects of antimicrobial agents used in food-producing animals.	Wagner RD, Johnson SJ, Cerniglia CE.	Antimicrob Agents Chemother	10.1128/aac.00852-07	2008
Metabolism	A novel mechanism for desulfation of mucin: identification and cloning of a mucin-desulfating glycosidase (sulfoglycosidase) from Prevotella strain RS2.	Rho JH, Wright DP, Christie DL, Clinch K, Furneaux RH, Roberton AM.	J Bacteriol	10.1128/jb.187.5.1543-1551.2005	2005
Metabolism	Isolation and characterization of outer membranes of Bacteroides thetaiotaomicron grown on different carbohydrates.	Kotarski SF, Salyers AA.	J Bacteriol	10.1128/jb.158.1.102-109.1984	1984
	Analysis of rRNA restriction fragment length polymorphisms from Bacteroides spp. and Bacteroides fragilis isolates associated with diarrhea in humans and animals.	Smith CJ, Callihan DR.	J Clin Microbiol	10.1128/jcm.30.4.806-812.1992	1992
Metabolism	Evidence that polygalacturonic acid may not be a major source of carbon and energy for some colonic Bacteroides species.	McCarthy RE, Salyers AA.	Appl Environ Microbiol	10.1128/aem.52.1.9-16.1986	1986
	Development of an in vitro integration assay for the Bacteroides conjugative transposon CTnDOT.	Cheng Q, Wesslund N, Shoemaker NB, Salyers AA, Gardner JF.	J Bacteriol	10.1128/jb.184.17.4829-4837.2002	2002
Metabolism	Production of two proteins encoded by the Bacteroides mobilizable transposon NBU1 correlates with time-dependent accumulation of the excised NBu1 circular form.	Wang J, Wang GR, Shoemaker NB, Salyers AA.	J Bacteriol	10.1128/jb.183.21.6335-6343.2001	2001
Metabolism	Cloning of a mucin-desulfating sulfatase gene from Prevotella strain RS2 and its expression using a Bacteroides recombinant system.	Wright DP, Knight CG, Parkar SG, Christie DL, Roberton AM.	J Bacteriol	10.1128/jb.182.11.3002-3007.2000	2000
Metabolism	Metabolism of 6-nitrochrysene by intestinal microflora.	Manning BW, Campbell WL, Franklin W, Delclos KB, Cerniglia CE.	Appl Environ Microbiol	10.1128/aem.54.1.197-203.1988	1988
Phylogeny	A highly specific and sensitive DNA probe derived from chromosomal DNA of Helicobacter pylori is useful for typing H. pylori isolates.	Li C, Ferguson DA, Ha T, Chi DS, Thomas E.	J Clin Microbiol	10.1128/jcm.31.8.2157-2162.1993	1993
	Cloning and characterization of the endogenous cephalosporinase gene, cepA, from Bacteroides fragilis reveals a new subgroup of Ambler class A beta-lactamases.	Rogers MB, Parker AC, Smith CJ.	Antimicrob Agents Chemother	10.1128/aac.37.11.2391	1993
Metabolism	Properties of the penicillin-binding proteins of four species of the genus Bacteroides.	Piddock LJ, Wise R.	Antimicrob Agents Chemother	10.1128/aac.29.5.825	1986
Genetics	Development of the human infant intestinal microbiota.	Palmer C, Bik EM, DiGiulio DB, Relman DA, Brown PO.	PLoS Biol	10.1371/journal.pbio.0050177	2007
Phylogeny	Enumeration of polysaccharide-degrading Bacteroides species in human feces by using species-specific DNA probes.	Kuritza AP, Shaughnessy P, Salyers AA.	Appl Environ Microbiol	10.1128/aem.51.2.385-390.1986	1986
Phylogeny	DNA probes for identification of clinically important Bacteroides species.	Kuritza AP, Getty CE, Shaughnessy P, Hesse R, Salyers AA.	J Clin Microbiol	10.1128/jcm.23.2.343-349.1986	1986
	Compilation of 5S rRNA and 5S rRNA gene sequences.	Specht T, Wolters J, Erdmann VA.	Nucleic Acids Res	10.1093/nar/18.suppl.2215	1990
Enzymology	Use of a species-specific DNA hybridization probe for enumerating Bacteroides vulgatus in human feces.	Kuritza AP, Salyers AA.	Appl Environ Microbiol	10.1128/aem.50.4.958-964.1985	1985
	An In Vitro Approach to Study Effects of Prebiotics and Probiotics on the Faecal Microbiota and Selected Immune Parameters Relevant to the Elderly.	Liu Y, Gibson GR, Walton GE.	PLoS One	10.1371/journal.pone.0162604	2016
Phylogeny	Mucosa-associated bacteria in two middle-aged women diagnosed with collagenous colitis.	Gustafsson RJ, Ohlsson B, Benoni C, Jeppsson B, Olsson C.	World J Gastroenterol	10.3748/wjg.v18.i14.1628	2012
Enzymology	Cephalosporinases associated with outer membrane vesicles released by Bacteroides spp. protect gut pathogens and commensals against beta-lactam antibiotics.	Stentz R, Horn N, Cross K, Salt L, Brearley C, Livermore DM, Carding SR.	J Antimicrob Chemother	10.1093/jac/dku466	2015
Phylogeny	A 16S rRNA Gene and Draft Genome Database for the Murine Oral Bacterial Community.	Joseph S, Aduse-Opoku J, Hashim A, Hanski E, Streich R, Knowles SCL, Pedersen AB, Wade WG, Curtis MA.	mSystems	10.1128/msystems.01222-20	2021
Enzymology	Detection of unculturable bacteria in periodontal health and disease by PCR.	Harper-Owen R, Dymock D, Booth V, Weightman AJ, Wade WG.	J Clin Microbiol	10.1128/jcm.37.5.1469-1473.1999	1999
Enzymology	Superoxide dismutase in Bacteroides fragilis and related Bacteroides species.	Carlsson J, Wrethen J, Beckman G.	J Clin Microbiol	10.1128/jcm.6.3.280-284.1977	1977
Enzymology	Enterohepatic helicobacter in ulcerative colitis: potential pathogenic entities?	Thomson JM, Hansen R, Berry SH, Hope ME, Murray GI, Mukhopadhya I, McLean MH, Shen Z, Fox JG, El-Omar E, Hold GL.	PLoS One	10.1371/journal.pone.0017184	2011
Phylogeny	Characterization of bacterial communities in feces from healthy elderly volunteers and hospitalized elderly patients by using real-time PCR and effects of antibiotic treatment on the fecal microbiota.	Bartosch S, Fite A, Macfarlane GT, McMurdo ME.	Appl Environ Microbiol	10.1128/aem.70.6.3575-3581.2004	2004
	Nature, type of linkage, quantity, and absolute configuration of (3-hydroxy) fatty acids in lipopolysaccharides from Bacteroides fragilis NCTC 9343 and related strains.	Wollenweber HW, Rietschel ET, Hofstad T, Weintraub A, Lindberg AA.	J Bacteriol	10.1128/jb.144.3.898-903.1980	1980
	Opsonization of four Bacteroides species: role of the classical complement pathway and immunoglobulin.	Tofte RW, Peterson PK, Schmeling D, Bracke J, Kim Y, Quie PG.	Infect Immun	10.1128/iai.27.3.784-792.1980	1980
	Extraction and Evaluation of Outer Membrane Vesicles from Two Important Gut Microbiota Members, Bacteroides fragilis and Bacteroides thetaiotaomicron.	Ahmadi Badi S, Moshiri A, Ettehad Marvasti F, Mojtahedzadeh M, Kazemi V, Siadat SD.	Cell J	10.22074/cellj.2020.6499	2020
	Downregulation of ACE, AGTR1, and ACE2 genes mediating SARS-CoV-2 pathogenesis by gut microbiota members and their postbiotics on Caco-2 cells.	Ahmadi Badi S, Malek A, Paolini A, Rouhollahi Masoumi M, Seyedi SA, Amanzadeh A, Masotti A, Khatami S, Siadat SD.	Microb Pathog	10.1016/j.micpath.2022.105798	2022
	The regulation of Niemann-Pick C1-Like 1 (NPC1L1) gene expression in opposite direction by Bacteroides spp. and related outer membrane vesicles in Caco-2 cell line.	Badi SA, Motahhary A, Bahramali G, Masoumi M, Khalili SFS, Ebrahimzadeh N, Nouri P, Rahimi A, Masotti A, Moshiri A, Siadat SD.	J Diabetes Metab Disord	10.1007/s40200-020-00522-3	2020
	Phages infecting Bacteroides thetaiotaomicron.	Steczynska JP, Williams KP.	Microbiol Resour Announc	10.1128/mra.00760-25	2025
	Larch Arabinogalactan Alleviates Colitis by Modulating Gut Microbiota and Promoting Bacteroides thetaiotaomicron.	Zhang S, Sun Y, Bian X, Liu F, Nie S.	J Agric Food Chem	10.1021/acs.jafc.5c09920	2025
	Lessons from the model gut Bacteroidales Bacteroides fragilis and Bacteroides thetaiotaomicron and future opportunities.	Comstock LE.	J Bacteriol	10.1128/jb.00346-25	2025
Metabolism	Extracellular Vesicle-Linked Vitamin B12 Acquisition via Novel Binding Proteins in Bacteroides thetaiotaomicron.	Juodeikis R, Ulrich R, Clarke C, Banasik M, Deery E, Saalbach G, Krautler B, Carding SR, Geeves MA, Pickersgill R, Warren MJ.	Biochem J	10.1042/bcj20253340	2025
Metabolism	Insights into gut microbiota and metabolite profiles during in vitro fermentation of Volvaria volvacea polysaccharides: unraveling the central role of Bacteroides thetaiotaomicron.	Ye Z, Yu L, Zhang C, Wei X, Zhao J, Chen W, Zhai Q, Tian F.	Food Chem	10.1016/j.foodchem.2025.146197	2025
	Modulation of butyrate-induced stress responses in Bacteroides by lotus seed resistant starch and its sugar degradation products	Jiang Y, Zhang G, Su J, Zhang Y, Chang Q, Zeng H.	Carbohydrate polymers.		2025
Transcriptome	Low biomass bacterial transcriptomics takes shape.	Yang Q, Martens EC.	Trends Microbiol	10.1016/j.tim.2025.06.015	2025
	Identification of strain-specific cues that regulate biofilm formation in Bacteroides thetaiotaomicron.	Glowacki RW, Engelhart MJ, Till JM, Kadam A, Nemet I, Sangwan N, Ahern PP.	Microbiol Spectr	10.1128/spectrum.03419-24	2025
Metabolism	DNA-utilization loci enable exogenous DNA metabolism in gut Bacteroidales.	Sharan D, Nurek A, Stemczynski J, Turan K, Little AS, Coyne MJ, McMillin M, Sidebottom AM, Comstock LE, Light SH.	Proc Natl Acad Sci U S A	10.1073/pnas.2505388122	2025
	Comparison of novel alpha-glucosidases in glycoside hydrolase family 97 isolated from Bacteroides thetaiotaomicron.	Ko DS, Jeong HM, Shin YJ, Jeong DW, Kim NR, Shim JH.	Enzyme Microb Technol	10.1016/j.enzmictec.2025.110696	2025
Transcriptome	Preparation, characterization, fermentation properties of pectin with specific structures, and the analysis of microbial enzymes and genes involved in their degradation.	Cao W, Liu Y, Chen N, Wang Y, Nushrat YM, Qiao S, Tang L, Sun Z, Lu R, Liu C, Hua X.	Carbohydr Polym	10.1016/j.carbpol.2025.124162	2025
	Industrial and agricultural chemicals exhibit antimicrobial activity against human gut bacteria in vitro.	Roux I, Lindell AE, Griesshammer A, Smith T, Krishna S, Guan R, Rad D, Faria L, Blasche S, Patil KR, Kleinstreuer NC, Maier L, Kamrad S, Patil KR.	Nat Microbiol	10.1038/s41564-025-02182-6	2025
Genetics	Inverse Association between Serum Vitamin B₁₂ Level and Abundance of Potential B₁₂-Producing Gut Microbes in Indian Children.	Chandel N, Patel P, Somvanshi PR, Verma AK, Thakur V.	J Nutr	10.1016/j.tjnut.2025.10.021	2025
	Low-input RNA-seq suggests metabolic specialization underlying morphological heterogeneity in a gut commensal bacterium.	Bornet E, Prezza G, Cecchino L, Jenniches L, Behrends J, Tawk C, Huang KC, Strowig T, Vogel J, Barquist L, Saliba AE, Westermann AJ.	Cell Rep	10.1016/j.celrep.2025.115844	2025
	beta1,6-Selective Enzymatic N-Acetylglucosamination Catalyzed by the Family GH84 N-Acetyl-beta-D-glucosaminidase from Bacteroides thetaiotaomicron and its Glycosyl Acceptor Specificity.	Okuno R, Nakada S, Tonomura K, Aso Y, Takeshita D, Ohnuma T, Tanaka T.	Chem Asian J	10.1002/asia.202500142	2025
	Impact of donor human milk pasteurization methods on the gut microbiome of preterm infants.	Ocampo-Chih C, Hendricks H, Weitkamp S, Gowda NS, Singh H, Banerjee R, Rajagopala SV, Weitkamp JH.	Pediatr Res	10.1038/s41390-025-04386-2	2025
	Metabolic profiling of polysaccharides from Leccinum crocipodium (Letellier.) Watliag stem fermented by Bacteroides thetaiotaomicron and their immunomodulatory effects.	Fan Y, Zheng T, Liang S, Niu Y, Xiao Z, Fan J.	Int J Biol Macromol	10.1016/j.ijbiomac.2025.142026	2025
Metabolism	Bacteroides thetaiotaomicron: A symbiotic ally against diarrhea along with modulation of gut microbial ecological networks via tryptophan metabolism and AHR-Nrf2 signaling.	Luo Y, Lan C, Ren W, Wu A, Yu B, He J, Chen D.	J Adv Res	10.1016/j.jare.2025.04.016	2025
Metabolism	Acetylated cellulose suppresses body mass gain through gut commensals consuming host-accessible carbohydrates.	Takeuchi T, Miyauchi E, Nakanishi Y, Ito Y, Kato T, Yaguchi K, Kawasumi M, Tachibana N, Ito A, Shimamoto S, Matsuyama A, Sasaki N, Kimura I, Ohno H.	Cell Metab	10.1016/j.cmet.2025.04.013	2025
	Bifidobacterium animalis subsp. lactis BLa80 for preventing allergic, respiratory, and gastrointestinal diseases in young children in China: a randomized double-blind placebo-controlled trial.	Chen K, Zhang X, Zeng K, Zhong J, Jin S, Nie Y, Yang P, He N, Chen H, Cao Y, Fu Y, Fang Z, Jiang W, Liu C.	Clin Exp Pediatr	10.3345/cep.2025.01256	2025
	Liver abscess caused by Bacteroides thetaiotaomicron complicated by purulent pericarditis: a case report.	Liu Y, Zhang Y, Li Y, Yang J.	Am J Transl Res	10.62347/ffjx7040	2025
	Investigating Polyreactivity of CD4⁺ T Cells to the Intestinal Microbiota.	Saadawi A, Mair F, Rosenwald E, Hoces D, Slack E, Kopf M.	Eur J Immunol	10.1002/eji.202451484	2025
Genetics	Genomic characterization of a clinical Enterocloster aldenensis strain: First report in Thailand.	Yaikhan T, Yingkajorn M, Duangsi-Ngoen W, Thant EP, Chaichana N, Suwannasin S, Singkhamanan K, Churi S, Surachat K.	Infect Genet Evol	10.1016/j.meegid.2025.105800	2025
	An engineered gut bacterium protects against dietary methylmercury exposure in pregnant mice.	Yu KB, Chandra F, Coley-O'Rourke EJ, Paulson ET, Novoselov A, Zhang D, Finnigan D, Paramo J, Lopez-Romero A, Dong TS, Schartup AT, Hsiao EY.	Cell Host Microbe	10.1016/j.chom.2025.04.009	2025
	Targeting symbionts by apolipoprotein L proteins modulates gut immunity.	Yang T, Hu X, Cao F, Yun F, Jia K, Zhang M, Kong G, Nie B, Liu Y, Zhang H, Li X, Gao H, Shi J, Liang G, Hu G, Kasper DL, Song X, Qian Y.	Nature	10.1038/s41586-025-08990-4	2025
	Synergistic effects of human-origin novel postbiotic Bacteroides & Phocaeicola on obesity and thermogenesis in high-fat diet-induced metabolic dysfunction.	Wu L, Wang JH, Park SH, Cui Y, Han K, Kim H.	Benef Microbes	10.1163/18762891-bja00080	2025
Pathogenicity	A Nitrate/Nitrite Biosensor Designed with an Antiterminator for In Vivo Diagnosis of Colitis Based on Bacteroides thetaiotaomicron.	Yang X, Ye M, Wang F, Yang X, Gao X, Yu J, Liu W.	ACS Synth Biol	10.1021/acssynbio.4c00602	2025
	[Development of a miniaturized CRISPR/Cas gene editing tool for human gut Bacteroides].	Zhan Y, Zheng L, Shen J, Hu Y, Luo X, Dai L.	Sheng Wu Gong Cheng Xue Bao	10.13345/j.cjb.240959	2025
	Gut Microbiome Interventions: From Dysbiosis to Next-Generation Probiotics (NGPs) for Disease Management.	Gupta MK, Srivastava R.	Probiotics Antimicrob Proteins	10.1007/s12602-025-10582-7	2025
Phenotype	Modulation of butyrate-induced stress responses in Bacteroides by lotus seed resistant starch and its sugar degradation products.	Jiang Y, Zhang G, Su J, Zhang Y, Chang Q, Zeng H.	Carbohydr Polym	10.1016/j.carbpol.2025.123944	2025
	A novel cholesterol-reducing mechanism of polygonati rhizoma: Dual action via Bacteroides-mediated cholesterol sulfonation and feedback inhibition of ACAT2 by sulfated metabolite.	Wang X, Chen M, Su Y, Zhang X, Chen J, Huang Z, Xie J, Xie Q, He L, Su L, Su Z, Wang H, Li Y.	J Ethnopharmacol	10.1016/j.jep.2025.120619	2026
	Probiotic Engraftment of Akkermansia muciniphila in an In Vitro Synthetic Microbial Community.	Berkhout MD, de Ram C, Boeren S, Plugge CM, Belzer C.	Microb Ecol	10.1007/s00248-025-02605-1	2025
	Comprehensive profiling of genomic invertons in defined gut microbial community reveals associations with intestinal colonization and surface adhesion.	Jin X, Cheng AG, Chanin RB, Yu FB, Dimas A, Jasper M, Weakley A, Yan J, Bhatt AS, Pollard KS.	Microbiome	10.1186/s40168-025-02052-7	2025
	Saliva-driven surface-engineered Bacteroides thetaiotaomicron alleviates hypertension.	Xu S, Luo H, Du LJ, Dong T, Zhou LJ, Chen BY, Li YL, Tian GC, Meng XQ, Bai XB, Ye HL, Zhang J, Lin WZ, Zhang WC, Liu J, Duan SZ.	Bioact Mater	10.1016/j.bioactmat.2025.11.007	2026
	Distinct Adjacent Substrate Binding Pocket Regulates the Activity of a Decameric Feruloyl Esterase from Bacteroides thetaiotaomicron.	Wang Y, Du G, Zhang Y, Yu H, Liu S, Wang Z, Ma X, Wei X, Wen B, Li Z, Fan S, Xin F.	J Agric Food Chem	10.1021/acs.jafc.4c06286	2024
	Investigation of bacterial gut microbiome in diverse Egyptian populations "pilot study".	Mohamed KT, Shabayek S, Fahmy Mahmoud N, Tawfick MM, Hanora AMS.	Cell Mol Biol (Noisy-le-grand)	10.14715/cmb/2025.70.1.8	2025
	Ursolic acid attenuates sarcopenia through IL-17a-related gut-muscle axis in senile diabetic mice and myotube model.	She M, Li T, Zhou L, Deng Z, Huang M, Yan Y, Zhang M, Yang Y, Wang D.	J Nutr Biochem	10.1016/j.jnutbio.2025.109940	2025
	A rationally designed microbial consortium modulates neurodegeneration in a Drosophila melanogaster model of Parkinson's disease.	Ovalle A, Lopez E, Sierralta J, Paricio N, Garrido D.	NPJ Biofilms Microbiomes	10.1038/s41522-025-00797-5	2025
	Colonisation of Newborn Piglets with a Mixture of Bacteroides Species Improves Their Gut Health and Performance.	Matiasovicova J, Nechvatalova K, Karasova D, Sebkova A, Matiasovic J, Volf J, Babak V, Rychlik I.	Microorganisms	10.3390/microorganisms13102356	2025
	Antimicrobial resistance pattern of the Bacteroides fragilis group strains isolated at a teaching hospital in China.	Wu ZC, Feng HX, Wu L, Zhang M, Gu Z.	Acta Microbiol Immunol Hung	10.1556/030.2025.02400	2025
Metabolism	The association of objective daytime sleepiness with impaired glucose metabolism in patients with obstructive sleep apnea: a multi-omics study.	Chen L, Chen B, Dai Y, Sun Q, Wu J, Zheng D, Vgontzas AN, Tang X, Li Y.	Sleep	10.1093/sleep/zsae240	2025
Pathogenicity	Spatially resolved lipidomics shows conditional transfer of lipids produced by Bacteroides thetaiotaomicron into the mouse gut.	Mirretta Barone C, Heaver SL, Gruber L, Zundel F, Vu DL, Ley RE.	Cell Host Microbe	10.1016/j.chom.2024.04.021	2024
	Screening for Genes Involved in Outer Membrane Vesicle Biogenesis in Bacteroides thetaiotaomicron.	Pardue EJ, Feldman MF.	Methods Mol Biol	10.1007/978-1-0716-4055-5_5	2024
Pathogenicity	The effects of human volatiles produced by skin microbiota on Forcipomyia (Lasiohelea) taiwana host preference.	Lu T, Zhang Y, Gou D, Chen H, Hou X.	Pest Manag Sci	10.1002/ps.70089	2025
Enzymology	Enzyme Machinery for Bacterial Glucoside Metabolism through a Conserved Non-hydrolytic Pathway.	Kastner K, Bitter J, Pfeiffer M, Grininger C, Oberdorfer G, Pavkov-Keller T, Weber H, Nidetzky B.	Angew Chem Int Ed Engl	10.1002/anie.202410681	2024
	Bile-induced biofilm formation in Bacteroides thetaiotaomicron requires magnesium efflux by an RND pump.	Lopes A-A, Vendrell-Fernandez S, Deschamps J, Georgeault S, Cokelaer T, Briandet R, Ghigo J-M.	mBio	10.1128/mbio.03488-23	2024
	Expanded Diversity of Microbial Groups Capable of Anaerobic Pyrite Reduction and Assimilation of Dissolution Products.	Boyd ES, Payne D.	Environ Microbiol	10.1111/1462-2920.70125	2025
	Gut microbiota-based discovery of Houttuyniae Herba as a novel prebiotic of Bacteroides thetaiotaomicron with anti-colitis activity.	Zou LE, Yang YN, Zhan J, Cheng J, Fu Y, Cao Y, Yan X, Wang Y, Wu C.	Biomed Pharmacother	10.1016/j.biopha.2024.116302	2024
Metabolism	Carbohydrates and the oxidative branch of the pentose phosphate pathway modify Bacteroides thetaiotaomicron phage resistance by phase-variable S-layers.	Fuentes JJ, Singh S, Pudlo NA, Heaver SL, Ley RE, Martens EC.	J Bacteriol	10.1128/jb.00178-25	2025
	Comparison of clinical characteristics, risk factors, and outcomes of patients infected with Bacteroides fragilis group at a tertiary care hospital in central China between 2017 and March 2024.	Li Y, Zhao J, Ma Q, Xu J, Yuan Y, Zhang Q, Yan W, Xu W, Yang Z, Li G, Gao L, Wang B.	Anaerobe	10.1016/j.anaerobe.2024.102922	2025
	Discovery, structural characterization, and functional insights into a novel apiosidase from the GH140 family, isolated from a lignocellulolytic-enriched mangrove microbial community	Liberato MV, Paixao DAA, Tomazetto G, Ndeh D, Bolam DN, Squina FM.	Biotechnol Lett.		2024
	peu-MIR2916-p3-enriched garlic exosomes ameliorate murine colitis by reshaping gut microbiota, especially by boosting the anti-colitic Bacteroides thetaiotaomicron.	Wang X, Liu Y, Dong X, Duan T, Wang C, Wang L, Yang X, Tian H, Li T.	Pharmacol Res	10.1016/j.phrs.2024.107071	2024
	Hypolipidemic Effects of Mesona chinensis Benth Polysaccharides with Different Structures and Molecular Weights.	Du JL, Xiao LH, Yang JH, Luo Q, Li JW, Feng YS, Zhan RT, Yan P.	Chem Biodivers	10.1002/cbdv.202401210	2024
Pathogenicity	A perfusion host-microbe bioreactor (HMB) system that captures dynamic interactions of secreted metabolites between epithelial cells cocultured with a human gut anaerobe.	Yang J, Cassaday J, Wyche TP, Squadroni B, Newhard W, Trinh H, Cabral D, Hett E, Sana TR, Lee K, Kasper S.	Biotechnol Bioeng	10.1002/bit.28730	2024
Enzymology	Immobilized high-performance heparin lyase III for efficient preparation of low molecular weight heparin.	Yang F, Sun X, Lu J, Zhang L, Du G, Li J, Xu R, Kang Z.	Int J Biol Macromol	10.1016/j.ijbiomac.2024.135833	2024
	Adaptations in gut Bacteroidales facilitate stable co-existence with their lytic bacteriophages.	Cortes-Martin A, Buttimer C, Maier JL, Tobin CA, Draper LA, Ross RP, Kleiner M, Hill C, Shkoporov AN.	Gut Microbes	10.1080/19490976.2025.2507775	2025
	Bacteroides thetaiotaomicron metabolic activity decreases with polysaccharide molecular weight.	Wong JPH, Chillier N, Fischer-Stettler M, Zeeman SC, Battin TJ, Persat A.	mBio	10.1128/mbio.02599-23	2024
Genetics	Limitations of MALDI-TOF MS in identifying anaerobic bacteremia: challenges in polymicrobial infections and the role of whole-genome sequencing.	Hosoda T, Suzuki M, Matsuno T, Matsui K, Ohyama K, Doi Y.	Microbiol Spectr	10.1128/spectrum.01014-25	2025
	Intragenic DNA inversions expand bacterial coding capacity.	Chanin RB, West PT, Wirbel J, Gill MO, Green GZM, Park RM, Enright N, Miklos AM, Hickey AS, Brooks EF, Lum KK, Cristea IM, Bhatt AS.	Nature	10.1038/s41586-024-07970-4	2024
	Bacteroides thetaiotaomicron and its inactivated bacteria ameliorate colitis by inhibiting macrophage activation.	Yinhe S, Lixiang L, Yan L, Xiang G, Yanqing L, Xiuli Z.	Clin Res Hepatol Gastroenterol	10.1016/j.clinre.2023.102276	2024
	CRISPRi-Driven Genetic Screening for Designing Novel Microbial Phenotypes.	Kang M, Kim K, Cho BK.	Methods Mol Biol	10.1007/978-1-0716-3658-9_7	2024
	Novel Signal Peptides and Episomal Plasmid System for Enhanced Protein Secretion in Engineered Bacteroides Species.	Kim TH, Ju K, Kim SK, Woo SG, Lee JS, Lee CH, Rha E, Shin J, Kwon KK, Lee H, Kim H, Lee SG, Lee DH.	ACS Synth Biol	10.1021/acssynbio.3c00649	2024
Pathogenicity	What is the link between the dietary inflammatory index and the gut microbiome? A systematic review.	Mirhosseini SM, Mahdavi A, Yarmohammadi H, Razavi A, Rezaei M, Soltanipur M, Karimi Nemch M, Jafari Naeini S, Siadat SD.	Eur J Nutr	10.1007/s00394-024-03470-3	2024
	Infection-relevant conditions dictate differential versus coordinate expression of Salmonella chaperones and cochaperones.	Chan C, Mukai K, Groisman EA.	mBio	10.1128/mbio.00227-25	2025
	Quantification and Correlation Analysis of Bacteroides Species with Diabetes-Related Amino Acids in Individuals with Prediabetes and Type 2 Diabetes Mellitus.	Safari-Alighiarloo N, Bostanghadiri N, Sedighi M, Mohebbi A, Vafaei E, Mirshekar M, Razavi S, Alaei-Shahmiri F.	Metab Syndr Relat Disord	10.1089/met.2024.0071	2024
	Modulation of satiety hormones by Bacteroides thetaiotaomicron, Bacteroides fragilis and their derivatives.	Vaezijoze S, Irani S, Siadat SD, Zali M.	AMB Express	10.1186/s13568-025-01852-2	2025
	Bacteroides thetaiotaomicron With Concomitant Streptococcus milleri as a Cause of Purulent Pericarditis: A Case Report.	Mohammed F, Haider S, Akbar M, Saleem S, Lin C.	Cureus	10.7759/cureus.63153	2024
Metabolism	Metabolite dependence of antibiotic susceptibility in a gut microbe.	Allison KR.	mSphere	10.1128/msphere.00600-24	2024
	Can our microbiome break our hearts? Collaborative production of p-cresol sulfate and indoxyl sulfate by commensal microbes increases susceptibility to thrombosis.	Machado Ribeiro TR, Brito CB, Byndloss MX.	mBio	10.1128/mbio.02692-23	2024
	Discovery, structural characterization, and functional insights into a novel apiosidase from the GH140 family, isolated from a lignocellulolytic-enriched mangrove microbial community.	Liberato MV, Paixao DAA, Tomazetto G, Ndeh D, Bolam DN, Squina FM.	Biotechnol Lett	10.1007/s10529-023-03460-1	2024
	Not losing sight of the bigger picture of complications associated with post-polypectomy syndrome: A case report and review of literature.	Suarez M, Martinez R, Santiago-Ramos PC.	World J Clin Cases	10.12998/wjcc.v13.i31.110734	2025
	Peanut supplementation affects compositions and functions of gut microbiome in Ugandan children.	Wang JS, Xue K, Li Z, Ssempebwa J, Wamuyu-Maina G, Musinguzi G, Rhoads J, Hoisington D, Tang L.	Food Funct	10.1039/d3fo04645a	2024
Genetics	Unveiling the causal effects of gut microbiome on trimethylamine N-oxide: evidence from Mendelian randomization.	Yu Y, Yin Y, Deng J, Yang X, Bai S, Yu R.	Front Microbiol	10.3389/fmicb.2024.1465455	2024
	Abdominal Necrotizing Fasciitis Secondary to Perforated Colon Cancer.	Devkota A, Shrestha A, Bilalaga MM, Gaddipati G, Haas CJ.	J Community Hosp Intern Med Perspect	10.55729/2000-9666.1516	2025
Enzymology	A mathematical model of competition between fiber and mucin degraders in the gut provides a possible explanation for mucus thinning.	Jegatheesan T, Moorthy AS, Eberl HJ.	J Theor Biol	10.1016/j.jtbi.2024.111824	2024
Pathogenicity	Escherichia coli is implicated in the development and manifestation of host susceptibility to the roundworm Trichostrongylus colubriformis infections in sheep.	Liu F, McNally J, Fleming DS, Ingham AB, Hunt PW, Li RW.	Vet Res	10.1186/s13567-025-01565-1	2025
Genetics	CRISPR Interference-Based Functional Small RNA Genomics.	Prezza G, Westermann AJ.	Methods Mol Biol	10.1007/978-1-0716-3565-0_6	2024
	Exploring the interactive mechanism of acarbose with the amylase SusG in the starch utilization system of the human gut symbiont Bacteroides thetaiotaomicron through molecular modeling.	Kwain S, Dominy BN, Whitehead KJ, Miller BA, Whitehead DC.	Chem Biol Drug Des	10.1111/cbdd.14251	2023
Metabolism	Exploring potential polysaccharide utilization loci involved in the degradation of typical marine seaweed polysaccharides by Bacteroides thetaiotaomicron.	Yu B, Lu Z, Zhong S, Cheong KL.	Front Microbiol	10.3389/fmicb.2024.1332105	2024
	The use of a multicellular in vitro model to investigate uptake and migration of bacterial extracellular vesicles derived from the human gut commensal Bacteroides thetaiotaomicron.	Modasia AA, Jones EJ, Martel LM, Louvel H, Couraud PO, Blackshaw LA, Carding SR.	J Extracell Biol	10.1002/jex2.93	2023
	Screening competition and cross-feeding interactions during utilization of human milk oligosaccharides by gut microbes.	Diaz R, Garrido D.	Microbiome Res Rep	10.20517/mrr.2023.61	2024
	Collateral pathways arising from internal jugular venous occlusion in Lemierre's syndrome.	Ishikawa K, Mori N.	Clin Case Rep	10.1002/ccr3.9338	2024
	High-fat diet increases circulating palmitic acid produced by gut Bacteroides thetaiotaomicron to promote thrombosis.	Huang X, Tang X, He Q, Tadese DA, Cao K, Gao J, Xu Q, Cheng R, Lu Q, Chen Y, Yang M, Du Y, Mwangi J, Ni H, Lai R.	Cell Rep Med	10.1016/j.xcrm.2025.102260	2025
Enzymology	Novel beta-galactosidase activity and first crystal structure of Glycoside Hydrolase family 154.	Hameleers L, Pijning T, Gray BB, Faure R, Jurak E.	N Biotechnol	10.1016/j.nbt.2023.12.011	2024
	Understanding the substrate recognition and catalytic mechanism of 2-O-methyl fucosidases from glycoside hydrolase family 139.	McIver Z, Moraleda-Montoya A, Chen Z, Epa R, Starns D, Davy M, Garcia-Alija M, Basle A, Schubert M, Ndeh D, Trastoy B, Williams SJ, Guerin ME, Cartmell A.	J Biol Chem	10.1016/j.jbc.2025.110407	2025
	Trifecta of Abscesses of the Prostate, Bilateral Seminal Vesicles, and Left Epididymis Caused by Staphylococcus aureus: A Report of a Rare Case.	Nakamura M, Matsukawa M.	Cureus	10.7759/cureus.75573	2024
	WITHDRAWN: Bacteroides thetaiotaomicron necrotizing fasciitis as presentation of colorectal cancer, with subsequent cutaneous exteriorization.	Ferrer Inaebnit E, Gil Catalan A, Alfonso Garcia M, Fernandez Isaart M, Coll Sastre M, Gamundi Cuesta M, Gonzalez Argente FX.	Rev Esp Enferm Dig	10.17235/reed.2023.9606/2023	2023
Pathogenicity	Salmonella Typhimurium expansion in the inflamed murine gut is dependent on aspartate derived from ROS-mediated microbiota lysis.	Yoo W, Shealy NG, Zieba JK, Torres TP, Baltagulov M, Thomas JD, Shelton CD, McGovern AG, Foegeding NJ, Olsan EE, Byndloss MX.	Cell Host Microbe	10.1016/j.chom.2024.05.001	2024
	Arylsulfamates inhibit colonic Bacteroidota growth through a sulfatase-independent mechanism.	Crawford CJ, Tomlinson CWE, Gunawan C, Chen Z, Byrne DP, Darby C, Conti MLG, Larson T, Luis AS, Elli S, Yates EA, Bolam DN, van der Post S, Williams SJ, Cartmell A.	Proc Natl Acad Sci U S A	10.1073/pnas.2414331122	2025
Genetics	nf-UnO pipeline: A metagenomic co-assembly pipeline for novel pathogen detection from mNGS outbreak sets.	Guzman-Cole C, Huang AD.	Bioinformatics	10.1093/bioinformatics/btaf436	2025
	Chemoproteomic identification of a DPP4 homolog in Bacteroides thetaiotaomicron.	Keller LJ, Nguyen TH, Liu LJ, Hurysz BM, Lakemeyer M, Guerra M, Gelsinger DJ, Chanin R, Ngo N, Lum KM, Faucher F, Ipock P, Niphakis MJ, Bhatt AS, O'Donoghue AJ, Huang KC, Bogyo M.	Nat Chem Biol	10.1038/s41589-023-01357-8	2023
	Gut Commensal Bacteroides thetaiotaomicron Promote Atherothrombosis via Regulating L-Tryptophan Metabolism.	Liu H, Feng S, Tang M, Tian R, Zhang S.	Rev Cardiovasc Med	10.31083/j.rcm2511395	2024
	Multiple TonB homologs are important for carbohydrate utilization by Bacteroides thetaiotaomicron.	Pollet RM, Foley MH, Kumar SS, Elmore A, Jabara NT, Venkatesh S, Vasconcelos Pereira G, Martens EC, Koropatkin NM.	J Bacteriol	10.1128/jb.00218-23	2023
	Cas9-assisted biological containment of a genetically engineered human commensal bacterium and genetic elements.	Hayashi N, Lai Y, Fuerte-Stone J, Mimee M, Lu TK.	Nat Commun	10.1038/s41467-024-45893-w	2024
	Does schistosome infection affect behavior through the gut-brain axis?	Combrink L, Spaan JM, Perret A, Maehara T, Hyun B, Parker D, Johns JL, Blouin MS, Magnusson K, Steinauer ML.	PLoS Negl Trop Dis	10.1371/journal.pntd.0013088	2025
	A pectic polysaccharide isolated from Achyranthes bidentata is metabolized by human gut Bacteroides spp.	Wen C, Li T, Wang B, Jin C, Li S, Li Y, Li M, Ding K.	Int J Biol Macromol	10.1016/j.ijbiomac.2023.125785	2023
	Outer membrane utilisomes mediate glycan uptake in gut Bacteroidetes.	White JBR, Silale A, Feasey M, Heunis T, Zhu Y, Zheng H, Gajbhiye A, Firbank S, Basle A, Trost M, Bolam DN, van den Berg B, Ranson NA.	Nature	10.1038/s41586-023-06146-w	2023
	Enzyme-functionalized alginate microparticles enable anaerobic culture under ambient oxygen.	Williams TJ, Daboin C, Kim P, Guo F, de Figueiredo P, Alge DL.	Biotechnol Bioeng	10.1002/bit.28566	2024
Proteome	Mapping multi-omics characteristics related to short-term PM_2.5 trajectory and their impact on type 2 diabetes in middle-aged and elderly adults in Southern China.	Wang JT, Hu W, Xue Z, Cai X, Zhang SY, Li FQ, Lin LS, Chen H, Miao Z, Xi Y, Guo T, Zheng JS, Chen YM, Lin HL.	J Hazard Mater	10.1016/j.jhazmat.2024.133784	2024
	Gut microbiota of the small intestine as an antimicrobial barrier against foodborne pathogens: Impact of diet on the survival of S. Typhimurium and L. monocytogenes during in vitro digestion	Akritidou T, Akkermans S, Smet C, Gaspari S, Sharma C, Matthews E, Van Impe JFM.	Food Research International.		2023
	Polysaccharide utilization loci encoded DUF1735 likely functions as membrane-bound spacer for carbohydrate active enzymes.	Hameleers L, Gaenssle LA, Bertran-Llorens S, Pijning T, Jurak E.	FEBS Open Bio	10.1002/2211-5463.13816	2024
	A taxon-specific measurement of disruption in a multi-modal study of microbiomes and metabolomes reveals system-wide dysbiosis preceding HIV-1 infection.	Fouladi F, Chen Y, Bera S, Jarmusch AK, Van Tyne D, Palella FJ, Margolick JB, Chew KW, Sun J, Martinson J, Rinaldo CR, Peddada SD.	Nat Commun	10.1038/s41467-025-64822-z	2025
	Bacteroides methylmalonyl-CoA mutase produces propionate that promotes intestinal goblet cell differentiation and homeostasis.	Wang X, Cai Z, Wang Q, Wu C, Sun Y, Wang Z, Xu X, Xue W, Cao Z, Zhang M, Zhu Y, Lin H, Zhang Y, Yuan M, Zhao Y, Gao A, Yu Y, Bi Y, Ning G, Wang W, Wang J, Liu R.	Cell Host Microbe	10.1016/j.chom.2023.11.005	2024
	Tracking and characterization of a novel conjugative transposon identified by shotgun transposon mutagenesis.	Ortanez J, Degnan PH.	Front Microbiol	10.3389/fmicb.2024.1241582	2024
	Dietary carbohydrates alter immune-modulatory functionalities and DNA inversions in Bacteroides thetaiotaomicron.	Gal-Mandelbaum N, Carasso S, Kedem A, Ziv T, Keshet-David R, Abboud R, Zaatry R, Gefen T, Geva-Zatorsky N.	Nat Commun	10.1038/s41467-025-60202-9	2025
	Functional annotation of haloacid dehalogenase superfamily structural genomics proteins.	Pathira Kankanamge LS, Ruffner LA, Touch MM, Pina M, Beuning PJ, Ondrechen MJ.	Biochem J	10.1042/bcj20230057	2023
	Discrete genetic loci in human gut Bacteroides thetaiotaomicron confer pectin metabolism	Li M, Li S, Guo X, Guo C, Wang Y, Du Z, Zhang Z, Xie C, Ding K.	Carbohydrate polymers.		2022
	Combinatorial effects of tryptophan derivatives serotonin and indole on virulence modulation of enteric pathogens.	Hoskan MA, Sperandio V.	mBio	10.1128/mbio.02067-25	2025
	Human gut microbes express functionally distinct endoglycosidases to metabolize the same N-glycan substrate.	Sastre DE, Sultana N, V A S Navarro M, Huliciak M, Du J, Cifuente JO, Flowers M, Liu X, Lollar P, Trastoy B, Guerin ME, Sundberg EJ.	Nat Commun	10.1038/s41467-024-48802-3	2024
Enzymology	Novel Endo-beta-N-Acetylglucosaminidases Derived from Human Fecal Samples Selectively Release N-Glycans from Model Glycoproteins.	Bolino M, Haththotuwe Gamage N, Duman H, Abiodun O, De Mello AS, Karav S, Frese SA.	Foods	10.3390/foods14081288	2025
	Coordinated regulation of Bacteroides thetaiotaomicron glutamate decarboxylase activity by multiple elements under different pH.	Liu S, Wen B, Du G, Wang Y, Ma X, Yu H, Zhang J, Fan S, Zhou H, Xin F.	Food Chem	10.1016/j.foodchem.2022.134436	2023
Genetics	Structure-dependent degradation of milk oligosaccharides by newly isolated intestinal commensal bacterial strains from suckling piglets and rabbits.	Rumeau M, Chadi S, Pepke F, Beaumont M, Vicente CM, Juppeau A, Vandecasteele C, Cauquil L, Pascal G, Langella P, Knudsen C, Combes S, Martin R.	BMC Microbiol	10.1186/s12866-025-04205-y	2025
Genetics	Micromix: web infrastructure for visualizing and remixing microbial 'omics data.	Hayward RJ, Ebbecke T, Fricke H, Nguyen VQ, Barquist L.	Gigascience	10.1093/gigascience/giae120	2025
	A high-resolution genomic and phenotypic analysis of resistance evolution of an Escherichia coli strain from a critically unwell patient treated with piperacillin/tazobactam.	Fraser AJ, Ball R, Cantillon D, Brettell LE, Graf FE, Munnoch JT, Hoskisson PA, Lewis JM, van Aartsen JJ, Parry CM, Heinz E, Edwards T.	J Med Microbiol	10.1099/jmm.0.002018	2025
	Structural insights into the oligomeric effects on catalytic activity of a decameric feruloyl esterase and its application in ferulic acid production.	Du G, Wang Y, Zhang Y, Yu H, Liu S, Ma X, Cao H, Wei X, Wen B, Li Z, Fan S, Zhou H, Xin F.	Int J Biol Macromol	10.1016/j.ijbiomac.2023.126540	2023
	PD-L1 deficiency exacerbates colitis severity by remodeling gut microbiota in inflammatory bowel disease.	Ma Y, Suo J, Sheng S, Chen L.	Front Immunol	10.3389/fimmu.2025.1622744	2025
	Adjuvant A-PRF Application in Patients with Various Stages of Medication-Related Osteonecrosis of the Jaw (MRONJ): Case Series.	Vasilcenko I, Cema I, Bagante I.	Reports (MDPI)	10.3390/reports8040240	2025
	Exploring the mediating role of the plasma lipidome in the pathway from the gut microbiota to dementia: a Mendelian randomization study.	Li B, Sun X, Luo X, Kan Y, Wang W, Wang T, Wu C, Hu Y, Bi X.	Arch Med Sci	10.5114/aoms/201447	2025
	Gut microbiota, immune cells, and chronic sinusitis: A Mendelian randomization analysis.	Huang J, Zhu X, Yao J, Yang W, Zhu Z.	Medicine (Baltimore)	10.1097/md.0000000000041093	2025
	Otogenic Cerebellar Abscess with Polymicrobial Anaerobic Infection in a Young Female- A Rare Presentation.	Sharma B, Sreenivasan P, Singh A, Mondal PS, Ray P, Angrup A.	Indian J Otolaryngol Head Neck Surg	10.1007/s12070-023-04218-x	2024
	Diagnostic and epidemiological landscape of anaerobic bacteria in Europe, 2020-2023 (ANAEuROBE).	Boattini M, Bianco G, Bastos P, Mavromanolaki VE, Maraki S, Spiliopoulou A, Kakouris V, Kalchev Y, Budimir A, Bedenic B, Rubic Z, Licker M, Musuroi C, Juhasz E, Kristof K, Pirs M, Velimirovic I, Berktold M, Liptakova A, Krajcikova A, Drevinek P, Gryndlerova A, Brzychczy-Wloch M, Olechowska-Jarzab A, Bielec F, Brauncajs M, Podsiadly E, Nurzynska G, Zalas-Wiecek P, Riesbeck K, Andersson HS, Tonjum T, Berild JC, Leegaard TM, Rasmussen AN, Schonning K, Glockner S, Rodel J, Badr MT, Hacker GA, Stark D, Hamprecht A, Dudakova A, Jantsch J, Mancini S, Quiblier C, Jacot D, Greub G, Ferniani T, Ambretti S, Calvo M, Stefani S, Schade R, Yusuf E, Koeveringe SVK, Vandamme S, Verroken A, Rodriguez-Villalobos H, Duigou F, Corvec S, Floch P, Massip C, Chainier D, Barraud O, Louissaint MB, Mizrahi A, Ali S, Doyle M, Egan C, McNicholas S, Colomina-Rodriguez J, Torres I, Luengo RG, Escartin MNL, Perez MBV, Halperin AV, Garcia SF, Canton R, Seruca M, Mendes VS, Carvalho D, Cavallo R, Cristino JM, Costa C.	Int J Antimicrob Agents	10.1016/j.ijantimicag.2025.107478	2025
Genetics	Multi-cohort metagenomics reveals strain functional heterogeneity and demonstrates fecal microbial load correction improves colorectal cancer diagnostic models.	Li Q, Liu F, Zhong J, Fang X, Zhang X, Xiong H, Li G, Chen H.	Front Microbiol	10.3389/fmicb.2025.1656016	2025
	Effect of antibiotic administration on Blastocystis persistence and gut microbiome-metabolome dynamics in an irritable bowel syndrome longitudinal case study.	Newton JM, Edwards WJS, Thompson GS, Gentekaki E, Tsaousis AD.	Access Microbiol	10.1099/acmi.0.000926.v4	2025
	Substrate Selectivities of GH78 alpha-L-Rhamnosidases from Human Gut Bacteria on Dietary Flavonoid Glycosides.	Li BC, Wu B, Hou X, Ding GB.	Molecules	10.3390/molecules30050980	2025
Genetics	Highly efficient CRISPR-mediated base editing for the gut Bacteroides spp. with pnCasBS-CBE.	Liang J, Tan Y.	Biotechnol J	10.1002/biot.202200504	2023
	A Bacteroides thetaiotaomicron genetic locus encodes activities consistent with mucin O-glycoprotein processing and N-acetylgalactosamine metabolism.	Ndeh DA, Nakjang S, Kwiatkowski KJ, Sawyers C, Koropatkin NM, Hirt RP, Bolam DN.	Nat Commun	10.1038/s41467-025-58660-2	2025
	A dietary intervention for postmenopausal hot flashes: A potential role of gut microbiome. An exploratory analysis.	Kahleova H, Holtz DN, Strom N, La Reau A, Kolipaka S, Schmidt N, Hata E, Znayenko-Miller T, Holubkov R, Barnard ND.	Complement Ther Med	10.1016/j.ctim.2023.103002	2023
	The intracellular proteome of the gut bacterium Bacteroides thetaiotaomicron is widely unaffected by a switch from glucose to sucrose as main carbohydrate source.	Genth J, Kaleja P, Treitz C, Schafer K, Graspeuntner S, Rupp J, Tholey A.	Proteomics	10.1002/pmic.202200189	2022
	Gut microbiota of the small intestine as an antimicrobial barrier against foodborne pathogens: Impact of diet on the survival of S. Typhimurium and L. monocytogenes during in vitro digestion.	Akritidou T, Akkermans S, Smet C, Gaspari S, Sharma C, Matthews E, Van Impe JFM.	Food Res Int	10.1016/j.foodres.2023.113292	2023
	BAV-LLPS: a database of bacterial, archaea, and virus liquid-liquid phase separation proteins.	Rodriguez CB, Tunque Cahui RR, Demitroff N, Hirsh L, Devos DP, Boccaccio G, Parisi G.	Bioinformatics	10.1093/bioinformatics/btaf550	2025
	Bacteroides thetaiotaomicron enhances oxidative stress tolerance through rhamnose-dependent mechanisms.	Xie S, Ma J, Lu Z.	Front Microbiol	10.3389/fmicb.2024.1505218	2024
Enzymology	Linker-peptide-mediated one-step purification and immobilization of alpha-L-rhamnosidase from Bacteroides thetaiotaomicron for direct biotransformation from epimedin C to icariin.	Lu C, Zou K, Guo B, Li Q, Wang Z, Xiao W, Zhao L.	Enzyme Microb Technol	10.1016/j.enzmictec.2022.110131	2023
	Structural changes of polysaccharides from Astragulus after honey processing and their bioactivities on human gut microbiota.	Tian Y, Wu J, Zheng Y, Li M, Xu X, Chen H, Rui W.	J Sci Food Agric	10.1002/jsfa.12808	2023
	Engineering the human gut commensal Bacteroides thetaiotaomicron with synthetic biology.	Lai Y, Hayashi N, Lu TK.	Curr Opin Chem Biol	10.1016/j.cbpa.2022.102178	2022
	A Possible Aquatic Origin of the Thiaminase TenA of the Human Gut Symbiont Bacteroides thetaiotaomicron.	Stentz R, Cheema J, Philo M, Carding SR.	J Mol Evol	10.1007/s00239-023-10101-8	2023
	CRISPR-based screening of small RNA modulators of bile susceptibility in Bacteroides thetaiotaomicron.	Prezza G, Liao C, Reichardt S, Beisel CL, Westermann AJ.	Proc Natl Acad Sci U S A	10.1073/pnas.2311323121	2024
	The aerobic electron flux is deficient in fumarate respiration of a strict anaerobe Bacteroides thetaiotaomicron.	Lin L, Zou M, Lu Z.	Biochem Biophys Res Commun	10.1016/j.bbrc.2022.05.017	2022
	Biocatalytic synthesis of phenyl benzoate esters using the amide ligase ClxA.	Ascham A, Tang Q, Fairlamb IJS, Grogan G.	RSC Chem Biol	10.1039/d5cb00205b	2025
Genetics	O-Mucin-degrading carbohydrate-active enzymes and their possible implication in inflammatory bowel diseases.	Labourel A, Parrou JL, Deraison C, Mercier-Bonin M, Lajus S, Potocki-Veronese G.	Essays Biochem	10.1042/ebc20220153	2023
	Tumor Tissue Microbiota in Colorectal Cancer: PCR Profile of FFPE Blocks in Associations with Metastatic Status.	Shakhpazyan NK, Mikhaleva LM, Sadykhov NK, Midiber KY, Buchaka AS, Gioeva ZV, Mikhalev AI, Bedzhanyan AL.	Cells	10.3390/cells14191508	2025
	An Eleven-Year Retrospective Survey of Anaerobic Bloodstream Infection in Adults in a General Hospital.	Yang R, Wang W, Yin G, Ma T, Tao J.	Infect Drug Resist	10.2147/idr.s482698	2024
	Crystal Structure of CcGH131B, a Protein Belonging to Glycoside Hydrolase Family 131 from the Basidiomycete Coprinopsis cinerea.	Shiojima Y, Sano R, Kozono T, Nishikawa A, Kojima Y, Yoshida M, Sunagawa N, Igarashi K, Tonozuka T.	J Appl Glycosci (1999)	10.5458/jag.7202104	2025
	Diagnostic accuracy and clinical impact of filmarray multiplex PCR system in bloodstream infections: A comparative study with conventional methods in a tertiary health care setting.	Aygar IS, Hosbul T.	Medicine (Baltimore)	10.1097/md.0000000000043263	2025
	Metagenome-wide association study of gut microbiome features for myositis.	Li Y, Xu J, Hong Y, Li Z, Xing X, Zhufeng Y, Lu D, Liu X, He J, Li Y, Sun X.	Clin Immunol	10.1016/j.clim.2023.109738	2023
	Steamed broccoli sprouts alleviate DSS-induced inflammation and retain gut microbial biogeography in mice.	Holman JM, Colucci L, Baudewyns D, Balkan J, Hunt T, Hunt B, Kinney M, Holcomb L, Stratigakis A, Chen G, Moses PL, Mawe GM, Zhang T, Li Y, Ishaq SL.	mSystems	10.1128/msystems.00532-23	2023
Proteome	Proteomics of Bacterial and Mouse Extracellular Vesicles Released in the Gastrointestinal Tracts of Nutrient-Stressed Animals Reveals an Interplay Between Microbial Serine Proteases and Mammalian Serine Protease Inhibitors.	Stentz R, Jones E, Gul L, Latousakis D, Parker A, Brion A, Goldson AJ, Gotts K, Carding SR.	Int J Mol Sci	10.3390/ijms26094080	2025
	Ruminococcus torques is a keystone degrader of intestinal mucin glycoprotein, releasing oligosaccharides used by Bacteroides thetaiotaomicron.	Schaus SR, Vasconcelos Pereira G, Luis AS, Madlambayan E, Terrapon N, Ostrowski MP, Jin C, Henrissat B, Hansson GC, Martens EC.	mBio	10.1128/mbio.00039-24	2024
	Production of deoxycholic acid by low-abundant microbial species is associated with impaired glucose metabolism.	Wahlstrom A, Brumbaugh A, Sjoland W, Olsson L, Wu H, Henricsson M, Lundqvist A, Makki K, Hazen SL, Bergstrom G, Marschall HU, Fischbach MA, Backhed F.	Nat Commun	10.1038/s41467-024-48543-3	2024
	An expanded transcriptome atlas for Bacteroides thetaiotaomicron reveals a small RNA that modulates tetracycline sensitivity.	Ryan D, Bornet E, Prezza G, Alampalli SV, Franco de Carvalho T, Felchle H, Ebbecke T, Hayward RJ, Deutschbauer AM, Barquist L, Westermann AJ.	Nat Microbiol	10.1038/s41564-024-01642-9	2024
	Structure of a distinct beta-barrel assembly machinery complex in the Bacteroidota.	Silale A, Madej M, Mikruta K, Frey AM, Hart AJ, Basle A, Scavenius C, Enghild JJ, Trost M, Hirt RP, van den Berg B.	Nat Microbiol	10.1038/s41564-025-02132-2	2025
	Metagenomic Analysis of Gut Microbiota for Abdominal Aortic Aneurysm.	Ito E, Ohki T, Toya N, Emoto T, Yamashita T, Sugiyama T, Yamada T, Mori H, Toyoda A, Hirata KI.	Ann Vasc Dis	10.3400/avd.oa.24-00105	2025
	Microbiome engineering: unlocking therapeutic potential in inflammatory bowel disease.	Kong C, Huang LB, Yang MF, Yue NN, Luo D, Zhang Y, Tian CM, Song Y, Wei DR, Shi RY, Liang YJ, Yao J, Wang LS, Li DF.	Front Microbiol	10.3389/fmicb.2025.1610029	2025
	Production, Isolation, and Characterization of Bioengineered Bacterial Extracellular Membrane Vesicles Derived from Bacteroides thetaiotaomicron and Their Use in Vaccine Development.	Stentz R, Miquel-Clopes A, Carding SR.	Methods Mol Biol	10.1007/978-1-0716-1900-1_11	2022
	Disruption and adaptation: infant gut microbiota's dynamic response to SARS-CoV-2 infection.	Zhu LT, Zhao L, Zhu Y, Xu XL, Lin JJ, Duan YF, Long L, Wu YY, Xu WJ, Chen JY, Yin YH, Obeten AU, Huang Q.	Microbiome	10.1186/s40168-025-02029-6	2025
Metabolism	A mucin-responsive hybrid two-component system controls Bacteroides thetaiotaomicron colonization and gut homeostasis.	Lee JH, Kwon SJ, Han JY, Cho SH, Cho YJ, Park JH.	J Microbiol	10.1007/s12275-022-1649-3	2022
	Multiomics approach reveals the comprehensive interactions between nutrition and children's gut microbiota, and microbial and host metabolomes.	Zhu M, Wang Q, Yang Y, Liu X, Zhang J, Li G, Liu W, Xiang X, Chen J.	Nutr J	10.1186/s12937-025-01116-6	2025
Genetics	Metagenomic analysis demonstrates distinct changes in the gut microbiome of Kawasaki diseases children.	Han L, Liu X, Lan Y, Hua Y, Fan Z, Li Y.	Front Immunol	10.3389/fimmu.2024.1416185	2024
Pathogenicity	Human-derived microRNA 21 regulates indole and L-tryptophan biosynthesis transcripts in the gut commensal Bacteroides thetaiotaomicron.	Flanagan K, Gassner K, Lang M, Ozelyte J, Hausmann B, Crepaz D, Pjevac P, Gasche C, Berry D, Vesely C, Pereira FC.	mBio	10.1128/mbio.03928-24	2025
	Ruminococcus bromii enables the growth of proximal Bacteroides thetaiotaomicron by releasing glucose during starch degradation.	Rangarajan AA, Chia HE, Azaldegui CA, Olszewski MH, Pereira GV, Koropatkin NM, Biteen JS.	Microbiology (Reading)	10.1099/mic.0.001180	2022
	Folate Production by Streptococcus thermophilus IDCC 2201 and Its Impact on Human Gut Microbiota.	Nam EH, Lee M, Kim D, Jung YH, Yang J, Shin M.	J Microbiol Biotechnol	10.4014/jmb.2502.02045	2025
	The first report of enzymatic transglycosylation catalyzed by family GH84 N-acetyl-beta-d-glucosaminidase using a sugar oxazoline derivative as a glycosyl donor.	Tanaka T, Habuchi Y, Okuno R, Nishimura S, Tsuji S, Aso Y, Ohnuma T.	Carbohydr Res	10.1016/j.carres.2023.108740	2023
	The global RNA-binding protein RbpB is a regulator of polysaccharide utilization in Bacteroides thetaiotaomicron.	Ruttiger AS, Ryan D, Spiga L, Lamm-Schmidt V, Prezza G, Reichardt S, Langford M, Barquist L, Faber F, Zhu W, Westermann AJ.	Nat Commun	10.1038/s41467-024-55383-8	2025
	Omental infarction following robotic-assisted laparoscopic inguinal hernia repair.	Hassanesfahani M, Tian J, Keating L, Khan N, Louis MA, Malhotra R.	J Surg Case Rep	10.1093/jscr/rjae343	2024
	Diet leaves a genetic signature in a keystone member of the gut microbiota.	Dapa T, Ramiro RS, Pedro MF, Gordo I, Xavier KB.	Cell Host Microbe	10.1016/j.chom.2022.01.002	2022
Metabolism	The human symbiont Bacteroides thetaiotaomicron promotes diet-induced obesity by regulating host lipid metabolism.	Cho SH, Cho YJ, Park JH.	J Microbiol	10.1007/s12275-022-1614-1	2022
	Childhood obesity and insulin resistance is correlated with gut microbiome serum protein: an integrated metagenomic and proteomic analysis.	Liu L, Li M, Qin Y, Liu Y, Li M, Lian B, Guo R, Xiao Y, Yin C.	Sci Rep	10.1038/s41598-025-07357-z	2025
	Development and application of a multiplex PCR system for forensic salivary identification.	Liang X, Liu X, Ye L, Du W, Huang L, Liu C, Xiao G, Huang M, Zheng Y, Shi M, Liu C, Chen L.	Int J Legal Med	10.1007/s00414-023-03004-2	2023
	Gut microbiota is associated with persistence of longer-term BNT162b2 vaccine immunogenicity.	Ng HY, Liao Y, Cheung CL, Zhang R, Chan KH, Seto WK, Leung WK, Hung IFN, Lam TTY, Cheung KS.	Front Immunol	10.3389/fimmu.2025.1534787	2025
	Metabolic changes associated with polysaccharide utilization reduce susceptibility to some beta-lactams in Bacteroides thetaiotaomicron.	Nilson R, Penumutchu S, Pagano FS, Belenky P.	mSphere	10.1128/msphere.00103-24	2024
	Unfolding and de-confounding: biologically meaningful causal inference from longitudinal multi-omic networks using METALICA.	Ruiz-Perez D, Gimon I, Sazal M, Mathee K, Narasimhan G.	mSystems	10.1128/msystems.01303-23	2024
	Differential temporal release and lipoprotein loading in B. thetaiotaomicron bacterial extracellular vesicles.	Juodeikis R, Martins C, Saalbach G, Richardson J, Koev T, Baker DJ, Defernez M, Warren M, Carding SR.	J Extracell Vesicles	10.1002/jev2.12406	2024
	Dacryocystitis Involving Parvimonas micra and Bacteroides thetaiotaomicron Infection.	Abouodah H, Nasrazadani DA, Sokol JA.	Kans J Med	10.17161/kjm.vol15.18273	2022
	Slackia exigua, an emerging anaerobic pathogen - isolation from a case of polymicrobial peritonitis and review of literature.	Kumaresan M, Agarwal R H, Fysel AM, Jayagandan S, Biswas R, Sundaramurthi S.	IDCases	10.1016/j.idcr.2024.e02008	2024
	A Globally Distributed Bacteroides caccae Strain Is the Most Prevalent Mother-Child Shared Bacteroidaceae Strain in a Large Scandinavian Cohort.	Nilsen M, Rehbinder EM, Lodrup Carlsen KC, Haugen G, Hedlin G, Jonassen CM, Killingstad ME, Nordlund B, Ormaasen I, Skjerven HO, Snipen L, Staff AC, Soderhall C, Sorensen R, Vettukattil R, Wilborn LM, Rudi K.	Appl Environ Microbiol	10.1128/aem.00789-23	2023
	Identification of mixed anaerobic infections after inguinal hernia repair based on metagenomic next-generation sequencing: A case report.	Zhang J, Zhou Y, Zhong Z, Lv Y, Yang X, Liu X.	Open Med (Wars)	10.1515/med-2023-0887	2024
	Breast Milk-Derived Limosilactobacillus reuteri Prevents Atopic Dermatitis in Mice via Activating Retinol Absorption and Metabolism in Peyer's Patches.	Qi C, Tu H, Zhao Y, Zhou J, Chen J, Hu H, Yu R, Sun J.	Mol Nutr Food Res	10.1002/mnfr.202200444	2023
	Effect of Bifidobacterium longum subsp. infantis YLGB-1496 on common diseases in pediatrics: a randomized, blinded, placebo-controlled trial.	Zhang X, Chen K, Lan H, Chen H, Chen H, Yang P, He N, Hung W, Zeng Z, Liu C.	Front Nutr	10.3389/fnut.2025.1585504	2025
Metabolism	Dynamic genetic adaptation of Bacteroides thetaiotaomicron during murine gut colonization.	Kennedy MS, Zhang M, DeLeon O, Bissell J, Trigodet F, Lolans K, Temelkova S, Carroll KT, Fiebig A, Deutschbauer A, Sidebottom AM, Lake J, Henry C, Rice PA, Bergelson J, Chang EB.	Cell Rep	10.1016/j.celrep.2023.113009	2023
	Detailed analysis of metabolism reveals growth-rate-promoting interactions between Anaerostipes caccae and Bacteroides spp.	Kattel A, Morell I, Aro V, Lahtvee PJ, Vilu R, Joers A, Nahku R.	Anaerobe	10.1016/j.anaerobe.2022.102680	2023
Phylogeny	Difficult-to-culture micro-organisms specifically isolated using the liquid-liquid co-culture method - towards the identification of bacterial species and metabolites supporting their growth.	Hisatomi A, Yoshida T, Hasunuma T, Ohkuma M, Sakamoto M.	Microbiology (Reading)	10.1099/mic.0.001581	2025
	Decoding anaerobes: a comprehensive evaluation of MALDI-TOF Sirius and VITEK MS PRIME in clinical settings.	Rocca MF, Etcheverry P, D Angiolo G, Prieto M.	Microbiol Spectr	10.1128/spectrum.01870-25	2025
	The Role of the Gut Microbiota in Sanfilippo Syndrome's Physiopathology: An Approach in Two Affected Siblings.	Barbero-Herranz R, Garriga-Garcia M, Moreno-Blanco A, Palacios E, Ruiz-Sala P, Vicente-Santamaria S, Stanescu S, Belanger-Quintana A, Pintos-Morell G, Arconada B, Del Campo R, Avendano-Ortiz J.	Int J Mol Sci	10.3390/ijms25168856	2024
	Hadza Prevotella require diet-derived microbiota-accessible carbohydrates to persist in mice.	Gellman RH, Olm MR, Terrapon N, Enam F, Higginbottom SK, Sonnenburg JL, Sonnenburg ED.	Cell Rep	10.1016/j.celrep.2023.113233	2023
Metabolism	Bacteroides thetaiotaomicron ameliorates mouse hepatic steatosis through regulating gut microbial composition, gut-liver folate and unsaturated fatty acids metabolism.	Li H, Wang XK, Tang M, Lei L, Li JR, Sun H, Jiang J, Dong B, Li HY, Jiang JD, Peng ZG.	Gut Microbes	10.1080/19490976.2024.2304159	2024
	Optimal Representative Strain selector-a comprehensive pipeline for selecting next-generation reference strains of bacterial species.	Tarracchini C, Fontana F, Petraro S, Lugli GA, Mancabelli L, Turroni F, Ventura M, Milani C.	NAR Genom Bioinform	10.1093/nargab/lqae173	2024
Genetics	Engineering Bacteroides thetaiotaomicron to produce non-native butyrate based on a genome-scale metabolic model-guided design.	Kim K, Choe D, Song Y, Kang M, Lee SG, Lee DH, Cho BK.	Metab Eng	10.1016/j.ymben.2021.10.005	2021
	Interbacterial warfare in the human gut: insights from Bacteroidales' perspective.	Jiang K, Pang X, Li W, Xu X, Yang Y, Shang C, Gao X.	Gut Microbes	10.1080/19490976.2025.2473522	2025
	Infection leaves a genetic and functional mark on the gut population of a commensal bacterium.	Tawk C, Lim B, Bencivenga-Barry NA, Lees HJ, Ramos RJF, Cross J, Goodman AL.	Cell Host Microbe	10.1016/j.chom.2023.04.005	2023
Metabolism	Dissecting the respective roles of microbiota and host genetics in the susceptibility of Card9^-/- mice to colitis.	Danne C, Lamas B, Lavelle A, Michel ML, Da Costa G, Pham HP, Lefevre A, Bridonneau C, Bredon M, Planchais J, Straube M, Emond P, Langella P, Sokol H.	Microbiome	10.1186/s40168-024-01798-w	2024
	Microbial succinate promotes the response to metformin by upregulating secretory immunoglobulin a in intestinal immunity.	Zhang Y, Wang A, Zhao W, Qin J, Zhang Y, Liu B, Yao C, Long J, Yuan M, Yan D.	Gut Microbes	10.1080/19490976.2025.2450871	2025
Enzymology	Structure and function of microbial alpha-l-fucosidases: a mini review.	Wu H, Owen CD, Juge N.	Essays Biochem	10.1042/ebc20220158	2023
Pathogenicity	Nutrient smuggling: Commensal gut bacteria-derived extracellular vesicles scavenge vitamin B12 and related cobamides for microbe and host acquisition.	Juodeikis R, Jones E, Deery E, Beal DM, Stentz R, Krautler B, Carding SR, Warren MJ.	J Extracell Biol	10.1002/jex2.61	2022
Genetics	Compositional and functional gut microbiota alterations in mild cognitive impairment: links to Alzheimer's disease pathology.	Fan KC, Lin CC, Chiu YL, Koh SH, Liu YC, Chuang YF.	Alzheimers Res Ther	10.1186/s13195-025-01769-9	2025
	Glycan-mediated interactions between bacteria, rotavirus and the host cells provide an additional mechanism of antiviral defence.	Raev SA, Omwando AM, Guo Y, Raque MS, Amimo JO, Saif LJ, Vlasova AN.	Benef Microbes	10.3920/bm2022.0026	2022
	In vivo systematic analysis of microbiota-prebiotic crosstalk reveals a synbiotic that effectively ameliorates DSS-induced colitis in mice.	Peng Q, Jiang P, Yi L, Li Y, Yang Q, Wan X, He J, Mo Z, Niu H, Lan Q, Jia H, Xu D, Wang C, Yang H, Liu Z, Chen WH.	Gut Microbes	10.1080/19490976.2025.2541028	2025
Genetics	Multi-omics study unravels gut microbiota and metabolites alteration in patients with Wilson's disease.	Cai X, Dai J, Xie Y, Xu S, Liu M.	Sci Rep	10.1038/s41598-024-71740-5	2024
	Chemical and nutritional characteristics, and microbial degradation of rapeseed meal recalcitrant carbohydrates: A review.	Long C, Qi XL, Venema K.	Front Nutr	10.3389/fnut.2022.948302	2022
	Gut microbiome and metabolome profiling in Framingham heart study reveals cholesterol-metabolizing bacteria.	Li C, Strazar M, Mohamed AMT, Pacheco JA, Walker RL, Lebar T, Zhao S, Lockart J, Dame A, Thurimella K, Jeanfavre S, Brown EM, Ang QY, Berdy B, Sergio D, Invernizzi R, Tinoco A, Pishchany G, Vasan RS, Balskus E, Huttenhower C, Vlamakis H, Clish C, Shaw SY, Plichta DR, Xavier RJ.	Cell	10.1016/j.cell.2024.03.014	2024
Genetics	TolRad, a model for predicting radiation tolerance using Pfam annotations, identifies novel radiosensitive bacterial species from reference genomes and MAGs.	Sweet P, Burroughs M, Jang S, Contreras L.	Microbiol Spectr	10.1128/spectrum.03838-23	2024
Phylogeny	BN-BacArena: Bayesian network extension of BacArena for the dynamic simulation of microbial communities.	Blasco T, Balzerani F, Valcarcel LV, Larranaga P, Bielza C, Francino MP, Rufian-Henares JA, Planes FJ, Perez-Burillo S.	Bioinformatics	10.1093/bioinformatics/btae266	2024
Genetics	Antibiotics-induced depression in mice via the microbiota-gut-brain axis.	Fan X, Deng H, Qiu J, Ji H, Shen X.	J Affect Disord	10.1016/j.jad.2022.08.059	2022
	Modeling human pollution in water bodies using somatic coliphages and bacteriophages that infect Bacteroides thetaiotaomicron strain GA17.	Mendez J, Garcia-Aljaro C, Muniesa M, Pascual-Benito M, Balleste E, Lopez P, Monleon A, Blanch AR, Lucena F.	J Environ Manage	10.1016/j.jenvman.2021.113802	2022
	Community living causes changes in metabolic behavior and is permitted by specific growth conditions in two bacterial co-culture systems.	Ellis E, Fulte S, Boylan S, Flory A, Paine K, Lopez S, Allen G, Warya K, Ortiz-Merino J, Blacketer S, Thompson S, Sanchez S, Burdette K, Duchscherer A, Pinkham N, Shih JD, Rahn-Lee L.	J Bacteriol	10.1128/jb.00075-25	2025
	Acarbose impairs gut Bacteroides growth by targeting intracellular glucosidases.	Brown HA, Morris AL, Pudlo NA, Hopkins AE, Martens EC, Golob JL, Koropatkin NM.	mBio	10.1128/mbio.01506-24	2024
	A mathematical model of Bacteroides thetaiotaomicron, Methanobrevibacter smithii, and Eubacterium rectale interactions in the human gut.	Adrian MA, Ayati BP, Mangalam AK.	Sci Rep	10.1038/s41598-023-48524-4	2023
	Clinical features, treatments and prognosis of COVID-19 (Omicron) and hemorrhagic colitis: a case series study.	Li J, Xu C, Chen K, Zhang Q.	BMC Gastroenterol	10.1186/s12876-025-04254-7	2025
	The gut microbiome, mild cognitive impairment, and probiotics: A randomized clinical trial in middle-aged and older adults.	Aljumaah MR, Bhatia U, Roach J, Gunstad J, Azcarate Peril MA.	Clin Nutr	10.1016/j.clnu.2022.09.012	2022
	Integrative multiomics analysis reveals association of gut microbiota and its metabolites with susceptibility to keloids.	Li D, Li M, Gao H, Hu K, Xie R, Fan J, Huang M, Liao C, Han C, Guo Z, Chen X, Li M.	Front Microbiol	10.3389/fmicb.2024.1475984	2024
	B.uniformis IM01-derived IAA alleviates asthma via AhR/NLRP3 pathways in mice.	He Y, Yang T, Mi J, He S, Yang Z, Lu S, Yue K, Huang Y, Song L, Xiao Y, Ren Z.	Cell Mol Life Sci	10.1007/s00018-025-05910-7	2025
	Starvation responses impact interaction dynamics of human gut bacteria Bacteroides thetaiotaomicron and Roseburia intestinalis.	Liu B, Garza DR, Gonze D, Krzynowek A, Simoens K, Bernaerts K, Geirnaert A, Faust K.	ISME J	10.1038/s41396-023-01501-1	2023
	Perspective: on the future of fecal microbiota transplantation.	Larsen OFA, Brummer RJM.	Front Microbiol	10.3389/fmicb.2024.1449133	2024
	Persimmon Fiber-Rich Ingredients Promote Anti-Inflammatory Responses and the Growth of Beneficial Anti-Inflammatory Firmicutes Species from the Human Colon.	Lopez-Bermudo L, Moreno-Chamba B, Salazar-Bermeo J, Hayward NJ, Morris A, Duncan GJ, Russell WR, Cardenas A, Ortega A, Escudero-Lopez B, Berna G, Marti Bruna N, Duncan SH, Neacsu M, Martin F.	Nutrients	10.3390/nu16152518	2024
	The Emergence of Bacteroides pyogenes as a Human Pathogen of Animal Origin: A Narrative Review.	Mauri C, Giubbi C, Consonni A, Briozzo E, Meroni E, Luzzaro F, Tonolo S.	Microorganisms	10.3390/microorganisms13061200	2025
	Construction and characterization of a genome-scale ordered mutant collection of Bacteroides thetaiotaomicron.	Arjes HA, Sun J, Liu H, Nguyen TH, Culver RN, Celis AI, Walton SJ, Vasquez KS, Yu FB, Xue KS, Newton D, Zermeno R, Weglarz M, Deutschbauer A, Huang KC, Shiver AL.	BMC Biol	10.1186/s12915-022-01481-2	2022
	Incomplete lytic cycle of a widespread Bacteroides bacteriophage leads to the formation of defective viral particles.	Vendrell-Fernandez S, Beamud B, Abou Haydar Y, Am de Sousa J, Burlaud-Gaillard J, Kornobis E, Raynal B, Vinh J, Bikard D, Ghigo JM.	PLoS Biol	10.1371/journal.pbio.3002787	2025
Metabolism	Discrete genetic loci in human gut Bacteroides thetaiotaomicron confer pectin metabolism.	Li M, Li S, Guo X, Guo C, Wang Y, Du Z, Zhang Z, Xie C, Ding K.	Carbohydr Polym	10.1016/j.carbpol.2021.118534	2021
Pathogenicity	The underlying rationality of Chinese medicine herb pair Coptis chinensis and Dolomiaea souliei: From the perspective of metabolomics and intestinal function.	Wang T, Zhang C, Li H, Zhou R, Ye X, Yang Y, He K.	J Ethnopharmacol	10.1016/j.jep.2022.115065	2022
	The gut microbial metabolite indole-3-aldehyde alleviates impaired intestinal development by promoting intestinal stem cell expansion in weaned piglets.	Zhang J, Chen Y, Guo X, Li X, Zhang R, Wang M, Zhu W, Yu K.	J Anim Sci Biotechnol	10.1186/s40104-024-01111-7	2024
	Selenium-Enriched Black Soybean Protein Prevents Benzo(a)pyrene-Induced Pyroptotic Colon Damage and Gut Dysbacteriosis.	Wang Z, Shi L, Li H, Song W, Li J, Yuan L.	J Agric Food Chem	10.1021/acs.jafc.2c04526	2022
	The Complex Role of Gut Microbiota in Systemic Lupus Erythematosus and Lupus Nephritis: From Pathogenetic Factor to Therapeutic Target.	Parodi E, Novi M, Bottino P, La Porta E, Merlotti G, Castello LM, Gotta F, Rocchetti A, Quaglia M.	Microorganisms	10.3390/microorganisms13020445	2025
	Antimicrobial susceptibility profile of clinically relevant Bacteroides, Phocaeicola, Parabacteroides and Prevotella species, isolated by eight laboratories in the Netherlands.	Boiten KE, Notermans DW, Rentenaar RJ, van Prehn J, Bode LGM, Maat I, van der Zwet W, Jansz A, Siebers TJH, Rossen JWA, de Greeff SC, Hendrickx APA, Kuijper EJ, Veloo ACM.	J Antimicrob Chemother	10.1093/jac/dkae043	2024
	An unusual presentation of Pseudomonas citronellolis bacteraemia and Campylobacter gastroenteritis infection in a human - a case report and literature review.	Hwang CS, Rahmati E, Gerbino AJ, Rose TM, Verma P, Schwartz MA.	Access Microbiol	10.1099/acmi.0.000479.v3	2023
	Infective Endocarditis Secondary to Bacteroides Thetaiotaomicron in a Patient With Uterine Smooth Muscle Tumor of Uncertain Malignant Potential: A Case Report and Review of the Literature.	Beshai R, Wadehra R.	Cureus	10.7759/cureus.23403	2022
	A case report of Pseudomonas citronellolis and Escherichia coli isolated from acute suppurative appendicitis: reveals the potential intestinal colonization and pathogenicity of Pseudomonas citronellolis.	Lin Y, Li Y, Lin C.	Front Cell Infect Microbiol	10.3389/fcimb.2024.1280188	2024
Genetics	Dietary protein source alters gut microbiota composition and function.	Blakeley-Ruiz JA, Bartlett A, McMillan AS, Awan A, Walsh MV, Meyerhoffer AK, Vintila S, Maier JL, Richie TG, Theriot CM, Kleiner M.	ISME J	10.1093/ismejo/wraf048	2025
	Gut microbiota of preterm infants in the neonatal intensive care unit: a study from a tertiary care center in northern India.	Devarajalu P, Kumar J, Dutta S, Attri SV, Kabeerdoss J.	Front Microbiol	10.3389/fmicb.2024.1329926	2024
	Bifidobacterial GH146 beta-L-arabinofuranosidase for the removal of beta1,3-L-arabinofuranosides on plant glycans.	Fujita K, Tsunomachi H, Lixia P, Maruyama S, Miyake M, Dakeshita A, Kitahara K, Tanaka K, Ito Y, Ishiwata A, Fushinobu S.	Appl Microbiol Biotechnol	10.1007/s00253-024-13014-8	2024
Enzymology	Loss of Bacteroides thetaiotaomicron bile acid-altering enzymes impacts bacterial fitness and the global metabolic transcriptome.	McMillan AS, Foley MH, Perkins CE, Theriot CM.	Microbiol Spectr	10.1128/spectrum.03576-23	2024
	[The role of the microbiome in lupus and antiphospholipid syndrome].	Redanz S, Kriegel MA.	Z Rheumatol	10.1007/s00393-022-01184-7	2022
Genetics	Comparative genomics provides structural and functional insights into Bacteroides RNA biology.	Prezza G, Ryan D, Madler G, Reichardt S, Barquist L, Westermann AJ.	Mol Microbiol	10.1111/mmi.14793	2022
	Gut microbiota in regulatory T cell generation and function: mechanisms and health implications.	Sharma A, Sharma G, Im SH.	Gut Microbes	10.1080/19490976.2025.2516702	2025
	Determinants of raffinose family oligosaccharide use in Bacteroides species.	Basu A, Adams AND, Degnan PH, Vanderpool CK.	J Bacteriol	10.1128/jb.00235-24	2024
	Genetically predicted plasma metabolites mediate the causal relationship between gut microbiota and osteosarcoma.	Qin X, Fan Z, Qiao S, Li J, Lv J.	Sci Rep	10.1038/s41598-025-91869-1	2025
	The His23 and Lys79 pair determines the high catalytic efficiency of the inorganic pyrophosphatase of the haloacid dehalogenase superfamily.	Zhang M, Yang L, Ding W, Zhang H.	Biochim Biophys Acta Gen Subj	10.1016/j.bbagen.2022.130128	2022
	Characteristics and function of the gut microbiota in patients with rectal neuroendocrine tumors.	Gao Y, Zheng H, Ye M, Zhou G, Chen J, Qiang X, Bai J, Lu X, Tang Q.	J Cancer	10.7150/jca.103297	2025
	Diagnostic performance of an automated robot for MALDI target preparation in microbial identification.	Pranada AB, Cicatka M, Hess C, Karasek J.	J Clin Microbiol	10.1128/jcm.00434-24	2024
	Using phenotyping to visualize and identify selfish bacteria: a methods guide.	Reintjes G, Giljan G, Fuchs BM, Arnosti C, Amann R.	Microbiol Spectr	10.1128/spectrum.01602-24	2025
	Healthy Ageing and Gut Microbiota: A Study on Longevity in Adults.	Deng L, Xu J, Xue Q, Wei Y, Wang J.	Microorganisms	10.3390/microorganisms13071657	2025
Pathogenicity	Protective effects of patchouli alcohol against DSS-induced ulcerative colitis.	Han H, Gao M, Wang F, Luo Z, Jiang X, Qiu Y, Su J, Duan X, Luo S, Tang S, Khan A, Zou Z, Chen C, Yin Q, Qiu J, Zhang H.	Sci Rep	10.1038/s41598-024-66259-8	2024
	Longitudinal changes in gut microbiota composition during endocrine therapy in hormone receptor-positive breast cancer patients.	Tsai CH, Huang WL, Su YW, Lee F, Lee CC, Li FY, Yang HW, Lu CY, Yang PS.	NPJ Breast Cancer	10.1038/s41523-025-00810-2	2025
	Cloning and Characterization of a Novel N-Acetyl-D-galactosamine-4-O-sulfate Sulfatase, SulA1, from a Marine Arthrobacter Strain.	Christensen MD, Allahgholi L, Linares-Pasten JA, Fridjonsson O, Gudmundsson H, Kale V, Sardari RRR, Hreggvidsson GO, Karlsson EN.	Mar Drugs	10.3390/md22030104	2024
Phylogeny	Early life exposure to broccoli sprouts confers stronger protection against enterocolitis development in an immunological mouse model of inflammatory bowel disease.	Holcomb L, Holman JM, Hurd M, Lavoie B, Colucci L, Hunt B, Hunt T, Kinney M, Pathak J, Mawe GM, Moses PL, Perry E, Stratigakis A, Zhang T, Chen G, Ishaq SL, Li Y.	mSystems	10.1128/msystems.00688-23	2023
	Bacteriophage-mediated lysis supports robust growth of amino acid auxotrophs.	Pherribo GJ, Taga ME.	ISME J	10.1038/s41396-023-01452-7	2023
	Changes in Human Colonic Microbiota Promoted by Synbiotic Açai Juice Composed of Gluco-Oligosaccharides, Dextran, and Bifidobacterium breve NRRL B-41408.	Reges BM, da Silva Oliveira FA, Fonteles TV, Rodrigues S.	Foods	10.3390/foods13244121	2024
	Dual membrane-spanning anti-sigma factors regulate vesiculation in Bacteroides thetaiotaomicron.	Pardue EJ, Sartorio MG, Jana B, Scott NE, Beatty WL, Ortiz-Marquez JC, Van Opijnen T, Hsu FF, Potter RF, Feldman MF.	Proc Natl Acad Sci U S A	10.1073/pnas.2321910121	2024
Metabolism	Methods for Cultivation of Bacteroides thetaiotaomicron and Analysis of Heme Metabolism by Mass Spectrometry and Spectroscopic Approaches.	da Silva RR, Adedoyin V, DuBois JL.	Methods Mol Biol	10.1007/978-1-0716-4043-2_7	2024
Metabolism	Interactions between gut microbiota and parkinson's disease: the role of tryptophan metabolism.	Fan X, Xiao Z, Chen Y, Yang H, Diao M, Hu W, Wang S.	Cell Commun Signal	10.1186/s12964-025-02393-8	2025
	Blood cell perturbation responses mediate the causal relationship between the gut microbiota and asthma: a bidirectional Mendelian randomization study.	Bi J, Zhao L, Liu X, Zhang J, Zhang W.	BMC Med Genomics	10.1186/s12920-025-02196-3	2025
	The Sdp-SH3b2 domain contained in Lactobacillus johnsonii N6.2-derived extracellular vesicles inhibit murine norovirus replication.	da Silva DR, Sharjeel AB, Beliakoff R, Teixeira LD, Kima PE, Jones MK, Gonzalez CF, Lorca GL.	Front Immunol	10.3389/fimmu.2024.1490755	2024
	Measuring and understanding information storage and transfer in a simulated human gut microbiome.	Zoller H, Garcia Perez C, Betel Geijo Fernandez J, Zu Castell W.	PLoS Comput Biol	10.1371/journal.pcbi.1012359	2024
	Effects of Clostridium butyricum Capsules Combined with Rosuvastatin on Intestinal Flora, Lipid Metabolism, Liver Function and Inflammation in NAFLD Patients.	Zhu W, Yan M, Cao H, Zhou J, Xu Z.	Cell Mol Biol (Noisy-le-grand)	10.14715/cmb/2022.68.2.10	2022
	Protection of Anaerobic Microbes from Processing Stressors Using Metal-Phenolic Networks.	Fan G, Wasuwanich P, Rodriguez-Otero MR, Furst AL.	J Am Chem Soc	10.1021/jacs.1c09018	2022
	Investigations into the biosynthesis of stieleriacines and related N-acyl tyrosines by comparative genomics, knock-out studies and total synthesis of epi-stieleriacine C.	Sauer M, Staack M, Balluff S, Jogler C, Kallscheuer N, Beemelmanns C.	Commun Chem	10.1038/s42004-025-01654-4	2025
Metabolism	Unifying themes and distinct features of carbon and nitrogen assimilation by polysaccharide-degrading bacteria: a summary of four model systems.	Gardner JG, Schreier HJ.	Appl Microbiol Biotechnol	10.1007/s00253-021-11614-2	2021
	Microbiome and gut-liver interactions: From mechanisms to therapies.	Anis MA, Shahid Y, Majeed AA, Abid S.	World J Gastroenterol	10.3748/wjg.v31.i40.111409	2025
	Synthetic beta-d-Glucuronides: Substrates for Exploring Glucuronide Degradation by Human Gut Bacteria.	Gorecka A, Schacht H, Fraser MK, Teriosina A, London JA, Barsukov IL, Powell AK, Cartmell A, Stachulski AV, Yates EA.	ACS Omega	10.1021/acsomega.4c09036	2025
	Akkermansia muciniphila is associated with normal muscle mass and Eggerthella is related with sarcopenia in cirrhosis.	Efremova I, Alieva A, Maslennikov R, Poluektova E, Zharkova M, Kudryavtseva A, Krasnov G, Zharikov Y, Nerestyuk Y, Karchevskaya A, Ivashkin V.	Front Nutr	10.3389/fnut.2024.1438897	2024
Pathogenicity	Identification and characterization of 3-ketosphinganine reductase activity encoded at the BT_0972 locus in Bacteroides thetaiotaomicron.	Lee MT, Le HH, Besler KR, Johnson EL.	J Lipid Res	10.1016/j.jlr.2022.100236	2022
	Coptis chinensis shows distinct effects on hyperlipidemia and gut microbiota in high-fat diet induced mice with cold or hot syndrome.	Yang Y, Zhan J, Cheng J, Cao Y, Wu C.	Chin Herb Med	10.1016/j.chmed.2025.04.009	2025
Metabolism	Investigation and Alteration of Organic Acid Synthesis Pathways in the Mammalian Gut Symbiont Bacteroides thetaiotaomicron.	Porter NT, Larsbrink J.	Microbiol Spectr	10.1128/spectrum.02312-21	2022
Metabolism	A strain of Bacteroides thetaiotaomicron attenuates colonization of Clostridioides difficile and affects intestinal microbiota and bile acids profile in a mouse model.	Li X, Kang Y, Huang Y, Xiao Y, Song L, Lu S, Ren Z.	Biomed Pharmacother	10.1016/j.biopha.2021.111290	2021
	TonB-dependent transporters in the Bacteroidetes: Unique domain structures and potential functions.	Pollet RM, Martin LM, Koropatkin NM.	Mol Microbiol	10.1111/mmi.14683	2021
	Effects of a Low-Carbohydrate, High-Protein Diet on Gut Microbiome Composition in Insulin-Resistant Individuals With Chronic Spinal Cord Injury: Preliminary Results From a Randomized Controlled Trial.	Li J, Morrow C, McLain A, Womack ED, Yarar-Fisher C.	Arch Phys Med Rehabil	10.1016/j.apmr.2022.03.014	2022
	Acteoside, the Main Bioactive Compound in Osmanthus fragrans Flowers, Palliates Experimental Colitis in Mice by Regulating the Gut Microbiota.	Liu Y, Huang W, Zhu Y, Zhao T, Xiao F, Wang Y, Lu B.	J Agric Food Chem	10.1021/acs.jafc.1c07583	2022
	The structure of a Bacteroides thetaiotaomicron carbohydrate-binding module provides new insight into the recognition of complex pectic polysaccharides by the human microbiome.	Trovao F, Correia VG, Lourenco FM, Ribeiro DO, Carvalho AL, Palma AS, Pinheiro BA.	J Struct Biol X	10.1016/j.yjsbx.2022.100084	2023
	Human colitis-associated colorectal carcinoma progression is accompanied by dysbiosis with enriched pathobionts.	Masaadeh AH, Eletrebi M, Parajuli B, De Jager N, Bosch DE.	Gut Microbes	10.1080/19490976.2025.2479774	2025
Phylogeny	Comprehensive analyses of a large human gut Bacteroidales culture collection reveal species- and strain-level diversity and evolution.	Zhang ZJ, Cole CG, Coyne MJ, Lin H, Dylla N, Smith RC, Pappas TE, Townson SA, Laliwala N, Waligurski E, Ramaswamy R, Woodson C, Burgo V, Little JC, Moran D, Rose A, McMillin M, McSpadden E, Sundararajan A, Sidebottom AM, Pamer EG, Comstock LE.	Cell Host Microbe	10.1016/j.chom.2024.08.016	2024
Metabolism	Bacteroides thetaiotaomicron relieves colon inflammation by activating aryl hydrocarbon receptor and modulating CD4⁺T cell homeostasis.	Li K, Hao Z, Du J, Gao Y, Yang S, Zhou Y.	Int Immunopharmacol	10.1016/j.intimp.2020.107183	2021
Pathogenicity	Yeast mannan increases Bacteroides thetaiotaomicron abundance and suppresses putrefactive compound production in in vitro fecal microbiota fermentation.	Oba S, Washida K, Shimada Y, Sunagawa T, Tanihiro R, Sugiyama H, Nakamura Y.	Biosci Biotechnol Biochem	10.1080/09168451.2020.1784704	2020
Biotechnology	CtGH76, a Glycoside Hydrolase 76 from Chaetomium thermophilum, with Elongated Glycan-Binding Canyon.	Ruppenthal SR, Po-Hsun W, Watad M, Rosner CJ, Vogt MS, Friedrich M, Voigt AL, Petz A, Gnau P, Essen LO.	Int J Mol Sci	10.3390/ijms26146589	2025
	Polysaccharides catabolism by the human gut bacterium -Bacteroides thetaiotaomicron: advances and perspectives.	Ye M, Yu J, Shi X, Zhu J, Gao X, Liu W.	Crit Rev Food Sci Nutr	10.1080/10408398.2020.1803198	2021
	Metagenomic Next-Generation Sequencing Direct Diagnosis of Mixed Bacterial Meningitis in a Child: A Case Report.	Wang W, Wang Y, Xin X, Yin Y, Zhao C, Jin Y.	Infect Drug Resist	10.2147/idr.s476781	2024
	Parallel Alterations in Gut and Tumor Microbiota in Pediatric Oncology: Potential Impacts on Disease Progression and Treatment Response.	Szabo PJ, Sagi V, Kassai LK, Kiss-Miki RM, Makra N, Szabo D, Garami M.	Cancers (Basel)	10.3390/cancers17213426	2025
Pathogenicity	Moderate altitude exposure impacts extensive host-microbiota multi-kingdom connectivity with serum metabolome and fasting blood glucose.	Huang X, Gao X, Fan Y, Wang D, Chen X, Qi X, Yang Z, Wang YE, Meng J, Zou G, Liu Z, Li X.	Virulence	10.1080/21505594.2025.2530660	2025
Genetics	CRISPR/Cas-Based Genome Editing for Human Gut Commensal Bacteroides Species.	Zheng L, Tan Y, Hu Y, Shen J, Qu Z, Chen X, Ho CL, Leung EL, Zhao W, Dai L.	ACS Synth Biol	10.1021/acssynbio.1c00543	2022
	In Vitro Gastrointestinal Digestion of Grifola frondosa Polysaccharides and Their Enhancement of GABA Production via Gut Microbiota Modulation.	Wang Q, Luo Y, Zhu H, Liu X, Xue M, Yang G, Chen Y, Chen S, Wen Z.	Nutrients	10.3390/nu17213332	2025
	Extensively acquired antimicrobial-resistant bacteria restructure the individual microbial community in post-antibiotic conditions.	Baek JW, Lim S, Park N, Song B, Kirtipal N, Nielsen J, Mardinoglu A, Shoaie S, Kim JI, Son JW, Koh A, Lee S.	NPJ Biofilms Microbiomes	10.1038/s41522-025-00705-x	2025
	A conserved inhibitory interdomain interaction regulates DNA-binding activities of hybrid two-component systems in Bacteroides.	Gao R, Wu T, Stock AM.	mBio	10.1128/mbio.01220-24	2024
	Hungatella hathewayi, an Efficient Glycosaminoglycan-Degrading Firmicutes from Human Gut and Its Chondroitin ABC Exolyase with High Activity and Broad Substrate Specificity.	Rawat PS, Li Y, Zhang W, Meng X, Liu W.	Appl Environ Microbiol	10.1128/aem.01546-22	2022
Metabolism	Mobilization of vitamin B₁₂ transporters alters competitive dynamics in a human gut microbe.	Frye KA, Piamthai V, Hsiao A, Degnan PH.	Cell Rep	10.1016/j.celrep.2021.110164	2021
	Extracellular vesicles produced by the human gut commensal bacterium Bacteroides thetaiotaomicron elicit anti-inflammatory responses from innate immune cells.	Fonseca S, Carvalho AL, Miquel-Clopes A, Jones EJ, Juodeikis R, Stentz R, Carding SR.	Front Microbiol	10.3389/fmicb.2022.1050271	2022
	Dissection and enhancement of prebiotic properties of yeast cell wall oligosaccharides through metabolic engineering.	Kwak S, Robinson SJ, Lee JW, Lim H, Wallace CL, Jin YS.	Biomaterials	10.1016/j.biomaterials.2022.121379	2022
	Food colorant brilliant blue causes persistent functional and structural changes in an in vitro simplified microbiota model system.	Castaneda-Monsalve V, Haange SB, Frohlich LF, Fu Q, Rolle-Kampczyk U, von Bergen M, Jehmlich N.	ISME Commun	10.1093/ismeco/ycaf050	2025
Metabolism	Beneficial metabolic effects of PAHSAs depend on the gut microbiota in diet-induced obese mice but not in chow-fed mice.	Lee J, Wellenstein K, Rahnavard A, Nelson AT, Holter MM, Cummings BP, Yeliseyev V, Castoldi A, Clish CB, Bry L, Siegel D, Kahn BB.	Proc Natl Acad Sci U S A	10.1073/pnas.2318691121	2024
	A child with recurrent otitis media due to Bacteroides thetaiotaomicron.	Kanaujia R, Gupta S, Singla N, Jani P, Angrup A.	Anaerobe	10.1016/j.anaerobe.2020.102203	2020
	MAIT cell activation is reduced by direct and microbiota-mediated exposure to bisphenols.	Krause JL, Engelmann B, Nunes da Rocha U, Pierzchalski A, Chang HD, Zenclussen AC, von Bergen M, Rolle-Kampczyk U, Herberth G.	Environ Int	10.1016/j.envint.2021.106985	2022
	Bioavailability, Human Metabolism, and Dietary Interventions of Glucosinolates and Isothiocyanates: Critical Insights and Future Perspectives	Narra F, Galgani G, Harris C, Moreno D, Nunez-Gomez V.	Foods		2025
	Microbiome Alterations Driven by Trypanosoma cruzi Infection in Two Disjunctive Murine Models.	Castaneda S, Munoz M, Hotez PJ, Bottazzi ME, Paniz-Mondolfi AE, Jones KM, Mejia R, Poveda C, Ramirez JD.	Microbiol Spectr	10.1128/spectrum.00199-23	2023
Pathogenicity	Association Between the Inflammatory Potential of Diet and Constipation Among Adults in the United States: A Cross-sectional Study.	Lu WF, Liu L, Zhang YH, Liu H.	J Clin Gastroenterol	10.1097/mcg.0000000000002060	2025
	Necrotizing fasciitis wound after debridement could be successfully treated with negative-pressure wound therapy with instillation and dwelling: A case report.	Kobayashi N, Toyama S, Yoshida H, Shiraso S, Kawaguchi S.	Trauma Case Rep	10.1016/j.tcr.2023.100957	2023
	Gut Bacteria Shape Intestinal Microhabitats Occupied by the Fungus Candida albicans.	Eckstein MT, Moreno-Velasquez SD, Perez JC.	Curr Biol	10.1016/j.cub.2020.09.027	2020
	The Human Gut Microbe Bacteroides thetaiotaomicron Suppresses Toxin Release from Clostridium difficile by Inhibiting Autolysis.	Elahi M, Nakayama-Imaohji H, Hashimoto M, Tada A, Yamasaki H, Nagao T, Kuwahara T.	Antibiotics (Basel)	10.3390/antibiotics10020187	2021
	Development of two compatible plasmids to assess sRNA-mediated post-transcriptional regulation in Acinetobacter baumannii.	Mogre A, Connell O, White J, Shaibah A, Hokamp K, Hamrock FJ, Schauer K, Kroger C.	Microbiology (Reading)	10.1099/mic.0.001639	2025
	Farnesoid X Receptor Agonist GW4064 Protects Lipopolysaccharide-Induced Intestinal Epithelial Barrier Function and Colorectal Tumorigenesis Signaling through the alphaKlotho/betaKlotho/FGFs Pathways in Mice.	Liu HM, Chang ZY, Yang CW, Chang HH, Lee TY.	Int J Mol Sci	10.3390/ijms242316932	2023
	Challenging Diagnosis of Late Abdominal Pregnancy: A Case Study of Misdiagnosis and Fetal Death in the Third Trimester.	Alwafai Z, Kolbe C, Kruse-Wieczorek J, Khanji MN, Zygmunt M.	Am J Case Rep	10.12659/ajcr.943625	2024
	Milk sialyl-oligosaccharides mediate the early colonization of gut commensal microbes in piglets.	Hashimoto R, Nishiyama K, Namai F, Suzuki K, Sakuma T, Fukuda I, Sugiyama Y, Okano K, Shanoh T, Toyoshi E, Ohgi R, Saha S, Tsuchida S, Nishiyama E, Mukai T, Furukawa M, Nochi T, Villena J, Ikeda-Ohtsubo W, Yoshioka G, Nakazaki E, Suda Y, Kitazawa H.	Microbiome	10.1186/s40168-025-02129-3	2025
	A biosynthetic pathway for the selective sulfonation of steroidal metabolites by human gut bacteria.	Yao L, D'Agostino GD, Park J, Hang S, Adhikari AA, Zhang Y, Li W, Avila-Pacheco J, Bae S, Clish CB, Franzosa EA, Huttenhower C, Huh JR, Devlin AS.	Nat Microbiol	10.1038/s41564-022-01176-y	2022
Metabolism	Iron Deficiency Modulates Metabolic Landscape of Bacteroidetes Promoting Its Resilience during Inflammation.	Lewis JP, Gui Q.	Microbiol Spectr	10.1128/spectrum.04733-22	2023
	Ammonia-Assimilating Bacteria Promote Wheat (Triticum aestivum) Growth and Nitrogen Utilization.	Gao Y, Zhang Q, Chen Y, Yang Y, Zhou C, Yu J, Li Y, Qiu L.	Microorganisms	10.3390/microorganisms13010043	2024
	Prebiotic Effect of Oxidized Hydroxypropyl Starch via In Vitro and In Vivo.	Zheng H, Xu Z, Fan Y, Han J, Zhou L, Li H, Pan X, Ma R, Liu C, Tian Y.	Foods	10.3390/foods14132217	2025
	The effect of culturing temperature on the growth of the most dominant bacterial species of human gut microbiota and harmful bacterial species.	Shimokawa H, Sakakibara H, Ami Y, Hirano R, Kurihara S.	Biosci Microbiota Food Health	10.12938/bmfh.2024-087	2025
	Dietary Polyphenols in Relation to Gut Microbiota Composition in Saudi Arabian Females.	Alsuhaibani MN, Aljuraiban GS, Aljazairy EA, Abudawood M, Hussain SD, Alnaami A, Sabico S, Al-Daghri NM, Al-Musharaf S.	Metabolites	10.3390/metabo13010006	2022
Metabolism	Nutrient-dependent morphological variability of Bacteroides thetaiotaomicron.	Rangarajan AA, Koropatkin NM, Biteen JS.	Microbiology (Reading)	10.1099/mic.0.000924	2020
Metabolism	Carrot-Derived Rhamnogalacturonan-I Consistently Increases the Microbial Production of Health-Promoting Indole-3-Propionic Acid Ex Vivo.	Mercenier A, Vu LD, Poppe J, Albers R, McKay S, Van den Abbeele P.	Metabolites	10.3390/metabo14120722	2024
Pathogenicity	Theabrownin-targeted regulation of intestinal microorganisms to improve glucose and lipid metabolism in Goto-Kakizaki rats.	Yue S, Shan B, Peng C, Tan C, Wang Q, Gong J.	Food Funct	10.1039/d1fo03374c	2022
	Assessment of Human Health Risks in Tropical Environmental Waters with Microbial Source Tracking Markers.	Goh SG, Liang L, Gin KYH.	Water Res	10.1016/j.watres.2021.117748	2021
	Dysregulated Intestinal Host-Microbe Interactions in Systemic Lupus Erythematosus: Insights from Patients and Mouse Models.	Kume M, Din J, Zegarra-Ruiz DF.	Microorganisms	10.3390/microorganisms13030556	2025
	Evaluation of the Disk Diffusion Test for Bacteroides fragilis Group Clinical Isolates.	Lee Y, Bae MH, Lee H, Kim M, Lee K.	Ann Lab Med	10.3343/alm.2024.0159	2025
	Serum Vitamin D Level and Gut Microbiota in Women.	Al-Khaldy NS, Al-Musharaf S, Aljazairy EA, Hussain SD, Alnaami AM, Al-Daghri N, Aljuraiban G.	Healthcare (Basel)	10.3390/healthcare11030351	2023
	Gut microbiota Turicibacter strains differentially modify bile acids and host lipids.	Lynch JB, Gonzalez EL, Choy K, Faull KF, Jewell T, Arellano A, Liang J, Yu KB, Paramo J, Hsiao EY.	Nat Commun	10.1038/s41467-023-39403-7	2023
	The physiological functions of the Cbp2D and Cbp2E proteins are important for insoluble cellulose-dependent growth in Cellvibrio japonicus.	Kakacek BE, Liang J, Dickerson KA, Gardner JG.	Appl Environ Microbiol	10.1128/aem.00818-25	2025
	In Vitro Probiotic Modulation of Specific Dietary Complex Sugar Consumption in Fecal Cultures in Infants.	Mollova D, Baev V, Iliev I.	Microorganisms	10.3390/microorganisms13102352	2025
Proteome	The Proteome of Extracellular Vesicles Produced by the Human Gut Bacteria Bacteroides thetaiotaomicron In Vivo Is Influenced by Environmental and Host-Derived Factors.	Stentz R, Jones E, Juodeikis R, Wegmann U, Guirro M, Goldson AJ, Brion A, Booth C, Sudhakar P, Brown IR, Korcsmaros T, Carding SR.	Appl Environ Microbiol	10.1128/aem.00533-22	2022
Phylogeny	The impact of different gastrointestinal reconstruction techniques on gut microbiota after gastric cancer surgery.	Yang Y, Zhou HY, Zhou GM, Chen J, Ming R, Zhang D, Jiang HW.	Front Microbiol	10.3389/fmicb.2024.1494049	2024
	Minimizing endogenous cryptic plasmids to construct antibiotic-free expression systems for Escherichia coli Nissle 1917.	Zhou S, Zhao L, Zuo W, Zheng Y, Zhang P, Sun Y, Wang Y, Du G, Kang Z.	Synth Syst Biotechnol	10.1016/j.synbio.2024.01.006	2024
	Metagenomic Shotgun Sequencing Reveals Specific Human Gut Microbiota Associated with Insulin Resistance and Body Fat Distribution in Saudi Women.	Aljuraiban GS, Alfhili MA, Aldhwayan MM, Aljazairy EA, Al-Musharaf S.	Biomolecules	10.3390/biom13040640	2023
	Extraintestinal Clostridioides difficile Infection (CDI): A Recurrent Battle with Resilient Abdominal Wall Abscess.	Chinnappan J, Hussain M, Awuah D, Ogbon E, Bachuwa G, McDonald P.	Eur J Case Rep Intern Med	10.12890/2023_003711	2023
	Symbiotic biofilms formed by Clostridioides difficile and bacteroides thetaiotaomicron in the presence of vancomycin.	Yang J, Rui W, Zhong S, Li X, Liu W, Meng L, Li Y, Huang H.	Gut Microbes	10.1080/19490976.2024.2390133	2024
	N-Carbamoylputrescine Amidohydrolase of Bacteroides thetaiotaomicron, a Dominant Species of the Human Gut Microbiota.	Shimokawa H, Sakanaka M, Fujisawa Y, Ohta H, Sugiyama Y, Kurihara S.	Biomedicines	10.3390/biomedicines11041123	2023
Enzymology	Reduced Enterohepatic Recirculation of Mycophenolate and Lower Blood Concentrations Are Associated with the Stool Bacterial Microbiome after Hematopoietic Cell Transplantation.	Saqr A, Carlson B, Staley C, Rashidi A, Al-Kofahi M, Kaiser T, Holtan S, MacMillan M, Young JA, Jurdi NE, Weisdorf D, Khoruts A, Jacobson PA.	Transplant Cell Ther	10.1016/j.jtct.2022.04.018	2022
Pathogenicity	Mucormycosis after liver transplant: Case series and literature review.	Aceves-Sanchez B, Rojas-Castaneda E, Ponce-de-Leon A, Lopez-Iniguez A, Rangel-Cordero A, Sanchez E, Salgado-Nesme N, Gonzalez-Lara MF.	Med Mycol Case Rep	10.1016/j.mmcr.2024.100686	2024
Genetics	Construction of antibiotic-induced depression mice model and the function of intestinal microbiota.	Deng H, Yu Y, Sha Q, Sun W, Liang L, Ren F, Ji H, Shen X, Fan X.	Front Microbiol	10.3389/fmicb.2023.1093486	2023
Phylogeny	Bacteroides thetaiotaomicron-Infecting Bacteriophage Isolates Inform Sequence-Based Host Range Predictions.	Hryckowian AJ, Merrill BD, Porter NT, Van Treuren W, Nelson EJ, Garlena RA, Russell DA, Martens EC, Sonnenburg JL.	Cell Host Microbe	10.1016/j.chom.2020.06.011	2020
	Ocular Surface Microbiota and Corneal Transplant Outcome: Is There a Link?	Potenza M, Moramarco A, Astolfi A, Ciavarella C, Fontana L, Versura P.	Biomedicines	10.3390/biomedicines13040972	2025
	Exploring the Relationship between Gut Microbiome Composition and Blood Indole-3-acetic Acid in Hemodialysis Patients.	Wu PH, Tseng YF, Liu W, Chuang YS, Tai CJ, Tung CW, Lai KY, Kuo MC, Chiu YW, Hwang SJ, Hung WC, Lin YT.	Biomedicines	10.3390/biomedicines12010148	2024
Metabolism	Characterization of novel alpha-galactosidase in glycohydrolase family 97 from Bacteroides thetaiotaomicron and its immobilization for industrial application.	Shin YJ, Woo SH, Jeong HM, Kim JS, Ko DS, Jeong DW, Lee JH, Shim JH.	Int J Biol Macromol	10.1016/j.ijbiomac.2020.02.232	2020
	Polysaccharide Protection: How Bacteroides thetaiotaomicron Survives an Antibiotic Attack.	Jogia W, Maurice CF.	Cell Metab	10.1016/j.cmet.2019.09.011	2019
	The relationship of Megamonas species with nonalcoholic fatty liver disease in children and adolescents revealed by metagenomics of gut microbiota.	Zhou J, Zhang Q, Zhao Y, Zou Y, Chen M, Zhou S, Wang Z.	Sci Rep	10.1038/s41598-022-25140-2	2022
Pathogenicity	Microbe-derived uremic solutes enhance thrombosis potential in the host.	Nemet I, Funabashi M, Li XS, Dwidar M, Sangwan N, Skye SM, Romano KA, Cajka T, Needham BD, Mazmanian SK, Hajjar AM, Rey FE, Fiehn O, Tang WHW, Fischbach MA, Hazen SL.	mBio	10.1128/mbio.01331-23	2023
Metabolism	Biochemical and structural characterization reveals Rv3400 codes for beta-phosphoglucomutase in Mycobacterium tuberculosis.	Singh L, Karthikeyan S, Thakur KG.	Protein Sci	10.1002/pro.4943	2024
	Relationships between diet and gut microbiome in an Italian and Dutch cohort: does the dietary protein to fiber ratio play a role?	Tagliamonte S, Puhlmann ML, De Filippis F, Guerville M, Ercolini D, Vitaglione P.	Eur J Nutr	10.1007/s00394-023-03308-4	2024
	Identification of Intestinal Microbial Community in Gallstone Patients with Metagenomic Next-Generation Sequencing.	Ding L, Wang S, Jiang W, Miao Y, Liu W, Yang F, Zhang J, Chi W, Liu T, Liu Y, Wang S, Zhang Y, Zhao H.	Diagnostics (Basel)	10.3390/diagnostics13162712	2023
	ProkDBP: Toward more precise identification of prokaryotic DNA binding proteins.	Pradhan UK, Meher PK, Naha S, Das R, Gupta A, Parsad R.	Protein Sci	10.1002/pro.5015	2024
	The structure of a pectin-active family 1 polysaccharide lyase from the marine bacterium Pseudoalteromonas fuliginea.	Hobbs JK, Boraston AB.	Acta Crystallogr F Struct Biol Commun	10.1107/s2053230x2400596x	2024
Metabolism	Engineering the heparin-binding pocket to enhance the catalytic efficiency of a thermostable heparinase III from Bacteroides thetaiotaomicron.	Wang H, Zhang L, Wang Y, Li J, Du G, Kang Z.	Enzyme Microb Technol	10.1016/j.enzmictec.2020.109549	2020
	Association between low vitamin B-12 status and latent tuberculosis infection among adults.	Jiang L, Yan T, Zhang X, Liu C, Yan Q, Chai Y, Li Y, Tan Y, Gao X, Wang Q.	Asia Pac J Clin Nutr	10.6133/apjcn.202508_34(4).0014	2025
Genetics	The interactions between host genome and gut microbiome increase the risk of psychiatric disorders: Mendelian randomization and biological annotation.	Xiao L, Liu S, Wu Y, Huang Y, Tao S, Liu Y, Tang Y, Xie M, Ma Q, Yin Y, Dai M, Zhang M, Llamocca E, Gui H, Wang Q.	Brain Behav Immun	10.1016/j.bbi.2023.08.003	2023
	Gut microbial CAZymes markers for depression.	Xie P, Zhou X, Li Y, Wu J, Zhang H, Huang Y, Tan X, Wen L, Olasunkanmi OI, Zhou J, Sun Z, Liu M, Zhang G, Wang Y, Xie P, Yang J, Zheng P.	Transl Psychiatry	10.1038/s41398-024-02850-x	2024
Genetics	RFW captures species-level metagenomic functions by integrating genome annotation information.	Mi K, Xu R, Liu X.	Cell Rep Methods	10.1016/j.crmeth.2024.100932	2024
	Quorum Sensing System in Bacteroides thetaiotaomicron Strain Identified by Genome Sequence Analysis.	Wu ZC, Feng HX, Wu L, Zhang M, Zhou WL.	ACS Omega	10.1021/acsomega.0c03986	2020
	A core human gut microbe, Mediterraneibacter gnavus, produces a broad-spectrum bacteriocin mediterrocin.	Mingolelli G, Raherisoanjato J, Trinh D, Gao Y, Henke M.	mBio	10.1128/mbio.01523-25	2025
	Comparative analysis of dietary fiber impact on bile acid metabolism and gut microbiota composition in mice.	Zochling A, Seneca J, Pjevac P, Aunon-Lopez A, Zebeli Q, Pignitter M, Duszka K.	NPJ Gut Liver	10.1038/s44355-025-00041-z	2025
Phylogeny	Fecal microbiomes from screening sampling tubes are stable despite varying sampling and storage conditions.	Jorgensen AB, Almer L, Brandstrup B, Friis-Hansen L.	Sci Rep	10.1038/s41598-025-12506-5	2025
	Stevens-Johnson syndrome-toxic epidermal necrolysis overlap in a patient taking quetiapine and famotidine: a case report.	Su CS, Kao CL.	J Med Case Rep	10.1186/s13256-024-04629-6	2024
	Increased mucin-degrading bacteria by high protein diet leads to thinner mucus layer and aggravates experimental colitis.	Chen L, Wang J, Yi J, Liu Y, Yu Z, Chen S, Liu X.	J Gastroenterol Hepatol	10.1111/jgh.15562	2021
Genetics	Whole-genome sequencing and comparative analysis of the genomes of Bacteroides thetaiotaomicron and Escherichia coli isolated from a healthy resident in Vietnam.	Mohsin M, Tanaka K, Kawahara R, Kondo S, Noguchi H, Motooka D, Nakamura S, Khong DT, Nguyen TN, Hoang TN, Yamamoto Y.	J Glob Antimicrob Resist	10.1016/j.jgar.2020.02.034	2020
	Dietary inflammatory index and its relationship with gut microbiota in individuals with intestinal constipation: a cross-sectional study.	Costa LM, Mendes MM, Oliveira AC, Magalhaes KG, Shivappa N, Hebert JR, da Costa THM, Botelho PB.	Eur J Nutr	10.1007/s00394-021-02649-2	2022
	Polymicrobial Osteomyelitis in a Patient With Isolation of Trueperella bernardiae: A Case Report and Literature Review.	Delaye-Martinez MA, Vanegas-Rodriguez ES, Mendez-Sotelo B, Garcia-Hernandez ML, Colin-Castro CA, Franco-Cendejas R, Lopez-Jacome LE.	Case Rep Infect Dis	10.1155/crdi/6010539	2025
	Bacterial polysaccharide lyase family 33: Specificity from an evolutionarily conserved binding tunnel.	Loiodice M, Drula E, McIver Z, Antonyuk S, Basle A, Lima M, Yates EA, Byrne DP, Coughlan J, Leech A, Mesdaghi S, Rigden DJ, Drouillard S, Helbert W, Henrissat B, Terrapon N, Wright GSA, Couturier M, Cartmell A.	Proc Natl Acad Sci U S A	10.1073/pnas.2421623122	2025
	Multiscale study of the oral and gut environments in children with high- and low-threshold peanut allergy.	Zhang L, Chun Y, Ho HE, Arditi Z, Lo T, Sajja S, Rose R, Jones D, Wang J, Sicherer S, Bunyavanich S.	J Allergy Clin Immunol	10.1016/j.jaci.2022.04.026	2022
Enzymology	Bioinformatic Analysis of Sulfotransferases from an Unexplored Gut Microbe, Sutterella wadsworthensis 3_1_45B: Possible Roles towards Detoxification via Sulfonation by Members of the Human Gut Microbiome.	Langford L, Shah DD.	Int J Mol Sci	10.3390/ijms25052983	2024
Pathogenicity	Lactoferrin and lactoferricin B reduce adhesion and biofilm formation in the intestinal symbionts Bacteroides fragilis and Bacteroides thetaiotaomicron.	de Sa Almeida JS, de Oliveira Marre AT, Teixeira FL, Boente RF, Domingues RMCP, de Paula GR, Lobo LA.	Anaerobe	10.1016/j.anaerobe.2020.102232	2020
	Coarse-grained model of serial dilution dynamics in synthetic human gut microbiome.	Mahajan T, Maslov S.	PLoS Comput Biol	10.1371/journal.pcbi.1013222	2025
	Extraction of Seed Oil from Heracleum persicum Desf. ex Fischer and Investigation of Its Composition, Qualitative and Nutraceutical Properties.	Dadazadeh A, Azadmard-Damirchi S, Piravi-Vanak Z, Torbati M, Martinez F.	Foods	10.3390/foods14203486	2025
	Acetate differentially regulates IgA reactivity to commensal bacteria.	Takeuchi T, Miyauchi E, Kanaya T, Kato T, Nakanishi Y, Watanabe T, Kitami T, Taida T, Sasaki T, Negishi H, Shimamoto S, Matsuyama A, Kimura I, Williams IR, Ohara O, Ohno H.	Nature	10.1038/s41586-021-03727-5	2021
Metabolism	Selective Utilization of the Human Milk Oligosaccharides 2'-Fucosyllactose, 3-Fucosyllactose, and Difucosyllactose by Various Probiotic and Pathogenic Bacteria.	Salli K, Hirvonen J, Siitonen J, Ahonen I, Anglenius H, Maukonen J.	J Agric Food Chem	10.1021/acs.jafc.0c06041	2021
Pathogenicity	Rifaximin reduces gut-derived inflammation in severe acute pancreatitis: an experimental animal model and randomized controlled trial.	Zou Y-y, Yu B-j, He C, Ding L, Xu X, Wan J-h, Lei Y-p, Huang X, Xiong H-f, He W-h, Luo L-y, Xia L, Lv N-h, Zhu Y.	Microbiol Spectr	10.1128/spectrum.01299-25	2025
Metabolism	Gut microbiota-mediated modulation of host amino acid availability and metabolism.	Han Z, Zhao L, Hu Q, Hung I, Liu C, Liu S, Mei X, Zeng X, Bin P, Wang J.	Gut Microbes	10.1080/19490976.2025.2552345	2025
	Alterations of the gut microbiota in the lupus nephritis: a systematic review.	Wang A, Zhao J, Qin Y, Zhang Y, Xing Y, Wang Y, Yu Z, Yan J, Han M, Yuan J, Hui Y, Guo S, Ning X, Sun S.	Ren Fail	10.1080/0886022x.2023.2285877	2023
	Longitudinal analysis of gut microbiome and metabolome correlates of response and toxicity with idecabtagene vicleucel.	Saha S, Rehman L, Rehman A, Darbaniyan F, Weber DM, Becnel M, Gaballa M, Thomas SK, Lee HC, Chang CC, Arora R, Menges M, Corallo S, Davila ML, Locke FL, Tanner MR, Neelapu SS, Shpall EJ, Flowers CR, Orlowski RZ, Jenq RR, Jain MD, Peterson C, Hansen DK, Saini NY, Patel KK.	Blood Adv	10.1182/bloodadvances.2024014476	2025
	Erratum for Townsend et al., "A Master Regulator of Bacteroides thetaiotaomicron Gut Colonization Controls Carbohydrate Utilization and an Alternative Protein Synthesis Factor".	Townsend GE, Han W, Schwalm ND, Hong X, Bencivenga-Barry NA, Goodman AL, Groisman EA.	mBio	10.1128/mbio.00301-20	2020
	MicroSTNet: a spatio-temporal graph-based framework for time-series microbiome analysis.	Gao S, Li L, Wang J, Wang Y, Dong Y.	Microb Genom	10.1099/mgen.0.001519	2025
	Hospital-Acquired Sacral Pressure Ulcer Complicated by a Spinal Epidural Abscess.	Carlson TL, Alba R, Alfaori Q, Bies JJ, Lane M, Htay T.	Cureus	10.7759/cureus.60379	2024
Metabolism	Anaerobic heme recycling by gut microbes: Important methods for monitoring porphyrin production.	da Silva RR, Nath AK, Adedoyin V, Akpoto E, DuBois JL.	Methods Enzymol	10.1016/bs.mie.2024.07.002	2024
	Clinical Evaluation of VITEK MS PRIME with PICKME Pen for Bacteria and Yeasts, and RUO Database for Filamentous Fungi.	Lee H, Koo J, Oh J, Cho SI, Lee H, Lee HJ, Sung GH, Kim J.	Microorganisms	10.3390/microorganisms12050964	2024
	Human gene and microbial analyses in rectal cancer complete responses to radiotherapy.	Sulit AK, Wilson K, Pearson J, Silander OK, Sampurno S, Michael M, Ramsay R, Heriot A, Frizelle F, Purcell RV.	BJS Open	10.1093/bjsopen/zrad035	2023
	Short-chain fatty acids of various lengths differentially inhibit Klebsiella pneumoniae and Enterobacteriaceae species.	Chang KC, Nagarajan N, Gan Y-H.	mSphere	10.1128/msphere.00781-23	2024
	[Bacteremia due to strict anaerobes].	Pina Delgado C, Bolanos Rivero M, Carmona Tello MC, Ramirez Estupinan CJ, Hernandez Cabrera PM, de Miguel Martinez I.	Rev Esp Quimioter	10.37201/req/063.2024	2025
	East meets west: integrating Yin-Yang theory with immunology teaching.	Wang Z, Wang M, Lin M, Lu Y, Xia Q, Wei P.	Front Immunol	10.3389/fimmu.2024.1441863	2024
	Author Correction: Metabolism of multiple glycosaminoglycans by Bacteroides thetaiotaomicron is orchestrated by a versatile core genetic locus.	Ndeh D, Basle A, Strahl H, Yates EA, McClurgg UL, Henrissat B, Terrapon N, Cartmell A.	Nat Commun	10.1038/s41467-020-18097-1	2020
	A retrospective study of the detection of sepsis pathogens comparing blood culture and culture-independent digital PCR.	Zhao Z, Wang Y, Kang Y, Wu G, He J, Wang Z, Yang J, Wang Y, Yang X, Jia W.	Heliyon	10.1016/j.heliyon.2024.e27523	2024
	Engineered probiotics: a new era in treating inflammatory bowel disease.	Duan S, Wang Y, Zhan S, Ye Z, Luo T, Zhou Y, Xu H, Huang H.	J Transl Med	10.1186/s12967-025-07271-y	2025
	Switching from a High-Fat to a Regular Chow Diet Improves Obesity Progression in Mice.	Wang Y, Chen F, Wang X, Wang S, Ding L.	Curr Issues Mol Biol	10.3390/cimb47100791	2025
	Inter-phylum circulation of a beta-lactamase-encoding gene: a rare but observable event.	Gschwind R, Petitjean M, Fournier C, Lao J, Clermont O, Nordmann P, Mellmann A, Denamur E, Poirel L, Ruppe E.	Antimicrob Agents Chemother	10.1128/aac.01459-23	2024
	Association between monosodium glutamate consumption with changes in gut microbiota and related metabolic dysbiosis-A systematic review.	Ahangari H, Bahramian B, Khezerlou A, Tavassoli M, Kiani-Salmi N, Tarhriz V, Ehsani A.	Food Sci Nutr	10.1002/fsn3.4198	2024
	An RNA-centric view on gut Bacteroidetes.	Ryan D, Prezza G, Westermann AJ.	Biol Chem	10.1515/hsz-2020-0230	2020
	Intestinal dysbiosis associated with non-nutritive sweeteners intake: an effect without a cause?	Marongiu L, Brzozowska E, Hetjens S, Hoelzle LE, Venturelli S.	Front Nutr	10.3389/fnut.2025.1694264	2025
Enzymology	Metagenomic insights into the effects of Urtica dioica vegetable on the gut microbiota of C57BL/6J obese mice, particularly the composition of Clostridia.	Fan S, Raychaudhuri S, Page R, Shahinozzaman M, Obanda DN.	J Nutr Biochem	10.1016/j.jnutbio.2021.108594	2021
	Effects of adding eubiotic lignocellulose on the performance, the gut microbiota, and short-chain fatty acids of layer chickens.	Sun B, Hou L, Yang Y.	Braz J Microbiol	10.1007/s42770-022-00796-0	2022
Metabolism	Extracellular vesicles produced by the human commensal gut bacterium Bacteroides thetaiotaomicron affect host immune pathways in a cell-type specific manner that are altered in inflammatory bowel disease.	Gul L, Modos D, Fonseca S, Madgwick M, Thomas JP, Sudhakar P, Booth C, Stentz R, Carding SR, Korcsmaros T.	J Extracell Vesicles	10.1002/jev2.12189	2022
	Fluid flow structures gut microbiota biofilm communities by distributing public goods.	Wong JPH, Fischer-Stettler M, Zeeman SC, Battin TJ, Persat A.	Proc Natl Acad Sci U S A	10.1073/pnas.2217577120	2023
	Gut Microbiota Composition in Rats Consuming Sucralose or Rebaudioside A at Recommended Doses Under Two Dietary Interventions.	Ramos-Garcia M, Genis-Mendoza AD, Garcia-Vazquez C, Martinez-Magana JJ, Olvera-Hernandez V, Martinez-Lopez MC, Diaz-Zagoya JC, Alvarez-Villagomez CS, Juarez-Rojop IE, Nicolini H, Ble-Castillo JL.	Metabolites	10.3390/metabo15080529	2025
Genetics	Infant Gut Microbial Metagenome Mining of alpha-l-Fucosidases with Activity on Fucosylated Human Milk Oligosaccharides and Glycoconjugates.	Moya-Gonzalvez EM, Pena-Gil N, Rubio-Del-Campo A, Coll-Marques JM, Gozalbo-Rovira R, Monedero V, Rodriguez-Diaz J, Yebra MJ.	Microbiol Spectr	10.1128/spectrum.01775-22	2022
	Gut Microbiota Profile and Functional Gastrointestinal Disorders in Infants: A Longitudinal Study.	Pantazi AC, Mihai CM, Lupu A, Balasa AL, Chisnoiu T, Mihai L, Frecus CE, Ungureanu A, Chirila SI, Nori W, Lupu VV, Stoicescu RM, Baciu G, Cambrea SC.	Nutrients	10.3390/nu17040701	2025
	A novel system to culture human intestinal organoids under physiological oxygen content to study microbial-host interaction.	Fofanova TY, Karandikar UC, Auchtung JM, Wilson RL, Valentin AJ, Britton RA, Grande-Allen KJ, Estes MK, Hoffman K, Ramani S, Stewart CJ, Petrosino JF.	PLoS One	10.1371/journal.pone.0300666	2024
Metabolism	Structure of a gut microbial diltiazem-metabolizing enzyme suggests possible substrate binding mode.	Zhou S, Ko TP, Huang JW, Liu W, Zheng Y, Wu S, Wang Q, Xie Z, Liu Z, Chen CC, Guo RT.	Biochem Biophys Res Commun	10.1016/j.bbrc.2020.04.116	2020
	Probing the Broad-Spectrum Virus-Neutralizing Epitopes Using the High-Density Oligomannose-Conjugates and Carbohydrate Microarrays.	Toonstra C, Wu L, Wang LX, Wang D.	Bioconjug Chem	10.1021/acs.bioconjchem.5c00361	2025
	Gut microbiome is associated with asthma and race in children with food allergy.	Mahdavinia M, Fyolek JP, Jiang J, Thivalapill N, Bilaver LA, Warren C, Fox S, Nimmagadda SR, Newmark PJ, Sharma H, Assa'ad A, Seed PC, Gupta RS.	J Allergy Clin Immunol	10.1016/j.jaci.2023.07.024	2023
	Narrowing Down Key Players in Autoimmunity via Single-Cell Multiomics.	Gjurgjaj A, Conde CD.	Eur J Immunol	10.1002/eji.202451233	2025
	Human gut bacteria tailor extracellular vesicle cargo for the breakdown of diet- and host-derived glycans.	Sartorio MG, Pardue EJ, Scott NE, Feldman MF.	Proc Natl Acad Sci U S A	10.1073/pnas.2306314120	2023
	Moderate altitude exposure induced gut microbiota enterotype shifts impacting host serum metabolome and phenome.	Ma Y, Wang D, Yu X, Fan Y, Yang Z, Gao X, Huang X, Meng J, Cheng P, Liu X, Liu Z, Li X.	BMC Microbiol	10.1186/s12866-025-04245-4	2025
	Ultra-Processed Foods and the Impact on Cardiometabolic Health: The Role of Diet Quality.	Wang X, Sun Q.	Diabetes Metab J	10.4093/dmj.2024.0659	2024
	Gut microbiome is associated with radiotherapy response in lung cancer patients with brain metastases.	Liang F, Sun Y, Yang J, Shen Z, Wang G, Zhu J, Zhou C, Xia Y.	Front Cell Infect Microbiol	10.3389/fcimb.2025.1562831	2025
	The role of the gut microbiota in chemotherapy response, efficacy and toxicity: a systematic review.	Bohm D, Russ E, Guchelaar HJ, Ziemons J, Penders J, Smidt ML, van Best N, Deenen MJ.	NPJ Precis Oncol	10.1038/s41698-025-01034-0	2025
	Mucin-driven ecological interactions in an in vitro synthetic community of human gut microbes.	Berkhout MD, Ioannou A, de Ram C, Boeren S, Plugge CM, Belzer C.	Glycobiology	10.1093/glycob/cwae085	2024
	Designing function-specific minimal microbiomes from large microbial communities.	Raghu AK, Palanikumar I, Raman K.	NPJ Syst Biol Appl	10.1038/s41540-024-00373-1	2024
Genetics	Characteristics of intestinal flora in patients with cerebral infarction complicated with Type 2 diabetes mellitus.	Cheng X, Zhang Z, Dong W, Lun Y, Liu B.	Zhong Nan Da Xue Xue Bao Yi Xue Ban	10.11817/j.issn.1672-7347.2023.220558	2023
	FucR Functions as a Transcriptional Regulator for L-Fucose Utilization in Campylobacter jejuni.	Muraoka WT, Lizer N, Liu P, Shen Z, Xia Q, Ilgu M, Zhang Q.	Microorganisms	10.3390/microorganisms13102364	2025
Enzymology	Production of N-Acetyl-d-neuraminic Acid by Whole Cells Expressing Bacteroides thetaiotaomicron N-Acetyl-d-glucosamine 2-Epimerase and Escherichia coli N-Acetyl-d-neuraminic Acid Aldolase.	Gao X, Zhang F, Wu M, Wu Z, Shang G.	J Agric Food Chem	10.1021/acs.jafc.9b01839	2019
	Idiopathic aplastic anemia with concurrent complications of colonic perforation and mucormycosis: Case report.	Li ZP, Yang JC, Ma T, He XX, Gong YF, Xue J, Xue XY.	Heliyon	10.1016/j.heliyon.2024.e34091	2024
	Diaphragmatic Injury with Empyema Development after Microwave Ablation of a Liver Dome Lesion.	Jing R, Merritt T, Gemmete JJ.	Semin Intervent Radiol	10.1055/s-0043-1769774	2023
	Modulatory Role of Hesperetin-Copper(II) on Gut Microbiota in Type 2 Diabetes Mellitus Mice.	Peng X, Wei Y, Gong D, Zhang G.	Foods	10.3390/foods14132390	2025
	Prognostic value of 24-hour cultivation of peritoneal fluid to distinguish complicated from uncomplicated acute appendicitis: a prospective cohort study.	Mark-Christensen A, Bro Sorensen D, Qvist N, Justesen US, Moller S, Ellebaek MB.	Langenbecks Arch Surg	10.1007/s00423-024-03428-3	2024
Pathogenicity	Gut microbiota-derived indoleacetic acid attenuates neuroinflammation and neurodegeneration in glaucoma through ahr/rage pathway.	Wang N, Sun C, Yang Y, Zhang D, Huang L, Xu C, Wang M, Xu M, Yan T, Wu Y, Xu L, Ju Y, Sun H, Guo W.	J Neuroinflammation	10.1186/s12974-025-03505-4	2025
Phylogeny	Full-length 16S rRNA Sequencing Reveals Gut Microbiome Signatures Predictive of MASLD in children with obesity.	Lin YC, Wu CC, Li YE, Chen CL, Lin CR, Ni YH.	BMC Microbiol	10.1186/s12866-025-03849-0	2025
	Host hepatic metabolism is modulated by gut microbiota-derived sphingolipids.	Le HH, Lee MT, Besler KR, Johnson EL.	Cell Host Microbe	10.1016/j.chom.2022.05.002	2022
	CO₂ Is Beneficial to Gut Microbiota Homeostasis during Colonoscopy: Randomized Controlled Trial.	Yang X, Xiu WB, Wang JX, Li LP, He C, Gao CP.	J Clin Med	10.3390/jcm11185281	2022
	The Role of Gut Microbiota in Mice With Bile Duct Ligation-Evoked Cholestatic Liver Disease-Related Cognitive Dysfunction.	Yang B, Sun T, Chen Y, Xiang H, Xiong J, Bao S.	Front Microbiol	10.3389/fmicb.2022.909461	2022
	Tryptophan Metabolism and Gut Microbiota: A Novel Regulatory Axis Integrating the Microbiome, Immunity, and Cancer.	Hou Y, Li J, Ying S.	Metabolites	10.3390/metabo13111166	2023
	Shotgun EM of mycobacterial protein complexes during stationary phase stress.	Kirykowicz AM, Woodward JD.	Curr Res Struct Biol	10.1016/j.crstbi.2020.09.002	2020
	Biochemical Characterization of Two Rhamnogalacturonan Lyases From Bacteroides ovatus ATCC 8483 With Preference for RG-I Substrates.	Wang W, Wang Y, Yi H, Liu Y, Zhang G, Zhang L, Mayo KH, Yuan Y, Zhou Y.	Front Microbiol	10.3389/fmicb.2021.799875	2021
	Areca catechu L. extract powder ameliorates Eimeria tenella-induced coccidiosis in chicks through anti-inflammatory effects, growth promotion, hematological restoration, and gut microbiota modulation.	Ma D, Wu S, Hou S, Hui Q, Gong Y, Han C, Hao Z.	Poult Sci	10.1016/j.psj.2025.105498	2025
	Rapeseed Meal as an Alternative Protein Source in Fish Feed and Its Impact on Growth Parameters, Digestive Tract, and Gut Microbiota.	Karolina WA, Justyna N.	Animals (Basel)	10.3390/ani15091264	2025
	A Continuous Battle for Host-Derived Glycans Between a Mucus Specialist and a Glycan Generalist in vitro and in vivo.	Kostopoulos I, Aalvink S, Kovatcheva-Datchary P, Nijsse B, Backhed F, Knol J, de Vos WM, Belzer C.	Front Microbiol	10.3389/fmicb.2021.632454	2021
Enzymology	X-ray Structures of Two Bacteroides thetaiotaomicron C11 Proteases in Complex with Peptide-Based Inhibitors.	Roncase EJ, Gonzalez-Paez GE, Wolan DW.	Biochemistry	10.1021/acs.biochem.9b00098	2019
Pathogenicity	Integrative machine learning identifies robust inflammation-related diagnostic biomarkers and stratifies immune-heterogeneous subtypes in Kawasaki disease	Wang X, Zhang L.	Pediatr Rheumatol Online J		2025
Metabolism	Phase-variable bacteria simultaneously express multiple capsules.	Hsieh SA, Donermeyer DL, Horvath SC, Allen PM.	Microbiology (Reading)	10.1099/mic.0.001066	2021
Phenotype	Shared and Distinct Gut Microbial Profiles in Saudi Women with Metabolically Healthy and Unhealthy Obesity.	Aljuraiban GS, Alfhili MA, Aldhwayan MM, Aljazairy EA, Al-Musharaf S.	Microorganisms	10.3390/microorganisms11061430	2023
Metabolism	Analysis of Active Site Architecture and Reaction Product Linkage Chemistry Reveals a Conserved Cleavage Substrate for an Endo-alpha-mannanase within Diverse Yeast Mannans.	Jones DR, Xing X, Tingley JP, Klassen L, King ML, Alexander TW, Abbott DW.	J Mol Biol	10.1016/j.jmb.2019.12.048	2020
	The association between dietary live microbes intake and PhenoAge in US non-diabetes adults and the mediating effect of insulin resistance: NHANES 2007-2018.	Yang Y, Sun Z, Lin J, Wang Q, Sun X, Tong T, Zhang X, Li C, Yao K.	Aging Clin Exp Res	10.1007/s40520-025-03104-6	2025
	Reference Whole Genome Sequence Analyses and Characterization of a Novel Carnobacterium maltaromaticum Distinct Sequence Type Isolated from a North American Gray Wolf (Canis lupus) Gastrointestinal Tract.	Klews CC, Bryant JL, McCabe J, Atchley AN, Cousins TW, Barnard-Davidson M, Ackermann MR, Netherland M, Hasan NA, Jordan PA, Forsythe ES, Ball PN, Seal BS.	Vet Sci	10.3390/vetsci12050410	2025
	Gut microbes modulate (p)ppGpp during a time-restricted feeding regimen.	Ontai-Brenning A, Hamchand R, Crawford JM, Goodman AL.	mBio	10.1128/mbio.01907-23	2023
	Development of a dual-flow tissue perfusion device for modeling the gastrointestinal tract-brain axis.	Baldwin L, Jones EJ, Iles A, Carding SR, Pamme N, Dyer CE, Greenman J.	Biomicrofluidics	10.1063/5.0168953	2023
	In Situ Imaging of O-Linked beta-N-Acetylglucosamine Using On-Tissue Hydrolysis and MALDI Mass Spectrometry.	Escobar EE, Seeley EH, Serrano-Negron JE, Vocadlo DJ, Brodbelt JS.	Cancers (Basel)	10.3390/cancers15041224	2023
	Fermentation of Alginate and Its Oligosaccharides by the Human Gut Microbiota: Structure-Property Relationships and New Findings Focusing on Bacteroides xylanisolvens.	Li J, Lv Y, Shao M, Lv D, Fu Z, Guo P, Li Q, Shang Q.	Nutrients	10.3390/nu17091424	2025
	Exploring the Catalytic Mechanisms of a Newly Identified Salt-Activated Alginate Lyase from Pseudoalteromonas carrageenovora ASY5.	Zhuang X, Jiao C, Guo Z, Xiao Q, Chen J, Chen F, Yang Q, Ru Y, Weng H, Wang S, Xiao A, Zhang Y.	Mar Drugs	10.3390/md23060254	2025
	Barcoded overexpression screens in gut Bacteroidales identify genes with roles in carbon utilization and stress resistance.	Huang YY, Price MN, Hung A, Gal-Oz O, Tripathi S, Smith CW, Ho D, Carion H, Deutschbauer AM, Arkin AP.	Nat Commun	10.1038/s41467-024-50124-3	2024
	Dietary polyunsaturated fatty acids effect on cecal microbiome profile of maturing broiler chicken.	Jadhav VV, Fasina YO, Harrison SH.	Poult Sci	10.1016/j.psj.2025.105167	2025
Pathogenicity	The current landscape of fecal microbiota transplantation in treating inflammatory bowel disease.	Bi Y, Cheng B, Zou B, Liu S, Cui Z.	Transl Gastroenterol Hepatol	10.21037/tgh-24-138	2025
Metabolism	A metabolomics pipeline for the mechanistic interrogation of the gut microbiome.	Han S, Van Treuren W, Fischer CR, Merrill BD, DeFelice BC, Sanchez JM, Higginbottom SK, Guthrie L, Fall LA, Dodd D, Fischbach MA, Sonnenburg JL.	Nature	10.1038/s41586-021-03707-9	2021
Enzymology	Diversity of bacterial endophyte in Eucalyptus clones and their implications in water stress tolerance.	Dasgupta MG, Burragoni S, Amrutha S, Muthupandi M, Parveen ABM, Sivakumar V, Ulaganathan K.	Microbiol Res	10.1016/j.micres.2020.126579	2020
	Characteristics and Clinical Significance of Gut Microbiota in Patients with Invasive Pulmonary Aspergillosis.	Cao J, He Q, Zhang M, Zhou R, Feng C.	Pol J Microbiol	10.33073/pjm-2025-011	2025
	Evolutionary insights into elongation factor G using AlphaFold and ancestral analysis.	Rahaman S, Steele JH, Zeng Y, Xu S, Wang Y.	Comput Biol Med	10.1016/j.compbiomed.2025.110188	2025
	E.PathDash, pathway activation analysis of publicly available pathogen gene expression data.	Taub L, Hampton TH, Sarkar S, Doing G, Neff SL, Finger CE, Ferreira Fukutani K, Stanton BA.	mSystems	10.1128/msystems.01030-24	2024
Genetics	Structural and functional characterization of gut microbiota in dyslipidemic patients from high-altitude Tibetan pastoral areas.	Chen J, Luo Y, Hao Y, Wang Q, Wang Q.	Front Nutr	10.3389/fnut.2025.1676238	2025
	Utilization of glycosaminoglycans by the human gut microbiota: participating bacteria and their enzymatic machineries.	Rawat PS, Seyed Hameed AS, Meng X, Liu W.	Gut Microbes	10.1080/19490976.2022.2068367	2022
Pathogenicity	Iron acquisition by a commensal bacterium modifies host nutritional immunity during Salmonella infection.	Spiga L, Fansler RT, Perera YR, Shealy NG, Munneke MJ, David HE, Torres TP, Lemoff A, Ran X, Richardson KL, Pudlo N, Martens EC, Folta-Stogniew E, Yang ZJ, Skaar EP, Byndloss MX, Chazin WJ, Zhu W.	Cell Host Microbe	10.1016/j.chom.2023.08.018	2023
Metabolism	Microbiota and short chain fatty acid relationships underlie clinical heterogeneity and identify key microbial targets in irritable bowel syndrome (IBS).	Shin AS, Xing Y, Waseem MR, Siwiec R, James-Stevenson T, Rogers N, Bohm M, Wo J, Lockett C, Gupta A, Kadariya J, Toh E, Anderson R, Dong A, Xu H, Gao X.	Sci Rep	10.1038/s41598-025-19363-2	2025
Genetics	Coupling culturomics and metagenomics sequencing to characterize the gut microbiome of patients with cancer treated with immune checkpoint inhibitors.	Diop K, Mbaye B, Nili S, Filin A, Benlaifaoui M, Malo J, Renaud AS, Belkaid W, Hunter S, Messaoudene M, Lee KA, Elkrief A, Routy B.	Gut Pathog	10.1186/s13099-025-00694-4	2025
	Bacteroides thetaiotaomicron.	Porter NT, Luis AS, Martens EC.	Trends Microbiol	10.1016/j.tim.2018.08.005	2018
	Gut bacteria: protective mediators, pathogenic contributors and novel therapeutic targets in Candida albicans infections.	Song J, Yang X, Liu X, Li J.	Gut Pathog	10.1186/s13099-025-00755-8	2025
Phylogeny	Polymicrobial anaerobic meningitis caused by Bacteroides fragilis, Bacteroides thetaiotaomicron, Fusobacterium necrophorum and Slackia exigua in a patient with mastoiditis following otitis media.	Kalay GN, Dalgic N, Bozan T, Ulger-Toprak N, Bayraktar B, Soyletir G.	Anaerobe	10.1016/j.anaerobe.2019.02.003	2019
	Long-term health outcomes in adolescents with obesity treated with faecal microbiota transplantation: 4-year follow-up	Wilson B, Zuppi M, Derraik J, Albert B, Tweedie-Cullen R, Leong K, Beck K, Vatanen T, O'Sullivan J, Cutfield W.	Nat Commun		2025
Phylogeny	Stage-specific fecal and salivary microbiota signatures for noninvasive detection of colorectal cancer.	Wu Z, Zhu Z, Zhou C, Lin Z, Yang H, Jiang G, Ding S, Yu J, Sun L.	Front Microbiol	10.3389/fmicb.2025.1658693	2025
	Recent advances in understanding the role of extracellular vesicles from probiotics in intestinal immunity signaling.	Kurata A, Uegaki K.	Biochem Soc Trans	10.1042/bst20240150	2025
	Gut microbiome and NAFLD: impact and therapeutic potential.	Li L, Cai F, Guo C, Liu Z, Qin J, Huang J.	Front Microbiol	10.3389/fmicb.2024.1500453	2024
	Isolation, Characterization, and Application of Bacteriophage for Salmonella Control in Broiler Chickens.	Wanasawaeng W, Thomrongsuwannakij T, Chansiripornchai N.	Vet Med Int	10.1155/vmi/6502225	2025
	Cefadroxil-Induced Clostridium difficile Infection Following Total Knee Arthroplasty.	Angerett N, Ferguson C, Kahan M, Fitz D, Hallock R.	Arthroplast Today	10.1016/j.artd.2022.08.016	2022
	Synthesis and biological evaluation of lipid A derived from commensal Bacteroides.	Verpalen ECJM, Ehlers AM, van Wingaarden ACA, Brouwer AJ, Boons GJ.	Org Biomol Chem	10.1039/d4ob01340a	2024
	Xylo-oligosaccharide-based prebiotics upregulate the proteins of the Sus-like system in caecal Bacteroidetes of the chicken: evidence of stimbiotic mechanism.	Amir SE, Naeem M, Boocock D, Coveney C, O'Neill HM, Bedford MR, Burton EJ.	Poult Sci	10.1016/j.psj.2023.103113	2023
	Engineering strategies and biomedical applications of bacterial extracellular vesicles.	Liang X, Li Q, Zheng L, Situ B.	Biomater Transl	10.12336/bmt.24.00032	2025
	Complex carbohydrate utilization by gut bacteria modulates host food consumption.	Yu KB, Son C, Ozcan E, Chandra A, Paramo J, Varghese A, Roice A, Finnigan D, Chandra F, Novoselov A, Kazmi SA, Lum GR, Lopez-Romero A, Lynch JB, Hsiao EY.	Nat Commun	10.1038/s41467-025-63372-8	2025
	The Selective Advantage of the lac Operon for Escherichia coli Is Conditional on Diet and Microbiota Composition.	Pinto C, Melo-Miranda R, Gordo I, Sousa A.	Front Microbiol	10.3389/fmicb.2021.709259	2021
	Enhancement of oxaliplatin efficacy and amelioration of intestinal epithelial damage by Lactobacillus rhamnosus GG through modulation of gut microbiota.	Zhang Z, Li R, Ren Y, Ni Y, Shen X, Yi D, Xu ZH, Geng Y, You Q.	Front Microbiol	10.3389/fmicb.2025.1565880	2025
Enzymology	Structural and functional characterization of a family GH53 beta-1,4-galactanase from Bacteroides thetaiotaomicron that facilitates degradation of prebiotic galactooligosaccharides.	Boger M, Hekelaar J, van Leeuwen SS, Dijkhuizen L, Lammerts van Bueren A.	J Struct Biol	10.1016/j.jsb.2018.12.002	2019
Pathogenicity	A bacterial sialidase mediates early-life colonization by a pioneering gut commensal.	Buzun E, Hsu CY, Sejane K, Oles RE, Vasquez Ayala A, Loomis LR, Zhao J, Rossitto LA, McGrosso DM, Gonzalez DJ, Bode L, Chu H.	Cell Host Microbe	10.1016/j.chom.2023.12.014	2024
	Microscopic messengers: microbiota-derived bacterial extracellular vesicles in inflammatory bowel disease.	Zubair M, Abouelnazar FA, Dawood AS, Pan J, Zheng X, Chen T, Liu P, Mao F, Yan Y, Chu Y.	Front Microbiol	10.3389/fmicb.2024.1481496	2024
	Gut microbiota-derived 4-hydroxyphenylacetic acid (4-HPAA) inhibits weight gain and is negatively associated with childhood obesity.	Li Q, Zhang J, Fan M, Wu N, Li T, Wang M, Zhang L.	Transl Pediatr	10.21037/tp-2025-158	2025
	Systematic review of the impact of intestinal microbiota on vaccine responses.	Ardura-Garcia C, Curtis N, Zimmermann P.	NPJ Vaccines	10.1038/s41541-024-01000-0	2024
	Causal Associations Between the Gut Microbiota and Hypertension-Related Traits Through Mendelian Randomization: A Cross-Sectional Cohort Study.	Tian Y, Gu M, Chen D, Dong Q, Wang Y, Sun W, Kong X.	J Clin Hypertens (Greenwich)	10.1111/jch.14925	2025
	Gut microbiome compositional and functional features associate with Alzheimer's disease pathology.	Kang JW, Khatib LA, Heston MB, Dilmore AH, Labus JS, Deming Y, Schimmel L, Blach C, McDonald D, Gonzalez A, Bryant M, Ulland TK, Johnson SC, Asthana S, Carlsson CM, Chin NA, Blennow K, Zetterberg H, Rey FE, Alzheimer Gut Microbiome Project Consortium, Kaddurah-Daouk R, Knight R, Bendlin BB.	Alzheimers Dement	10.1002/alz.70417	2025
Phylogeny	Alterations of ileal mucosa-associated microbiota in hypercholesterolemia patients.	Li J, Ma J, Wang W, Du H, Tang S, Li Y, Zhu W, Zhang R, Wan J.	Heliyon	10.1016/j.heliyon.2023.e22116	2023
Metabolism	Activation of a Specific Gut Bacteroides-Folate-Liver Axis Benefits for the Alleviation of Nonalcoholic Hepatic Steatosis.	Qiao S, Bao L, Wang K, Sun S, Liao M, Liu C, Zhou N, Ma K, Zhang Y, Chen Y, Liu SJ, Liu H.	Cell Rep	10.1016/j.celrep.2020.108005	2020
	Weissella confusa alleviates experimental colitis in mice by regulating inflammatory pathways and gut microbiota.	Tang H, Fan Q, Lu Y, Lin X, Lan R, Hu D, Zhang S, Wang R, Zhao R, Liu L, Xu J.	Front Microbiol	10.3389/fmicb.2025.1574548	2025
Enzymology	Biochemical characterisation of four rhamnosidases from thermophilic bacteria of the genera Thermotoga, Caldicellulosiruptor and Thermoclostridium.	Baudrexl M, Schwarz WH, Zverlov VV, Zverlov VV, Liebl W.	Sci Rep	10.1038/s41598-019-52251-0	2019
	Hierarchical glycolytic pathways control the carbohydrate utilization regulator in human gut Bacteroides.	Kabonick SG, Verma K, Modesto JL, Pearce VH, Winokur KM, Groisman EA, Townsend GE.	Nat Commun	10.1038/s41467-025-59704-3	2025
Metabolism	In-Vitro Prebiotic Analysis of Microbiota Accessible Pectic Polysaccharides.	Tingirikari JMR.	Curr Microbiol	10.1007/s00284-019-01781-x	2019
	Effects of Antimicrobial Flavonoids Against Representative Bacteria and Fungi: A Review of the Literature.	Hamid ME, Alamri F, Abdelrahim IM, Joseph M, Elamin MM, Alraih AM.	Cureus	10.7759/cureus.62765	2024
	Bacillus coagulans 198 and L-glutamine in combination attenuated intestinal mucositis in a 5-FU-induced BALB/c mouse model via modulation of gut microbial community structure and diversity.	Chen WJ, Shen SR, Hsu WH, Lee BH, Wei YS, Chu HF, Tseng MC, Shen TL.	J Food Drug Anal	10.38212/2224-6614.3535	2025
	Interactions between gut microbiota and cardiovascular drugs: effects on drug therapeutic effect and side effect.	Wang T, Lan Q, Deng H, Han W, Zhang R, Zhong J.	Front Cardiovasc Med	10.3389/fcvm.2025.1570008	2025
	Comparative study of rebaudioside A and rebaudioside Aalpha: physicochemical properties and in vivo metabolism.	Kim HJ, Kang HJ, Lim S, Kim OC, Yoon KN, Lee J, Matienzo ME, Park MJ, Park BS, Cho JY, Hong SJ, Kim DI, Kim YM.	NPJ Sci Food	10.1038/s41538-025-00585-7	2025
	A spectrophotometric method for high-throughput screening of alpha-l-rhamnosidase activity on rutin coupled with a beta-d-glucosidase assay.	Li BC, Peng B, Zhang T, Li YQ, Ding GB.	3 Biotech	10.1007/s13205-019-1753-1	2019
	The Role of Beneficial Microbiota in COVID-19: Insights from Key Bacterial Genera.	Rampelotto PH, Taufer CR, da Silva J.	Microorganisms	10.3390/microorganisms13051029	2025
	The First Infant Anaerobic Meningitis Infected by Prevotella bivia: A Case Report and Literature Review.	Sun Y, Li Z, Li Y, Zhang C, Wang M, Yu W, Liu G, Wang S.	Infect Drug Resist	10.2147/idr.s452189	2024
	QseC sensor kinase modulates the human microbiota during enterohemorrhagic Escherichia coli O157:H7 infection in the Simulator of the Human Intestinal Microbial Ecosystem (SHIME®).	Melchior K, Salgaco MK, Sivieri K, Moreira CG.	Braz J Microbiol	10.1007/s42770-022-00877-0	2023
	Single-molecule dynamics of surface lipoproteins in bacteroides indicate similarities and cooperativity.	Geffroy L, Brown HA, DeVeaux AL, Koropatkin NM, Biteen JS.	Biophys J	10.1016/j.bpj.2022.10.024	2022
	A self-designed Chinese herbal formula alleviates GAstV infection-induced gout in goslings by inhibiting xanthine oxidase (XOD) and regulating intestinal microbiota.	Zhang X, Zhu M, Cui H, Fan J, Yang M, Jin Y, Mao S, Zhang H.	Poult Sci	10.1016/j.psj.2025.106062	2025
Genetics	Genome analysis reveals a biased distribution of virulence and antibiotic resistance genes in the genus Enterococcus and an abundance of safe species.	Tadesse BT, Zhao S, Gu L, Jers C, Mijakovic I, Solem C.	Appl Environ Microbiol	10.1128/aem.00415-25	2025
	Association between the Blautia/Bacteroides Ratio and Altered Body Mass Index after Bariatric Surgery.	Kim Y, Son D, Kim BK, Kim KH, Seo KW, Jung K, Park SJ, Lim S, Kim JH.	Endocrinol Metab (Seoul)	10.3803/enm.2022.1481	2022
Metabolism	Genetic Variation of the SusC/SusD Homologs from a Polysaccharide Utilization Locus Underlies Divergent Fructan Specificities and Functional Adaptation in Bacteroides thetaiotaomicron Strains.	Joglekar P, Sonnenburg ED, Higginbottom SK, Earle KA, Morland C, Shapiro-Ward S, Bolam DN, Sonnenburg JL.	mSphere	10.1128/mspheredirect.00185-18	2018
	Metagenome-wide association analysis identifies microbial determinants of post-antibiotic ecological recovery in the gut.	Chng KR, Ghosh TS, Tan YH, Nandi T, Lee IR, Ng AHQ, Li C, Ravikrishnan A, Lim KM, Lye D, Barkham T, Raman K, Chen SL, Chai L, Young B, Gan YH, Nagarajan N.	Nat Ecol Evol	10.1038/s41559-020-1236-0	2020
	Prevotella timonensis Bacteria Associated With Vaginal Dysbiosis Enhance Human Immunodeficiency Virus Type 1 Susceptibility Of Vaginal CD4+ T Cells.	van Teijlingen NH, van Smoorenburg MY, Sarrami-Forooshani R, Zijlstra-Willems EM, van Hamme JL, Borgdorff H, van de Wijgert JHHM, van Leeuwen E, van der Post JAM, Strijbis K, Ribeiro CMS, Geijtenbeek TBH.	J Infect Dis	10.1093/infdis/jiae166	2024
	Bacteriophages Are Good Estimators of Human Viruses Present in Water.	Balleste E, Blanch AR, Mendez J, Sala-Comorera L, Maunula L, Monteiro S, Farnleitner AH, Tiehm A, Jofre J, Garcia-Aljaro C.	Front Microbiol	10.3389/fmicb.2021.619495	2021
Metabolism	Culture of salivary methanogens assisted by chemically produced hydrogen.	Guindo CO, Terrer E, Chabriere E, Aboudharam G, Drancourt M, Grine G.	Anaerobe	10.1016/j.anaerobe.2019.102128	2020
	Microbial succession at weaning is guided by microbial metabolism of host glycans.	Lubin JB, Planet PJ, Silverman MA.	Microbiome	10.1186/s40168-025-02193-9	2025
	Efficient production of icariin and baohuoside I from Epimedium Folium flavonoids by fungal alpha-L-rhamnosidase hydrolysing regioselectively the terminal rhamnose of epimedin C.	Zhang S, Lu C, Cao S, Li Q, Wu G, Zhao L.	Biotechnol Biofuels Bioprod	10.1186/s13068-023-02348-6	2023
Metabolism	Inulin-type fructan intervention restricts the increase in gut microbiome-generated indole in patients with peritoneal dialysis: a randomized crossover study.	Li L, Xiong Q, Zhao J, Lin X, He S, Wu N, Yao Y, Liang W, Zuo X, Ying C.	Am J Clin Nutr	10.1093/ajcn/nqz337	2020
	Metagenomic Comparison of Gut Microbes of Lemur catta in Captive and Semi-Free-Range Environments.	Xu C, Guo X, Li L.	Animals (Basel)	10.3390/ani15101442	2025
Pathogenicity	Working together: gut microbe-microbe interactions shape host inflammation.	Lawing A, Bleich R.	Infect Immun	10.1128/iai.00512-24	2025
Pathogenicity	Age-diet interactions significantly influence intratumoral gene expression, gut microbiome signature and tumor microenvironment in colorectal cancer.	Soni S, Mittal P, Lo JH, Yang Y, Smbatyan G, Lee K, Wan J, Kumagai H, Yen K, Mehta HH, Miller B, Torres-Gonzalez L, Battaglin F, Shah UH, Bartolini M, Zhang W, Craig DW, Millstein J, Cohen P, Lenz HJ.	Neoplasia	10.1016/j.neo.2025.101245	2025
	Open Label Vancomycin in Primary Sclerosing Cholangitis-Inflammatory Bowel Disease: Improved Colonic Disease Activity and Associations With Changes in Host-Microbiome-Metabolomic Signatures.	Quraishi MN, Cheesbrough J, Rimmer P, Mullish BH, Sharma N, Efstathiou E, Acharjee A, Gkoutus G, Patel A, Marchesi JR, Camuzeaux S, Chappell K, Valdivia-Garcia MA, Ferguson J, Brookes MJ, Walmsley M, Rossiter AE, van Schaik W, McInnes RS, Cooney R, Trauner M, Beggs AD, Iqbal TH, Trivedi PJ.	J Crohns Colitis	10.1093/ecco-jcc/jjae189	2025
	Isoxanthohumol improves obesity and glucose metabolism via inhibiting intestinal lipid absorption with a bloom of Akkermansia muciniphila in mice.	Watanabe Y, Fujisaka S, Morinaga Y, Watanabe S, Nawaz A, Hatta H, Kado T, Nishimura A, Bilal M, Aslam MR, Honda K, Nakagawa Y, Softic S, Hirabayashi K, Nakagawa T, Nagai Y, Tobe K.	Mol Metab	10.1016/j.molmet.2023.101797	2023
	Seeing is believing: Illuminating the Gram-negative outer membrane with molecular dynamics simulations.	Gutishvili G, Yang L, Gumbart JC.	Curr Opin Struct Biol	10.1016/j.sbi.2024.102828	2024
	The impact of Streptococcus thermophilus IDCC 2201 on gut microbiota and its potential as a prophylactic agent for colorectal cancer.	Nam EH, Lee M, Kim H, Kim D, Lee Y, Jung YH, Yang J, Shin M.	Sci Rep	10.1038/s41598-025-20976-w	2025
	Correction: Dynamic properties of dipeptidyl peptidase III from Bacteroides thetaiotaomicron and the structural basis for its substrate specificity - a computational study.	Tomin M, Tomic S.	Mol Biosyst	10.1039/c7mb90042b	2017
	GapMind: Automated Annotation of Amino Acid Biosynthesis.	Price MN, Deutschbauer AM, Arkin AP.	mSystems	10.1128/msystems.00291-20	2020
	Long-term TCDD oral exposure changes gut microbial glycosylation patterns in female but not male C57BL/6 mice.	Reichert D, Janssen S, Rossi A, Esser C.	Arch Toxicol	10.1007/s00204-025-04137-6	2025
Metabolism	Conserved unique peptide patterns (CUPP) online platform: peptide-based functional annotation of carbohydrate active enzymes.	Barrett K, Hunt CJ, Lange L, Meyer AS.	Nucleic Acids Res	10.1093/nar/gkaa375	2020
	Oregano Essential Oils Promote Rumen Digestive Ability by Modulating Epithelial Development and Microbiota Composition in Beef Cattle.	Zhang R, Wu J, Lei Y, Bai Y, Jia L, Li Z, Liu T, Xu Y, Sun J, Wang Y, Zhang K, Lei Z.	Front Nutr	10.3389/fnut.2021.722557	2021
	New Orange Ligand-Dependent Fluorescent Reporter for Anaerobic Imaging.	Chia HE, Koebke KJ, Rangarajan AA, Koropatkin NM, Marsh ENG, Biteen JS.	ACS Chem Biol	10.1021/acschembio.1c00391	2021
	Unraveling the Gut Microbiota-mediated Anti-tumor Mechanisms of ShenXia KuanZhong Decoction in Gastric Cancer: a Systems Biology and Dose-weighted Network Pharmacology Approach.	Zhou Z, Fang Y, Song L, Wang Y, Fang Z.	Biol Proced Online	10.1186/s12575-025-00304-2	2025
	Oleic Acid and Palmitic Acid from Bacteroides thetaiotaomicron and Lactobacillus johnsonii Exhibit Anti-Inflammatory and Antifungal Properties.	Charlet R, Le Danvic C, Sendid B, Nagnan-Le Meillour P, Jawhara S.	Microorganisms	10.3390/microorganisms10091803	2022
Genetics	A Spatiotemporal Atlas of the Gut Microbiota in Macaca mulatta brevicaudus: Implications for Health and Environment.	Yuan J, Sun Z, Sun R, Wang J, Wu C, Liu B, Zhao X, Li Q, Zhao J, Cai K.	Biology (Basel)	10.3390/biology14080980	2025
Metabolism	Salmonella enterica serovar Typhimurium uses anaerobic respiration to overcome propionate-mediated colonization resistance.	Shelton CD, Yoo W, Shealy NG, Torres TP, Zieba JK, Calcutt MW, Foegeding NJ, Kim D, Kim J, Ryu S, Byndloss MX.	Cell Rep	10.1016/j.celrep.2021.110180	2022
	Bibliometric analysis of research hotspots and trends on the relationship between the gut microbiota and depression from 2020 to 2024.	Xu D, Wu J, Lu Z, Zhao X, Feng Y, Zhang W, Jiang S, Zhang L, Wang T, Zhao Z.	Front Microbiol	10.3389/fmicb.2024.1479703	2024
	Crystal structure of beta-d-galactofuranosidase from Streptomyces sp. JHA19 in complex with an inhibitor provides insights into substrate specificity.	Fujio N, Yamada C, Kashima T, Matsunaga E, Nash RJ, Takegawa K, Fushinobu S.	FEBS Lett	10.1002/1873-3468.15056	2024
	LC-MS analysis of serum lipidomic and metabolomic signatures in pediatric patients with acute lymphoblastic leukemia.	Yan F, Wang S, Wang Y, Sun Y, Yang J, Sun L, Zaytseva YY, Deng P, Wang L.	Ital J Pediatr	10.1186/s13052-025-01921-z	2025
	Diet-microbiome interactions promote enteric nervous system resilience following spinal cord injury.	Hamilton AM, Blackmer-Raynolds L, Li Y, Kelly SD, Kebede N, Williams AE, Chang J, Garraway SM, Srinivasan S, Sampson TR.	NPJ Biofilms Microbiomes	10.1038/s41522-024-00556-y	2024
Phylogeny	In Search of Healthy Ageing: A Microbiome-Based Precision Nutrition Approach for Type 2 Diabetes Prevention.	Gonzalez A, Fullaondo A, Odriozola A.	Nutrients	10.3390/nu17111877	2025
	Microbial orchestration of neuroimmune crosstalk: from homeostasis to disease.	Ouyang H, Yang Y, Zhang X, Cui Y, Zhang Y.	Front Immunol	10.3389/fimmu.2025.1679286	2025
Pathogenicity	CRISPR-based genetic tools for the study of host-microbe interactions.	Echavarria Galindo M, Lai Y.	Infect Immun	10.1128/iai.00510-24	2025
	Metaproteomics-based stable isotope fingerprinting links intestinal bacteria to their carbon source and captures diet-induced substrate switching.	Mordant A, Blakeley-Ruiz JA, Kleiner M.	ISME J	10.1093/ismejo/wraf127	2025
	Elemental iron protects gut microbiota against oxygen-induced dysbiosis.	Ostrov I, Gong Y, Zuk JB, Wickramasinghe PCK, Tmenova I, Roopchand DE, Zhao L, Raskin I.	PLoS One	10.1371/journal.pone.0298592	2024
Genetics	Research in etiology of Floppy Kid Syndrome.	Cheng C, Zheng Y, Wang X, Tao J, Cheng D.	Front Vet Sci	10.3389/fvets.2025.1557951	2025
	Uncovering Predictive Factors and Interventions for Restoring Microecological Diversity after Antibiotic Disturbance.	Chen J, Zhu J, Lu W, Wang H, Pan M, Tian P, Zhao J, Zhang H, Chen W.	Nutrients	10.3390/nu15183925	2023
Metabolism	Phase-variable capsular polysaccharides and lipoproteins modify bacteriophage susceptibility in Bacteroides thetaiotaomicron.	Porter NT, Hryckowian AJ, Merrill BD, Fuentes JJ, Gardner JO, Glowacki RWP, Singh S, Crawford RD, Snitkin ES, Sonnenburg JL, Martens EC.	Nat Microbiol	10.1038/s41564-020-0746-5	2020
Pathogenicity	A host-adapted auxotrophic gut symbiont induces mucosal immunodeficiency.	Lu Q, Hitch TCA, Zhou JY, Dwidar M, Sangwan N, Lawrence D, Nolan LS, Espenschied ST, Newhall KP, Han Y, Karell PE, Salazar V, Baldridge MT, Clavel T, Stappenbeck TS.	Science	10.1126/science.adk2536	2024
Pathogenicity	Intestinal microbiota controls graft-versus-host disease independent of donor-host genetic disparity.	Koyama M, Hippe DS, Srinivasan S, Proll SC, Miltiadous O, Li N, Zhang P, Ensbey KS, Hoffman NG, Schmidt CR, Yeh AC, Minnie SA, Strenk SM, Fiedler TL, Hattangady N, Kowalsky J, Grady WM, Degli-Esposti MA, Varelias A, Clouston AD, van den Brink MRM, Dey N, Randolph TW, Markey KA, Fredricks DN, Hill GR.	Immunity	10.1016/j.immuni.2023.06.024	2023
	New 24-Membered Macrolactines from an Arctic Bacterium Bacillus amyloliquefaciens SCSIO 41392 and Their Anti-Pathogenicity Evaluation.	Song Y, Zhou Y, Cong M, Deng S, Chen Y, Pang X, Liu Y, Liao L, Yang L, Wang J.	Mar Drugs	10.3390/md22110484	2024
	Alpha-glucans from bacterial necromass indicate an intra-population loop within the marine carbon cycle.	Beidler I, Steinke N, Schulze T, Sidhu C, Bartosik D, Zuhlke MK, Martin LT, Krull J, Dutschei T, Ferrero-Bordera B, Rielicke J, Kale V, Sura T, Trautwein-Schult A, Kirstein IV, Wiltshire KH, Teeling H, Becher D, Bengtsson MM, Hehemann JH, Bornscheuer UT, Amann RI, Schweder T.	Nat Commun	10.1038/s41467-024-48301-5	2024
	Gender-Based Differences in Gut Microbiota Composition in Response to Anxiety and Stress in Shooting and Archery Athletes.	Wei Y, Huo S, Liang R, Cui Y, Wang L, Zhao Y, Zhao C, Shao C.	Brain Behav	10.1002/brb3.70933	2025
Pathogenicity	Microbiome-based prediction of allogeneic hematopoietic stem cell transplantation outcome.	Shtossel O, Eshel A, Fried S, Geva M, Danylesko I, Yerushalmi R, Shem-Tov N, Fein JA, Fabbrini M, Shimoni A, Turjeman S, Louzoun Y, Nagler A, Koren O, Shouval R.	Genome Med	10.1186/s13073-025-01507-8	2025
Metabolism	A versatile genetic toolbox for Prevotella copri enables studying polysaccharide utilization systems.	Li J, Galvez EJC, Amend L, Almasi E, Iljazovic A, Lesker TR, Bielecka AA, Schorr EM, Strowig T.	EMBO J	10.15252/embj.2021108287	2021
	Identification and characterization of the lipoprotein N-acyltransferase in Bacteroides.	Armbruster KM, Jiang J, Sartorio MG, Scott NE, Peterson JM, Sexton JZ, Feldman MF, Koropatkin NM.	Proc Natl Acad Sci U S A	10.1073/pnas.2410909121	2024
	What makes a small RNA work?	Alquethamy S, Lalaouna D, Tree JJ.	Nucleic Acids Res	10.1093/nar/gkaf563	2025
	Synthesis of N-(3-Acyloxyacyl)glycines, Small Molecules with Potential Role in Gut Microbiome-Endocannabinoidome Communication.	Villano R, Di Marzo V.	Molecules	10.3390/molecules29153703	2024
	Exploring the Dynamic Relationship between the Gut Microbiome and Body Composition across the Human Lifespan: A Systematic Review.	Komodromou I, Andreou E, Vlahoyiannis A, Christofidou M, Felekkis K, Pieri M, Giannaki CD.	Nutrients	10.3390/nu16050660	2024
Pathogenicity	Nonmicrobicidal Small Molecule Inhibition of Polysaccharide Metabolism in Human Gut Microbes: A Potential Therapeutic Avenue.	Santilli AD, Dawson EM, Whitehead KJ, Whitehead DC.	ACS Chem Biol	10.1021/acschembio.8b00309	2018
	Structure and dynamics analysis of a new member heparinase II/III of family 12 polysaccharide lyase from Pseudopedobacter saltans by computational modeling and small-angle X-ray scattering.	Balasubramaniam K, Sharma K, Goyal A.	J Biomol Struct Dyn	10.1080/07391102.2019.1622453	2020
	Position preference of essential genes in prokaryotic operons.	Liu T, Luo H, Gao F.	PLoS One	10.1371/journal.pone.0250380	2021
	Gut colonization by Bacteroides requires translation by an EF-G paralog lacking GTPase activity.	Han W, Peng BZ, Wang C, Townsend GE, Barry NA, Peske F, Goodman AL, Liu J, Rodnina MV, Groisman EA.	EMBO J	10.15252/embj.2022112372	2023
Genetics	Machine learning integrates region-specific microbial signatures to distinguish geographically adjacent populations within a province.	Luo L, Chen B, Zeng S, Li Y, Chen X, Zhang J, Guo X, Li S, Ruan L, Zhu S, Gao C, Zhang C, Li T.	Front Microbiol	10.3389/fmicb.2025.1586195	2025
	Nutrient niche specificity for glycosaminoglycans is reflected in polysaccharide utilization locus architecture of gut Bacteroides species.	Overbeeke A, Hausmann B, Nikolov G, Pereira FC, Herbold CW, Berry D.	Front Microbiol	10.3389/fmicb.2022.1033355	2022
	Bacteroidetes Species Are Correlated with Disease Activity in Ulcerative Colitis.	Nomura K, Ishikawa D, Okahara K, Ito S, Haga K, Takahashi M, Arakawa A, Shibuya T, Osada T, Kuwahara-Arai K, Kirikae T, Nagahara A.	J Clin Med	10.3390/jcm10081749	2021
	Short-Term Dietary Intervention with Whole Oats Protects from Antibiotic-Induced Dysbiosis.	Costa SK, Antosca K, Beekman CN, Peterson RL, Penumutchu S, Belenky P.	Microbiol Spectr	10.1128/spectrum.02376-23	2023
Metabolism	Xenosiderophore Utilization Promotes Bacteroides thetaiotaomicron Resilience during Colitis.	Zhu W, Winter MG, Spiga L, Hughes ER, Chanin R, Mulgaonkar A, Pennington J, Maas M, Behrendt CL, Kim J, Sun X, Beiting DP, Hooper LV, Winter SE.	Cell Host Microbe	10.1016/j.chom.2020.01.010	2020
	Bifidobacterium adolescentis CCFM1447 effectively alleviates osteoporosis by enriching intestinal flora capable of vitamin D conversion.	Yu X, Tian G, Wang Y, Li L, Huang L, Zhao Y, Feng L, Zhao Y, Fang H, Lu W, Lu S, Wang H.	Front Nutr	10.3389/fnut.2025.1647671	2025
	Nervous system-gut microbiota-immune system axis: future directions for preventing tumor.	Wang J, Cheng W, Yang R.	Front Immunol	10.3389/fimmu.2025.1535955	2025
Enzymology	Metabolic engineering of Yarrowia lipolytica for the biosynthesis of crotonic acid.	Wang L, Zong Z, Liu Y, Zheng M, Li D, Wang C, Zheng F, Madzak C, Liu Z.	Bioresour Technol	10.1016/j.biortech.2019.121484	2019
	In vitro antibacterial activity of antiretroviral drugs on key commensal bacteria from the human microbiota.	Rubio-Garcia E, Ferrando N, Martin N, Balleste-Delpierre C, Miro JM, Paredes R, Casals-Pascual C, Vila J.	Front Cell Infect Microbiol	10.3389/fcimb.2023.1306430	2023
	A Highly Active Chondroitin Sulfate Lyase ABC for Enzymatic Depolymerization of Chondroitin Sulfate.	Fan XM, Huang JY, Ling XM, Wei W, Su WB, Zhang YW.	Polymers (Basel)	10.3390/polym14091770	2022
	Effect of red yeast rice on the growth of male SD rats: a 90-day feeding study	Lee H, Do B, Kwon H.	Toxicol Res		2025
Metabolism	Gut microbiome alterations and hepatic encephalopathy post-TIPS in liver cirrhosis patients.	Li S, Xu Z, Diao H, Zhou A, Tu D, Wang S, Feng Y, Feng X, Lai Y, Yang S, Tang B.	J Transl Med	10.1186/s12967-025-06774-y	2025
	Acidipropionibacterium acidipropionici, a propionate-producing bacterium, contributes to GPR41 signaling and metabolic regulation in high-fat diet-induced obesity in mice.	Miyamoto J, Ando Y, Yamano M, Nishida A, Murakami K, Kimura I.	Front Nutr	10.3389/fnut.2025.1542196	2025
Pathogenicity	Bridging two worlds: Host Microbiota crosstalk in health and dysregulation.	Sanam M, Hossain CFTZ, Hyder TB, Tarannum R, Oishi JF, Rahman KMM, Islam SBU, Bulbul N, Sultana Jime J, Shishir MA, Safa A, Fakruddin M.	Innate Immun	10.1177/17534259251392993	2025
	Two different sulfotransferases modify sugars of the N-linked tetrasaccharide decorating Halobacterium salinarum glycoproteins.	Zaretsky M, Vershinin Z, Erez L, Grossman-Haham I, Eichler J.	mBio	10.1128/mbio.03534-24	2025
	Intermittent fasting modulates the intestinal microbiota and improves obesity and host energy metabolism.	Hu X, Xia K, Dai M, Han X, Yuan P, Liu J, Liu S, Jia F, Chen J, Jiang F, Yu J, Yang H, Wang J, Xu X, Jin X, Kristiansen K, Xiao L, Chen W, Han M, Duan S.	NPJ Biofilms Microbiomes	10.1038/s41522-023-00386-4	2023
	Neurodegeneration rewires the tumor microenvironment via the neuro-immune-cancer axis.	Bautista J, Coral-Riofrio EC, Suarez Urresta S, Palacios-Zavala D, Echeverria CE, Araujo-Abad S, Lopez-Cortes A.	iScience	10.1016/j.isci.2025.113550	2025
Pathogenicity	Prevotella copri variants among a single host diverge in sphingolipid production.	Xiao X, Le HH, Lee M-T, Lamm D, Johnson EL, Brito IL.	mBio	10.1128/mbio.02409-23	2024
	Big data analytics frameworks for the influence of gut microbiota on the development of tic disorder.	Fan F, Bian Z, Zhang X, Wu H, Wang S, Zhang S, Wang Q, Han F.	Front Comput Neurosci	10.3389/fncom.2022.986591	2022
Pathogenicity	Dietary prevention of antibiotic-induced dysbiosis and mortality upon aging in mice.	Smith KM, Francisco SG, Zhu Y, LeRoith T, Davis ML, Crott JW, Barger K, Greenberg AS, Smith DE, Taylor A, Yeruva L, Rowan S.	FASEB J	10.1096/fj.202402262r	2024
Metabolism	A Novel Family of RNA-Binding Proteins Regulate Polysaccharide Metabolism in Bacteroides thetaiotaomicron.	Adams AND, Azam MS, Costliow ZA, Ma X, Degnan PH, Vanderpool CK.	J Bacteriol	10.1128/jb.00217-21	2021
	Rebalancing the Gut: Glucagon-Like Peptide-1 Agonists as a Strategy for Obesity and Metabolic Health.	Singh K, Aulakh SK, Nijjar GS, Singh S, Sandhu APS, Luthra S, Tanvir F, Kaur Y, Singla A, Kaur MS.	Cureus	10.7759/cureus.64738	2024
Metabolism	Quantifying fluorescent glycan uptake to elucidate strain-level variability in foraging behaviors of rumen bacteria.	Klassen L, Reintjes G, Tingley JP, Jones DR, Hehemann JH, Smith AD, Schwinghamer TD, Arnosti C, Jin L, Alexander TW, Amundsen C, Thomas D, Amann R, McAllister TA, Abbott DW.	Microbiome	10.1186/s40168-020-00975-x	2021
	Design and application of synthetic human gut microbial communities.	Kim MS, Bisanz JE.	Gut Microbes	10.1080/19490976.2025.2575923	2025
Phylogeny	Intratumoral microbiome of adenoid cystic carcinomas and comparison with other head and neck cancers.	Karpinets TV, Mitani Y, Chang CC, Wu X, Song X, Flores II, McDaniel LK, Hoballah YM, Veguilla FJ, Ferrarotto R, Colbert LE, Ajami NJ, Jenq RR, Zhang J, Futreal AP, El-Naggar AK.	Sci Rep	10.1038/s41598-024-65939-9	2024
	Prebiotic Effects of alpha- and beta-Galactooligosaccharides: The Structure-Function Relation.	Ignatova I, Arsov A, Petrova P, Petrov K.	Molecules	10.3390/molecules30040803	2025
	In vitro interactions between Blautia hydrogenotrophica, Desulfovibrio piger and Methanobrevibacter smithii under hydrogenotrophic conditions.	Wang T, Leibrock N, Plugge CM, Smidt H, Zoetendal EG.	Gut Microbes	10.1080/19490976.2023.2261784	2023
	Mucosal Hub Bacteria as Potential Targets for Improving High-Fat Diet-Related Intestinal Barrier Injury.	Shao L, Zhang B, Song Y, Lyu Z, Zhang W, Yang W, Fu J, Li J, Shi J.	Can J Infect Dis Med Microbiol	10.1155/cjid/3652740	2024
	Harnessing gut microbiota for colorectal cancer therapy: from clinical insights to therapeutic innovations.	Chen C, Su Q, Zi M, Hua X, Zhang Z.	NPJ Biofilms Microbiomes	10.1038/s41522-025-00818-3	2025
Pathogenicity	The Porphyromonas gingivalis RNA-binding protein is required for growth in high levels of zinc and persistence with host cells.	Yanamandra S, Marsh H, Cvitkovic R, Gui Q, Belvin BR, Lewis JP.	Front Cell Infect Microbiol	10.3389/fcimb.2025.1569544	2025
	A genetically tractable branch of environmental Pedobacter from the phylum Bacteroidota represents a hotspot for natural product discovery.	Liu Y, Linares-Otoya L, Kersten C, Marner M, Mihajlovic S, Abdeldayem MH, Semmler S, Bletz MC, Vences M, Spohn M, Zumkeller CM, Schaberle TF.	Sci Rep	10.1038/s41598-025-03955-z	2025
	In Vitro Fermentation of Polysaccharide from Edible Alga Enteromorpha clathrata by the Gut Microbiota of Patients with Ulcerative Colitis.	Ma M, Quan M, Zhang J, Zhang A, Gao P, Shang Q, Yu G.	Nutrients	10.3390/nu15194122	2023
Genetics	Bacterial Systematic Genetics and Integrated Multi-Omics: Beyond Static Genomics Toward Predictive Models.	Sakaguchi T, Irifune Y, Kamada R, Sakaguchi K.	Int J Mol Sci	10.3390/ijms26199326	2025
Pathogenicity	Early-Life Microbial Restitution Reduces Colitis Risk Promoted by Antibiotic-Induced Gut Dysbiosis in Interleukin 10^-/- Mice.	Miyoshi J, Miyoshi S, Delmont TO, Cham C, Lee STM, Sakatani A, Yang K, Shan Y, Kennedy M, Kiefl E, Yousef M, Crosson S, Sogin M, Antonopoulos DA, Eren AM, Leone V, Chang EB.	Gastroenterology	10.1053/j.gastro.2021.05.054	2021
	Systematic review: The gut microbiota as a link between colorectal cancer and obesity.	Ruiz-Malagon AJ, Rodriguez-Sojo MJ, Redondo E, Rodriguez-Cabezas ME, Galvez J, Rodriguez-Nogales A.	Obes Rev	10.1111/obr.13872	2025
Transcriptome	Dissecting microbial communities with single-cell transcriptome analysis.	Pountain AW, Yanai I.	Science	10.1126/science.adp6252	2025
	Carbohydrate-active enzymes from Akkermansia muciniphila break down mucin O-glycans to completion.	Bakshani CR, Ojuri TO, Pilgaard B, Holck J, McInnes R, Kozak RP, Zakhour M, Cakaj S, Kerouedan M, Newton E, Bolam DN, Crouch LI.	Nat Microbiol	10.1038/s41564-024-01911-7	2025
	The Cecal Distribution of Microalgal Pigments in Rats: Do Carotenoids and Chlorophylls Play a Pharmacobiotic Role?	Nascimento TCD, Caetano PA, da Silveira MV, Lobo LE, Riste UDS, Depra MC, Schetinger MRC, de Menezes CR, Wagner R, Jacob-Lopes E, Zepka LQ.	Foods	10.3390/foods14132172	2025
Metabolism	Dynamic properties of dipeptidyl peptidase III from Bacteroides thetaiotaomicron and the structural basis for its substrate specificity - a computational study.	Tomin M, Tomic S.	Mol Biosyst	10.1039/c7mb00310b	2017
	Etiological diagnostic performance of probe capture-based targeted next-generation sequencing in bloodstream infection.	Cai S, Yuan J, Li Y, Guo F, Lin Z, Li H, Miao Q, Fang T, Wu Y, Gao X, Li P, Liu J, Hu C, Hu B.	J Thorac Dis	10.21037/jtd-24-400	2024
Metabolism	Isolation and culture of Methanobrevibacter smithii by co-culture with hydrogen-producing bacteria on agar plates.	Traore SI, Khelaifia S, Armstrong N, Lagier JC, Raoult D.	Clin Microbiol Infect	10.1016/j.cmi.2019.04.008	2019
	Baseline intestinal microbiota composition influences response to a real-world dietary fiber intervention.	Hoffmann Sarda FA, Giuntini EB, Oliveira A, Souza GS, Prado SBR, Taddei CR, Tadini CC, Bittinger K, Bushman FD, Menezes EW, Hoffmann C.	NPJ Biofilms Microbiomes	10.1038/s41522-025-00817-4	2025
	Beneficial Effects of In Vitro Reconstructed Human Gut Microbiota by Ginseng Extract Fermentation on Intestinal Cell Lines.	Finazzi M, Bovio F, Forcella M, Lasagni M, Fusi P, Di Gennaro P.	Microorganisms	10.3390/microorganisms13010192	2025
Metabolism	A Metabolic Pathway for Activation of Dietary Glucosinolates by a Human Gut Symbiont.	Liou CS, Sirk SJ, Diaz CAC, Klein AP, Fischer CR, Higginbottom SK, Erez A, Donia MS, Sonnenburg JL, Sattely ES.	Cell	10.1016/j.cell.2020.01.023	2020
	Interaction of the Vagus Nerve and Serotonin in the Gut-Brain Axis.	Hwang YK, Oh JS.	Int J Mol Sci	10.3390/ijms26031160	2025
Metabolism	A Data-Driven Approach to Enhance the Prediction of Bacteria-Metabolite Interactions in the Human Gut Microbiome Using Enzyme Encodings and Metabolite Structural Embeddings.	Srivastava G, Brylinski M.	Nutrients	10.3390/nu17030469	2025
	Surface Properties of Parabacteroides distasonis and Impacts of Stress-Induced Molecules on Its Surface Adhesion and Biofilm Formation Capacities.	Chamarande J, Cunat L, Caillet C, Mathieu L, Duval JFL, Lozniewski A, Frippiat JP, Alauzet C, Cailliez-Grimal C.	Microorganisms	10.3390/microorganisms9081602	2021
	Targeting the Gut Microbiota in Kidney Disease: The Future in Renal Nutrition and Metabolism.	Lambert K, Rinninella E, Biruete A, Sumida K, Stanford J, Raoul P, Mele MC, Wang AY, Mafra D.	J Ren Nutr	10.1053/j.jrn.2022.12.004	2023
Pathogenicity	Intestinal Bacteroides modulates inflammation, systemic cytokines, and microbial ecology via propionate in a mouse model of cystic fibrosis.	Price CE, Valls RA, Ramsey AR, Loeven NA, Jones JT, Barrack KE, Schwartzman JD, Royce DB, Cramer RA, Madan JC, Ross BD, Bliska J, O'Toole GA.	mBio	10.1128/mbio.03144-23	2024
Phylogeny	Exploring the Genetic and Functional Diversity of Porphyromonas gingivalis Survival Factor RagAB.	Montz PG, Dafni E, Neumann B, Deng D, Abdelbary MMH, Conrads G.	Int J Mol Sci	10.3390/ijms26031073	2025
	CrAssphage distribution analysis in an Amazonian river based on metagenomic sequencing data and georeferencing.	Martins DT, Alegria OVC, Dantas CWD, De Los Santos EFF, Pontes PRM, Cavalcante RBL, Ramos RTJ.	Appl Environ Microbiol	10.1128/aem.01470-24	2025
Biotechnology	Unraveling the Potential of gamma-Aminobutyric Acid: Insights into Its Biosynthesis and Biotechnological Applications.	Zhu L, Wang Z, Gao L, Chen X.	Nutrients	10.3390/nu16162760	2024
	A Novel Subfamily GH13_46 of the alpha-Amylase Family GH13 Represented by the Cyclomaltodextrinase from Flavobacterium sp. No. 92.	Marecek F, Janecek S.	Molecules	10.3390/molecules27248735	2022
	Structural and digestive characters of a heteropolysaccharide fraction from tea (Camellia sinensis L.) flower.	Chen D, Wang A, Lv J, Tang C, Jin CH, Liu J, Zeng X, Wang L.	Food Chem X	10.1016/j.fochx.2023.101058	2024
Pathogenicity	Microscopic messengers: Extracellular vesicles shaping gastrointestinal health and disease.	Yu Z, Swift KA, Hedges MA, Theiss AL, Andres SF.	Physiol Rep	10.14814/phy2.70292	2025
Pathogenicity	Protocol for predicting host-microbe interactions and their downstream effect on host cells using MicrobioLink.	Gul L, Elias AJ, Tambaku T, Olbei M, Watters E, Bohar B, Modos D, Madgwick M, Korcsmaros T.	STAR Protoc	10.1016/j.xpro.2024.103570	2025
	Culturable Human Microorganisms and the Impact of Transportation Conditions on Cultivability.	Fan X, Lv N, Quan Z.	Microorganisms	10.3390/microorganisms13030549	2025
Metabolism	Synthetic Microbiomes on the Rise-Application in Deciphering the Role of Microbes in Host Health and Disease.	Bolsega S, Bleich A, Basic M.	Nutrients	10.3390/nu13114173	2021
Genetics	Metagenomic Microbial Signatures for Noninvasive Detection of Pancreatic Cancer.	Chen Y, Nian F, Chen J, Jiang Q, Yuan T, Feng H, Shen X, Dong L.	Biomedicines	10.3390/biomedicines13041000	2025
	Utilization of machine learning to predict antibiotic resistant event outcomes in acute myeloid leukemia patients undergoing induction chemotherapy.	McMahon S, Franklin S, Galloway-Pena J.	Front Cell Infect Microbiol	10.3389/fcimb.2025.1629422	2025
	Proteomic insight into arabinogalactan utilization by particle-associated Maribacter sp. MAR_2009_72.	Kalenborn S, Zuhlke D, Riedel K, Amann RI, Harder J.	FEMS Microbiol Ecol	10.1093/femsec/fiae045	2024
	Nutritional, Therapeutic, and Functional Food Perspectives of Kale (Brassica oleracea var. acephala): An Integrative Review.	Lukaszyk A, Kwiecien I, Kanik A, Blicharska E, Tatarczak-Michalewska M, Bialowas W, Czarnek K, Szopa A.	Molecules	10.3390/molecules30214214	2025
Metabolism	Synthesis of Branched-Chain Sugars with a DHAP-Dependent Aldolase: Ketones are Electrophile Substrates of Rhamnulose-1-phosphate Aldolases.	Laurent V, Darii E, Aujon A, Debacker M, Petit JL, Helaine V, Liptaj T, Breza M, Mariage A, Nauton L, Traikia M, Salanoubat M, Lemaire M, Guerard-Helaine C, de Berardinis V.	Angew Chem Int Ed Engl	10.1002/anie.201712851	2018
	Revealing the antimicrobial potential of traditional Chinese medicine through text mining and molecular computation.	Chung MC, Su LJ, Chen CL, Wu LC.	Brief Bioinform	10.1093/bib/bbaf077	2024
	Gut Microbiota Composition Positively Correlates with Sports Performance in Competitive Non-Professional Female and Male Runners.	Shalmon G, Ibrahim R, Israel-Elgali I, Grad M, Shlayem R, Shapira G, Shomron N, Youngster I, Scheinowitz M.	Life (Basel)	10.3390/life14111397	2024
	Evaluating the link between the dietary intake of vitamin B and constipation: a population-based study.	Yang W, Jiang C, Shao Y, Gu S, Hong M.	Front Nutr	10.3389/fnut.2025.1594644	2025
	Expression of xylanase XynB is synergistically controlled by two two-component systems in Ruminiclostridium cellulolyticum.	Zhang W, Qiu Z, Zhao Q, Liu Z, Zhang X, Song H, Xu C.	Appl Environ Microbiol	10.1128/aem.00062-25	2025
	Database-assisted, globally optimized targeted secondary electrospray ionization high resolution mass spectrometry (dGOT-SESI-HRMS) and spectral stitching enhanced volatilomics analysis of bacterial metabolites.	Choueiry F, Xu R, Meyrath K, Zhu J.	Analyst	10.1039/d3an01487h	2023
	Individual variations in glycemic responses to carbohydrates and underlying metabolic physiology.	Wu Y, Ehlert B, Metwally AA, Perelman D, Park H, Brooks AW, Abbasi F, Michael B, Celli A, Bejikian C, Ayhan E, Lu Y, Lancaster SM, Hornburg D, Ramirez L, Bogumil D, Pollock S, Wong F, Bradley D, Gutjahr G, Rangan ES, Wang T, McGuire L, Venkat Rangan P, Raeder H, Shipony Z, Lipson D, McLaughlin T, Snyder MP.	Nat Med	10.1038/s41591-025-03719-2	2025
Metabolism	Quantitative metabolomics of a xylose-utilizing Saccharomyces cerevisiae strain expressing the Bacteroides thetaiotaomicron xylose isomerase on glucose and xylose.	Mert MJ, Rose SH, la Grange DC, Bamba T, Hasunuma T, Kondo A, van Zyl WH.	J Ind Microbiol Biotechnol	10.1007/s10295-017-1969-1	2017
	In-depth characterization of a selection of gut commensal bacteria reveals their functional capacities to metabolize dietary carbohydrates with prebiotic potential.	Bedu-Ferrari C, Biscarrat P, Pepke F, Vati S, Chaudemanche C, Castelli F, Chollet C, Rue O, Hennequet-Antier C, Langella P, Cherbuy C.	mSystems	10.1128/msystems.01401-23	2024
	Interactions between Kluyveromyces marxianus from cheese origin and the intestinal symbiont Bacteroides thetaiotaomicron: Impressive antioxidative effects	Ceugniez A, Tourret M, Dussert E, Coucheney F, Deracinois B, Jacques P, Flahaut C, Heuson E, Drider D, Behra-Miellet J.	Lebensm Wiss Technol	10.1016/j.lwt.2017.03.056	2017
	Clostridioides difficile infection: microbe-microbe interactions and live biotherapeutics.	Wang R.	Front Microbiol	10.3389/fmicb.2023.1182612	2023
	mulea: An R package for enrichment analysis using multiple ontologies and empirical false discovery rate.	Turek C, Olbei M, Stirling T, Fekete G, Tasnadi E, Gul L, Bohar B, Papp B, Jurkowski W, Ari E.	BMC Bioinformatics	10.1186/s12859-024-05948-7	2024
Pathogenicity	Impact of Early-Life Brain Injury on Gut Microbiota Composition in Rodents: Systematic Review with Implications for Neurodevelopment.	Souza VDS, Manhaes-de-Castro R, Pereira SDC, de Silveira BS, Calado CMSDS, Gouveia HJCB, Coq JO, Toscano AE.	Cells	10.3390/cells14141063	2025
Enzymology	Preparation and biological activities of an extracellular polysaccharide from Rhodopseudomonas palustris.	Zhang P, Sun F, Cheng X, Li X, Mu H, Wang S, Geng H, Duan J.	Int J Biol Macromol	10.1016/j.ijbiomac.2019.03.139	2019
	Bacteria require phase separation for fitness in the mammalian gut.	Krypotou E, Townsend GE, Gao X, Tachiyama S, Liu J, Pokorzynski ND, Goodman AL, Groisman EA.	Science	10.1126/science.abn7229	2023
Metabolism	Function and structure relationships of a beta-1,2-glucooligosaccharide-degrading beta-glucosidase.	Ishiguro R, Tanaka N, Abe K, Nakajima M, Maeda T, Miyanaga A, Takahashi Y, Sugimoto N, Nakai H, Taguchi H.	FEBS Lett	10.1002/1873-3468.12911	2017
Enzymology	Frogs host faecal bacteria typically associated with humans.	Gibb K, Schobben X, Christian K.	Can J Microbiol	10.1139/cjm-2017-0119	2017
	Research progress on the impact of intratumoral microbiota on the immune microenvironment of malignant tumors and its role in immunotherapy.	Xu J, Cheng M, Liu J, Cui M, Yin B, Liang J.	Front Immunol	10.3389/fimmu.2024.1389446	2024
	Sequence and characterization of shuttle vectors for molecular cloning in Porphyromonas, Bacteroides and related bacteria.	Jones KR, Belvin BR, Macrina FL, Lewis JP.	Mol Oral Microbiol	10.1111/omi.12304	2020
Genetics	The gut virome and the relevance of temperate phages in human health.	Avellaneda-Franco L, Dahlman S, Barr JJ.	Front Cell Infect Microbiol	10.3389/fcimb.2023.1241058	2023
Enzymology	Two distinct gut microbial pathways contribute to meta-organismal production of phenylacetylglutamine with links to cardiovascular disease.	Zhu Y, Dwidar M, Nemet I, Buffa JA, Sangwan N, Li XS, Anderson JT, Romano KA, Fu X, Funabashi M, Wang Z, Keranahalli P, Battle S, Tittle AN, Hajjar AM, Gogonea V, Fischbach MA, DiDonato JA, Hazen SL.	Cell Host Microbe	10.1016/j.chom.2022.11.015	2023
	Genetic insights into the gut microbiota and risk of psoriasis: a bidirectional mendelian randomization study.	Qian M, Shi J, Zhang Z, Bi D, Tan C.	Front Microbiol	10.3389/fmicb.2024.1434521	2024
	Understanding the Role of Exercise and Probiotic Interventions on Non-Alcoholic Fatty Liver Disease Alleviation in Zebrafish: Dialogue Between the Gut and Liver.	Gu X, Yuan L, Gan L, Zhang Z, Zhou S, Fu Z, Liu Y, Xin Z, Cheng S, Zhou X, Yan H, Wang Q.	Int J Mol Sci	10.3390/ijms26031360	2025
Metabolism	Microbiota-produced indole metabolites disrupt mitochondrial function and inhibit Cryptosporidium parvum growth.	Funkhouser-Jones LJ, Xu R, Wilke G, Fu Y, Schriefer LA, Makimaa H, Rodgers R, Kennedy EA, VanDussen KL, Stappenbeck TS, Baldridge MT, Sibley LD.	Cell Rep	10.1016/j.celrep.2023.112680	2023
	The gut microbiome and cancer response to immune checkpoint inhibitors.	Gazzaniga FS, Kasper DL.	J Clin Invest	10.1172/jci184321	2025
Pathogenicity	Unravelling three-way interactions between Clostridioides difficile, microbiota and the host.	Bywater-Brenna KK, Unnikrishnan M.	J Med Microbiol	10.1099/jmm.0.002067	2025
Phylogeny	Featured intestinal microbiota associated with hepatocellular carcinoma in various liver disease states.	Sun X, Zhou Z, Chi X, Cheng D, Zhang Y, Xu Y, Hao Y, Duan Y, Li W, Zhao Y, Liu S, Han M, Wang X, Yang S, Pan CQ, Xing H.	Front Immunol	10.3389/fimmu.2025.1674838	2025
	In Vitro Activity of Gepotidacin against Gram-Negative and Gram-Positive Anaerobes.	Hackel MA, Karlowsky JA, Canino MA, Sahm DF, Scangarella-Oman NE.	Antimicrob Agents Chemother	10.1128/aac.02165-21	2022
Metabolism	HIF-1 attenuates high-fiber diet-mediated proliferation and stemness of colonic epithelium.	Ribeiro Castro P, Correa RO, Servulo Cruz Angelim MK, de Rezende Rodovalho V, Font Fernandes M, Dias Nirello V, Dos Santos Pereira Gomes AB, de Souza Felipe J, Passarielo Pral L, de Oliveira S, Rodrigues PB, Fachi JL, Reis-de-Oliveira G, Smith BJ, Carregari VC, Shealy NG, Shelton C, Martins-de-Souza D, Moraes-Vieira PM, Xavier Byndloss M, Varga-Weisz P, Ramirez Vinolo MA.	Gut Microbes	10.1080/19490976.2025.2543123	2025
Metabolism	Enterococcus faecalis alpha1-2-mannosidase (EfMan-I): an efficient catalyst for glycoprotein N-glycan modification.	Li Y, Li R, Yu H, Sheng X, Wang J, Fisher AJ, Chen X.	FEBS Lett	10.1002/1873-3468.13618	2020
Metabolism	GH18 endo-beta-N-acetylglucosaminidases use distinct mechanisms to process hybrid-type N-linked glycans.	Trastoy B, Du JJ, Li C, Garcia-Alija M, Klontz EH, Roberts BR, Donahue TC, Wang LX, Sundberg EJ, Guerin ME.	J Biol Chem	10.1016/j.jbc.2021.101011	2021
	Gut microbiota-associated non-cholesterol sterol dysregulation modulates immune reconstitution during antiretroviral therapy in people living with HIV.	Pan J, Tian X, Wu K, Ji J, Dong M, Sun T, Lv D, Yao P, Lv L, Yao H.	Microbiol Spectr	10.1128/spectrum.01404-25	2025
	Characterization of inositol lipid metabolism in gut-associated Bacteroidetes.	Heaver SL, Le HH, Tang P, Basle A, Mirretta Barone C, Vu DL, Waters JL, Marles-Wright J, Johnson EL, Campopiano DJ, Ley RE.	Nat Microbiol	10.1038/s41564-022-01152-6	2022
Metabolism	Prebiotic effects of yeast mannan, which selectively promotes Bacteroides thetaiotaomicron and Bacteroides ovatus in a human colonic microbiota model.	Oba S, Sunagawa T, Tanihiro R, Awashima K, Sugiyama H, Odani T, Nakamura Y, Kondo A, Sasaki D, Sasaki K.	Sci Rep	10.1038/s41598-020-74379-0	2020
	Pharmacomicrobiomics.	Gronich N, Geva-Zatorsky N, Herren R, Kelly L, Cohen Z, Zhou H, Chen YC, Shah K, Robinson-Catala TA, Frisby G, Karnes JH, Shoda L.	Clin Pharmacol Ther	10.1002/cpt.70066	2025
	Lactiplantibacillus plantarum extracellular vesicles exert anti-PEDV effects through STING-dependent autophagy.	Zhang S, Shan X, Qu G, Sun A, Xing J, Liu Q, Liu Z, Wang Y, Zhang X, Cao X, Zeng Y, Wang J, Wang C, Hu J.	BMC Microbiol	10.1186/s12866-025-04019-y	2025
Metabolism	Prioritization of polysaccharide utilization and control of regulator activation in Bacteroides thetaiotaomicron.	Schwalm ND, Townsend GE, Groisman EA.	Mol Microbiol	10.1111/mmi.13609	2017
	Small intestinal perforation secondary to metastasis from skin squamous cell carcinoma: A case report and literature review.	Reynard ME, Strati TM, Egger B.	Int J Surg Case Rep	10.1016/j.ijscr.2023.108599	2023
Pathogenicity	Human gut microbes are susceptible to antimicrobial food additives in vitro.	Hrncirova L, Hudcovic T, Sukova E, Machova V, Trckova E, Krejsek J, Hrncir T.	Folia Microbiol (Praha)	10.1007/s12223-018-00674-z	2019
Metabolism	A novel glycoside hydrolase family 97 enzyme: Bifunctional beta-l-arabinopyranosidase/alpha-galactosidase from Bacteroides thetaiotaomicron.	Kikuchi A, Okuyama M, Kato K, Osaki S, Ma M, Kumagai Y, Matsunaga K, Klahan P, Tagami T, Yao M, Kimura A.	Biochimie	10.1016/j.biochi.2017.08.003	2017
	Role of probiotic extracellular vesicles in inter-kingdom communication and current technical limitations in advancing their therapeutic utility.	Sanwlani R, Bramich K, Mathivanan S.	Extracell Vesicles Circ Nucl Acids	10.20517/evcna.2024.39	2024
	B. thetaiotaomicron-derived acetic acid modulate immune microenvironment and tumor growth in hepatocellular carcinoma.	Ma H, Yang L, Liang Y, Liu F, Hu J, Zhang R, Li Y, Yuan L, Feng F.	Gut Microbes	10.1080/19490976.2023.2297846	2024
	Temporal network analysis of gut microbiota unveils aging trajectories associated with colon cancer.	Chen Z, Zhang Z, Nie BN, Huang W, Zhu Y, Zhang L, Xu M, Wang M, Yuan C, Liu N, Wang X, Tian J, Ba Q, Wang Z.	mSystems	10.1128/msystems.01188-24	2025
Genetics	Exploring the dynamics of gut microbiota, antibiotic resistance, and chemotherapy impact in acute leukemia patients: A comprehensive metagenomic analysis.	Luo Y, Sheikh TMM, Li X, Yuan Y, Yao F, Wang M, Guo X, Wu J, Shafiq M, Xie Q, Jiao X.	Virulence	10.1080/21505594.2024.2428843	2024
Metabolism	Composition and metabolism of fecal microbiota from normal and overweight children are differentially affected by melibiose, raffinose and raffinose-derived fructans.	Adamberg K, Adamberg S, Ernits K, Larionova A, Voor T, Jaagura M, Visnapuu T, Alamae T.	Anaerobe	10.1016/j.anaerobe.2018.06.009	2018
	Impact of Ex Vivo Bisphenol A Exposure on Gut Microbiota Dysbiosis and Its Association with Childhood Obesity.	Luque G, Ortiz P, Torres-Sanchez A, Ruiz-Rodriguez A, Lopez-Moreno A, Aguilera M.	J Xenobiot	10.3390/jox15010014	2025
Metabolism	The study of the relationship between food additives and the childhood asthma based on metabolome analysis.	Chen M, Xu X, Jiang X, Hui J, Tao X, Bao Y, Cao S, Wu Q.	Front Immunol	10.3389/fimmu.2025.1671022	2025
Transcriptome	Highly multiplexed spatial transcriptomics in bacteria.	Sarfatis A, Wang Y, Twumasi-Ankrah N, Moffitt JR.	Science	10.1126/science.adr0932	2025
	Dissecting the molecular interactions between botanical extracts and the human gut microbiota.	Mancabelli L, Tarracchini C, Longhi G, Alessandri G, Ventura M, Turroni F.	Front Microbiol	10.3389/fmicb.2025.1610170	2025
	A hybrid machine learning model with attention mechanism and multidimensional multivariate feature coding for essential gene prediction.	Yan W, Yu F, Tan L, Mengshan L, Xiaojun X, Weihong Z, Sheng S, Jun W, Fu-An W.	BMC Biol	10.1186/s12915-025-02209-8	2025
	Associations between sleep and the gut microbiome in adults with colorectal cancer and their caregivers.	Barb JJ, Lee LJ, Ahmed A, Son EH, Nanda S, Yang L, Ban Y, Ting A, Tsai TC, Kim Y.	Sci Rep	10.1038/s41598-025-18402-2	2025
	Efficacy and safety of Bacteroides fragilis BF839 for pediatric autism spectrum disorder: a randomized clinical trial.	Lin CH, Zeng T, Lu CW, Li DY, Liu YY, Li BM, Chen SQ, Deng YH.	Front Nutr	10.3389/fnut.2024.1447059	2024
Phylogeny	Subspecies phylogeny in the human gut revealed by co-evolutionary constraints across the bacterial kingdom.	Doran BA, Chen RY, Giba H, Behera V, Barat B, Sundararajan A, Lin H, Sidebottom A, Pamer EG, Raman AS.	Cell Syst	10.1016/j.cels.2024.12.008	2025
	Profiling the heterogeneity of microbial populations and communities at the single-cell level.	Wu L, Zuo W, Cao Z, Qu Z, Dai L.	mLife	10.1002/mlf2.70047	2025
	The increased tendency for anemia in traditional Chinese medicine deficient body constitution is associated with the gut microbiome.	Liang Y, Chen Y, Lin Y, Huang W, Qiu Q, Sun C, Yuan J, Xu N, Chen X, Xu F, Shang X, Deng Y, Liu Y, Tan F, He C, Li J, Deng Q, Zhang X, Guan H, Liang Y, Fang X, Jiang X, Han L, Huang L, Yang Z.	Front Nutr	10.3389/fnut.2024.1359644	2024
	Electroacupuncture relieves portal hypertension by improving vascular angiogenesis and linking gut microbiota in bile duct ligation rats.	Huang PY, Liu HM, Ko YR, Chang ZY, Lee TY.	Front Microbiol	10.3389/fmicb.2023.1207137	2023
Genetics	Developmental dynamics and functional adaptation of gut microbiota in Mongolian wild asses (Equus hemionus hemionus) across ontogenetic stages in arid desert ecosystems.	Wang J, Gu H, Gao H, Zhang T, Li B, Zhang M, Jiang F, Song P, Liang C, Fan Q, Xu Y, Zhang R.	Front Microbiol	10.3389/fmicb.2025.1659661	2025
Pathogenicity	Mechanism-based inhibition of gut microbial tryptophanases reduces serum indoxyl sulfate.	Graboski AL, Kowalewski ME, Simpson JB, Cao X, Ha M, Zhang J, Walton WG, Flaherty DP, Redinbo MR.	Cell Chem Biol	10.1016/j.chembiol.2023.07.015	2023
	Identification of Indicative Gut Microbial Guilds in a Natural Aging Mouse Model.	Koh YC, Kuo LH, Tung YC, Weerawatanakorn M, Pan MH.	ACS Omega	10.1021/acsomega.3c05949	2023
Enzymology	Division of the large and multifunctional glycoside hydrolase family 2: high functional specificity and biochemical assays in the uncharacterized subfamilies.	Lebreton A, Garron ML, Vuillemin M, Pilgaard B, Hornung BVH, Drula E, Lombard V, Helbert W, Henrissat B, Terrapon N.	Biotechnol Biofuels Bioprod	10.1186/s13068-025-02669-8	2025
	Indole intercepts the communication between enteropathogenic E. coli and Vibrio cholerae.	Gorelik O, Rogad A, Holoidovsky L, Meijler MM, Sal-Man N.	Gut Microbes	10.1080/19490976.2022.2138677	2022
	Glycoprotein In Vitro N-Glycan Processing Using Enzymes Expressed in E. coli.	Zhang L, Li Y, Li R, Yang X, Zheng Z, Fu J, Yu H, Chen X.	Molecules	10.3390/molecules28062753	2023
	Bidirectional Interplay Among Non-Coding RNAs, the Microbiome, and the Host During Development and Diseases.	Nai S, Song J, Su W, Liu X.	Genes (Basel)	10.3390/genes16020208	2025
Pathogenicity	Fermented Momordica charantia L. juice modulates hyperglycemia, lipid profile, and gut microbiota in type 2 diabetic rats.	Gao H, Wen JJ, Hu JL, Nie QX, Chen HH, Xiong T, Nie SP, Xie MY.	Food Res Int	10.1016/j.foodres.2019.03.055	2019
	Dietary Pea Fibre Improves Obesity, Intestinal Barrier, Reproductive Performance, Offspring Health of Parent Mice Deprived of Dietary Fibre.	Tian S, Zhang M, Chen Y, Sun H, Li Q, Yang Y, Guo A.	Animals (Basel)	10.3390/ani15050655	2025
	Sortase-encoding genes, srtA and srtC, mediate Enterococcus faecalis OG1RF persistence in the Helicoverpa zea gastrointestinal tract.	Jackson JJ, Heyer S, Bell G.	Front Microbiol	10.3389/fmicb.2024.1322303	2024
	Epilactose as a Promising Butyrate-Promoter Prebiotic via Microbiota Modulation.	Cardoso BB, Amorim C, Franco-Duarte R, Alves JI, Barbosa SG, Silverio SC, Rodrigues LR.	Life (Basel)	10.3390/life14050643	2024
Metabolism	Microbial interaction between the succinate-utilizing bacterium Phascolarctobacterium faecium and the gut commensal Bacteroides thetaiotaomicron.	Ikeyama N, Murakami T, Toyoda A, Mori H, Iino T, Ohkuma M, Sakamoto M.	Microbiologyopen	10.1002/mbo3.1111	2020
Phylogeny	Odontogenic Cervicofacial Necrotizing Fasciitis: Microbiological Characterization and Management of Four Clinical Cases.	Bottger S, Zechel-Gran S, Schmermund D, Streckbein P, Wilbrand JF, Knitschke M, Pons-Kuhnemann J, Hain T, Weigel M, Imirzalioglu C, Howaldt HP, Domann E, Attia S.	Pathogens	10.3390/pathogens11010078	2022
	Milk and mucin glycans orchestrate a synthetic infant gut microbiota structure.	Berkhout MD, Ioannou A, Kavanal Jayaprakash Y, Plugge CM, Belzer C.	FEMS Microbiol Ecol	10.1093/femsec/fiaf069	2025
	Bacteroides salyersiae Is a Candidate Probiotic Species with Potential Anti-Colitis Properties in the Human Colon: First Evidence from an In Vivo Mouse Model.	Dai W, Lv Y, Quan M, Ma M, Shang Q, Yu G.	Nutrients	10.3390/nu16172918	2024
	Effects of combined ciprofloxacin and Neulasta therapy on intestinal pathology and gut microbiota after high-dose irradiation in mice.	Horseman TS, Frank AM, Cannon G, Zhai M, Olson MG, Lin B, Li X, Hull L, Xiao M, Kiang JG, Burmeister DM.	Front Public Health	10.3389/fpubh.2024.1365161	2024
	Succinate-producing microbiota drives tuft cell hyperplasia to protect against Clostridioides difficile.	Kellogg TD, Ceglia S, Mortzfeld BM, Tanna TM, Zeamer AL, Mancini MR, Foley SE, Ward DV, Bhattarai SK, McCormick BA, Reboldi A, Bucci V.	J Exp Med	10.1084/jem.20232055	2025
Transcriptome	A high-resolution transcriptome map identifies small RNA regulation of metabolism in the gut microbe Bacteroides thetaiotaomicron.	Ryan D, Jenniches L, Reichardt S, Barquist L, Westermann AJ.	Nat Commun	10.1038/s41467-020-17348-5	2020
Metabolism	Methanogenesis associated with altered microbial production of short-chain fatty acids and human-host metabolizable energy.	Dirks B, Davis TL, Carnero EA, Corbin KD, Smith SR, Rittmann BE, Krajmalnik-Brown R.	ISME J	10.1093/ismejo/wraf103	2025
	Methanobrevibacter smithii cell variants in human physiology and pathology: A review.	Malat I, Drancourt M, Grine G.	Heliyon	10.1016/j.heliyon.2024.e36742	2024
	Dietary prophage inducers and antimicrobials: toward landscaping the human gut microbiome.	Boling L, Cuevas DA, Grasis JA, Kang HS, Knowles B, Levi K, Maughan H, McNair K, Rojas MI, Sanchez SE, Smurthwaite C, Rohwer F.	Gut Microbes	10.1080/19490976.2019.1701353	2020
	SARS-CoV-2 infectivity can be modulated through bacterial grooming of the glycocalyx.	Martino C, Kellman BP, Sandoval DR, Clausen TM, Cooper R, Benjdia A, Soualmia F, Clark AE, Garretson AF, Marotz CA, Song SJ, Wandro S, Zaramela LS, Salido RA, Zhu Q, Armingol E, Vazquez-Baeza Y, McDonald D, Sorrentino JT, Taylor B, Belda-Ferre P, Das P, Ali F, Liang C, Zhang Y, Schifanella L, Covizzi A, Lai A, Riva A, Basting C, Broedlow CA, Havulinna AS, Jousilahti P, Estaki M, Kosciolek T, Kuplicki R, Victor TA, Paulus MP, Savage KE, Benbow JL, Spielfogel ES, Anderson CAM, Martinez ME, Lacey JV, Huang S, Haiminen N, Parida L, Kim H-C, Gilbert JA, Sweeney DA, Allard SM, Swafford AD, Cheng S, Inouye M, Niiranen T, Jain M, Salomaa V, Zengler K, Klatt NR, Hasty J, Berteau O, Carlin AF, Esko JD, Lewis NE, Knight R.	mBio	10.1128/mbio.04015-24	2025
Enzymology	RiboRid: A low cost, advanced, and ultra-efficient method to remove ribosomal RNA for bacterial transcriptomics.	Choe D, Szubin R, Poudel S, Sastry A, Song Y, Lee Y, Cho S, Palsson B, Cho BK.	PLoS Genet	10.1371/journal.pgen.1009821	2021
	Delivery mode and maternal gestational diabetes are important factors in shaping the neonatal initial gut microbiota.	Shi X, Liu Y, Ma T, Jin H, Zhao F, Sun Z.	Front Cell Infect Microbiol	10.3389/fcimb.2024.1397675	2024
Enzymology	Unlocking the Hydrolytic Mechanism of GH92 alpha-1,2-Mannosidases: Computation Inspires the use of C-Glycosides as Michaelis Complex Mimics.	Alonso-Gil S, Parkan K, Kaminsky J, Pohl R, Miyazaki T.	Chemistry	10.1002/chem.202200148	2022
Metabolism	High-fat diet-induced colonocyte dysfunction escalates microbiota-derived trimethylamine N-oxide.	Yoo W, Zieba JK, Foegeding NJ, Torres TP, Shelton CD, Shealy NG, Byndloss AJ, Cevallos SA, Gertz E, Tiffany CR, Thomas JD, Litvak Y, Nguyen H, Olsan EE, Bennett BJ, Rathmell JC, Major AS, Baumler AJ, Byndloss MX.	Science	10.1126/science.aba3683	2021
Enzymology	Development and Validation of an Enzymatic Method To Determine Stevioside Content from Stevia rebaudiana.	Udompaisarn S, Arthan D, Somana J.	J Agric Food Chem	10.1021/acs.jafc.6b05793	2017
	Interkingdom signaling between gastrointestinal hormones and the gut microbiome.	Zhao X, Qiu Y, Liang L, Fu X.	Gut Microbes	10.1080/19490976.2025.2456592	2025
	Dose-Responsive Effects of Iron Supplementation on the Gut Microbiota in Middle-Aged Women.	Shearer J, Shah S, MacInnis MJ, Shen-Tu G, Mu C.	Nutrients	10.3390/nu16060786	2024
	Human resident gut microbe Bacteroides thetaiotaomicron regulates colonic neuronal innervation and neurogenic function.	Aktar R, Parkar N, Stentz R, Baumard L, Parker A, Goldson A, Brion A, Carding S, Blackshaw A, Peiris M.	Gut Microbes	10.1080/19490976.2020.1766936	2020
	Machine learning analysis of sex and menopausal differences in the gut microbiome in the HELIUS study.	Vriend EMC, Galenkamp H, Herrema H, Nieuwdorp M, van den Born BH, Verhaar BJH.	NPJ Biofilms Microbiomes	10.1038/s41522-024-00628-z	2024
	Dietary Fiber Lacks a Consistent Effect on Immune Checkpoint Blockade Efficacy Across Diverse Murine Tumor Models.	Roichman A, Reyes-Castellanos G, Chen Z, Chen Z, Mitchell SJ, MacArthur MR, Sawant A, Levett L, Powers JR, Burgo V, Gomez-Jenkins M, Ibrahim M, Xu X, Tomlinson B, Hang X, Pamer EG, Wei Y, Kang Y, White EP, Rabinowitz JD.	Cancer Res	10.1158/0008-5472.can-24-4378	2025
	A beta-1,2-glucan-associated glycoside hydrolase family 1 beta-glucosidase from Streptomyces griseus.	Kumakura H, Motouchi S, Kobayashi K, Inoue M, Kariuda N, Nakai H, Nakajima M.	Protein Sci	10.1002/pro.70255	2025
Metabolism	Bacteroidota polysaccharide utilization system for branched dextran exopolysaccharides from lactic acid bacteria.	Nakamura S, Kurata R, Tonozuka T, Funane K, Park EY, Miyazaki T.	J Biol Chem	10.1016/j.jbc.2023.104885	2023
	Both viable Bifidobacterium longum subsp. infantis B8762 and heat-killed cells alleviate the intestinal inflammation of DSS-induced IBD rats.	Li Z, Peng C, Sun Y, Zhang T, Feng C, Zhang W, Huang T, Yao G, Zhang H, He Q.	Microbiol Spectr	10.1128/spectrum.03509-23	2024
Metabolism	Do Primocolonizing Bacteria Enable Bacteroides thetaiotaomicron Intestinal Colonization Independently of the Capacity To Consume Oxygen?	Halpern D, Morvan C, Derre-Bobillot A, Meylheuc T, Guillemet M, Rabot S, Gruss A.	mSphere	10.1128/msphere.00232-19	2021
	Microcosms for evaluating microbial indicator persistence and mobilization in fluvial sediments during rainfall events.	Martin-Diaz J, Garcia-Aljaro C, Pascual-Benito M, Galofre B, Blanch AR, Lucena F.	Water Res	10.1016/j.watres.2017.07.017	2017
	Is There an Interplay between Environmental Factors, Microbiota Imbalance, and Cancer Chemotherapy-Associated Intestinal Mucositis?	Fernandes C, Miranda MCC, Roque CR, Paguada ALP, Mota CAR, Florencio KGD, Pereira AF, Wong DVT, Oria RB, Lima-Junior RCP.	Pharmaceuticals (Basel)	10.3390/ph17081020	2024
	Potential application of pig (Sus scrofa domestica) skin peptide-iron chelates in the treatment of iron deficiency anemia and regulation of intestinal flora metabolism.	Huang S, Deng H, Liang K, Zhao X, Zhang J.	Front Nutr	10.3389/fnut.2025.1553668	2025
	Solvent induced amyloid polymorphism and the uncovering of the elusive class 3 amyloid topology.	Durvanger Z, Bencs F, Menyhard DK, Horvath D, Perczel A.	Commun Biol	10.1038/s42003-024-06621-8	2024
	The Glycine Lipids of Bacteroides thetaiotaomicron Are Important for Fitness during Growth In Vivo and In Vitro.	Lynch A, Tammireddy SR, Doherty MK, Whitfield PD, Clarke DJ.	Appl Environ Microbiol	10.1128/aem.02157-18	2019
	Evaluation of the therapeutic effect of pomegranate peel ginger ultrafine powder on chronic enteritis in mice by regulating intestinal microbiota.	Guo Z, Wang X, Li Y, Zhang Y, Guo P, Zhang J, Zhang Z, Ma X.	Front Immunol	10.3389/fimmu.2025.1563225	2025
	Serotonergic and immunomodulatory properties of the psychobiotic candidate Bacteroides finegoldii UO.H1052 and its extracellular vesicles.	Yousuf B, Esmail GA, Nazemof N, Bouhlel NE, Minic Z, Hammami R.	Appl Environ Microbiol	10.1128/aem.00891-25	2025
Metabolism	Biochemical and structural basis of sialic acid utilization by gut microbes.	Bell A, Severi E, Owen CD, Latousakis D, Juge N.	J Biol Chem	10.1016/j.jbc.2023.102989	2023
	Small RNAs Go Global in Human Gut Bacteroides.	Pudlo NA, Martens EC.	J Bacteriol	10.1128/jb.00383-21	2021
	Disturbances in the gut microbiota potentially associated with metabolic syndrome among patients living with HIV-1 and on antiretroviral therapy at Bafoussam Regional Hospital, Cameroon.	Diesse JM, Jadhav S, Tamekou SL, Simo G, Dzoyem JP, Souopgui J, Kuiate JR, Nema V.	Diabetol Metab Syndr	10.1186/s13098-025-01653-4	2025
	Polymicrobial Solitary Retroperitoneal Abscess Due to Sigmoid Colon Perforation.	Takase Y, Yang YM, Kitagawa K, Nakano Y, Miura S, Oshikiri T, Kakeji Y, Shigemura K, Fujisawa M.	Kobe J Med Sci		2021
	Gut Bacteria in Alcohol-Associated Liver Disease.	Yang Y, Schnabl B.	Clin Liver Dis	10.1016/j.cld.2024.06.008	2024
Pathogenicity	Host interactions of novel Crassvirales species belonging to multiple families infecting bacterial host, Bacteroides cellulosilyticus WH2.	Papudeshi B, Vega AA, Souza C, Giles SK, Mallawaarachchi V, Roach MJ, An M, Jacobson N, McNair K, Fernanda Mora M, Pastrana K, Boling L, Leigh C, Harker C, Plewa WS, Grigson SR, Bouras G, Decewicz P, Luque A, Droit L, Handley SA, Wang D, Segall AM, Dinsdale EA, Edwards RA.	Microb Genom	10.1099/mgen.0.001100	2023
	Intestinal Microbiota and Vaccinations: A Systematic Review of the Literature.	Loddo F, Lagana P, Rizzo CE, Calderone SM, Romeo B, Venuto R, Maisano D, Fedele F, Squeri R, Nicita A, Nirta A, Genovese G, Bartucciotto L, Genovese C.	Vaccines (Basel)	10.3390/vaccines13030306	2025
Pathogenicity	Bile modulates phage-host interactions in multidrug-resistant Pseudomonas aeruginosa.	Khan MSI, Wu J, Hou S, Ji S, Li H, Chang Y, Sui B, Tan D, Yin J.	BMC Microbiol	10.1186/s12866-025-04379-5	2025
	Bacteroides thetaiotaomicron Starch Utilization Promotes Quercetin Degradation and Butyrate Production by Eubacterium ramulus.	Rodriguez-Castano GP, Dorris MR, Liu X, Bolling BW, Acosta-Gonzalez A, Rey FE.	Front Microbiol	10.3389/fmicb.2019.01145	2019
	Cordyceps militaris extract and cordycepin ameliorate LPS-challenged colonic damage in piglets by modulating the microbiota and metabolite profiles.	Xiong S, Wan F, Jiang J, Liu Y, Hang Y, Xue H, Lu Y, Su Y.	Front Immunol	10.3389/fimmu.2025.1530098	2025
	Gut Microbiota and Plasma Bile Acids Associated with Non-Alcoholic Fatty Liver Disease Resolution in Bariatric Surgery Patients.	Perez-Rubio A, Soluyanova P, Moro E, Quintas G, Rienda I, Perianez MD, Painel A, Vizuete J, Perez-Rojas J, Castell JV, Trullenque-Juan R, Pareja E, Jover R.	Nutrients	10.3390/nu15143187	2023
Metabolism	Body Mass Index as a Determinant of Systemic Exposure to Gallotannin Metabolites during 6-Week Consumption of Mango (Mangifera indica L.) and Modulation of Intestinal Microbiota in Lean and Obese Individuals.	Barnes RC, Kim H, Fang C, Bennett W, Nemec M, Sirven MA, Suchodolski JS, Deutz N, Britton RA, Mertens-Talcott SU, Talcott ST.	Mol Nutr Food Res	10.1002/mnfr.201800512	2019
	The Obesity-Epigenetics-Microbiome Axis: Strategies for Therapeutic Intervention.	Nohesara S, Mostafavi Abdolmaleky H, Pirani A, Pettinato G, Thiagalingam S.	Nutrients	10.3390/nu17091564	2025
	A compendium of predicted growths and derived symbiotic relationships between 803 gut microbes in 13 different diets.	Singh R, Dutta A, Bose T, Mande SS.	Curr Res Microb Sci	10.1016/j.crmicr.2022.100127	2022
	Accurate identification and quantification of commensal microbiota bound by host immunoglobulins.	Jackson MA, Pearson C, Ilott NE, Huus KE, Hegazy AN, Webber J, Finlay BB, Macpherson AJ, Powrie F, Lam LH.	Microbiome	10.1186/s40168-020-00992-w	2021
Genetics	A novel computational approach for the mining of signature pathways using species co-occurrence networks in gut microbiomes.	Kim S, Thapa I, Ali H.	BMC Microbiol	10.1186/s12866-024-03633-6	2024
	Microbiome engineering to enhance disease resistance in aquaculture: current strategies and future directions.	Tayyab M, Zhao Y, Zhang Y.	Front Microbiol	10.3389/fmicb.2025.1625265	2025
Genetics	A Metagenome-Wide Association Study of the Gut Microbiome and Metabolic Syndrome.	Qin Q, Yan S, Yang Y, Chen J, Li T, Gao X, Yan H, Wang Y, Wang J, Wang S, Ding S.	Front Microbiol	10.3389/fmicb.2021.682721	2021
Genetics	Using gut microbiome metagenomic hypervariable features for diabetes screening and typing through supervised machine learning.	Chavarria X, Park HS, Oh S, Kang D, Choi JH, Kim M, Cho YH, Yi MH, Kim JY.	Microb Genom	10.1099/mgen.0.001365	2025
Metabolism	Formate oxidation in the intestinal mucus layer enhances fitness of Salmonella enterica serovar Typhimurium.	Winter MG, Hughes ER, Muramatsu MK, Jimenez AG, Chanin RB, Spiga L, Gillis CC, McClelland M, Andrews-Polymenis H, Winter SE.	mBio	10.1128/mbio.00921-23	2023
	Histo-Blood Group Antigen-Producing Bacterial Cocktail Reduces Rotavirus A, B, and C Infection and Disease in Gnotobiotic Piglets.	Raev SA, Kick MK, Chellis M, Amimo JO, Saif LJ, Vlasova AN.	Viruses	10.3390/v16050660	2024
Metabolism	Carboxyspermidine decarboxylase of the prominent intestinal microbiota species Bacteroides thetaiotaomicron is required for spermidine biosynthesis and contributes to normal growth.	Sakanaka M, Sugiyama Y, Kitakata A, Katayama T, Kurihara S.	Amino Acids	10.1007/s00726-016-2233-0	2016
Enzymology	Efficient synthesis of alpha-galactosyl oligosaccharides using a mutant Bacteroides thetaiotaomicron retaining alpha-galactosidase (BtGH97b).	Okuyama M, Matsunaga K, Watanabe KI, Yamashita K, Tagami T, Kikuchi A, Ma M, Klahan P, Mori H, Yao M, Kimura A.	FEBS J	10.1111/febs.14018	2017
	Exploring the CDCA-Scd1 Axis: Molecular Mechanisms Linking the Colitis Microbiome to Neurological Deficits.	Du D, Li Q, Wei Z, Wang Z, Xu L.	Int J Mol Sci	10.3390/ijms26052111	2025
	Gut microbiota dysbiosis and metabolic perturbations of bile/glyceric acids in major depressive disorder with IBS comorbidity.	Du J-Y, Zhang Z-J, Tan L, Yang J-Y, Yang R-N, Chen Y-L, Tan G-F, Li J, Li W-J, Yang L, Cai J, Shen D-L, Zhu H-R, Fan Z-X, Yuan M-L, Zhang W.	mBio	10.1128/mbio.02447-25	2025
	Tetracycline-modifying enzyme SmTetX from Stenotrophomonas maltophilia.	Maly M, Kolenko P, Stransky J, Svecova L, Duskova J, Koval' T, Skalova T, Trundova M, Adamkova K, Cerny J, Bozikova P, Dohnalek J.	Acta Crystallogr F Struct Biol Commun	10.1107/s2053230x23005381	2023
	Research article network analysis of polymicrobial chronic wound infections in Masanga, Sierra Leone.	Sandmann S, Nunes JV, Grobusch MP, Sesay M, Kriegel MA, Varghese J, Schaumburg F.	BMC Infect Dis	10.1186/s12879-023-08204-0	2023
	Bioinformatic Assessment of Factors Affecting the Correlation between Protein Abundance and Elongation Efficiency in Prokaryotes.	Korenskaia AE, Matushkin YG, Lashin SA, Klimenko AI.	Int J Mol Sci	10.3390/ijms231911996	2022
Enzymology	Novel dipeptidyl hydroxamic acids that inhibit human and bacterial dipeptidyl peptidase III.	Cvitesic A, Sabljic I, Makarevic J, Abramic M.	J Enzyme Inhib Med Chem	10.1080/14756366.2016.1186021	2016
Pathogenicity	Metabolic modeling of host-microbe interactions.	Srinak N, Kruger F, Kaleta C, Taubenheim J.	Comput Struct Biotechnol J	10.1016/j.csbj.2025.10.006	2025
Pathogenicity	Transplantation of fecal microbiota from different breeds improved intestinal barrier condition and modulated ileal microflora of recipient pigs.	Yang T, Liu Y, Yin J, Yv T, Zhou F, Li Y, Yang L, Han L, Huang X.	J Anim Sci	10.1093/jas/skae314	2024
Metabolism	Targeting the Gut Microbiota's Role in Host Energy Absorption With Precision Nutrition Interventions for the Prevention and Treatment of Obesity.	Corbin KD, Igudesman D, Smith SR, Zengler K, Krajmalnik-Brown R.	Nutr Rev	10.1093/nutrit/nuaf046	2025
Genetics	An integrated strain-level analytic pipeline utilizing longitudinal metagenomic data.	Zhou B, Wang C, Putzel G, Hu J, Liu M, Wu F, Chen Y, Pironti A, Li H.	Microbiol Spectr	10.1128/spectrum.01431-24	2024
Metabolism	Spatial organization of bacterial sphingolipid synthesis enzymes.	Uchendu CG, Guan Z, Klein EA.	J Biol Chem	10.1016/j.jbc.2024.107276	2024
Pathogenicity	Association of gut microbiota and inflammatory markers in obese patients with type 2 diabetes mellitus: post hoc analysis of a synbiotic interventional study.	Sugawara Y, Kanazawa A, Aida M, Yoshida Y, Yamashiro Y, Watada H.	Biosci Microbiota Food Health	10.12938/bmfh.2021-081	2022
	Gut microbiota dysbiosis and associated immune response in systemic lupus erythematosus: impact of disease and treatment.	Ali AY, Zahran SA, Eissa M, Kashef MT, Ali AE.	Gut Pathog	10.1186/s13099-025-00683-7	2025
	The Ketone Bridge Between the Heart and the Bladder: How Fast Should We Go?	Faria-Costa G, Oliveira J, Vilas-Boas I, Campelo I, Silva EA, Bras-Silva C, Silva SM, Antunes-Lopes T, Charrua A.	Int Neurourol J	10.5213/inj.2346250.125	2024
Metabolism	Suggested alternative starch utilization system from the human gut bacterium Bacteroides thetaiotaomicron.	Chaudet MM, Rose DR.	Biochem Cell Biol	10.1139/bcb-2016-0002	2016
	Non-invasive monitoring of microbiota and host metabolism using secondary electrospray ionization-mass spectrometry.	Lan J, Greter G, Streckenbach B, Wanner B, Arnoldini M, Zenobi R, Slack E.	Cell Rep Methods	10.1016/j.crmeth.2023.100539	2023
Genetics	Specialized Bacteroidetes dominate the Arctic Ocean during marine spring blooms.	Redondo-Rio A, Mundy CJ, Tamames J, Pedros-Alio C.	Front Microbiol	10.3389/fmicb.2024.1481702	2024
Genetics	Influence of gender, age, and body mass index on the gut microbiota of individuals from South China.	Li S, Fan S, Ma Y, Xia C, Yan Q.	Front Cell Infect Microbiol	10.3389/fcimb.2024.1419884	2024
	Bacteriophage-driven DNA inversions shape bacterial functionality and long-term co-existence in Bacteroides fragilis.	Carasso S, Keshet-David R, Zhang J, Hajjo H, Kadosh-Kariti D, Gefen T, Geva-Zatorsky N.	Gut Microbes	10.1080/19490976.2025.2501492	2025
	Impact of Blastocystis carriage and colonization intensity on gut microbiota composition in a non-westernized rural population from Colombia.	Castaneda S, Tomiak J, Andersen LO, Acosta CP, Vasquez-A LR, Stensvold CR, Ramirez JD.	PLoS Negl Trop Dis	10.1371/journal.pntd.0013111	2025
	Mobilisation of microbial indicators, microbial source tracking markers and pathogens after rainfall events.	Garcia-Aljaro C, Martin-Diaz J, Vinas-Balada E, Calero-Caceres W, Lucena F, Blanch AR.	Water Res	10.1016/j.watres.2017.02.003	2017
	Discovery of Anomer-Inverting Transglycosylase: Cyclic Glucohexadecaose-Producing Enzyme from Xanthomonas, a Phytopathogen.	Motouchi S, Komba S, Nakai H, Nakajima M.	J Am Chem Soc	10.1021/jacs.4c02579	2024
	NOBIAS: Analyzing anomalous diffusion in single-molecule tracks with nonparametric Bayesian inference.	Chen Z, Geffroy L, Biteen JS.	Front Bioinform	10.3389/fbinf.2021.742073	2021
	Sulforaphane and Sulforaphane-Nitrile Metabolism in Humans Following Broccoli Sprout Consumption: Inter-individual Variation, Association with Gut Microbiome Composition, and Differential Bioactivity.	Bouranis JA, Beaver LM, Wong CP, Choi J, Hamer S, Davis EW, Brown KS, Jiang D, Sharpton TJ, Stevens JF, Ho E.	Mol Nutr Food Res	10.1002/mnfr.202300286	2024
	Chemical composition and in vitro leishmanicidal, antibacterial and cytotoxic activities of essential oils of the Myrtaceae family occurring in the Cerrado biome	da Silva VP, Alves CCF, Miranda MLD, Bretanha LC, Balleste MP, Micke GA, Silveira EV, Martins CHG, Ambrosio MALV, de Souza Silva T, Tavares DC, Magalhaes LG, Silva FG, Egea MB.	Industrial crops and products.	10.1016/j.indcrop.2018.07.033	2018
	Bacteroides thetaiotaomicron-derived outer membrane vesicles promote regulatory dendritic cell responses in health but not in inflammatory bowel disease.	Durant L, Stentz R, Noble A, Brooks J, Gicheva N, Reddi D, O'Connor MJ, Hoyles L, McCartney AL, Man R, Pring ET, Dilke S, Hendy P, Segal JP, Lim DNF, Misra R, Hart AL, Arebi N, Carding SR, Knight SC.	Microbiome	10.1186/s40168-020-00868-z	2020
	Fluorescence activated cell sorting and fermentation analysis to study rumen microbiome responses to administered live microbials and yeast cell wall derived prebiotics.	Klassen L, Reintjes G, Li M, Jin L, Amundsen C, Xing X, Dridi L, Castagner B, Alexander TW, Abbott DW.	Front Microbiol	10.3389/fmicb.2022.1020250	2022
	Plant-based diets and the gut microbiome: findings from the Baltimore Longitudinal Study of Aging.	Shen X, Tilves C, Kim H, Tanaka T, Spira AP, Chia CW, Talegawkar SA, Ferrucci L, Mueller NT.	Am J Clin Nutr	10.1016/j.ajcnut.2024.01.006	2024
	Bibliometric analysis of the top 100 most cited articles on Th17/Treg balance and rheumatoid arthritis.	Liu X, Wang Y, Wen Q.	Heliyon	10.1016/j.heliyon.2024.e32832	2024
Phylogeny	PhyloFunc: phylogeny-informed functional distance as a new ecological metric for metaproteomic data analysis.	Wang L, Simopoulos CMA, Serrana JM, Ning Z, Li Y, Sun B, Yuan J, Figeys D, Li L.	Microbiome	10.1186/s40168-024-02015-4	2025
	Clostridia isolated from helminth-colonized humans promote the life cycle of Trichuris species.	Sargsian S, Chen Z, Lee SC, Robertson A, Thur RS, Sproch J, Devlin JC, Tee MZ, Er YX, Copin R, Heguy A, Pironti A, Torres VJ, Ruggles KV, Lim YAL, Bethony J, Loke P, Cadwell K.	Cell Rep	10.1016/j.celrep.2022.111725	2022
	Transmembrane Transcription Regulators Are Widespread in Bacteria and Archaea.	Demey LM, Gumerov VM, Xing J, Zhulin IB, DiRita VJ.	Microbiol Spectr	10.1128/spectrum.00266-23	2023
Genetics	Fecal Pharmacokinetics and Gut Microbiome Effects of Oral Omadacycline Versus Vancomycin in Healthy Volunteers.	Jo J, Hu C, Begum K, Wang W, Le TM, Agyapong S, Hanson BM, Ayele H, Lancaster C, Jahangir Alam M, Gonzales-Luna AJ, Garey KW.	J Infect Dis	10.1093/infdis/jiad537	2024
Metabolism	Branched-chain amino acids induce hyperammonemia via gut-liver axis-mediated ammonia overproduction in laying hens.	Jian H, Xu M, Liu F, Zhang L, Huang Q, Ma J, Zou X, Dong X.	Anim Nutr	10.1016/j.aninu.2025.03.012	2025
	The probability of detecting host-specific microbial source tracking markers in surface waters was strongly associated with method and season.	Murphy CM, Weller DL, Love TMT, Danyluk MD, Strawn LK.	Microbiol Spectr	10.1128/spectrum.01972-24	2025
Pathogenicity	Metronidazole- and carbapenem-resistant bacteroides thetaiotaomicron isolated in Rochester, Minnesota, in 2014.	Sadarangani SP, Cunningham SA, Jeraldo PR, Wilson JW, Khare R, Patel R.	Antimicrob Agents Chemother	10.1128/aac.00677-15	2015
	Prescription opioids induced microbial dysbiosis worsens severity of chronic pancreatitis and drives pain hypersensitivity.	Kesh K, Tao J, Ghosh N, Jalodia R, Singh S, Dawra R, Roy S.	Gut Microbes	10.1080/19490976.2024.2310291	2024
Pathogenicity	Aluminum-induced oxidative stress promotes changes in the structure of the gut microbiota and liver deficiency.	Feng R, Chen L, Yang M.	Heliyon	10.1016/j.heliyon.2024.e36165	2024
	Efficacy and safety of novel carbapenem-beta-lactamase inhibitor combinations: imipenem-cilastatin/relebactam results from randomized controlled trials.	Yang Q, Yang Y, He R, Yu B, Zhong Y, Lin F.	Front Med (Lausanne)	10.3389/fmed.2023.1304369	2023
	Lipidomic Analysis Reveals Differences in Bacteroides Species Driven Largely by Plasmalogens, Glycerophosphoinositols and Certain Sphingolipids.	Ryan E, Gonzalez Pastor B, Gethings LA, Clarke DJ, Joyce SA.	Metabolites	10.3390/metabo13030360	2023
	A molecular toolkit for heterologous protein secretion across Bacteroides species.	Yeh YH, Kelly VW, Rahman Pour R, Sirk SJ.	Nat Commun	10.1038/s41467-024-53845-7	2024
	Heterologous Expression and Characterization of Cellouronate (beta-1,4-Glucuronan) Lyase from a Human Intestinal Bacterium Bacteroides luhongzhouii.	Tanaka Y, Matsumura K, Ariga M, Konno N, Ogata M, Habu N.	J Appl Glycosci (1999)	10.5458/jag.7203102	2025
	Development of culture methods capable of culturing a wide range of predominant species of intestinal bacteria.	Hirano R, Nishita I, Nakai R, Bito A, Sasabe R, Kurihara S.	Front Cell Infect Microbiol	10.3389/fcimb.2023.1056866	2023
Phylogeny	In Situ Profiling of the Three Dominant Phyla Within the Human Gut Using TaqMan PCR for Pre-Hospital Diagnosis of Gut Dysbiosis.	Jo YJ, Tagele SB, Pham HQ, Jung Y, Ibal JC, Choi S, Kang GU, Park S, Kang Y, Kim S, Koh H, Shin JH.	Int J Mol Sci	10.3390/ijms21061916	2020
Metabolism	Probiotics in human gut microbiota can degrade host glycosaminoglycans.	Kawai K, Kamochi R, Oiki S, Murata K, Hashimoto W.	Sci Rep	10.1038/s41598-018-28886-w	2018
Metabolism	Gut microbial carbohydrate metabolism contributes to insulin resistance.	Takeuchi T, Kubota T, Nakanishi Y, Tsugawa H, Suda W, Kwon AT, Yazaki J, Ikeda K, Nemoto S, Mochizuki Y, Kitami T, Yugi K, Mizuno Y, Yamamichi N, Yamazaki T, Takamoto I, Kubota N, Kadowaki T, Arner E, Carninci P, Ohara O, Arita M, Hattori M, Koyasu S, Ohno H.	Nature	10.1038/s41586-023-06466-x	2023
	Comparison of Yacon (Smallanthus sonchifolius) Tuber with Commercialized Fructo-oligosaccharides (FOS) in Terms of Physiology, Fermentation Products and Intestinal Microbial Communities in Rats.	Utami NW, Sone T, Tanaka M, Nakatsu CH, Saito A, Asano K.	Biosci Microbiota Food Health	10.12938/bmfh.32.167	2013
	Bacteroides ovatus as the predominant commensal intestinal microbe causing a systemic antibody response in inflammatory bowel disease.	Saitoh S, Noda S, Aiba Y, Takagi A, Sakamoto M, Benno Y, Koga Y.	Clin Diagn Lab Immunol	10.1128/cdli.9.1.54-59.2002	2002
Metabolism	Chitosan Oligosaccharides Show Protective Effects in Coronary Heart Disease by Improving Antioxidant Capacity via the Increase in Intestinal Probiotics.	Jiang T, Xing X, Zhang L, Liu Z, Zhao J, Liu X.	Oxid Med Cell Longev	10.1155/2019/7658052	2019
Metabolism	Modification to increase the thermostability and catalytic efficiency of alpha-L-rhamnosidase from Bacteroides thetaiotaomicron and high-level expression.	Lu C, Dong Y, Ke K, Zou K, Wang Z, Xiao W, Pei J, Zhao L	Enzyme Microb Technol	10.1016/j.enzmictec.2022.110040	2022
Metabolism	Bacteroides thetaiotaomicron uses a widespread extracellular DNase to promote bile-dependent biofilm formation.	Bechon N, Mihajlovic J, Lopes AA, Vendrell-Fernandez S, Deschamps J, Briandet R, Sismeiro O, Martin-Verstraete I, Dupuy B, Ghigo JM	Proc Natl Acad Sci U S A	10.1073/pnas.2111228119	2022
Metabolism	Lipidomics Analysis of Outer Membrane Vesicles and Elucidation of the Inositol Phosphoceramide Biosynthetic Pathway in Bacteroides thetaiotaomicron.	Sartorio MG, Valguarnera E, Hsu FF, Feldman MF	Microbiol Spectr	10.1128/spectrum.00634-21	2022
Metabolism	Rational Design for Broadened Substrate Specificity and Enhanced Activity of a Novel Acetyl Xylan Esterase from Bacteroides thetaiotaomicron.	Wang L, Han X, Wang Y, Wei X, Liu S, Shao S, Yang S, Sun L, Xin F	J Agric Food Chem	10.1021/acs.jafc.1c00750	2021
Biotechnology	GABA Production by Human Intestinal Bacteroides spp.: Prevalence, Regulation, and Role in Acid Stress Tolerance.	Otaru N, Ye K, Mujezinovic D, Berchtold L, Constancias F, Cornejo FA, Krzystek A, de Wouters T, Braegger C, Lacroix C, Pugin B	Front Microbiol	10.3389/fmicb.2021.656895	2021
	Capsular Polysaccharide Cross-Regulation Modulates Bacteroides thetaiotaomicron Biofilm Formation.	Bechon N, Mihajlovic J, Vendrell-Fernandez S, Chain F, Langella P, Beloin C, Ghigo JM	mBio	10.1128/mBio.00729-20	2020
Pathogenicity	Endotoxin Producers Overgrowing in Human Gut Microbiota as the Causative Agents for Nonalcoholic Fatty Liver Disease.	Fei N, Bruneau A, Zhang X, Wang R, Wang J, Rabot S, Gerard P, Zhao L	mBio	10.1128/mBio.03263-19	2020
	Intestinal IgA Regulates Expression of a Fructan Polysaccharide Utilization Locus in Colonizing Gut Commensal Bacteroides thetaiotaomicron.	Joglekar P, Ding H, Canales-Herrerias P, Pasricha PJ, Sonnenburg JL, Peterson DA	mBio	10.1128/mBio.02324-19	2019
Phylogeny	Bifidobacterium adolescentis P2P3, a Human Gut Bacterium Having Strong Non-Gelatinized Resistant Starch-Degrading Activity.	Jung DH, Kim GY, Kim IY, Seo DH, Nam YD, Kang H, Song Y, Park CS	J Microbiol Biotechnol	10.4014/jmb.1909.09010	2019
Metabolism	Single cell fluorescence imaging of glycan uptake by intestinal bacteria.	Hehemann JH, Reintjes G, Klassen L, Smith AD, Ndeh D, Arnosti C, Amann R, Abbott DW	ISME J	10.1038/s41396-019-0406-z	2019
Pathogenicity	A Putative Type V Pilus Contributes to Bacteroides thetaiotaomicron Biofilm Formation Capacity.	Mihajlovic J, Bechon N, Ivanova C, Chain F, Almeida A, Langella P, Beloin C, Ghigo JM	J Bacteriol	10.1128/JB.00650-18	2019
Metabolism	Characterization of a alpha-l-rhamnosidase from Bacteroides thetaiotaomicron with high catalytic efficiency of epimedin C.	Wu T, Pei J, Ge L, Wang Z, Ding G, Xiao W, Zhao L	Bioorg Chem	10.1016/j.bioorg.2018.08.004	2018
Metabolism	The Biosynthesis of Lipooligosaccharide from Bacteroides thetaiotaomicron.	Jacobson AN, Choudhury BP, Fischbach MA	mBio	10.1128/mBio.02289-17	2018
	Characterization of a glycoside hydrolase family 78 alpha-l-rhamnosidase from Bacteroides thetaiotaomicron VPI-5482 and identification of functional residues.	Li B, Ji Y, Li Y, Ding G	3 Biotech	10.1007/s13205-018-1139-9	2018
Pathogenicity	Comprehensive evaluation of the bactericidal activities of free bile acids in the large intestine of humans and rodents.	Watanabe M, Fukiya S, Yokota A	J Lipid Res	10.1194/jlr.M075143	2017
Metabolism	Anaerobic utilization of Fe(III)-xenosiderophores among Bacteroides species and the distinct assimilation of Fe(III)-ferrichrome by Bacteroides fragilis within the genus.	Rocha ER, Krykunivsky AS	Microbiologyopen	10.1002/mbo3.479	2017
Metabolism	The microbiota shifts the iron sensing of intestinal cells.	Deschemin JC, Noordine ML, Remot A, Willemetz A, Afif C, Canonne-Hergaux F, Langella P, Karim Z, Vaulont S, Thomas M, Nicolas G	FASEB J	10.1096/fj.15-276840	2015
Metabolism	The gut bacterium Bacteroides thetaiotaomicron influences the virulence potential of the enterohemorrhagic Escherichia coli O103:H25.	Iversen H, Lindback T, L'Abee-Lund TM, Roos N, Aspholm M, Stenfors Arnesen L	PLoS One	10.1371/journal.pone.0118140	2015
	Evaluative profiling of arsenic sensing and regulatory systems in the human microbiome project genomes.	Isokpehi RD, Udensi UK, Simmons SS, Hollman AL, Cain AE, Olofinsae SA, Hassan OA, Kashim ZA, Enejoh OA, Fasesan DE, Nashiru O	Microbiol Insights	10.4137/MBI.S18076	2014
Genetics	Structural genomics analysis of uncharacterized protein families overrepresented in human gut bacteria identifies a novel glycoside hydrolase.	Sheydina A, Eberhardt RY, Rigden DJ, Chang Y, Li Z, Zmasek CC, Axelrod HL, Godzik A	BMC Bioinformatics	10.1186/1471-2105-15-112	2014
Biotechnology	Degradation of Fructans and Production of Propionic Acid by Bacteroides thetaiotaomicron are Enhanced by the Shortage of Amino Acids.	Adamberg S, Tomson K, Vija H, Puurand M, Kabanova N, Visnapuu T, Jogi E, Alamae T, Adamberg K	Front Nutr	10.3389/fnut.2014.00021	2014
Proteome	Filling out the structural map of the NTF2-like superfamily.	Eberhardt RY, Chang Y, Bateman A, Murzin AG, Axelrod HL, Hwang WC, Aravind L	BMC Bioinformatics	10.1186/1471-2105-14-327	2013
Metabolism	Discovery of beta-1,4-D-mannosyl-N-acetyl-D-glucosamine phosphorylase involved in the metabolism of N-glycans.	Nihira T, Suzuki E, Kitaoka M, Nishimoto M, Ohtsubo K, Nakai H	J Biol Chem	10.1074/jbc.M113.469080	2013
Enzymology	Bacteroides thetaiotaomicron VPI-5482 glycoside hydrolase family 66 homolog catalyzes dextranolytic and cyclization reactions.	Kim YM, Yamamoto E, Kang MS, Nakai H, Saburi W, Okuyama M, Mori H, Funane K, Momma M, Fujimoto Z, Kobayashi M, Kim D, Kimura A	FEBS J	10.1111/j.1742-4658.2012.08698.x	2012
Pathogenicity	A conformational switch in the active site of BT_2972, a methyltransferase from an antibiotic resistant pathogen B. thetaiotaomicron.	Kumar V, Sivaraman J	PLoS One	10.1371/journal.pone.0027543	2011
Enzymology	The X-ray crystallographic structure and specificity profile of HAD superfamily phosphohydrolase BT1666: comparison of paralogous functions in B. thetaiotaomicron.	Lu Z, Dunaway-Mariano D, Allen KN	Proteins	10.1002/prot.23137	2011
Pathogenicity	Use of a Bacteroides thetaiotaomicron-specific alpha-1-6, mannanase quantitative PCR to detect human faecal pollution in water.	Yampara-Iquise H, Zheng G, Jones JE, Carson CA	J Appl Microbiol	10.1111/j.1365-2672.2008.03895.x	2008
Enzymology	The catalytic scaffold of the haloalkanoic acid dehalogenase enzyme superfamily acts as a mold for the trigonal bipyramidal transition state.	Lu Z, Dunaway-Mariano D, Allen KN	Proc Natl Acad Sci U S A	10.1073/pnas.0710800105	2008
Metabolism	Crystal structures of two novel dye-decolorizing peroxidases reveal a beta-barrel fold with a conserved heme-binding motif.	Zubieta C, Krishna SS, Kapoor M, Kozbial P, McMullan D, Axelrod HL, Miller MD, Abdubek P, Ambing E, Astakhova T, Carlton D, Chiu HJ, Clayton T, Deller MC, Duan L, Elsliger MA, Feuerhelm J, Grzechnik SK, Hale J, Hampton E, Han GW, Jaroszewski L, Jin KK, Klock HE, Knuth MW, Kumar A, Marciano D, Morse AT, Nigoghossian E, Okach L, Oommachen S, Reyes R, Rife CL, Schimmel P, van den Bedem H, Weekes D, White A, Xu Q, Hodgson KO, Wooley J, Deacon AM, Godzik A, Lesley SA, Wilson IA	Proteins	10.1002/prot.21550	2007
Metabolism	Characterization of Bacteroides fragilis hemolysins and regulation and synergistic interactions of HlyA and HlyB.	Robertson KP, Smith CJ, Gough AM, Rocha ER	Infect Immun	10.1128/IAI.74.4.2304-2316.2006	2006
Enzymology	HAD superfamily phosphotransferase substrate diversification: structure and function analysis of HAD subclass IIB sugar phosphatase BT4131.	Lu Z, Dunaway-Mariano D, Allen KN	Biochemistry	10.1021/bi050009j	2005
Genetics	Genetic and structural analysis of the Bacteroides conjugative transposon CTn341.	Bacic M, Parker AC, Stagg J, Whitley HP, Wells WG, Jacob LA, Smith CJ	J Bacteriol	10.1128/JB.187.8.2858-2869.2005	2005
Phylogeny	Identification of Bacteroides thetaiotaomicron on the basis of an unexpected specific amplicon of universal 16S ribosomal DNA PCR.	Teng LJ, Hsueh PR, Huang YH, Tsai JC	J Clin Microbiol	10.1128/JCM.42.4.1727-1730.2004	2004
Metabolism	A heat labile soluble factor from Bacteroides thetaiotaomicron VPI-5482 specifically increases the galactosylation pattern of HT29-MTX cells.	Freitas M, Cayuela C, Antoine JM, Piller F, Sapin C, Trugnan G	Cell Microbiol	10.1046/j.1462-5822.2001.00113.x	2001
	Carbohydrate utilization patterns and substrate preferences in Bacteroides thetaiotaomicron.	Degnan BA, Macfarlane GT	Anaerobe	10.1016/s1075-9964(95)80392-0	1995
Phylogeny	[Use of cell-surface antigens of Bacteroides thetaiotaomicron in the passive hemagglutination test and in the inhibition of passive hemagglutination].	Rokosz A, Meisel-Mikolajczyk F	Med Dosw Mikrobiol		1995
Metabolism	Metabolism of 1,4-dinitro-2-methylpyrrole, a mutagen formed by a sorbic acid-nitrite reaction, by intestinal bacteria.	Shu YZ, Kingston DG, Van Tassell RL, Wilkins TD	Environ Mol Mutagen	10.1002/em.2850170307	1991
Pathogenicity	Growth of succinate consumer Dialister hominis is supported by Bacteroides thetaiotaomicron.	Sakamoto M, Ikeyama N, Iino T, Ohkuma M	Anaerobe	10.1016/j.anaerobe.2022.102642	2022
Phylogeny	Scrofimicrobium appendicitidis sp. nov., isolated from a patient with ruptured appendicitis.	Lao HY, Wong AYP, Ng TT, Wong RY, Yau MC, Lam JY, Siu GK.	Int J Syst Evol Microbiol	10.1099/ijsem.0.006633	2025
Phylogeny	Bacteroides reticulotermitis sp. nov., isolated from the gut of a subterranean termite (Reticulitermes speratus).	Sakamoto M, Ohkuma M	Int J Syst Evol Microbiol	10.1099/ijs.0.040931-0	2012
Phylogeny	Bacteroides faecis sp. nov., isolated from human faeces.	Kim MS, Roh SW, Bae JW	Int J Syst Evol Microbiol	10.1099/ijs.0.020024-0	2009

References

#714	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 2079
#20215	Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.: List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ. IJSEM ( DOI 10.1099/ijsem.0.004332 )
#20218	Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.: StrainInfo introduces electronic passports for microorganisms.. Syst Appl Microbiol. 37: 42 - 50 2014 ( DOI 10.1016/j.syapm.2013.11.002 , PubMed 24321274 )
#41048	; Curators of the CIP;
#42081	; Curators of the CIP;
#45331	Culture Collection University of Gothenburg (CCUG) ; Curators of the CCUG; CCUG 10774
#66792	Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann: Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) .
#67770	Japan Collection of Microorganism (JCM) ; Curators of the JCM;
#68367	Automatically annotated from API 20A .
#68380	Automatically annotated from API rID32A .
#124043	Isabel Schober, Julia Koblitz: Data extracted from sequence databases, automatically matched based on designation and taxonomy .
#125438	Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg Overmann: Predicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets. 2024 ( DOI 10.1101/2024.08.12.607695 )
#125439	Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardy: deepG: Deep Learning for Genome Sequence Data. R package version 0.3.1 .
#126262	A. Lissin, I. Schober, J. F. Witte, H. Lüken, A. Podstawka, J. Koblitz, B. Bunk, P. Dawyndt, P. Vandamme, P. de Vos, J. Overmann, L. C. Reimer: StrainInfo—the central database for linked microbial strain identifiers. ( DOI 10.1093/database/baaf059 )

Rate our new design

Content

About us

Bacteroides thetaiotaomicron (DSM 2079, ATCC 29148, NCTC 10582)

Name and taxonomic classification

Morphology

Cell morphology

Colony morphology

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Oxygen tolerance

Spore formation

Observation

Metabolite utilization

Metabolite production

Metabolite tests

Enzymes

API 20A

API rID32A

Isolation, sampling and environmental information

Isolation source categories

Isolation

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_014131755

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

Help

Social Media

@ref	URE	ADH (Arg)	alpha GAL	beta GAL	beta-Galactosidase 6-phosphatebeta GP	alpha GLU	beta GLU	alpha ARA	beta GUR	beta-N-Acetyl-beta-glucosaminidasebeta NAG	MNE	RAF	GDC	alpha FUC	Reduction of nitrateNIT	IND	PAL	L-arginine arylamidaseArgA	ProA	LGA	Phenylalanine arylamidasePheA	Leucine arylamidaseLeuA	PyrA	Tyrosine arylamidaseTyrA	Alanine arylamidaseAlaA	Glycin arylamidaseGlyA	Histidine arylamidaseHisA	Glutamyl-glutamate arylamidaseGGA	Serine arylamidaseSerA
714	-	-	+	+	-	+	+	+	-	+	+	+	+	+	-	+	+	+	-	+	+/-	+	-	+/-	+	-	+	+/-	-
714	-	-	+	+	-	+	+	+	-	+	+	+	+	+	-	+	+	+	-	+	+/-	+	-	-	+	-	+/-	+/-	-
714	-	-	+	+	-	+	+	+	-	+	+	+	+	+	-	+	+	+	-	+	+/-	+	-	-	+	-	+/-	+/-	-
714	-	-	+	+	-	+	+	+	-	+	+	+	+	+	-	+	+	+	-	+	+/-	+	-	-	+	-	+/-	-	-
714	-	-	+	+	-	+	+	+	-	+	+	+	+	+	-	+	+	+	-	+	+/-	+	-	-	+	-	+/-	+/-	-
714	-	-	+	+	-	+	+	+	-	+	+	+	+	+	-	+	+	+	-	+	-	+	-	-	+	-	+	+	-
714	-	-	+	+	-	+	+	+	-	+	+	+	+	+	-	+	+	+	-	+	-	+	-	-	+	-	-	-	-
714	-	-	+	+	-	+	+	+	-	+	+	+	+	+	-	+	+	+	-	+	-	+	-	-	+	-	-	-	-
714	-	-	+	+	-	+	+	+	-	+	+	+	+	+	-	+	+	+	-	+	-	+	-	-	+	-	-	-	-
714	-	-	+	+	-	+	+	+	-	+	+	+	+	+	-	+	+	+	-	+	-	+	-	-	+	-	-	+	-

@ref	URE	ADH (Arg)	alpha GAL	beta GAL	beta-Galactosidase 6-phosphatebeta GP	alpha GLU	beta GLU	alpha ARA	beta GUR	beta-N-Acetyl-beta-glucosaminidasebeta NAG	MNE	RAF	GDC	alpha FUC	Reduction of nitrateNIT	IND	PAL	L-arginine arylamidaseArgA	ProA	LGA	Phenylalanine arylamidasePheA	Leucine arylamidaseLeuA	PyrA	Tyrosine arylamidaseTyrA	Alanine arylamidaseAlaA	Glycin arylamidaseGlyA	Histidine arylamidaseHisA	Glutamyl-glutamate arylamidaseGGA	Serine arylamidaseSerA
714	-	-	+	+	-	+	+	+	-	+	+	+	+	+	-	+	+	+	-	+	+/-	+	-	+/-	+	-	+	+/-	-
714	-	-	+	+	-	+	+	+	-	+	+	+	+	+	-	+	+	+	-	+	+/-	+	-	-	+	-	+/-	+/-	-
714	-	-	+	+	-	+	+	+	-	+	+	+	+	+	-	+	+	+	-	+	+/-	+	-	-	+	-	+/-	+/-	-
714	-	-	+	+	-	+	+	+	-	+	+	+	+	+	-	+	+	+	-	+	+/-	+	-	-	+	-	+/-	-	-
714	-	-	+	+	-	+	+	+	-	+	+	+	+	+	-	+	+	+	-	+	+/-	+	-	-	+	-	+/-	+/-	-
714	-	-	+	+	-	+	+	+	-	+	+	+	+	+	-	+	+	+	-	+	-	+	-	-	+	-	+	+	-
714	-	-	+	+	-	+	+	+	-	+	+	+	+	+	-	+	+	+	-	+	-	+	-	-	+	-	-	-	-
714	-	-	+	+	-	+	+	+	-	+	+	+	+	+	-	+	+	+	-	+	-	+	-	-	+	-	-	-	-
714	-	-	+	+	-	+	+	+	-	+	+	+	+	+	-	+	+	+	-	+	-	+	-	-	+	-	-	-	-
714	-	-	+	+	-	+	+	+	-	+	+	+	+	+	-	+	+	+	-	+	-	+	-	-	+	-	-	+	-

@ref	URE	ADH (Arg)	alpha GAL	beta GAL	beta-Galactosidase 6-phosphatebeta GP	alpha GLU	beta GLU	alpha ARA	beta GUR	beta-N-Acetyl-beta-glucosaminidasebeta NAG	MNE	RAF	GDC	alpha FUC	Reduction of nitrateNIT	IND	PAL	L-arginine arylamidaseArgA	ProA	LGA	Phenylalanine arylamidasePheA	Leucine arylamidaseLeuA	PyrA	Tyrosine arylamidaseTyrA	Alanine arylamidaseAlaA	Glycin arylamidaseGlyA	Histidine arylamidaseHisA	Glutamyl-glutamate arylamidaseGGA	Serine arylamidaseSerA
714	-	-	+	+	-	+	+	+	-	+	+	+	+	+	-	+	+	+	-	+	+/-	+	-	+/-	+	-	+	+/-	-
714	-	-	+	+	-	+	+	+	-	+	+	+	+	+	-	+	+	+	-	+	+/-	+	-	-	+	-	+/-	+/-	-
714	-	-	+	+	-	+	+	+	-	+	+	+	+	+	-	+	+	+	-	+	+/-	+	-	-	+	-	+/-	+/-	-
714	-	-	+	+	-	+	+	+	-	+	+	+	+	+	-	+	+	+	-	+	+/-	+	-	-	+	-	+/-	-	-
714	-	-	+	+	-	+	+	+	-	+	+	+	+	+	-	+	+	+	-	+	+/-	+	-	-	+	-	+/-	+/-	-
714	-	-	+	+	-	+	+	+	-	+	+	+	+	+	-	+	+	+	-	+	-	+	-	-	+	-	+	+	-
714	-	-	+	+	-	+	+	+	-	+	+	+	+	+	-	+	+	+	-	+	-	+	-	-	+	-	-	-	-
714	-	-	+	+	-	+	+	+	-	+	+	+	+	+	-	+	+	+	-	+	-	+	-	-	+	-	-	-	-
714	-	-	+	+	-	+	+	+	-	+	+	+	+	+	-	+	+	+	-	+	-	+	-	-	+	-	-	-	-
714	-	-	+	+	-	+	+	+	-	+	+	+	+	+	-	+	+	+	-	+	-	+	-	-	+	-	-	+	-