Bacteroides eggerthii (DSM 20697, ATCC 27754, NCTC 11155)

Name: Bacteroides eggerthii (DSM 20697, ATCC 27754, NCTC 11155)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 1583

Type strain

Strain Designation 10128

Culture col. no. DSM 20697 ATCC 27754 NCTC 11155 CCUG 9559 CIP 104285 3 more

NCBI tax ID(s) 483216 28111

Special Collections DSMZ CCUG JCM CIP

History DSMZ <- NCTC; NCTC 11155 <- ATCC; ATCC 27754 <- L. V. Holdeman; VPI T5-42B-1 JCM <-- CCUG 9559 <-- NCTC 11155 <-- ATCC 27754 <-- L. V. Holdeman VPI T5-42B-1. CIP <- 1994, J.P. Carlier, Inst. Pasteur, Paris, France: strain 10128 <- NCTC <- ATCC <- L.V. Holdeman: strain VPI T5-42B-1

Links

Bacteroides eggerthii 10128 is an anaerobe bacterium that was isolated from human faeces.

anaerobe genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 125761

ATCC 27754,NCTC 11155,CCUG 9559,CIP 104285,DSM 20697,JCM 12986,KCTC 5122,VTT E-093118

@ref 20215

Last LPSN update 2026-05-29 08:25:17

Domain Bacteria

Phylum Bacteroidota

Class Bacteroidia

Order Bacteroidales

Family Bacteroidaceae

Genus Bacteroides

Species Bacteroides eggerthii

Full scientific name Bacteroides eggerthii Holdeman and Moore 1974 (Approved Lists 1980)

BacDive ID	Other strains from **Bacteroides eggerthii** (1)	Type strain
158880	B. eggerthii WCA3-601-WT-5E, DSM 107245

Morphology

Cell morphology

@ref	Gram stain	Confidence
125438	negative	94.865
125439	negative	97.503

Colony morphology

@ref	Type of hemolysis	Hemolysis ability	Incubation period
9017	gamma	0	1-2 days

Culture and growth conditions

Culture medium

@ref	Name	Medium link	Composition
9017	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
9017	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
9017	PYG MEDIUM (MODIFIED) (DSMZ Medium 104)	Medium recipe at MediaDive	Name: PYG MEDIUM (modified) (DSMZ Medium 104) Composition: Yeast extract 10.0 g/l Peptone 5.0 g/l Trypticase peptone 5.0 g/l Beef extract 5.0 g/l Glucose 5.0 g/l L-Cysteine HCl x H2O 0.5 g/l NaHCO3 0.4 g/l NaCl 0.08 g/l K2HPO4 0.04 g/l KH2PO4 0.04 g/l MgSO4 x 7 H2O 0.02 g/l CaCl2 x 2 H2O 0.01 g/l Hemin 0.005 g/l Ethanol 0.0038 g/l Resazurin 0.001 g/l Tween 80 Vitamin K1 NaOH Distilled water
41096	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)
118999	CIP Medium 20	Medium recipe at CIP

Culture temp

@ref	Growth	Type	Temperature (°C)
9017	positive	growth	37
41096	positive	growth	37
45195	positive	growth	37
67770	positive	growth	37

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
9017	anaerobe
45195	anaerobe
125439	obligate anaerobe	99.868

Spore formation

@ref	Spore formation	Confidence
125439		99.975
125438		92.479

Observation

67770

Observationquinones: MK-10, MK-11

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
68381	40585 ChEBI	alpha-cyclodextrin	+	builds acid from	from API rID32STR
68381	29016 ChEBI	arginine	-	hydrolysis	from API rID32STR
68380	29016 ChEBI	arginine	-	hydrolysis	from API rID32A
68381	18333 ChEBI	D-arabitol	-	builds acid from	from API rID32STR
68381	16899 ChEBI	D-mannitol	-	builds acid from	from API rID32STR
68380	16024 ChEBI	D-mannose	+	fermentation	from API rID32A
68381	16988 ChEBI	D-ribose	-	builds acid from	from API rID32STR
68381	16443 ChEBI	D-tagatose	-	builds acid from	from API rID32STR
68381	28087 ChEBI	glycogen	+	builds acid from	from API rID32STR
68381	606565 ChEBI	hippurate	-	hydrolysis	from API rID32STR
68381	30849 ChEBI	L-arabinose	+	builds acid from	from API rID32STR
68380	29985 ChEBI	L-glutamate	+	degradation	from API rID32A
68381	17716 ChEBI	lactose	+	builds acid from	from API rID32STR
68381	17306 ChEBI	maltose	+	builds acid from	from API rID32STR
68381	6731 ChEBI	melezitose	-	builds acid from	from API rID32STR
68381	28053 ChEBI	melibiose	-	builds acid from	from API rID32STR
68381	320055 ChEBI	methyl beta-D-glucopyranoside	-	builds acid from	from API rID32STR
68380	17632 ChEBI	nitrate	-	reduction	from API rID32A
68381	27941 ChEBI	pullulan	+	builds acid from	from API rID32STR
68381	16634 ChEBI	raffinose	-	builds acid from	from API rID32STR
68380	16634 ChEBI	raffinose	-	fermentation	from API rID32A
68381	30911 ChEBI	sorbitol	-	builds acid from	from API rID32STR
68381	17992 ChEBI	sucrose	-	builds acid from	from API rID32STR
68381	27082 ChEBI	trehalose	-	builds acid from	from API rID32STR
68380	27897 ChEBI	tryptophan	+	energy source	from API rID32A
68381	16199 ChEBI	urea	-	hydrolysis	from API rID32STR
68380	16199 ChEBI	urea	-	hydrolysis	from API rID32A

Metabolite production

@ref	Chebi-ID	Metabolite	Production
68381	15688 ChEBI	acetoin		from API rID32STR
68380	35581 ChEBI	indole		from API rID32A

Metabolite tests

@ref	Chebi-ID	Metabolite	Voges-proskauer-test	Indole test
68381	15688 ChEBI	acetoin	-		from API rID32STR
68380	35581 ChEBI	indole		+	from API rID32A

Enzymes

@ref	Value	Activity	Ec
68380	alanine arylamidase	+	3.4.11.2	from API rID32A
68381	Alanyl-Phenylalanyl-Proline arylamidase	+		from API rID32STR
68380	alkaline phosphatase	+	3.1.3.1	from API rID32A
68381	alkaline phosphatase	+	3.1.3.1	from API rID32STR
68380	alpha-arabinosidase	+	3.2.1.55	from API rID32A
68380	alpha-fucosidase	-	3.2.1.51	from API rID32A
68381	alpha-galactosidase	+	3.2.1.22	from API rID32STR
68380	alpha-galactosidase	-	3.2.1.22	from API rID32A
68380	alpha-glucosidase	+	3.2.1.20	from API rID32A
68381	arginine dihydrolase	-	3.5.3.6	from API rID32STR
68380	arginine dihydrolase	-	3.5.3.6	from API rID32A
68380	beta-galactosidase	+	3.2.1.23	from API rID32A
68381	beta-galactosidase	+	3.2.1.23	from API rID32STR
68380	beta-Galactosidase 6-phosphate	-		from API rID32A
68381	beta-glucosidase	+	3.2.1.21	from API rID32STR
68381	beta-glucuronidase	-	3.2.1.31	from API rID32STR
68380	beta-glucuronidase	-	3.2.1.31	from API rID32A
68381	beta-mannosidase	-	3.2.1.25	from API rID32STR
68380	glutamate decarboxylase	+	4.1.1.15	from API rID32A
68380	glutamyl-glutamate arylamidase	+		from API rID32A
68380	glycin arylamidase	-		from API rID32A
68381	glycyl tryptophan arylamidase	+		from API rID32STR
68380	histidine 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	phenylalanine arylamidase	-		from API rID32A
68380	proline-arylamidase	-	3.4.11.5	from API rID32A
68381	pyrrolidonyl arylamidase	-	3.4.19.3	from API rID32STR
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	tyrosine arylamidase	-		from API rID32A
68380	urease	-	3.5.1.5	from API rID32A
68381	urease	-	3.5.1.5	from API rID32STR

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
9017	-	-	-	+	-	+	-	+	-	+	+	-	+	-	-	+	+	-	-	+	-	-	-	-	+	-	-	+	-
9017	-	-	-	+	-	+	+	+	-	+	+	-	+	-	-	+	+	-	-	+	-	-	-	-	+	-	-	+	-

API rID32STR

@ref	ADH (Arg)	beta GLU	beta GAR	beta GUR	alpha GAL	PAL	RIB	MAN	SOR	LAC	TRE	RAF	SAC	LARA	DARL	Acid from alpha-cyclodextrinCDEX	Acetoin production (Voges Proskauer test)VP	Alanyl-Phenylalanyl-Proline arylamidaseAPPA	beta GAL	Pyrrolidonyl arylamidasePyrA	N-Acetyl-glucosaminidasebeta NAG	Glycyl-tryptophan arylamidaseGTA	HIP	GLYG	PUL	MAL	MEL	MLZ	Acidification of methyl beta-D-glucopyranosideMbeta DG	TAG	beta MAN	URE
9017	-	+	+	-	+	+	-	-	-	+	-	-	-	+	-	+	-	+	+	-	+/-	+	-	+	+	+	-	-	-	-	-	-

Isolation, sampling and environmental information

Isolation source categories

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

Isolation

@ref	Sample type	Host species	Sampling date	Isolation date
9017	human faeces	Homo sapiens
45195	Human feces	Homo sapiens	1972
67770	Human feces	Homo sapiens
118999	Human, Feces	Homo sapiens		1972

Taxonmaps

69479

Global distribution of 16S sequence AB510700 (>99% sequence identity) for Bacteroides eggerthii subclade from Microbeatlas

Aquatic Samples	9244
Soil Samples	2463
Animal Samples	163124
Plant Samples	713
Total Samples	175544

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
9017	2	Risk group (German classification) According to TRBA 466
118999	2	Risk group (French 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	ASM2514656v1 assembly for Bacteroides eggerthii DSM 20697	complete	GCA_025146565	28111.542	8119477866	28111	97.3
66792	48853_E02 assembly for Bacteroides eggerthii NCTC11155	contig	GCA_900445565	28111.20	2811995250	28111	76.87
67770	ASM15581v1 assembly for Bacteroides eggerthii DSM 20697	scaffold	GCA_000155815	483216.6	642979334	483216	64.49

16S sequences

@ref	Description	Accession	Length	NCBI tax ID
20218	Bacteroides eggerthii 16S-23S rDNA intergenic spacer region	AF176690	378	483216
9017	Bacteroides eggerthii gene for 16S rRNA, partial sequence	AB050107	1425	483216
67770	Bacteroides eggerthii gene for 16S ribosomal RNA, partial sequence, strain: JCM 12986	AB510700	1488	28111
124043	Bacteroides eggerthii strain JCM12986 16S ribosomal RNA gene, partial sequence.	EU136695	1991	28111

GC content

@ref	GC-content (mol%)	Method
9017	46.0	thermal denaturation, midpoint method (Tm)
9017	44.6	sequence analysis
67770	44.2	high performance liquid chromatography (HPLC)

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: ASM2514656v1 assembly for Bacteroides eggerthii DSM 20697
BV-BRC: 28111.542

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	oxygen_tolerance	BacteriaNetⓘ	obligate anaerobe	99.87	no
125439	gram_stain	BacteriaNetⓘ	negative	97.50	no
125439	motility	BacteriaNetⓘ	no	85.36	no
125439	spore_formation	BacteriaNetⓘ	no	99.98	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Bacteroides eggerthii DSM 20697
NCBI: GCA_025146565.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	94.87	no
125438	anaerobic	anaerobicⓘ	yes	89.74	no
125438	aerobic	aerobicⓘ	no	92.64	yes
125438	spore-forming	spore-formingⓘ	no	92.48	no
125438	thermophilic	thermophileⓘ	no	95.77	yes
125438	flagellated	motile2+ⓘ	no	89.00	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Pathogenicity	Hepatoprotective Potential of Bacteroides eggerthii on Fatty Liver Disease: A Mouse Model Study.	Chen LW, Wu IW, Cheng TC, Chang LC, Hsu CK, Yeung L, Chang LC, Su SC.	In Vivo	10.21873/invivo.14122	2025
Enzymology	Action and cooperation in alginate degradation by three enzymes from the human gut bacterium Bacteroides eggerthii DSM 20697.	Ronne ME, Dybdahl Andersen C, Teze D, Petersen AB, Fredslund F, Stender EGP, Chaberski EK, Holck J, Aachmann FL, Welner DH, Svensson B.	J Biol Chem	10.1016/j.jbc.2024.107596	2024
	A Porphyromonas gingivalis hypothetical protein controlled by the type I-C CRISPR-Cas system is a novel adhesin important in virulence.	Irfan M, Solbiati J, Duran-Pinedo A, Rocha FG, Gibson FC, Frias-Lopez J.	mSystems	10.1128/msystems.01231-23	2024
	When simplicity triumphs: niche specialization of gut bacteria exists even for simple fiber structures.	Xu H, Pudlo NA, Cantu-Jungles TM, Tuncil YE, Nie X, Kaur A, Reuhs BL, Martens EC, Hamaker BR.	ISME Commun	10.1093/ismeco/ycae037	2024
	Non-targeted metabolomics and microbial analyses of the impact of oat antimicrobial peptides on rats with dextran sulfate sodium-induced enteritis.	Wang H, Xie L, Liu S, Dai A, Chi X, Zhang D.	Front Nutr	10.3389/fnut.2022.1095483	2022
	Mapping the T cell repertoire to a complex gut bacterial community.	Nagashima K, Zhao A, Atabakhsh K, Bae M, Blum JE, Weakley A, Jain S, Meng X, Cheng AG, Wang M, Higginbottom S, Dimas A, Murugkar P, Sattely ES, Moon JJ, Balskus EP, Fischbach MA.	Nature	10.1038/s41586-023-06431-8	2023
	Comparison of the gut microbiota in older people with and without sarcopenia: a systematic review and meta-analysis.	Ren Y, He X, Wang L, Chen N.	Front Cell Infect Microbiol	10.3389/fcimb.2025.1480293	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
	Heterologous expression and antimicrobial potential of class II bacteriocins.	Elisa Heesemann Rosenkilde C, Olsen Lutzhoft D, Vazquez-Uribe R, Otto Alexander Sommer M.	Gut Microbes	10.1080/19490976.2024.2369338	2024
	Investigation on L-rhamnose metabolism of Loigolactobacillus coryniformis subsp. coryniformis DSM 20001 and its propionate-containing fermentates.	Elvan Gezer M, Gravlund Fonss K, Bambace MF, Marietou A, Sandberg Overby S, Sundekilde U, Schwab C.	Appl Environ Microbiol	10.1128/aem.01613-24	2025
	Early modifications of the gut microbiome in children with hepatic sinusoidal obstruction syndrome after hematopoietic stem cell transplantation.	Masetti R, Biagi E, Zama D, Muratore E, D'Amico F, Leardini D, Turroni S, Prete A, Brigidi P, Pession A.	Sci Rep	10.1038/s41598-021-93571-4	2021
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
Enzymology	Diversity and abundance of single-stranded DNA viruses in human feces.	Kim MS, Park EJ, Roh SW, Bae JW.	Appl Environ Microbiol	10.1128/aem.06331-11	2011
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
	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	Ancient acquisition of "alginate utilization loci" by human gut microbiota.	Mathieu S, Touvrey-Loiodice M, Poulet L, Drouillard S, Vincentelli R, Henrissat B, Skjak-Braek G, Helbert W.	Sci Rep	10.1038/s41598-018-26104-1	2018
Metabolism	Two new xylanases with different substrate specificities from the human gut bacterium Bacteroides intestinalis DSM 17393.	Hong PY, Iakiviak M, Dodd D, Zhang M, Mackie RI, Cann I.	Appl Environ Microbiol	10.1128/aem.03176-13	2014
	Illuminating vital surface molecules of symbionts in health and disease.	Hudak JE, Alvarez D, Skelly A, von Andrian UH, Kasper DL.	Nat Microbiol	10.1038/nmicrobiol.2017.99	2017
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
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	Strain dropouts reveal interactions that govern the metabolic output of the gut microbiome.	Wang M, Osborn LJ, Jain S, Meng X, Weakley A, Yan J, Massey WJ, Varadharajan V, Horak A, Banerjee R, Allende DS, Chan ER, Hajjar AM, Wang Z, Dimas A, Zhao A, Nagashima K, Cheng AG, Higginbottom S, Hazen SL, Brown JM, Fischbach MA.	Cell	10.1016/j.cell.2023.05.037	2023
	Eukaryote to gut bacteria transfer of a glycoside hydrolase gene essential for starch breakdown in plants.	Arias MC, Danchin EG, Coutinho P, Henrissat B, Ball S.	Mob Genet Elements	10.4161/mge.20375	2012
Enzymology	Xylan utilization in human gut commensal bacteria is orchestrated by unique modular organization of polysaccharide-degrading enzymes.	Zhang M, Chekan JR, Dodd D, Hong PY, Radlinski L, Revindran V, Nair SK, Mackie RI, Cann I.	Proc Natl Acad Sci U S A	10.1073/pnas.1406156111	2014
Metabolism	Diversity and abundance of phosphonate biosynthetic genes in nature.	Yu X, Doroghazi JR, Janga SC, Zhang JK, Circello B, Griffin BM, Labeda DP, Metcalf WW.	Proc Natl Acad Sci U S A	10.1073/pnas.1315107110	2013
Metabolism	Optimized Production of Xylitol from Xylose Using a Hyper-Acidophilic Candida tropicalis.	Tamburini E, Costa S, Marchetti MG, Pedrini P.	Biomolecules	10.3390/biom5031979	2015
	The prevalence of species and strains in the human microbiome: a resource for experimental efforts.	Kraal L, Abubucker S, Kota K, Fischbach MA, Mitreva M.	PLoS One	10.1371/journal.pone.0097279	2014
Metabolism	Polysaccharides utilization in human gut bacterium Bacteroides thetaiotaomicron: comparative genomics reconstruction of metabolic and regulatory networks.	Ravcheev DA, Godzik A, Osterman AL, Rodionov DA.	BMC Genomics	10.1186/1471-2164-14-873	2013
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
Metabolism	Purification and characterization of phosphonoglycans from Glycomyces sp. strain NRRL B-16210 and Stackebrandtia nassauensis NRRL B-16338.	Yu X, Price NP, Evans BS, Metcalf WW.	J Bacteriol	10.1128/jb.00036-14	2014
Metabolism	Crystal structures of three representatives of a new Pfam family PF14869 (DUF4488) suggest they function in sugar binding/uptake.	Kumar A, Punta M, Axelrod HL, Das D, Farr CL, Grant JC, Chiu HJ, Miller MD, Coggill PC, Klock HE, Elsliger MA, Deacon AM, Godzik A, Lesley SA, Wilson IA.	Protein Sci	10.1002/pro.2522	2014
Metabolism	Functional metagenomics to mine the human gut microbiome for dietary fiber catabolic enzymes.	Tasse L, Bercovici J, Pizzut-Serin S, Robe P, Tap J, Klopp C, Cantarel BL, Coutinho PM, Henrissat B, Leclerc M, Dore J, Monsan P, Remaud-Simeon M, Potocki-Veronese G.	Genome Res	10.1101/gr.108332.110	2010
Metabolism	Structural and sequence analysis of imelysin-like proteins implicated in bacterial iron uptake.	Xu Q, Rawlings ND, Farr CL, Chiu HJ, Grant JC, Jaroszewski L, Klock HE, Knuth MW, Miller MD, Weekes D, Elsliger MA, Deacon AM, Godzik A, Lesley SA, Wilson IA.	PLoS One	10.1371/journal.pone.0021875	2011
Metabolism	Biochemical analysis of a beta-D-xylosidase and a bifunctional xylanase-ferulic acid esterase from a xylanolytic gene cluster in Prevotella ruminicola 23.	Dodd D, Kocherginskaya SA, Spies MA, Beery KE, Abbas CA, Mackie RI, Cann IK.	J Bacteriol	10.1128/jb.01628-08	2009
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, construction, and in vivo augmentation of a complex gut microbiome.	Cheng AG, Ho PY, Aranda-Diaz A, Jain S, Yu FB, Meng X, Wang M, Iakiviak M, Nagashima K, Zhao A, Murugkar P, Patil A, Atabakhsh K, Weakley A, Yan J, Brumbaugh AR, Higginbottom S, Dimas A, Shiver AL, Deutschbauer A, Neff N, Sonnenburg JL, Huang KC, Fischbach MA.	Cell	10.1016/j.cell.2022.08.003	2022
	Type VI secretion systems of human gut Bacteroidales segregate into three genetic architectures, two of which are contained on mobile genetic elements.	Coyne MJ, Roelofs KG, Comstock LE.	BMC Genomics	10.1186/s12864-016-2377-z	2016
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
	Microviridae goes temperate: microvirus-related proviruses reside in the genomes of Bacteroidetes.	Krupovic M, Forterre P.	PLoS One	10.1371/journal.pone.0019893	2011
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
Enzymology	Variations of bacterial populations in human feces measured by fluorescent in situ hybridization with group-specific 16S rRNA-targeted oligonucleotide probes.	Franks AH, Harmsen HJ, Raangs GC, Jansen GJ, Schut F, Welling GW.	Appl Environ Microbiol	10.1128/aem.64.9.3336-3345.1998	1998
Enzymology	Domain analysis of a modular alpha-L-Arabinofuranosidase with a unique carbohydrate binding strategy from the fiber-degrading bacterium Fibrobacter succinogenes S85.	Yoshida S, Hespen CW, Beverly RL, Mackie RI, Cann IK.	J Bacteriol	10.1128/jb.00503-10	2010
Metabolism	Purification and characterization of brochocin A and brochocin B(10-43), a functional fragment generated by heterologous expression in Carnobacterium piscicola.	Garneau S, Ference CA, van Belkum MJ, Stiles ME, Vederas JC.	Appl Environ Microbiol	10.1128/aem.69.3.1352-1358.2003	2003
Metabolism	Transcriptomic analyses of xylan degradation by Prevotella bryantii and insights into energy acquisition by xylanolytic bacteroidetes.	Dodd D, Moon YH, Swaminathan K, Mackie RI, Cann IK.	J Biol Chem	10.1074/jbc.m110.141788	2010
Metabolism	Structure, Assembly, and Function of Tripartite Efflux and Type 1 Secretion Systems in Gram-Negative Bacteria.	Alav I, Kobylka J, Kuth MS, Pos KM, Picard M, Blair JMA, Bavro VN.	Chem Rev	10.1021/acs.chemrev.1c00055	2021
Pathogenicity	In Vitro and In Vivo Activities of DS-2969b, a Novel GyrB Inhibitor, against Clostridium difficile.	Mathur T, Barman TK, Kumar M, Singh D, Kumar R, Khera MK, Yamada M, Inoue SI, Upadhyay DJ, Masuda N.	Antimicrob Agents Chemother	10.1128/aac.02157-17	2018
	Genetic Manipulation of Wild Human Gut Bacteroides.	Bencivenga-Barry NA, Lim B, Herrera CM, Trent MS, Goodman AL.	J Bacteriol	10.1128/jb.00544-19	2020
Pathogenicity	In vitro activity of tomopenem (CS-023/RO4908463) against anaerobic bacteria.	Tanaka K, Mikamo H, Nakao K, Ichiishi T, Goto T, Yamagishi Y, Watanabe K.	Antimicrob Agents Chemother	10.1128/aac.00595-08	2009
Pathogenicity	In vitro antimicrobial activity of razupenem (SMP-601, PTZ601) against anaerobic bacteria.	Tran CM, Tanaka K, Yamagishi Y, Goto T, Mikamo H, Watanabe K.	Antimicrob Agents Chemother	10.1128/aac.01038-10	2011
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
Enzymology	pH gradient and distribution of streptococci, lactobacilli, prevotellae, and fusobacteria in carious dentine.	Kianoush N, Nguyen KA, Browne GV, Simonian M, Hunter N.	Clin Oral Investig	10.1007/s00784-013-1009-0	2014
Pathogenicity	In vitro antianaerobic activity of DX-619, a new des-fluoro(6) quinolone.	Tanaka K, Mikamo H, Nakao K, Watanabe K.	Antimicrob Agents Chemother	10.1128/aac.00639-06	2006
Enzymology	Quantification of bacterial groups within human fecal flora by oligonucleotide probe hybridization.	Sghir A, Gramet G, Suau A, Rochet V, Pochart P, Dore J.	Appl Environ Microbiol	10.1128/aem.66.5.2263-2266.2000	2000
Phylogeny	Use of PCR and sodium dodecyl sulfate-polyacrylamide gel electrophoresis techniques for differentiation of Prevotella intermedia sensu stricto and Prevotella nigrescens.	Premaraj T, Kato N, Fukui K, Kato H, Watanabe K.	J Clin Microbiol	10.1128/jcm.37.4.1057-1061.1999	1999
Phylogeny	Development of cpn60-based real-time quantitative PCR assays for the detection of 14 Campylobacter species and application to screening of canine fecal samples.	Chaban B, Musil KM, Himsworth CG, Hill JE.	Appl Environ Microbiol	10.1128/aem.00101-09	2009
	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
	Bacteroides eggerthii Ameliorates MASLD through Host-Microbe Signaling and Highlights 2-Hydroxyisocaproate as a Potential Effector.	Choi J, Yoon MG, Jang SH, Baek GO, Jung HS, Lee NR, Lee CH, Han JE, Cheong JY, Eun JW, Kim SS.	Clin Mol Hepatol	10.3350/cmh.2025.0475	2025
	Causal effects of gut microbiome on aortic dissection: A mendelian randomization study.	Tian Y, Hao F, Xu G, Qian Y, Liu J, Pan N, Yang T.	Clinics (Sao Paulo)	10.1016/j.clinsp.2025.100811	2025
Phylogeny	Fecal microbiome associated with egg production efficiency in laying hens.	Chen JW, Wang SY, Yang WY.	Anim Biosci	10.5713/ab.25.0256	2025
	Screening of Fecal Bacteroides Strains and Discovery of Bacteroides eggerthii S13-F8 with Protective Effects Against Chemotherapy-Induced Diarrhea.	Zhao Y, Dai Z, Lang Y, Li R, Zheng H, Mi J, He X, Liu J, Xiang R, Mei X, Liu Y, Wang Y, Guo H, Yang Q, Ren K, Yang T.	Probiotics Antimicrob Proteins	10.1007/s12602-025-10595-2	2025
Pathogenicity	The Role of 473 Intestinal Microbiota and 91 Inflammatory Factors in Breast Cancer Risk: Insights From Mendel Randomization and its Implications for Diagnosis and Treatment.	Zhu R, Qiu J, Xian D, Yang K.	Clin Breast Cancer	10.1016/j.clbc.2025.06.001	2025
	The human gut Bacteroides eggerthii expresses a new galactofuranose-containing lipooligosaccharide with weak immunostimulatory properties	Tiemblo Martin M, Coccimiglio M, Andretta E, De Simone Carone L, Bell A, Gerpe-Amor T, Di Carluccio C, Molinaro A, van Kooyk Y, Juge N, Chiodo F, Di Lorenzo F, Silipo A.	Carbohydrate polymers.		2025
	The human gut Bacteroides eggerthii expresses a new galactofuranose-containing lipooligosaccharide with weak immunostimulatory properties.	Tiemblo Martin M, Coccimiglio M, Andretta E, De Simone Carone L, Bell A, Gerpe-Amor T, Di Carluccio C, Molinaro A, van Kooyk Y, Juge N, Chiodo F, Di Lorenzo F, Silipo A.	Carbohydr Polym	10.1016/j.carbpol.2024.122833	2025
Pathogenicity	Gut microbiota alterations and their association with tumorigenic pathways in colorectal cancer: insights from a pooled analysis of 109 microbiome datasets.	Haque S, Bantun F, Jalal NA, Faidah H, Babalghith AO, Alobaidy MA, Aldairi AF, Ahmad F.	Gut Pathog	10.1186/s13099-025-00712-5	2025
	Maillard conjugates of whey protein isolate and gum Arabic: Enhanced functional properties and unique gut microbiota regulation	Kan X, Zhang K, Fan X, Chen L, Zeng X.	Food hydrocolloids.		2024
	Analysis of Gut Microbiota and Their Metabolites in CADASIL Patients.	Watanabe-Hosomi A, Inoue R, Mizuta I, Matsuura J, Matsuura H, Fukunaga D, Ohara T, Naito Y, Mizuno T.	J Clin Neurol	10.3988/jcn.2025.0231	2025
	Mediators linking gut microbiota and sporadic Creutzfeldt-Jakob disease: a Mendelian randomization study.	Shao J, Su T, Wang J, Yin X, Lang Y, Fu Y, Cui L.	AMB Express	10.1186/s13568-025-01932-3	2025
	Exploring the Interplay Between Gut Microbiota and the Melatonergic Pathway in Hormone Receptor-Positive Breast Cancer.	Laborda-Illanes A, Boutriq S, Aranega-Martin L, Castellano-Castillo D, Sanchez-Alcoholado L, Plaza-Andrades I, Peralta-Linero J, Alba E, Fernandez-Garcia JC, Gonzalez-Gonzalez A, Queipo-Ortuno MI.	Int J Mol Sci	10.3390/ijms26146801	2025
	[Faecal microbiota study reveals specific dysbiosis in spondyloarthritis according to subtype, disease activity and treatment].	Romero-Sanchez C, Ferrer-Santos C, Abril D, Acosta-Hernandez E, Avila J, Ramos-Casallas A, Escobar J, Bautista-Molano W, Jaimes D, Beltran-Ostos A, Bello-Gualtero JM, Florez-Sarmiento C, Parra-Izquierdo V, Calixto OJ.	Rev Alerg Mex	10.29262/ram.v71i1.1305	2024
Transcriptome	Microbiota Alters and Its Correlation with Molecular Regulation Underlying Depression in PCOS Patients.	Yu L, Chen X, Bai X, Fang J, Sui M.	Mol Neurobiol	10.1007/s12035-023-03744-7	2024
	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
	Gut microbiota characterization in ageing, mild cognitive impairment, and Alzheimer's disease in the context of mediterranean lifestyle in a Spanish population.	Cabrera C, Carrion N, Mateo D, Vicens P, Pinzon A, Heredia L, Forcadell-Ferreres E, Pino M, Yerga B, Zaragoza J, Vicente-Pascual M, Moral A, Arco T, Arjo M, Martinez E, Galvez S, Lozano MJ, Torrente M.	Alzheimers Res Ther	10.1186/s13195-025-01862-z	2025
	Exploring the role of acylated ghrelin and gut microbiome in delineating cognitive health in the elderly.	Rout S, Dash R, Satish V, Venugopal G, Rao BN, Bandhyopadhyay D, Bhoi SK, Ramadass B.	Aging (Albany NY)	10.18632/aging.206200	2025
	Assessment of ecological fidelity of human microbiome-associated mice in observational studies and an interventional trial.	Wong MK, Armstrong E, Heirali AA, Schneeberger PHH, Chen H, Cochrane K, Sherriff K, Allen-Vercoe E, Siu LL, Spreafico A, Coburn B.	mBio	10.1128/mbio.01904-25	2025
	Modulation of Gut Microbiota by Whole Encapsulated Brown Seaweed (Himanthalia elongata) in Overweight Subjects: A Randomized Double-Blind Placebo-Controlled Trial.	Lopez-Santamarina A, Cardelle-Cobas A, Mondragon ADC, Cepeda A, Rodriguez JA, Miranda JM.	Nutrients	10.3390/nu17122047	2025
	Red meat consumption in higher healthy eating index diets is associated with brain health critical nutritional adequacy, and fecal microbial diversity.	Dhakal S, Hossain M, Parajuli S.	Sci Rep	10.1038/s41598-025-18907-w	2025
Phylogeny	Exploring the Intestinal Microbiota Profile in Prostate Cancer Patients and Healthy Controls.	Cocomazzi G, Villani A, Mencarelli G, Contu V, De Ruvo D, Virgili E, Marino F, Baldini GM, Binda E, Parmegiani L, Ciampaglia W, Capone L, Perri F, Cisternino A, Pazienza V, Panebianco C.	Microorganisms	10.3390/microorganisms13092105	2025
	Circulating Inflammatory Proteins Mediate the Causal Effect of Gut Microbiota on Inflammatory Bowel Disease: Bayesian and Mediated Mendelian Randomization.	Li Z, Jia L, Huai S.	FASEB Bioadv	10.1096/fba.2025-00114	2025
	The gut microbiome and Alopecia areata: Implications for early diagnostic biomarkers and novel therapies.	Kang Y, Cai Y, Zhao Y, Yang Y.	Front Nutr	10.3389/fnut.2022.979876	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
	Multi-omics assessment of gut microbiota in circadian rhythm disorders: a cross-sectional clinical study.	Tian Y, Zhao R, Xiao S, Chen L, Cheng Y, Meng W, Tang Z, Cai Y, Xiao Z, Yi A, Chen M, Zhao X, Ruan G, Wei Y.	Front Cell Infect Microbiol	10.3389/fcimb.2025.1524987	2025
	¹H, ¹³C, ¹⁵N resonance assignment of the enzyme KdgF from Bacteroides eggerthii.	Petersen AB, Christensen IA, Ronne ME, Stender EGP, Teze D, Svensson B, Aachmann FL.	Biomol NMR Assign	10.1007/s12104-022-10102-6	2022
	The Bacterial Composition of the Gut Microbiota of Mexicans with Overweight and Obesity: A Systematic Review	Samudio-Cruz M, Luna-Angulo A, Cabrera-Ruiz E, Landa-Solis C, Rangel-Lopez E, Carrillo-Mora P, Rios-Martinez J, Toledo-Perez R, Paniagua-Perez R, Martinez-Canseco C, Lino-Gonzalez A, Saldana Solano A, Sanchez-Chapul L.	Microorganisms		2025
Phylogeny	Peritonitis with bacteremia due to Christensenella hongkongensis identified via ribosomal RNA sequencing in a Japanese patient with advanced colorectal adenocarcinoma: A case report.	Itoh N, Akazawa N, Ishibana Y, Murakami H.	IDCases	10.1016/j.idcr.2023.e01797	2023
	Safety, Tolerability, and Immunogenicity of a DNA Vaccine (pGX9501) Against SARS-CoV-2 in Healthy Volunteers: A Single-Center, Randomized, Double-Blind, Placebo-Controlled, and Dose-Ranging Phase I Trial.	Yang H, Zhou Y, Cheng X, Qiu C, Wang S, Xia Y, Huai X, Xiu Z, Wang J, He Y, Cao G, Wei Q, Wang J, Ai J, Zhang H, Zhang Y, Zhang J, Zhang W, Wang B.	Vaccines (Basel)	10.3390/vaccines13060573	2025
	Systematic review of bidirectional interaction between gut microbiome, miRNAs, and human pathologies.	Drago L, De La Motte LR, Deflorio L, Sansico DF, Salvatici M, Micaglio E, Biazzo M, Giarritiello F.	Front Microbiol	10.3389/fmicb.2025.1540943	2025
	The Efficacy of Cheonggukjang in Alleviating Menopausal Syndrome and Its Effects on the Gut Microbiome: A Randomized, Double-Blind Trial.	Han AL, Ryu MS, Yang HJ, Jeong DY, Choi KH.	Nutrients	10.3390/nu17030505	2025
	The Predictive Value of Gut Microbiota Composition for Sustained Immunogenicity following Two Doses of CoronaVac.	Ng HY, Liao Y, Zhang R, Chan KH, To WP, Hui CH, Seto WK, Leung WK, Hung IFN, Lam TTY, Cheung KS.	Int J Mol Sci	10.3390/ijms25052583	2024
	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
	Inflammatory Manifestations Associated With Gut Dysbiosis in Alzheimer's Disease.	Kozhakhmetov S, Kaiyrlykyzy A, Jarmukhanov Z, Vinogradova E, Zholdasbekova G, Alzhanova D, Kunz J, Kushugulova A, Askarova S.	Int J Alzheimers Dis	10.1155/2024/9741811	2024
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
	Concomitant decrease of double-positive lymphocyte population CD4CD8alphaalpha and Faecalibacterium prausnitzii in patients with colorectal cancer.	Touchefeu Y, Duchalais E, Bruley des Varannes S, Alameddine J, Mirallie E, Matysiak-Budnik T, Le Bastard Q, Javaudin F, Rimbert M, Jotereau F, Montassier E.	Eur J Gastroenterol Hepatol	10.1097/meg.0000000000001842	2021
	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
	Gut microbiota influences lung cancer risk through circulating cytokines-Insights from a Mendelian randomization study.	Shen W, Hou R, Zhang J, Liu C, Zhang C, Liu X.	Medicine (Baltimore)	10.1097/md.0000000000044897	2025
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
	Age-related Eye Disease Studies Supplements and Genetic Risk Score Are Crucial Determinants of Intestinal Microbial Alterations in Advanced Age-Related Macular Degeneration.	Dadgar N, Fung K, McClintic S, Metea C, Llorenc V, Saleh M, Nakamura YK, Jahrig C, Kiang L, Janowitz C, Davin S, Balter A, Le Cao KA, Karstens L, Martin TM, Klein ML, Lin P.	Ophthalmol Sci	10.1016/j.xops.2025.100920	2026
	Analysis of the gut microbiota in alopecia areata: identification of bacterial biomarkers.	Moreno-Arrones OM, Serrano-Villar S, Perez-Brocal V, Saceda-Corralo D, Morales-Raya C, Rodrigues-Barata R, Moya A, Jaen-Olasolo P, Vano-Galvan S.	J Eur Acad Dermatol Venereol	10.1111/jdv.15885	2020
Genetics	Alterations of Gut Microbiome in Patients with Colorectal Advanced Adenoma by Metagenomic Analyses.	Xiang J, Chai N, Li L, Hao X, Linghu E.	Turk J Gastroenterol	10.5152/tjg.2024.24294	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
	Identifying microbial signatures for patients with postmenopausal osteoporosis using gut microbiota analyses and feature selection approaches.	Huang D, Wang J, Zeng Y, Li Q, Wang Y.	Front Microbiol	10.3389/fmicb.2023.1113174	2023
	Gut microbiome and metabolome profiles in renal allograft rejection from multiomics integration.	Dai X, Cao Y, Li L, Gao Y-X, Wang J-X, Liu Y-J, Ma T-T, Zheng J-M, Zhan P-P, Shen Z-Y.	mSystems	10.1128/msystems.01626-24	2025
	Microbial Ecosystem Therapeutics 4 (MET4) elicits treatment-specific IgG responses associated with changes in gut microbiota in immune checkpoint inhibitor recipients with advanced solid tumors.	Wong MK, Boukhaled GM, Armstrong E, Liu R, Heirali AA, Yee NR, Tsang J, Spiliopoulou P, Schneeberger PHH, Wang BX, Cochrane K, Sherriff K, Allen-Vercoe E, Siu LL, Spreafico A, Coburn B.	J Immunother Cancer	10.1136/jitc-2024-010681	2025
Genetics	Infectious Keratitis: Characterization of Microbial Diversity through Species Richness and Shannon Diversity Index.	Schiano-Lomoriello D, Abicca I, Contento L, Gabrielli F, Alfonsi C, Di Pietro F, Papa FT, Ballesteros-Sanchez A, Sanchez-Gonzalez JM, Rocha-De-Lossada C, Mazzotta C, Giannaccare G, Bonzano C, Borroni D.	Biomolecules	10.3390/biom14040389	2024
	Dietary therapy of murine primary biliary cholangitis induces hepatocellular steatosis: A cautionary tale.	Zhang W, Al Tekreeti T, Leung PSC, Tsuneyama K, Dhillon H, Rojas M, Heuer LS, Ridgway WM, Ansari AA, Young HA, Mackay CR, Gershwin ME.	Liver Int	10.1111/liv.16060	2024
	Fecal Microbiota Transplantation Induces Sustained Gut Microbiome Changes in Pediatric Ulcerative Colitis: A Combined Randomized and Open-Label Study.	Le J, Hakimjavadi H, Parsana R, Chamala S, Michail S.	Gastro Hep Adv	10.1016/j.gastha.2025.100741	2025
Phylogeny	The role of intestinal microbiota in the humoral response to SARS-CoV-2 after mRNA-1273 vaccination.	Tarrino M, Gutierrez-Bautista JF, Duran MJO, Garcia-Diaz A, Cabrera-Serrano AJ, Sainz J, Cobo F, Rodriguez T, Reguera JA, Bernal M, Lopez-Nevot MA, Sampedro A.	Sci Rep	10.1038/s41598-025-11103-w	2025
Genetics	The Relationship Between Osteoporosis and Intestinal Microbes in the Henan Province of China.	Qin Q, Yan S, Yang Y, Chen J, Yan H, Li T, Gao X, Wang Y, Li A, Wang S, Ding S.	Front Cell Dev Biol	10.3389/fcell.2021.752990	2021
	Mendelian randomization study revealed a gut microbiota-immune system-kidney junction axis in chronic kidney disease.	Tan J, Xiong Z, Yu S, Lu W, Yu L.	Sci Rep	10.1038/s41598-025-05941-x	2025
Enzymology	Efficacy of Lacticaseibacillus rhamnosus probiotic strains in treating chromate induced dermatitis.	Ali M, Amin A, Abbas Z.	Sci Rep	10.1038/s41598-025-93732-9	2025
	Microbiota boost immunotherapy? A meta-analysis dives into fecal microbiota transplantation and immune checkpoint inhibitors.	Lin A, Huang L, Jiang A, Zhu L, Mou W, Li Y, Zhang C, Liu Z, Zhang J, Cheng Q, Wei T, Luo P.	BMC Med	10.1186/s12916-025-04183-y	2025
	Biotransformation of quercetin by Bacillus subtilis and anticancer activity evaluation: in vitro and in Silico.	El Gendy SN, Elmotayam AK, Samir R, Ezzat MI, Abo-Elfadl MT, El Sayed AM.	AMB Express	10.1186/s13568-025-01860-2	2025
	Neutrophil-to-Lymphocyte Ratio at Diagnosis Predicts Colonoscopic Activity in Pediatric Inflammatory Bowel Diseases.	Aziz B, Aziz B, Belaghi R, Huynh H, Jacobson K, Mack DR, Deslandres C, Otley A, DeBruyn J, El-Matary W, Crowley E, Sherlock M, Critch J, Ahmed N, Griffiths A, Walters T, Wine E, Canadian Children IBD Network.	Clin Transl Gastroenterol	10.14309/ctg.0000000000000824	2025
	Fecal Microbiota Transplantation May Represent a Good Approach for Patients with Focal Segmental Glomerulosclerosis: A Brief Report.	Zhi W, Yuan X, Song W, Jin G, Li Y.	J Clin Med	10.3390/jcm11226700	2022
	Mediation effect of gut microbiota on the relationship between physical activity and carotid plaque.	Ouyang W, Tang B, He Y, Wu H, Yang P, Yin L, Li X, Li Y, Huang X.	Front Microbiol	10.3389/fmicb.2024.1432008	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
Pathogenicity	Modified Zhujing pill regulates RPE cholesterol metabolism and gut microbiota in an age-related macular degeneration mouse model.	Cen S, Xie S, Ibrahim KS, Baran MR, Li X, Reilly J, Tan Z, He Z, Shu X.	Front Cell Infect Microbiol	10.3389/fcimb.2025.1691360	2025
	Immunomodulatory Role of Vitamin D on Gut Microbiome in Children.	Tabassum A, Ali A, Zahedi FD, Ismail NAS.	Biomedicines	10.3390/biomedicines11051441	2023
	Mucosal homeostasis is altered in the ileum of gnotobiotic mice.	Greig CJ, Alper A, Goodman AL, Cowles RA.	J Surg Res	10.1016/j.jss.2018.05.055	2018
	Understanding the role of the gut microbiome in solid tumor responses to immune checkpoint inhibitors for personalized therapeutic strategies: a review.	Lim MY, Hong S, Nam YD.	Front Immunol	10.3389/fimmu.2024.1512683	2024
	Exploring Gut Microbiota and the Influence of Physical Activity Interventions on Overweight and Obese Children and Adolescents: A Systematic Review.	Morgado MC, Sousa M, Coelho AB, Costa JA, Seabra A.	Healthcare (Basel)	10.3390/healthcare11172459	2023
	Effects of Low Protein Diet on Modulating Gut Microbiota in Patients with Chronic Kidney Disease: A Systematic Review and Meta-analysis of International Studies.	Hsu CK, Su SC, Chang LC, Shao SC, Yang KJ, Chen CY, Chen YT, Wu IW.	Int J Med Sci	10.7150/ijms.66451	2021
	Effects of OsomeFood Clean Label plant-based meals on the gut microbiome.	Jacky D, Bibi C, Meng LMC, Jason F, Gwendoline T, Jeremy L, Wie CC.	BMC Microbiol	10.1186/s12866-023-02822-z	2023
Phylogeny	Stressful events induce long-term gut microbiota dysbiosis and associated post-traumatic stress symptoms in healthcare workers fighting against COVID-19.	Gao F, Guo R, Ma Q, Li Y, Wang W, Fan Y, Ju Y, Zhao B, Gao Y, Qian L, Yang Z, He X, Jin X, Liu Y, Peng Y, Chen C, Chen Y, Gao C, Zhu F, Ma X.	J Affect Disord	10.1016/j.jad.2022.02.024	2022
	Investigating volatile compounds in the Bacteroides secretome.	Shagaleeva OY, Kashatnikova DA, Kardonsky DA, Konanov DN, Efimov BA, Bagrov DV, Evtushenko EG, Chaplin AV, Silantiev AS, Filatova JV, Kolesnikova IV, Vanyushkina AA, Stimpson J, Zakharzhevskaya NB.	Front Microbiol	10.3389/fmicb.2023.1164877	2023
	Machine learning framework for gut microbiome biomarkers discovery and modulation analysis in large-scale obese population.	Liu Y, Zhu J, Wang H, Lu W, Lee YK, Zhao J, Zhang H.	BMC Genomics	10.1186/s12864-022-09087-2	2022
	Combining Bifidobacterium longum subsp. infantis and human milk oligosaccharides synergistically increases short chain fatty acid production ex vivo.	De Bruyn F, James K, Cottenet G, Dominick M, Katja J.	Commun Biol	10.1038/s42003-024-06628-1	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
	Exploring the Gut Microbiota: Key Insights Into Its Role in Obesity, Metabolic Syndrome, and Type 2 Diabetes.	Sasidharan Pillai S, Gagnon CA, Foster C, Ashraf AP.	J Clin Endocrinol Metab	10.1210/clinem/dgae499	2024
	Correlation of Gut Microbiota with Children Obesity and Weight Loss.	Peng LJ, Chen YP, Qu F, Zhong Y, Jiang ZS.	Indian J Microbiol	10.1007/s12088-023-01088-3	2024
	Evaluation of the gut microbiome associated with COVID-19.	Maddah R, Goodarzi V, Asadi-Yousefabad SL, Abbasluo M, Shariati P, Shafiei Kafraj A.	Inform Med Unlocked	10.1016/j.imu.2023.101239	2023
Metabolism	In vitro gut microbiome response to carbohydrate supplementation is acutely affected by a sudden change in diet.	Pantoja-Feliciano IG, Karl JP, Perisin M, Doherty LA, McClung HL, Armstrong NJ, Renberg R, Racicot K, Branck T, Arcidiacono S, Soares JW.	BMC Microbiol	10.1186/s12866-023-02776-2	2023
Pathogenicity	Structure analysis of human gut microbiota associated with single-celled gut protists using Next-Generation Sequencing of 16S and 18S rRNA genes.	Belkessa S, Pasolli E, Medrouh B, Berg RPKD, Andersen LO', Nielsen HV, Stensvold CR.	Comput Struct Biotechnol J	10.1016/j.csbj.2025.06.006	2025
Metabolism	Characterization of a novel multidomain CE15-GH8 enzyme encoded by a polysaccharide utilization locus in the human gut bacterium Bacteroides eggerthii.	Kmezik C, Krska D, Mazurkewich S, Larsbrink J.	Sci Rep	10.1038/s41598-021-96659-z	2021
Pathogenicity	A Citrus Fruit Extract High in Polyphenols Beneficially Modulates the Gut Microbiota of Healthy Human Volunteers in a Validated In Vitro Model of the Colon.	Sost MM, Ahles S, Verhoeven J, Verbruggen S, Stevens Y, Venema K.	Nutrients	10.3390/nu13113915	2021
	Insights of gut-liver axis in hepatic diseases: Mechanisms, clinical implications, and therapeutic potentials.	Jeyaraman N, Jeyaraman M, Mariappan T, Muthu S, Ramasubramanian S, Sharma S, Santos GS, da Fonseca LF, Lana JF.	World J Gastrointest Pharmacol Ther	10.4292/wjgpt.v15.i6.98146	2024
Genetics	Mendelian randomization analyses support causal relationships between gut microbiome and longevity.	Chen S, Chen W, Wang X, Liu S.	J Transl Med	10.1186/s12967-024-05823-2	2024
	Changes in HLA-B27 Transgenic Rat Fecal Microbiota Following Tofacitinib Treatment and Ileocecal Resection Surgery: Implications for Crohn's Disease Management.	Blondeaux A, Valibouze C, Speca S, Rousseaux C, Dubuquoy C, Blanquart H, Zerbib P, Desreumaux P, Foligne B, Titecat M.	Int J Mol Sci	10.3390/ijms25042164	2024
	Effect of Benaglutide on Gut Microbiota and Fecal Metabolites in Patients with Type 2 Diabetes Mellitus.	Han CY, Ye XM, Lu JP, Jin HY, Wang P, Xu WW, Zhang M.	Diabetes Metab Syndr Obes	10.2147/dmso.s418757	2023
Metabolism	Multi-omic profiling reveals associations between the gut microbiome, host genome and transcriptome in patients with colorectal cancer.	Zou S, Yang C, Zhang J, Zhong D, Meng M, Zhang L, Chen H, Fang L.	J Transl Med	10.1186/s12967-024-04984-4	2024
	Composition of gut microbiota in obese and normal-weight Mexican school-age children and its association with metabolic traits.	Lopez-Contreras BE, Moran-Ramos S, Villarruel-Vazquez R, Macias-Kauffer L, Villamil-Ramirez H, Leon-Mimila P, Vega-Badillo J, Sanchez-Munoz F, Llanos-Moreno LE, Canizalez-Roman A, Del Rio-Navarro B, Ibarra-Gonzalez I, Vela-Amieva M, Villarreal-Molina T, Ochoa-Leyva A, Aguilar-Salinas CA, Canizales-Quinteros S.	Pediatr Obes	10.1111/ijpo.12262	2018
	Evaluating the Effects of Sugar Shift^® Symbiotic on Microbiome Composition and LPS Regulation: A Double-Blind, Placebo-Controlled Study.	Garcia G, Soto J, Netherland M, Hasan NA, Buchaca E, Martinez D, Carlin M, de Jesus Cano R.	Microorganisms	10.3390/microorganisms12122525	2024
	Dietary supplementary with ellagic acid improves the intestinal barrier function and flora structure of broiler chicken challenged with E. coli K88.	Li P, Zhao S, Teng Y, Han S, Yang Y, Wu M, Guo S, Ding B, Xiao L, Yi D.	Poult Sci	10.1016/j.psj.2024.104429	2024
Genetics	Metagenome-assembled microbial genomes from Parkinson's disease fecal samples.	Duru IC, Lecomte A, Shishido TK, Laine P, Suppula J, Paulin L, Scheperjans F, Pereira PAB, Auvinen P.	Sci Rep	10.1038/s41598-024-69742-4	2024
	The Relationship Between Gut Microbiome and Ophthalmologic Diseases: A Comprehensive Review.	Lima Barrientos J, Rojas Huerta A, Perez Mendoza A, Abreu Lopez BA, Salolin Vargas VP, Garcia Gonzalez OY, Saldana Ruiz MA, Diarte E, Torijano Sarria AJ.	Cureus	10.7759/cureus.66808	2024
	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
	Characterization of Gut Microbiome Composition in Patients with Triple-Negative Breast Cancer Treated with Neoadjuvant Chemotherapy.	Vernaci G, Savarino EV, Patuzzi I, Facchin S, Zingone F, Massa D, Faggioni G, Giarratano T, Miglietta F, Griguolo G, Fassan M, Lo Mele M, Gasparini E, Bisagni G, Guarneri V, Dieci MV.	Oncologist	10.1093/oncolo/oyad060	2023
	Quantitative differences in synthetic gut microbial inoculums do not affect the final stabilized in vitro community compositions.	Gnanasekaran T, Sarathi A, Fang Q, Azarm A, Assis Geraldo J, Nigro E, Arumugam M.	mSystems	10.1128/msystems.01249-22	2023
	Influence of saccharide modifications on heparin lyase III substrate specificities.	Wu J, Chopra P, Boons GJ, Zaia J.	Glycobiology	10.1093/glycob/cwab023	2022
	Deciphering the Physiological Responses to the Intake of Plant-Based Meat Analogues: On the Track of Microbiota and Biomarkers in Serum and Urine.	Sanchez-Terron G, Martinez R, Morcuende D, Estevez M.	J Agric Food Chem	10.1021/acs.jafc.5c02799	2025
	Evaluation of Menopausal Syndrome Relief and Anti-Obesity Efficacy of the Korean Fermented Food Doenjang: A Randomized, Double-Blind Clinical Trial.	Han AL, Ryu MS, Yang HJ, Jeong DY, Choi KH.	Nutrients	10.3390/nu16081194	2024
	High Cannabigerol Hemp Extract Moderates Colitis and Modulates the Microbiome in an Inflammatory Bowel Disease Model.	Anderson BD, Sepulveda DE, Nachnani R, Cortez-Resendiz A, Coates MD, Beckett A, Bisanz JE, Kellogg JJ, Raup-Konsavage WM.	J Pharmacol Exp Ther	10.1124/jpet.124.002204	2024
	Association of Gut Microbiota with Age-Related Macular Degeneration and Glaucoma: A Bidirectional Mendelian Randomization Study.	Li C, Lu P.	Nutrients	10.3390/nu15214646	2023
	Multi-omics analysis of fecal samples in colorectal cancer Egyptians patients: a pilot study.	Khattab RH, Abo-Hammam RH, Salah M, Hanora AM, Shabayek S, Zakeer S.	BMC Microbiol	10.1186/s12866-023-02991-x	2023
Pathogenicity	Perturbed gut microbiota and serum metabolites are associated with progressive renal fibrosis.	Wang RX, Zhou HB, Gao JX, Li XH, Bai WF, Wang J, Bai YC, Fan LY, Chang H, Shi SL.	Front Med (Lausanne)	10.3389/fmed.2025.1489100	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
Phylogeny	Gut Microbiota Profile Changes in Patients with Inflammatory Bowel Disease and Non-Alcoholic Fatty Liver Disease: A Metagenomic Study.	De Caro C, Spagnuolo R, Quirino A, Mazza E, Carrabetta F, Maurotti S, Cosco C, Bennardo F, Roberti R, Russo E, Giudice A, Giudice A, Pujia A, Doldo P, Matera G, Marascio N.	Int J Mol Sci	10.3390/ijms25105453	2024
	Aged Gut Microbiota Contributes to Cognitive Impairment and Hippocampal Synapse Loss in Mice.	Li M, Ren J, Bao Y, Wei W, Yu X, He X, Gulisima M, Sheng L, Zheng N, Wan J, Zhou H, Zhao L, Li H.	Aging Cell	10.1111/acel.70064	2025
	Exploration of three Dyadobacter fermentans enzymes uncovers molecular activity determinants in CE15.	Carbonaro M, Mazurkewich S, Fiorentino G, Lo Leggio L, Larsbrink J.	Appl Microbiol Biotechnol	10.1007/s00253-024-13175-6	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
Enzymology	Exploring bacterial heparinase II activities with defined substrates.	Bohlmann L, Chang CW, Beacham I, von Itzstein M.	Chembiochem	10.1002/cbic.201500081	2015
	Citrus Extract High in Flavonoids Beneficially Alters Intestinal Metabolic Responses in Subjects with Features of Metabolic Syndrome.	Maurer Sost M, Stevens Y, Salden B, Troost F, Masclee A, Venema K.	Foods	10.3390/foods12183413	2023
	Gut Microbiome Composition in Dystonia Patients.	Timmers ER, Swarte JC, Gacesa R, Bjork JR, Weersma RK, Tijssen MAJ, de Koning TJ, Harmsen HJM, Niezen-Koning KE.	Int J Mol Sci	10.3390/ijms24032383	2023
Enzymology	Alterations and correlations of the gut microbiome, metabolism and immunity in patients with primary biliary cirrhosis.	Lv LX, Fang DQ, Shi D, Chen DY, Yan R, Zhu YX, Chen YF, Shao L, Guo FF, Wu WR, Li A, Shi HY, Jiang XW, Jiang HY, Xiao YH, Zheng SS, Li LJ.	Environ Microbiol	10.1111/1462-2920.13401	2016
	Integrating Choline and Specific Intestinal Microbiota to Classify Type 2 Diabetes in Adults: A Machine Learning Based Metagenomics Study.	Zeng Q, Zhao M, Wang F, Li Y, Li H, Zheng J, Chen X, Zhao X, Ji L, Gao X, Liu C, Wang Y, Cheng S, Xu J, Pan B, Sun J, Li Y, Li D, He Y, Zheng L.	Front Endocrinol (Lausanne)	10.3389/fendo.2022.906310	2022
	Impact of urbanization on gut microbiome mosaics across geographic and dietary contexts.	Vinogradova E, Mukhanbetzhanov N, Nurgaziyev M, Jarmukhanov Z, Aipova R, Sailybayeva A, Bekbossynova M, Kozhakhmetov S, Kushugulova A.	mSystems	10.1128/msystems.00585-24	2024
Genetics	Effect of time-restricted eating regimen on weight loss is mediated by gut microbiome.	Huang C, Liu D, Yang S, Huang Y, Wei X, Zhang P, Lin J, Xu B, Liu Y, Guo D, Li Y, Li J, Zhang H.	iScience	10.1016/j.isci.2024.110202	2024
	Impact of cigarette smoking on gut microbial dysbiosis: a structured literature review.	Imade EE, Obayagbona NO.	Gut Microbiome (Camb)	10.1017/gmb.2024.3	2024
Phylogeny	Microbial dynamics with CRC progression: a study of the mucosal microbiota at multiple sites in cancers, adenomatous polyps, and healthy controls.	Senthakumaran T, Moen AEF, Tannaes TM, Endres A, Brackmann SA, Rounge TB, Bemanian V, Tunsjo HS.	Eur J Clin Microbiol Infect Dis	10.1007/s10096-023-04551-7	2023
	Alterations of the Gut Microbiome Associated to Methane Metabolism in Mexican Children with Obesity.	Murga-Garrido SM, Orbe-Orihuela YC, Diaz-Benitez CE, Castaneda-Marquez AC, Cornejo-Granados F, Ochoa-Leyva A, Sanchez-Flores A, Cruz M, Burguete-Garcia AI, Lagunas-Martinez A.	Children (Basel)	10.3390/children9020148	2022
	Novel Thermostable Heparinase Based on the Genome of Bacteroides Isolated from Human Gut Microbiota.	Zhang C, Yu L, Zhai Q, Zhao R, Wang C, Zhao J, Zhang H, Chen W, Tian F.	Foods	10.3390/foods11101462	2022
	Silk-derived sericin/fibroin mixture drink fermented with plant-derived Lactococcus lactis BM32-1 improves constipation and related microbiota: a randomized, double-blind, and placebo-controlled clinical trial.	Noda M, Danshiitsoodol N, Kanno K, Sugiyama M.	Biosci Microbiota Food Health	10.12938/bmfh.2023-102	2024
	Association between Neutrophil-to-Lymphocyte Ratio and Gut Microbiota in a Large Population: a Retrospective Cross-Sectional Study.	Yoon HY, Kim HN, Lee SH, Kim SJ, Chang Y, Ryu S, Shin H, Kim HL, Lee JH.	Sci Rep	10.1038/s41598-018-34398-4	2018
Genetics	Antibiotic resistance profiles of gut microbiota across various primate species in Guangxi.	Huang H, Pang X, Que T, Chen P, Li S, Wu A, He M, Qiu H, Hu Y.	Front Microbiol	10.3389/fmicb.2023.1309709	2023
	The Role of the Microbiome in Gastroentero-Pancreatic Neuroendocrine Neoplasms (GEP-NENs).	Mohamed A, Asa SL, McCormick T, Al-Shakhshir H, Dasari A, Mauricio R, Salem I, Ocuin LM, Bajor D, Lee RT, Selfridge JE, Kardan A, Lee Z, Avril N, Kopp S, Winter JM, Hardacre JM, Ammori JB, Ghannoum MA.	Curr Issues Mol Biol	10.3390/cimb44050136	2022
	Gut Microbiome Alterations in Patients With Carotid Atherosclerosis.	Chen J, Qin Q, Yan S, Yang Y, Yan H, Li T, Wang L, Gao X, Li A, Ding S.	Front Cardiovasc Med	10.3389/fcvm.2021.739093	2021
	Gut microbiota derived indole-3-acetic acid ameliorates precancerous inflammatory intestinal milieu to inhibit tumorigenesis through IL-35.	Wang J, Hao Y, Yang Y, Zhang Y, Xu C, Yang R.	J Immunother Cancer	10.1136/jitc-2024-011155	2025
Metabolism	Integrative metagenomic and metabolomic analyses reveal severity-specific signatures of gut microbiota in chronic kidney disease.	Wu IW, Gao SS, Chou HC, Yang HY, Chang LC, Kuo YL, Dinh MCV, Chung WH, Yang CW, Lai HC, Hsieh WP, Su SC.	Theranostics	10.7150/thno.41725	2020
	Microbial dysbiosis index for assessing colitis status in mouse models: A systematic review and meta-analysis.	Kim MJ, Jung DR, Lee JM, Kim I, Son H, Kim ES, Shin JH.	iScience	10.1016/j.isci.2023.108657	2024
	Evaluation of Body Changes and the Anti-Obesity Effect after Consumption of Korean Fermented Food, Cheonggukjang: Randomized, Double-Blind Clinical Trial.	Han AL, Jeong SJ, Ryu MS, Yang HJ, Jeong DY, Seo YB.	Foods	10.3390/foods12112190	2023
	Distinct microbial and metabolic shifts characterize acute coronary syndrome and recovery.	Xu J, Dai D, Yang Y, Gao S, Yang J, Dong C, Yang W, Yuan J, Wang T, Tian T, Yang Y, Luo F, Jiang P, Wu C, Sun X, Sui Y, Gao G, Ma W, Wu Y, Zhang J, Li J, Guo C, Cui C, Guo T, Zhao X, Yuan J, Qiao S, Hu F, Gao X, Luo X, Peng H, Wang D, Wu J, Wu C, He J, Chen WH, Yang Y, Fu J.	Imeta	10.1002/imt2.70079	2025
Phylogeny	Polyphenol-mediated microbiome modulation in STEMI patients: a pilot study	Issilbayeva A, Sergazy S, Zhashkeyev A, Gulyayev A, Kozhakhmetov S, Shulgau Z, Nurgaziyev M, Nurgaziyeva A, Zhetkenev S, Mukhanbetzhanov N, Jarmukhanov Z, Mukhanbetzhanova Z, Vinogradova E, Zhumadilov Z, Kushugulova A, Aljofan M.	Front Med (Lausanne)		2025
Pathogenicity	Common Oral Medications Lead to Prophage Induction in Bacterial Isolates from the Human Gut.	Sutcliffe SG, Shamash M, Hynes AP, Maurice CF.	Viruses	10.3390/v13030455	2021
Metabolism	Microbiota-derived tryptophan metabolism and AMPK/mTOR pathway mediate antidepressant-like effect of Shugan Hewei Decoction.	Yue Y, Ke Y, Zheng J, Wang Z, Liu H, Liu S.	Front Pharmacol	10.3389/fphar.2024.1466336	2024
Pathogenicity	Nutraceutical Blends Promote Weight Loss, Inflammation Reduction, and Better Sleep: The Role of Faecalibacterium prausnitzii in Overweight Adults-A Double-Blind Trial.	Santamarina AB, Filho VN, de Freitas JA, Franco LAM, Martins RC, Fonseca JV, Orellana Turri JA, Hufnagel MT, Demarque DP, da Silva BFRB, Gusmao AF, Olivieri EHR, de Souza E, de Souza EA, Otoch JP, Pessoa AFM.	Mol Nutr Food Res	10.1002/mnfr.202400806	2025
	Development of an In Vitro Model of the Gut Microbiota Enriched in Mucus-Adhering Bacteria.	Calvigioni M, Panattoni A, Biagini F, Donati L, Mazzantini D, Massimino M, Daddi C, Celandroni F, Vozzi G, Ghelardi E.	Microbiol Spectr	10.1128/spectrum.00336-23	2023
Pathogenicity	Integrative metagenomic and metabolomic analyses reveal gut microbiota-derived multiple hits connected to development of gestational diabetes mellitus in humans.	Ye D, Huang J, Wu J, Xie K, Gao X, Yan K, Zhang P, Tao Y, Li Y, Zang S, Rong X, Li J, Guo J.	Gut Microbes	10.1080/19490976.2022.2154552	2023
	Gut Microbiota Modulates the Protective Role of Ginsenoside Compound K Against Sodium Valproate-Induced Hepatotoxicity in Rat.	Zhou L, Zeng X, Liao J, Chen L, Ouyang D.	Front Microbiol	10.3389/fmicb.2022.936585	2022
	An Improved Validated Method for the Determination of Short-Chain Fatty Acids in Human Fecal Samples by Gas Chromatography with Flame Ionization Detection (GC-FID).	Smith M, Polite L, Christy A, Edirisinghe I, Burton-Freeman B, Sandhu A.	Metabolites	10.3390/metabo13111106	2023
	Changes of gut microbiota reflect the severity of major depressive disorder: a cross sectional study.	Hu X, Li Y, Wu J, Zhang H, Huang Y, Tan X, Wen L, Zhou X, Xie P, Olasunkanmi OI, Zhou J, Sun Z, Liu M, Zhang G, Yang J, Zheng P, Xie P.	Transl Psychiatry	10.1038/s41398-023-02436-z	2023
	Aging characteristics of colorectal cancer based on gut microbiota.	Wu Y, Zhuang J, Zhang Q, Zhao X, Chen G, Han S, Hu B, Wu W, Han S.	Cancer Med	10.1002/cam4.6414	2023
	Discovery of a bifunctional xylanolytic enzyme with arabinoxylan arabinofuranohydrolase-d3 and endo-xylanase activities and its application in the hydrolysis of cereal arabinoxylans.	Wang R, Zhang Y, Liu L, Yang J, Yuan H.	Microb Biotechnol	10.1111/1751-7915.14267	2023
	Short-chain fatty acid-producing bacterial strains attenuate experimental ulcerative colitis by promoting M2 macrophage polarization via JAK/STAT3/FOXO3 axis inactivation.	Zhao H, Zhou Y, Xu J, Zhang Y, Wang H, Zhao C, Huang H, Yang J, Huang C, Li Y, Wang L, Nie Y.	J Transl Med	10.1186/s12967-024-05122-w	2024
	Association between gut microbiota and gastrointestinal cancer: a two-sample bi-directional Mendelian randomization study.	Su Q, Jin C, Bo Z, Yang Y, Wang J, Wang J, Zhou J, Chen Y, Zeng H, Chen G, Wang Y.	Front Microbiol	10.3389/fmicb.2023.1181328	2023
	Associations between changes in the gut microbiota and liver cirrhosis: a systematic review and meta-analysis.	Liu Y, Chen Z, Li C, Sun T, Luo X, Jiang B, Liu M, Wang Q, Li T, Cao J, Li Y, Chen Y, Kuai L, Xiao F, Xu H, Cui H.	BMC Gastroenterol	10.1186/s12876-025-03589-5	2025
Genetics	Metagenomic signatures of balancing selection in the human gut.	Moeller AH.	Mol Ecol	10.1111/mec.16474	2023
Pathogenicity	Microbiome in Chronic Kidney Disease (CKD): An Omics Perspective.	Lohia S, Vlahou A, Zoidakis J.	Toxins (Basel)	10.3390/toxins14030176	2022
	Gut Microbiota in Chronic Kidney Disease: From Composition to Modulation towards Better Outcomes-A Systematic Review.	Voroneanu L, Burlacu A, Brinza C, Covic A, Balan GG, Nistor I, Popa C, Hogas S, Covic A.	J Clin Med	10.3390/jcm12051948	2023
Enzymology	Isolation of Bacteroides from fish and human fecal samples for identification of unique molecular markers.	Kabiri L, Alum A, Rock C, McLain JE, Abbaszadegan M.	Can J Microbiol	10.1139/cjm-2013-0518	2013
	A preliminary study for the clinical effect of one combinational physiotherapy and its potential influence on gut microbial composition in children with Tourette syndrome.	Bao C, Wei M, Pan H, Wen M, Liu Z, Xu Y, Jiang H.	Front Nutr	10.3389/fnut.2023.1184311	2023
Pathogenicity	The gut microbiome in bullous pemphigoid: implications of the gut-skin axis for disease susceptibility.	Liu X, van Beek N, Cepic A, Andreani NA, Chung CJ, Hermes BM, Yilmaz K, Benoit S, Drenovska K, Gerdes S, Glaser R, Goebeler M, Gunther C, von Georg A, Hammers CM, Holtsche MM, Hubner F, Kiritsi D, Schauer F, Linnenmann B, Huilaja L, Tasanen-Maatta K, Vassileva S, Zillikens D, Sadik CD, Schmidt E, Ibrahim S, Baines JF.	Front Immunol	10.3389/fimmu.2023.1212551	2023
	A microbial causal mediation analytic tool for health disparity and applications in body mass index.	Wang C, Ahn J, Tarpey T, Yi SS, Hayes RB, Li H.	Microbiome	10.1186/s40168-023-01608-9	2023
Genetics	Gut Microbiome Alterations in Patients With Visceral Obesity Based on Quantitative Computed Tomography.	Yan H, Qin Q, Chen J, Yan S, Li T, Gao X, Yang Y, Li A, Ding S.	Front Cell Infect Microbiol	10.3389/fcimb.2021.823262	2021
	Effects of the Brown Seaweed Laminaria japonica Supplementation on Serum Concentrations of IgG, Triglycerides, and Cholesterol, and Intestinal Microbiota Composition in Rats.	Kim JY, Kwon YM, Kim IS, Kim JA, Yu DY, Adhikari B, Lee SS, Choi IS, Cho KK.	Front Nutr	10.3389/fnut.2018.00023	2018
Metabolism	The dynamics of the gut microbiota in prediabetes during a four-year follow-up among European patients-an IMI-DIRECT prospective study.	Lyu L, Fan Y, Vogt JK, Clos-Garcia M, Bonnefond A, Pedersen HK, Dutta A, Koivula R, Sharma S, Allin KH, Brorsson C, Cederberg H, Chabanova E, De Masi F, Dermitzakis E, Elders PJ, Blom MT, Hollander M, Eriksen R, Forgie I, Frost G, Giordano GN, Grallert H, Haid M, Hansen TH, Jablonka B, Kokkola T, Mahajan A, Mari A, McDonald TJ, Musholt PB, Pavo I, Prehn C, Ridderstrale M, Ruetten H, Hart LM', Schwenk JM, Stankevic E, Thomsen HS, Vangipurapu J, Vestergaard H, Vinuela A, Walker M, Hansen T, Linneberg A, Nielsen HB, Brunak S, McCarthy MI, Froguel P, Adamski J, Franks PW, Laakso M, Beulens JWJ, Pearson E, Pedersen O.	Genome Med	10.1186/s13073-025-01508-7	2025
Enzymology	Techniques for RNA extraction from cells cultured in starPEG-heparin hydrogels.	Jaeschke A, Harvey NR, Tsurkan M, Werner C, Griffiths LR, Haupt LM, Bray LJ.	Open Biol	10.1098/rsob.200388	2021
Metabolism	Colonic microflora and plasma metabolite-based comparative analysis of unilateral ureteral obstruction-induced chronic kidney disease after treatment with the Chinese medicine FuZhengHuaYuJiangZhuTongLuo and AST-120.	Chen Z, Wu S, Huang L, Li J, Li X, Zeng Y, Chen Z, Chen M.	Heliyon	10.1016/j.heliyon.2024.e24987	2024
Genetics	Duck gut metagenome reveals the microbiome signatures linked to intestinal regional, temporal development, and rearing condition.	Ma L, Lyu W, Zeng T, Wang W, Chen Q, Zhao J, Zhang G, Lu L, Yang H, Xiao Y.	Imeta	10.1002/imt2.198	2024
	Alterations of the intestinal microbiota in age-related macular degeneration.	Zhang Y, Wang T, Wan Z, Bai J, Xue Y, Dai R, Wang M, Peng Q.	Front Microbiol	10.3389/fmicb.2023.1069325	2023
Metabolism	Gut Microbiota Alterations and Their Functional Differences in Depression According to Enterotypes in Asian Individuals.	Park S, Li C, Wu X, Zhang T.	Int J Mol Sci	10.3390/ijms241713329	2023
Genetics	Alterations of gut viral signals in atrial fibrillation: complex linkage with gut bacteriome.	Zuo K, Li J, Fang C, Zhong J, Xu L, Yang X.	Aging (Albany NY)	10.18632/aging.204222	2022
	Checkpoint inhibitor responses can be regulated by the gut microbiota - A systematic review.	Zeriouh M, Raskov H, Kvich L, Gogenur I, Bennedsen ALB.	Neoplasia	10.1016/j.neo.2023.100923	2023
	Consistent signatures in the human gut microbiome of longevous populations.	Chen S, Zhang Z, Liu S, Chen T, Lu Z, Zhao W, Mou X, Liu S.	Gut Microbes	10.1080/19490976.2024.2393756	2024
Metabolism	Major phenylpropanoid-derived metabolites in the human gut can arise from microbial fermentation of protein.	Russell WR, Duncan SH, Scobbie L, Duncan G, Cantlay L, Calder AG, Anderson SE, Flint HJ.	Mol Nutr Food Res	10.1002/mnfr.201200594	2013
	The Nursing Home Older Adult Gut Microbiome Composition Shows Time-dependent Dysbiosis and Is Influenced by Medication Exposures, Age, Environment, and Frailty.	Haran JP, Zeamer A, Ward DV, Dutta P, Bucci V, McCormick BA.	J Gerontol A Biol Sci Med Sci	10.1093/gerona/glab167	2021
	Anti-Obesity Effects of Traditional and Commercial Kochujang in Overweight and Obese Adults: A Randomized Controlled Trial.	Han AL, Jeong SJ, Ryu MS, Yang HJ, Jeong DY, Park DS, Lee HK.	Nutrients	10.3390/nu14142783	2022
	Childhood Obesity and the Cryptic Language of the Microbiota: Metabolomics' Upgrading.	Bosco A, Loi M, Pinna G, Pintus R, Fanos V, Dessi A.	Metabolites	10.3390/metabo13030414	2023
Phylogeny	Characterization of the gut microbiota in Chinese children with overweight and obesity using 16S rRNA gene sequencing.	Chen X, Zhang D, Sun H, Jiang F, Shen Y, Wei P, Shen X.	PeerJ	10.7717/peerj.11439	2021
	A signature of Prevotella copri and Faecalibacterium prausnitzii depletion, and a link with bacterial glutamate degradation in the Kenyan colorectal cancer patients.	Obuya S, Elkholy A, Avuthu N, Behring M, Bajpai P, Agarwal S, Kim HG, El-Nikhely N, Akinyi P, Orwa J, Afaq F, Abdalla M, Michael A, Farouk M, Bateman LB, Fouad M, Saleh M, Guda C, Manne U, Arafat W.	J Gastrointest Oncol	10.21037/jgo-22-116	2022
	Microbial richness and air chemistry in aerosols above the PBL confirm 2,000-km long-distance transport of potential human pathogens.	Rodo X, Pozdniakova S, Borras S, Matsuki A, Tanimoto H, Armengol MP, Pey I, Vila J, Munoz L, Santamaria S, Canas L, Morgui JA, Fontal A, Curcoll R.	Proc Natl Acad Sci U S A	10.1073/pnas.2404191121	2024
	Altered Fecal Microbiome and Metabolome in a Mouse Model of Choroidal Neovascularization.	Li Y, Cai Y, Huang Q, Tan W, Li B, Zhou H, Wang Z, Zou J, Ding C, Jiang B, Yoshida S, Zhou Y.	Front Microbiol	10.3389/fmicb.2021.738796	2021
	Database limitations for studying the human gut microbiome.	Dias CK, Starke R, Pylro VS, Morais DK.	PeerJ Comput Sci	10.7717/peerj-cs.289	2020
	Gut Microbiome and Plasma Metabolomic Analysis in Patients with Myelodysplastic Syndrome.	Jiang H, Zhao X, Zang M, Fu R, Shao Z, Liu C.	Oxid Med Cell Longev	10.1155/2022/1482811	2022
Pathogenicity	Oleuropein Ameliorates Advanced Stage of Type 2 Diabetes in db/db Mice by Regulating Gut Microbiota.	Zheng S, Wang Y, Fang J, Geng R, Li M, Zhao Y, Kang SG, Huang K, Tong T.	Nutrients	10.3390/nu13072131	2021
	Association of the Intestinal Microbiome with the Development of Neovascular Age-Related Macular Degeneration.	Zinkernagel MS, Zysset-Burri DC, Keller I, Berger LE, Leichtle AB, Largiader CR, Fiedler GM, Wolf S.	Sci Rep	10.1038/srep40826	2017
	Gene variations in autism spectrum disorder are associated with alteration of gut microbiota, metabolites and cytokines.	Liu Z, Mao X, Dan Z, Pei Y, Xu R, Guo M, Liu K, Zhang F, Chen J, Su C, Zhuang Y, Tang J, Xia Y, Qin L, Hu Z, Liu X.	Gut Microbes	10.1080/19490976.2020.1854967	2021
Phylogeny	Screening of Human Gut Bacterial Culture Collection Identifies Species That Biotransform Quercetin into Metabolites with Anticancer Properties.	Sankaranarayanan R, Sekhon PK, Ambat A, Nelson J, Jose D, Bhat GJ, Scaria J.	Int J Mol Sci	10.3390/ijms22137045	2021
	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
	Evaluation of Systemic Treatment Options for Gastrointestinal Stromal Tumours.	Golcic M, Jones RL, Huang P, Napolitano A.	Cancers (Basel)	10.3390/cancers15164081	2023
Phylogeny	Application of quantitative real-time PCR for rapid identification of Bacteroides fragilis group and related organisms in human wound samples.	Tong J, Liu C, Summanen P, Xu H, Finegold SM.	Anaerobe	10.1016/j.anaerobe.2011.03.004	2011
	Celiac disease gut microbiome studies in the third millennium: reviewing the findings and gaps of available literature.	Luz VCC, Pereira SG.	Front Med Technol	10.3389/fmedt.2024.1413637	2024
	Treadmill exercise has minimal impact on obesogenic diet-related gut microbiome changes but alters adipose and hypothalamic gene expression in rats.	Leigh SJ, Kaakoush NO, Escorihuela RM, Westbrook RF, Morris MJ.	Nutr Metab (Lond)	10.1186/s12986-020-00492-6	2020
	Compliance with Nutritional Recommendations and Gut Microbiota Profile in Galician Overweight/Obese and Normal-Weight Individuals.	Sinisterra-Loaiza L, Alonso-Lovera P, Cardelle-Cobas A, Miranda JM, Vazquez BI, Cepeda A.	Nutrients	10.3390/nu15153418	2023
	Comparative analysis of Parkinson's and inflammatory bowel disease gut microbiomes reveals shared butyrate-producing bacteria depletion.	Krueger ME, Boles JS, Simon ZD, Alvarez SD, McFarland NR, Okun MS, Zimmermann EM, Forsmark CE, Tansey MG.	NPJ Parkinsons Dis	10.1038/s41531-025-00894-4	2025
	Impacts of dietary exposure to pesticides on faecal microbiome metabolism in adult twins.	Mesnage R, Bowyer RCE, El Balkhi S, Saint-Marcoux F, Gardere A, Ducarmon QR, Geelen AR, Zwittink RD, Tsoukalas D, Sarandi E, Paramera EI, Spector T, Steves CJ, Antoniou MN.	Environ Health	10.1186/s12940-022-00860-0	2022
Metabolism	Gut Microbiota as Diagnostic Tools for Mirroring Disease Progression and Circulating Nephrotoxin Levels in Chronic Kidney Disease: Discovery and Validation Study.	Wu IW, Lin CY, Chang LC, Lee CC, Chiu CY, Hsu HJ, Sun CY, Chen YC, Kuo YL, Yang CW, Gao SS, Hsieh WP, Chung WH, Lai HC, Su SC.	Int J Biol Sci	10.7150/ijbs.37421	2020
	Gut Microbiota Modulation through Akkermansia spp. Supplementation Increases CAR T-cell Potency.	Marcos-Kovandzic L, Avagliano M, Ben Khelil M, Srikanthan J, Abdallah R, Petrocelli V, Rengassamy J, Alfaro A, Bied M, Fidelle M, Ferrere G, Daillere R, Arbab A, Amine-Hneineh R, Pages A, Dartigues P, Ly P, Simon S, Durand S, Gottschlich A, Ginhoux F, Bleriot C, Liu P, Zhao L, Creusot L, Rolhion N, Derosa L, Kroemer G, Menger L, Kobold S, Castilla-Llorente C, Sokol H, Casola S, Pasolli E, Zitvogel L, Bigenwald C.	Cancer Discov	10.1158/2159-8290.cd-24-1230	2025
Pathogenicity	Fecal microbiota transplantation in hematopoietic cell transplant and cellular therapy recipients: lessons learned and the path forward.	Habibi S, Rashidi A.	Gut Microbes	10.1080/19490976.2023.2229567	2023
	Characterization of the bacterial fecal microbiota composition of pigs preceding the clinical signs of swine dysentery.	Barbosa JA, Aguirre JCP, Nosach R, Harding JCS, Cantarelli VS, Costa MO.	PLoS One	10.1371/journal.pone.0294273	2023
Metabolism	Propionate-producing bacteria in the intestine may associate with skewed responses of IL10-producing regulatory T cells in patients with relapsing polychondritis.	Shimizu J, Kubota T, Takada E, Takai K, Fujiwara N, Arimitsu N, Murayama MA, Ueda Y, Wakisaka S, Suzuki T, Suzuki N.	PLoS One	10.1371/journal.pone.0203657	2018
	The synergistic effects of polyphenols and intestinal microbiota on osteoporosis.	Wang K, Hu S.	Front Immunol	10.3389/fimmu.2023.1285621	2023
	Human Fecal Microbiota Transplantation Reduces the Susceptibility to Dextran Sulfate Sodium-Induced Germ-Free Mouse Colitis.	Yang Y, Zheng X, Wang Y, Tan X, Zou H, Feng S, Zhang H, Zhang Z, He J, Cui B, Zhang X, Wu Z, Dong M, Cheng W, Tao S, Wei H.	Front Immunol	10.3389/fimmu.2022.836542	2022
	Could Infectious Agents Play a Role in the Onset of Age-related Macular Degeneration? A Scoping Review.	Larsen PP, Dinet V, Delcourt C, Helmer C, Linard M.	Ophthalmol Sci	10.1016/j.xops.2024.100668	2025
Genetics	Probiotics maintain the intestinal microbiome homeostasis of the sailors during a long sea voyage.	Zhang J, Zhao J, Jin H, Lv R, Shi H, De G, Yang B, Sun Z, Zhang H.	Gut Microbes	10.1080/19490976.2020.1722054	2020
	Plasma and urine proteomics and gut microbiota analysis reveal potential factors affecting COVID-19 vaccination response.	Hu C, Hu W, Tang B, Bao Q, Jiang X, Tang L, Wang H, He L, Lv M, Xiao Y, Liu C, Li X, Liu Y, Li J, Huang G, Dong Z, Li Z, Guo T, Yang S.	iScience	10.1016/j.isci.2024.108851	2024
	Changes in the gut microbiome associated with liver stiffness improvement in nonalcoholic steatohepatitis.	Sharpton SR, Podlaha O, Chuang JC, Gindin Y, Myers RP, Loomba R.	Therap Adv Gastroenterol	10.1177/17562848221098243	2022
Pathogenicity	Gut Microbiota Alteration Is Associated With Cognitive Deficits in Genetically Diabetic (Db/db) Mice During Aging.	Zhang J, Zhang Y, Yuan Y, Liu L, Zhao Y, Wang X.	Front Aging Neurosci	10.3389/fnagi.2021.815562	2021
Genetics	Association of distinct microbial signatures with premalignant colorectal adenomas.	Lee JWJ, Plichta DR, Asher S, Delsignore M, Jeong T, McGoldrick J, Staller K, Khalili H, Xavier RJ, Chung DC.	Cell Host Microbe	10.1016/j.chom.2023.04.007	2023
	Extracellular vesicles from mesenchymal stem cells alter gut microbiota and improve neuroinflammation and motor impairment in rats with mild liver damage.	Mincheva G, Felipo V, Moreno-Manzano V, Benitez-Paez A, Llansola M.	Neurotherapeutics	10.1016/j.neurot.2024.e00445	2024
	Immunological design of commensal communities to treat intestinal infection and inflammation.	Brown RL, Larkinson MLY, Clarke TB.	PLoS Pathog	10.1371/journal.ppat.1009191	2021
Metabolism	A highly active heparinase I from Bacteroides cellulosilyticus: Cloning, high level expression, and molecular characterization.	Gao LW, Zhu HT, Liu CY, Lv ZX, Fan XM, Zhang YW.	PLoS One	10.1371/journal.pone.0240920	2020
Pathogenicity	Engraftment of aging-related human gut microbiota and the effect of a seven-species consortium in a pre-clinical model.	Ye H, Ghosh TS, Hueston CM, Vlckova K, Golubeva AV, Hyland NP, O'Toole PW.	Gut Microbes	10.1080/19490976.2023.2282796	2023
	A powerful machine learning approach to identify interactions of differentially abundant gut microbial subsets in patients with metastatic and non-metastatic pancreatic cancer.	Villani A, Fontana A, Panebianco C, Ferro C, Copetti M, Pavlovic R, Drago D, Fiorentini C, Terracciano F, Bazzocchi F, Canistro G, Pisati F, Maiello E, Latiano TP, Perri F, Pazienza V.	Gut Microbes	10.1080/19490976.2024.2375483	2024
	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
	Comprehensive Analysis Reveals Novel Interactions between Circulating MicroRNAs and Gut Microbiota Composition in Human Obesity.	Assmann TS, Cuevas-Sierra A, Riezu-Boj JI, Milagro FI, Martinez JA.	Int J Mol Sci	10.3390/ijms21249509	2020
	Rhubarb Enema Increasing Short-Chain Fatty Acids that Improves the Intestinal Barrier Disruption in CKD May Be Related to the Regulation of Gut Dysbiosis.	Ji C, Lu F, Wu Y, Lu Z, Mo Y, Han L, Lin Q, Liu X, Zou C.	Biomed Res Int	10.1155/2022/1896781	2022
	Impact of Mediterranean Diet on Disease Activity and Gut Microbiota Composition of Rheumatoid Arthritis Patients.	Picchianti Diamanti A, Panebianco C, Salerno G, Di Rosa R, Salemi S, Sorgi ML, Meneguzzi G, Mariani MB, Rai A, Iacono D, Sesti G, Pazienza V, Lagana B.	Microorganisms	10.3390/microorganisms8121989	2020
Metabolism	Multi-omic Profiling Reveals that Intra-abdominal-Hypertension-Induced Intestinal Damage Can Be Prevented by Microbiome and Metabolic Modulations with 5-Hydroxyindoleacetic Acid as a Diagnostic Marker.	Li F, Jiang L, Pan S, Jiang S, Fan Y, Jiang C, Gao C, Leng Y.	mSystems	10.1128/msystems.01204-21	2022
	Multi-Omics Analysis Demonstrates the Critical Role of Non-Ethanolic Components of Alcoholic Beverages in the Host Microbiome and Metabolome: A Human- and Animal-Based Study.	Sarkar P, Kandimalla R, Bhattacharya A, Wahengbam R, Dehingia M, Kalita MC, Talukdar NC, Talukdar R, Khan MR.	Microorganisms	10.3390/microorganisms11061501	2023
Genetics	Alterations of the Gut Microbiota in Patients with Diabetic Nephropathy.	Zhang L, Wang Z, Zhang X, Zhao L, Chu J, Li H, Sun W, Yang C, Wang H, Dai W, Yan S, Chen X, Xu D.	Microbiol Spectr	10.1128/spectrum.00324-22	2022
	Safety and Modulatory Effects of Humanized Galacto-Oligosaccharides on the Gut Microbiome.	Arnold JW, Whittington HD, Dagher SF, Roach J, Azcarate-Peril MA, Bruno-Barcena JM.	Front Nutr	10.3389/fnut.2021.640100	2021
	Goat Milk Consumption Enhances Innate and Adaptive Immunities and Alleviates Allergen-Induced Airway Inflammation in Offspring Mice.	Kao HF, Wang YC, Tseng HY, Wu LS, Tsai HJ, Hsieh MH, Chen PC, Kuo WS, Liu LF, Liu ZG, Wang JY.	Front Immunol	10.3389/fimmu.2020.00184	2020
	Bacteriophage-Mediated Perturbation of Defined Bacterial Communities in an In Vitro Model of the Human Gut.	Attai H, Wilde J, Liu R, Chopyk J, Garcia AG, Allen-Vercoe E, Pride D.	Microbiol Spectr	10.1128/spectrum.01135-22	2022
	Weighted Gene Co-Expression Network Analysis Identifies a Functional Guild and Metabolite Cluster Mediating the Relationship between Mucosal Inflammation and Adherence to the Mediterranean Diet in Ulcerative Colitis.	Strauss JC, Haskey N, Ramay HR, Ghosh TS, Taylor LM, Yousuf M, Ohland C, McCoy KD, Ingram RJM, Ghosh S, Panaccione R, Raman M.	Int J Mol Sci	10.3390/ijms24087323	2023
Pathogenicity	Lessons learned from the anaerobe survey: historical perspective and review of the most recent data (2005-2007).	Snydman DR, Jacobus NV, McDermott LA, Golan Y, Hecht DW, Goldstein EJ, Harrell L, Jenkins S, Newton D, Pierson C, Rihs JD, Yu VL, Venezia R, Finegold SM, Rosenblatt JE, Gorbach SL.	Clin Infect Dis	10.1086/647940	2010
Pathogenicity	Microbiome as an endocrine organ and its relationship with eye diseases: Effective factors and new targeted approaches.	Haghshenas L, Banihashemi S, Malekzadegan Y, Catanzaro R, Moghadam Ahmadi A, Marotta F.	World J Gastrointest Pathophysiol	10.4291/wjgp.v15.i5.96446	2024
Genetics	Anti-diabetic effect of dicaffeoylquinic acids is associated with the modulation of gut microbiota and bile acid metabolism.	Huang Y, Xu W, Dong W, Chen G, Sun Y, Zeng X.	J Adv Res	10.1016/j.jare.2024.06.027	2025
Phylogeny	Gut Microbial Characteristics of Adult Patients With Epilepsy.	Dong L, Zheng Q, Cheng Y, Zhou M, Wang M, Xu J, Xu Z, Wu G, Yu Y, Ye L, Feng Z.	Front Neurosci	10.3389/fnins.2022.803538	2022
	Gut microbiota modify risk for dietary glycemia-induced age-related macular degeneration.	Rowan S, Taylor A.	Gut Microbes	10.1080/19490976.2018.1435247	2018
	Metagenomic analysis reveals crosstalk between gut microbiota and glucose-lowering drugs targeting the gastrointestinal tract in Chinese patients with type 2 diabetes: a 6 month, two-arm randomised trial.	Zhang X, Ren H, Zhao C, Shi Z, Qiu L, Yang F, Zhou X, Han X, Wu K, Zhong H, Li Y, Li J, Ji L.	Diabetologia	10.1007/s00125-022-05768-5	2022
	Nutritional Therapy Modulates Intestinal Microbiota and Reduces Serum Levels of Total and Free Indoxyl Sulfate and P-Cresyl Sulfate in Chronic Kidney Disease (Medika Study).	Di Iorio BR, Rocchetti MT, De Angelis M, Cosola C, Marzocco S, Di Micco L, di Bari I, Accetturo M, Vacca M, Gobbetti M, Di Iorio M, Bellasi A, Gesualdo L.	J Clin Med	10.3390/jcm8091424	2019
Metabolism	IgA-deficient humans exhibit gut microbiota dysbiosis despite secretion of compensatory IgM.	Catanzaro JR, Strauss JD, Bielecka A, Porto AF, Lobo FM, Urban A, Schofield WB, Palm NW.	Sci Rep	10.1038/s41598-019-49923-2	2019
	Oral and gut dysbiosis leads to functional alterations in Parkinson's disease.	Jo S, Kang W, Hwang YS, Lee SH, Park KW, Kim MS, Lee H, Yoon HJ, Park YK, Chalita M, Lee JH, Sung H, Lee JY, Bae JW, Chung SJ.	NPJ Parkinsons Dis	10.1038/s41531-022-00351-6	2022
Phylogeny	Dissection of the gut microbiota in mothers and children with chronic Trichuris trichiura infection in Pemba Island, Tanzania.	Chen H, Mozzicafreddo M, Pierella E, Carletti V, Piersanti A, Ali SM, Ame SM, Wang C, Miceli C.	Parasit Vectors	10.1186/s13071-021-04580-1	2021
Phylogeny	Gut Microbiota Analysis in Postoperative Lynch Syndrome Patients.	Mori G, Orena BS, Cultrera I, Barbieri G, Albertini AM, Ranzani GN, Carnevali I, Tibiletti MG, Pasca MR.	Front Microbiol	10.3389/fmicb.2019.01746	2019
	Comparative Study of Salivary, Duodenal, and Fecal Microbiota Composition Across Adult Celiac Disease.	Panelli S, Capelli E, Lupo GFD, Schiepatti A, Betti E, Sauta E, Marini S, Bellazzi R, Vanoli A, Pasi A, Cacciatore R, Bacchi S, Balestra B, Pastoris O, Frulloni L, Corazza GR, Biagi F, Ciccocioppo R.	J Clin Med	10.3390/jcm9041109	2020
	RWHMDA: Random Walk on Hypergraph for Microbe-Disease Association Prediction.	Niu YW, Qu CQ, Wang GH, Yan GY.	Front Microbiol	10.3389/fmicb.2019.01578	2019
	Cell-Free Supernatant of Odoribacter splanchnicus Isolated From Human Feces Exhibits Anti-colorectal Cancer Activity.	Oh BS, Choi WJ, Kim JS, Ryu SW, Yu SY, Lee JS, Park SH, Kang SW, Lee J, Jung WY, Kim YM, Jeong JH, Lee JH.	Front Microbiol	10.3389/fmicb.2021.736343	2021
	Distinct patterns in the gut microbiota after surgical or medical therapy in obese patients.	Medina DA, Pedreros JP, Turiel D, Quezada N, Pimentel F, Escalona A, Garrido D.	PeerJ	10.7717/peerj.3443	2017
Pathogenicity	Metformin Strongly Affects Gut Microbiome Composition in High-Fat Diet-Induced Type 2 Diabetes Mouse Model of Both Sexes.	Silamikele L, Silamikelis I, Ustinova M, Kalnina Z, Elbere I, Petrovska R, Kalnina I, Klovins J.	Front Endocrinol (Lausanne)	10.3389/fendo.2021.626359	2021
Pathogenicity	Altered Gut Microbial Profile Accompanied by Abnormal Fatty Acid Metabolism Activity Exacerbates Endometrial Cancer Progression.	Zhao SS, Chen L, Yang J, Wu ZH, Wang XY, Zhang Q, Liu WJ, Liu HX.	Microbiol Spectr	10.1128/spectrum.02612-22	2022
	A non-antibiotic-disrupted gut microbiome is associated with clinical responses to CD19-CAR-T cell cancer immunotherapy.	Stein-Thoeringer CK, Saini NY, Zamir E, Blumenberg V, Schubert ML, Mor U, Fante MA, Schmidt S, Hayase E, Hayase T, Rohrbach R, Chang CC, McDaniel L, Flores I, Gaiser R, Edinger M, Wolff D, Heidenreich M, Strati P, Nair R, Chihara D, Fayad LE, Ahmed S, Iyer SP, Steiner RE, Jain P, Nastoupil LJ, Westin J, Arora R, Wang ML, Turner J, Menges M, Hidalgo-Vargas M, Reid K, Dreger P, Schmitt A, Muller-Tidow C, Locke FL, Davila ML, Champlin RE, Flowers CR, Shpall EJ, Poeck H, Neelapu SS, Schmitt M, Subklewe M, Jain MD, Jenq RR, Elinav E.	Nat Med	10.1038/s41591-023-02234-6	2023
Genetics	Successful Fecal Microbiota Transplantation in a Patient Suffering From Irritable Bowel Syndrome and Recurrent Urinary Tract Infections.	Hocquart M, Pham T, Kuete E, Tomei E, Lagier JC, Raoult D.	Open Forum Infect Dis	10.1093/ofid/ofz398	2019
	Serum trimethylamine-N-oxide and gut microbiome alterations are associated with cholesterol deposition in the liver of laying hens fed with rapeseed meal.	Zhu L, Wang J, Ding X, Bai S, Zeng Q, Xuan Y, Fraley GS, Zhang K.	Anim Nutr	10.1016/j.aninu.2021.02.008	2021
	Differences in the oral and intestinal microbiotas in pregnant women varying in periodontitis and gestational diabetes mellitus conditions.	Zhang X, Wang P, Ma L, Guo R, Zhang Y, Wang P, Zhao J, Liu J.	J Oral Microbiol	10.1080/20002297.2021.1883382	2021
Pathogenicity	Antibiotics create a shift from mutualism to competition in human gut communities with a longer-lasting impact on fungi than bacteria.	Seelbinder B, Chen J, Brunke S, Vazquez-Uribe R, Santhaman R, Meyer AC, de Oliveira Lino FS, Chan KF, Loos D, Imamovic L, Tsang CC, Lam RP, Sridhar S, Kang K, Hube B, Woo PC, Sommer MOA, Panagiotou G.	Microbiome	10.1186/s40168-020-00899-6	2020
	Pglyrp-Regulated Gut Microflora Prevotella falsenii, Parabacteroides distasonis and Bacteroides eggerthii Enhance and Alistipes finegoldii Attenuates Colitis in Mice.	Dziarski R, Park SY, Kashyap DR, Dowd SE, Gupta D.	PLoS One	10.1371/journal.pone.0146162	2016
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
Pathogenicity	Tipping the Balance: Vitamin D Inadequacy in Children Impacts the Major Gut Bacterial Phyla.	Singh P, Rawat A, Saadaoui M, Elhag D, Tomei S, Elanbari M, Akobeng AK, Mustafa A, Abdelgadir I, Udassi S, Hendaus MA, Al Khodor S.	Biomedicines	10.3390/biomedicines10020278	2022
	Gut microbiome alterations and gut barrier dysfunction are associated with host immune homeostasis in COVID-19 patients.	Sun Z, Song ZG, Liu C, Tan S, Lin S, Zhu J, Dai FH, Gao J, She JL, Mei Z, Lou T, Zheng JJ, Liu Y, He J, Zheng Y, Ding C, Qian F, Zheng Y, Chen YM.	BMC Med	10.1186/s12916-021-02212-0	2022
Genetics	Microbial strain-level population structure and genetic diversity from metagenomes.	Truong DT, Tett A, Pasolli E, Huttenhower C, Segata N.	Genome Res	10.1101/gr.216242.116	2017
	Effects of enriched seafood sticks (heat-inactivated B. animalis subsp. lactis CECT 8145, inulin, omega-3) on cardiometabolic risk factors and gut microbiota in abdominally obese subjects: randomized controlled trial.	Companys J, Calderon-Perez L, Pla-Paga L, Llaurado E, Sandoval-Ramirez BA, Gosalbes MJ, Arregui A, Barandiaran M, Caimari A, Del Bas JM, Arola L, Valls RM, Sola R, Pedret A.	Eur J Nutr	10.1007/s00394-022-02904-0	2022
Pathogenicity	Effect of host breeds on gut microbiome and serum metabolome in meat rabbits.	Ye X, Zhou L, Zhang Y, Xue S, Gan QF, Fang S.	BMC Vet Res	10.1186/s12917-020-02732-6	2021
	Limosilactobacillus mucosae-derived extracellular vesicles modulates macrophage phenotype and orchestrates gut homeostasis in a diarrheal piglet model.	Li J, Feng S, Wang Z, He J, Zhang Z, Zou H, Wu Z, Liu X, Wei H, Tao S.	NPJ Biofilms Microbiomes	10.1038/s41522-023-00403-6	2023
Pathogenicity	The potential role of vitamin D supplementation as a gut microbiota modifier in healthy individuals.	Singh P, Rawat A, Alwakeel M, Sharif E, Al Khodor S.	Sci Rep	10.1038/s41598-020-77806-4	2020
	Identification and Analysis of Human Microbe-Disease Associations by Matrix Decomposition and Label Propagation.	Qu J, Zhao Y, Yin J.	Front Microbiol	10.3389/fmicb.2019.00291	2019
	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
Phylogeny	Gut Microbiota Composition Associated With Clostridium difficile-Positive Diarrhea and C. difficile Type in ICU Patients.	Duan J, Meng X, Liu S, Zhou P, Zeng C, Fu C, Dou Q, Wu A, Li C.	Front Cell Infect Microbiol	10.3389/fcimb.2020.00190	2020
Pathogenicity	The Salivary Microbiota of Patients With Primary Biliary Cholangitis Is Distinctive and Pathogenic.	Lv L, Jiang H, Chen X, Wang Q, Wang K, Ye J, Li Y, Fang D, Lu Y, Yang L, Gu S, Chen J, Diao H, Yan R, Li L.	Front Immunol	10.3389/fimmu.2021.713647	2021
	High prevalence of cfxA beta-lactamase in aminopenicillin-resistant Prevotella strains isolated from periodontal pockets.	Fosse T, Madinier I, Hannoun L, Giraud-Morin C, Hitzig C, Charbit Y, Ourang S.	Oral Microbiol Immunol	10.1046/j.0902-0055.2001.00096.x	2002
Metabolism	A comprehensive analysis of the faecal microbiome and metabolome of Strongyloides stercoralis infected volunteers from a non-endemic area.	Jenkins TP, Formenti F, Castro C, Piubelli C, Perandin F, Buonfrate D, Otranto D, Griffin JL, Krause L, Bisoffi Z, Cantacessi C.	Sci Rep	10.1038/s41598-018-33937-3	2018
Metabolism	Degradation of complex arabinoxylans by human colonic Bacteroidetes.	Pereira GV, Abdel-Hamid AM, Dutta S, D'Alessandro-Gabazza CN, Wefers D, Farris JA, Bajaj S, Wawrzak Z, Atomi H, Mackie RI, Gabazza EC, Shukla D, Koropatkin NM, Cann I.	Nat Commun	10.1038/s41467-020-20737-5	2021
	Identification of Protein Recognition Elements within Heparin Chains Using Enzymatic Foot-Printing in Solution and Online SEC/MS.	Niu C, Zhao Y, Bobst CE, Savinov SN, Kaltashov IA.	Anal Chem	10.1021/acs.analchem.0c00115	2020
	Heparinase Digestion of 3-O-Sulfated Sequences: Selective Heparinase II Digestion for Separation and Identification of Binding Sequences Present in ATIII Affinity Fractions of Bovine Intestinal Heparins.	Mourier P.	Front Med (Lausanne)	10.3389/fmed.2022.841726	2022
Transcriptome	Multi-omic profiling reveals associations between the gut mucosal microbiome, the metabolome, and host DNA methylation associated gene expression in patients with colorectal cancer.	Wang Q, Ye J, Fang D, Lv L, Wu W, Shi D, Li Y, Yang L, Bian X, Wu J, Jiang X, Wang K, Wang Q, Hodson MP, Thibaut LM, Ho JWK, Giannoulatou E, Li L.	BMC Microbiol	10.1186/s12866-020-01762-2	2020
Enzymology	Polysaccharide utilization loci-driven enzyme discovery reveals BD-FAE: a bifunctional feruloyl and acetyl xylan esterase active on complex natural xylans.	Hameleers L, Penttinen L, Ikonen M, Jaillot L, Faure R, Terrapon N, Deuss PJ, Hakulinen N, Master ER, Jurak E.	Biotechnol Biofuels	10.1186/s13068-021-01976-0	2021
Pathogenicity	Microbiome therapeutics for hepatic encephalopathy.	Bloom PP, Tapper EB, Young VB, Lok AS.	J Hepatol	10.1016/j.jhep.2021.08.004	2021
	Bacteroides uniformis and its preferred substrate, alpha-cyclodextrin, enhance endurance exercise performance in mice and human males.	Morita H, Kano C, Ishii C, Kagata N, Ishikawa T, Hirayama A, Uchiyama Y, Hara S, Nakamura T, Fukuda S.	Sci Adv	10.1126/sciadv.add2120	2023
Enzymology	Improved production of 2'-fucosyllactose in engineered Saccharomyces cerevisiae expressing a putative alpha-1, 2-fucosyltransferase from Bacillus cereus.	Xu M, Meng X, Zhang W, Shen Y, Liu W.	Microb Cell Fact	10.1186/s12934-021-01657-5	2021
Pathogenicity	Tibet plateau probiotic mitigates chromate toxicity in mice by alleviating oxidative stress in gut microbiota.	Feng P, Ye Z, Han H, Ling Z, Zhou T, Zhao S, Virk AK, Kakade A, Abomohra AE, El-Dalatony MM, Salama ES, Liu P, Li X.	Commun Biol	10.1038/s42003-020-0968-3	2020
	Neuroinflammation in Murine Cirrhosis Is Dependent on the Gut Microbiome and Is Attenuated by Fecal Transplant.	Liu R, Kang JD, Sartor RB, Sikaroodi M, Fagan A, Gavis EA, Zhou H, Hylemon PB, Herzog JW, Li X, Lippman RH, Gonzalez-Maeso J, Wade JB, Ghosh S, Gurley E, Gillevet PM, Bajaj JS.	Hepatology	10.1002/hep.30827	2020
	Structure of the fimbrial protein Mfa4 from Porphyromonas gingivalis in its precursor form: implications for a donor-strand complementation mechanism.	Kloppsteck P, Hall M, Hasegawa Y, Persson K.	Sci Rep	10.1038/srep22945	2016
	The Intestinal Microbiota in the Development of Chronic Liver Disease: Current Status.	Stojic J, Kukla M, Grgurevic I.	Diagnostics (Basel)	10.3390/diagnostics13182960	2023
Enzymology	Microbiology of the infected recurrent sacrococcygeal pilonidal sinus.	Ardelt M, Dittmar Y, Kocijan R, Rodel J, Schulz B, Scheuerlein H, Settmacher U.	Int Wound J	10.1111/iwj.12274	2016
Metabolism	Dairy Propionibacterium freudenreichii ameliorates acute colitis by stimulating MUC2 expression in intestinal goblet cell in a DSS-induced colitis rat model.	Ma S, Yeom J, Lim YH.	Sci Rep	10.1038/s41598-020-62497-8	2020
	MALDI-TOF MS versus VITEK 2 ANC card for identification of anaerobic bacteria.	Li Y, Gu B, Liu G, Xia W, Fan K, Mei Y, Huang P, Pan S.	J Thorac Dis	10.3978/j.issn.2072-1439.2014.02.15	2014
	Combined metabolic activators therapy ameliorates liver fat in nonalcoholic fatty liver disease patients.	Zeybel M, Altay O, Arif M, Li X, Yang H, Fredolini C, Akyildiz M, Saglam B, Gonenli MG, Ural D, Kim W, Schwenk JM, Zhang C, Shoaie S, Nielsen J, Uhlen M, Boren J, Mardinoglu A.	Mol Syst Biol	10.15252/msb.202110459	2021
Pathogenicity	In vitro interactions of Alternaria mycotoxins, an emerging class of food contaminants, with the gut microbiota: a bidirectional relationship.	Crudo F, Aichinger G, Mihajlovic J, Varga E, Dellafiora L, Warth B, Dall'Asta C, Berry D, Marko D.	Arch Toxicol	10.1007/s00204-021-03043-x	2021
	Association of Flavonifractor plautii, a Flavonoid-Degrading Bacterium, with the Gut Microbiome of Colorectal Cancer Patients in India.	Gupta A, Dhakan DB, Maji A, Saxena R, P K VP, Mahajan S, Pulikkan J, Kurian J, Gomez AM, Scaria J, Amato KR, Sharma AK, Sharma VK.	mSystems	10.1128/msystems.00438-19	2019
Metabolism	The 3-O-sulfation of heparan sulfate modulates protein binding and lyase degradation.	Chopra P, Joshi A, Wu J, Lu W, Yadavalli T, Wolfert MA, Shukla D, Zaia J, Boons GJ.	Proc Natl Acad Sci U S A	10.1073/pnas.2012935118	2021
	Permissive microbiome characterizes human subjects with a neurovascular disease cavernous angioma.	Polster SP, Sharma A, Tanes C, Tang AT, Mericko P, Cao Y, Carrion-Penagos J, Girard R, Koskimaki J, Zhang D, Stadnik A, Romanos SG, Lyne SB, Shenkar R, Yan K, Lee C, Akers A, Morrison L, Robinson M, Zafar A, Bittinger K, Kim H, Gilbert JA, Kahn ML, Shen L, Awad IA.	Nat Commun	10.1038/s41467-020-16436-w	2020
Pathogenicity	Probiotic-directed modulation of gut microbiota is basal microbiome dependent.	Hou Q, Zhao F, Liu W, Lv R, Khine WWT, Han J, Sun Z, Lee YK, Zhang H.	Gut Microbes	10.1080/19490976.2020.1736974	2020
	Faecal microbiota transplantation halts progression of human new-onset type 1 diabetes in a randomised controlled trial.	de Groot P, Nikolic T, Pellegrini S, Sordi V, Imangaliyev S, Rampanelli E, Hanssen N, Attaye I, Bakker G, Duinkerken G, Joosten A, Prodan A, Levin E, Levels H, Potter van Loon B, van Bon A, Brouwer C, van Dam S, Simsek S, van Raalte D, Stam F, Gerdes V, Hoogma R, Diekman M, Gerding M, Rustemeijer C, de Bakker B, Hoekstra J, Zwinderman A, Bergman J, Holleman F, Piemonti L, De Vos W, Roep B, Nieuwdorp M.	Gut	10.1136/gutjnl-2020-322630	2021
Enzymology	Genetic transformation of Porphyromonas gingivalis by electroporation.	Yoshimoto H, Takahashi Y, Hamada N, Umemoto T.	Oral Microbiol Immunol	10.1111/j.1399-302x.1993.tb00561.x	1993
	Eating Fermented: Health Benefits of LAB-Fermented Foods.	Castellone V, Bancalari E, Rubert J, Gatti M, Neviani E, Bottari B.	Foods	10.3390/foods10112639	2021
	Assessment of the microbiota in microdissected tissues of Crohn's disease patients.	De Hertogh G, Lemmens B, Verhasselt P, de Hoogt R, Sagaert X, Joossens M, Van Assche G, Rutgeerts P, Vermeire S, Aerssens J.	Int J Inflam	10.1155/2012/505674	2012
Pathogenicity	Alcohol-associated intestinal dysbiosis impairs pulmonary host defense against Klebsiella pneumoniae.	Samuelson DR, Shellito JE, Maffei VJ, Tague ED, Campagna SR, Blanchard EE, Luo M, Taylor CM, Ronis MJJ, Molina PE, Welsh DA.	PLoS Pathog	10.1371/journal.ppat.1006426	2017
Enzymology	Biliary Microbiota, Gallstone Disease and Infection with Opisthorchis felineus.	Saltykova IV, Petrov VA, Logacheva MD, Ivanova PG, Merzlikin NV, Sazonov AE, Ogorodova LM, Brindley PJ.	PLoS Negl Trop Dis	10.1371/journal.pntd.0004809	2016
Enzymology	Succinivibrionaceae is dominant family in fecal microbiota of Behçet's Syndrome patients with uveitis.	Tecer D, Gogus F, Kalkanci A, Erdogan M, Hasanreisoglu M, Ergin C, Karakan T, Kozan R, Coban S, Diker KS.	PLoS One	10.1371/journal.pone.0241691	2020
	A Multi-omics Approach to Unraveling the Microbiome-Mediated Effects of Arabinoxylan Oligosaccharides in Overweight Humans.	Benitez-Paez A, Kjolbaek L, Gomez Del Pulgar EM, Brahe LK, Astrup A, Matysik S, Schott HF, Krautbauer S, Liebisch G, Boberska J, Claus S, Rampelli S, Brigidi P, Larsen LH, Sanz Y.	mSystems	10.1128/msystems.00209-19	2019
	Early-Life Events, Including Mode of Delivery and Type of Feeding, Siblings and Gender, Shape the Developing Gut Microbiota.	Martin R, Makino H, Cetinyurek Yavuz A, Ben-Amor K, Roelofs M, Ishikawa E, Kubota H, Swinkels S, Sakai T, Oishi K, Kushiro A, Knol J.	PLoS One	10.1371/journal.pone.0158498	2016
Genetics	Abnormal fecal microbiota community and functions in patients with hepatitis B liver cirrhosis as revealed by a metagenomic approach.	Wei X, Yan X, Zou D, Yang Z, Wang X, Liu W, Wang S, Li X, Han J, Huang L, Yuan J.	BMC Gastroenterol	10.1186/1471-230x-13-175	2013
Metabolism	Intermedilysin cytolytic activity depends on heparan sulfates and membrane composition.	Drabavicius G, Drabavicius G, Daelemans D.	PLoS Genet	10.1371/journal.pgen.1009387	2021
Metabolism	Heparan sulfate is essential for thymus growth.	Hsu HP, Chen YT, Chen YY, Lin CY, Chen PY, Liao SY, Lim CCY, Yamaguchi Y, Hsu CL, Dzhagalov IL.	J Biol Chem	10.1016/j.jbc.2021.100419	2021
	Role of the gut microbiome in three major psychiatric disorders.	Borkent J, Ioannou M, Laman JD, Haarman BCM, Sommer IEC, Sommer IEC.	Psychol Med	10.1017/s0033291722000897	2022
	Distinct Microbiome-Neuroimmune Signatures Correlate With Functional Abdominal Pain in Children With Autism Spectrum Disorder.	Luna RA, Oezguen N, Balderas M, Venkatachalam A, Runge JK, Versalovic J, Veenstra-VanderWeele J, Anderson GM, Savidge T, Williams KC.	Cell Mol Gastroenterol Hepatol	10.1016/j.jcmgh.2016.11.008	2017
Metabolism	A novel approach for the prediction of species-specific biotransformation of xenobiotic/drug molecules by the human gut microbiota.	Sharma AK, Jaiswal SK, Chaudhary N, Sharma VK.	Sci Rep	10.1038/s41598-017-10203-6	2017
Enzymology	Microbial enterotypes, inferred by the prevotella-to-bacteroides ratio, remained stable during a 6-month randomized controlled diet intervention with the new nordic diet.	Roager HM, Licht TR, Poulsen SK, Larsen TM, Bahl MI.	Appl Environ Microbiol	10.1128/aem.03549-13	2014
Metabolism	Administration of Inulin-Supplemented Gluten-Free Diet Modified Calcium Absorption and Caecal Microbiota in Rats in a Calcium-Dependent Manner.	Krupa-Kozak U, Markiewicz LH, Lamparski G, Juskiewicz J.	Nutrients	10.3390/nu9070702	2017
	Identification of Specific Oral and Gut Pathogens in Full Thickness Colon of Colitis Patients: Implications for Colon Motility.	Dinakaran V, Mandape SN, Shuba K, Pratap S, Sakhare SS, Tabatabai MA, Smoot DT, Farmer-Dixon CM, Kesavalu LN, Adunyah SE, Southerland JH, Gangula PR.	Front Microbiol	10.3389/fmicb.2018.03220	2018
Phylogeny	Host contributes to longitudinal diversity of fecal microbiota in swine selected for lean growth.	Lu D, Tiezzi F, Schillebeeckx C, McNulty NP, Schwab C, Shull C, Maltecca C.	Microbiome	10.1186/s40168-017-0384-1	2018
Pathogenicity	Salmonella enterica Serovar Typhimurium Temporally Modulates the Enteric Microbiota and Host Responses To Overcome Colonization Resistance in Swine.	Bescucci DM, Moote PE, Ortega Polo R, Uwiera RRE, Inglis GD.	Appl Environ Microbiol	10.1128/aem.01569-20	2020
Pathogenicity	Impact of genistein on the gut microbiome of humanized mice and its role in breast tumor inhibition.	Paul B, Royston KJ, Li Y, Stoll ML, Skibola CF, Wilson LS, Barnes S, Morrow CD, Tollefsbol TO.	PLoS One	10.1371/journal.pone.0189756	2017
Genetics	The impact of sequence database choice on metaproteomic results in gut microbiota studies.	Tanca A, Palomba A, Fraumene C, Pagnozzi D, Manghina V, Deligios M, Muth T, Rapp E, Martens L, Addis MF, Uzzau S.	Microbiome	10.1186/s40168-016-0196-8	2016
Genetics	In vitro culture conditions for maintaining a complex population of human gastrointestinal tract microbiota.	Kim BS, Kim JN, Cerniglia CE.	J Biomed Biotechnol	10.1155/2011/838040	2011
	Structural and functional characterization of shaft, anchor, and tip proteins of the Mfa1 fimbria from the periodontal pathogen Porphyromonas gingivalis.	Hall M, Hasegawa Y, Yoshimura F, Persson K.	Sci Rep	10.1038/s41598-018-20067-z	2018
	Bacterial sensor Nod2 prevents inflammation of the small intestine by restricting the expansion of the commensal Bacteroides vulgatus.	Ramanan D, Tang MS, Bowcutt R, Loke P, Cadwell K.	Immunity	10.1016/j.immuni.2014.06.015	2014
Enzymology	Establishment of intestinal microbiota during early life: a longitudinal, explorative study of a large cohort of Danish infants.	Bergstrom A, Skov TH, Bahl MI, Roager HM, Christensen LB, Ejlerskov KT, Molgaard C, Michaelsen KF, Licht TR.	Appl Environ Microbiol	10.1128/aem.00342-14	2014
Pathogenicity	Occurrence of enterotoxigenic and nonenterotoxigenic Bacteroides fragilis in calves and evaluation of their antimicrobial susceptibility.	Almeida FS, Nakano V, Avila-Campos MJ.	FEMS Microbiol Lett	10.1111/j.1574-6968.2007.00732.x	2007
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
Phylogeny	Real-time analysis of gut flora in Entamoeba histolytica infected patients of Northern India.	Verma AK, Verma R, Ahuja V, Paul J.	BMC Microbiol	10.1186/1471-2180-12-183	2012
	Pathogenic potential of Campylobacter ureolyticus.	Burgos-Portugal JA, Kaakoush NO, Raftery MJ, Mitchell HM.	Infect Immun	10.1128/iai.06031-11	2012
Metabolism	Deorphanizing FAM19A proteins as pan-neurexin ligands with an unusual biosynthetic binding mechanism.	Khalaj AJ, Sterky FH, Sclip A, Schwenk J, Brunger AT, Fakler B, Sudhof TC.	J Cell Biol	10.1083/jcb.202004164	2020
Genetics	Comparative Genomic Analysis of the Human Gut Microbiome Reveals a Broad Distribution of Metabolic Pathways for the Degradation of Host-Synthetized Mucin Glycans and Utilization of Mucin-Derived Monosaccharides.	Ravcheev DA, Thiele I.	Front Genet	10.3389/fgene.2017.00111	2017
	Longitudinal analysis of the prevalence, maintenance, and IgA response to species of the order Bacteroidales in the human gut.	Zitomersky NL, Coyne MJ, Comstock LE.	Infect Immun	10.1128/iai.01348-10	2011
Metabolism	The induction of colitis and ileitis in mice is associated with marked increases in intestinal concentrations of stimulants of TLRs 2, 4, and 5.	Erridge C, Duncan SH, Bereswill S, Heimesaat MM.	PLoS One	10.1371/journal.pone.0009125	2010
Metabolism	Characterization of glycosaminoglycan (GAG) sulfatases from the human gut symbiont Bacteroides thetaiotaomicron reveals the first GAG-specific bacterial endosulfatase.	Ulmer JE, Vilen EM, Namburi RB, Benjdia A, Beneteau J, Malleron A, Bonnaffe D, Driguez PA, Descroix K, Lassalle G, Le Narvor C, Sandstrom C, Spillmann D, Berteau O.	J Biol Chem	10.1074/jbc.m114.573303	2014
Phylogeny	PCR-restriction fragment length polymorphism analysis for identification of Bacteroides spp. and characterization of nitroimidazole resistance genes.	Stubbs SL, Brazier JS, Talbot PR, Duerden BI.	J Clin Microbiol	10.1128/jcm.38.9.3209-3213.2000	2000
Phylogeny	New degenerate Cytophaga-Flexibacter-Bacteroides-specific 16S ribosomal DNA-targeted oligonucleotide probes reveal high bacterial diversity in River Taff epilithon.	O'Sullivan LA, Weightman AJ, Fry JC.	Appl Environ Microbiol	10.1128/aem.68.1.201-210.2002	2002
Enzymology	Quantitative multiplexing analysis of PCR-amplified ribosomal RNA genes by hierarchical oligonucleotide primer extension reaction.	Wu JH, Liu WT.	Nucleic Acids Res	10.1093/nar/gkm413	2007
	Ecological characterization of the colonic microbiota of normal and diarrheic dogs.	Bell JA, Kopper JJ, Turnbull JA, Barbu NI, Murphy AJ, Mansfield LS.	Interdiscip Perspect Infect Dis	10.1155/2008/149694	2008
Pathogenicity	Multicenter survey of the changing in vitro antimicrobial susceptibilities of clinical isolates of Bacteroides fragilis group, Prevotella, Fusobacterium, Porphyromonas, and Peptostreptococcus species.	Aldridge KE, Ashcraft D, Cambre K, Pierson CL, Jenkins SG, Rosenblatt JE.	Antimicrob Agents Chemother	10.1128/aac.45.4.1238-1243.2001	2001
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
Phylogeny	Genome-Based Taxonomic Classification of Bacteroidetes.	Hahnke RL, Meier-Kolthoff JP, Garcia-Lopez M, Mukherjee S, Huntemann M, Ivanova NN, Woyke T, Kyrpides NC, Klenk HP, Goker M.	Front Microbiol	10.3389/fmicb.2016.02003	2016
Phylogeny	Direct analysis of genes encoding 16S rRNA from complex communities reveals many novel molecular species within the human gut.	Suau A, Bonnet R, Sutren M, Godon JJ, Gibson GR, Collins MD, Dore J.	Appl Environ Microbiol	10.1128/aem.65.11.4799-4807.1999	1999
	Evidence for extensive resistance gene transfer among Bacteroides spp. and among Bacteroides and other genera in the human colon.	Shoemaker NB, Vlamakis H, Hayes K, Salyers AA.	Appl Environ Microbiol	10.1128/aem.67.2.561-568.2001	2001
Enzymology	Cloning, expression, and characterization of a novel heparinase I from Bacteroides eggerthii.	Liu CY, Su WB, Guo LB, Zhang YW	Prep Biochem Biotechnol	10.1080/10826068.2019.1709977	2020
Phylogeny	Paraphocaeicola brunensis gen. nov., sp. nov., Carrying Two Variants of nimB Resistance Gene from Bacteroides fragilis, and Caecibacteroides pullorum gen. nov., sp. nov., Two Novel Genera Isolated from Chicken Caeca.	Kralova S, Davidova-Gerzova L, Valcek A, Bezdicek M, Rychlik I, Rezacova V, Cizek A.	Microbiol Spectr	10.1128/spectrum.01954-21	2022
Phylogeny	Bacteroides barnesiae sp. nov., Bacteroides salanitronis sp. nov. and Bacteroides gallinarum sp. nov., isolated from chicken caecum.	Lan PTN, Sakamoto M, Sakata S, Benno Y	Int J Syst Evol Microbiol	10.1099/ijs.0.64517-0	2006

References

#9017	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 20697
#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 )
#41096	; Curators of the CIP;
#45195	Culture Collection University of Gothenburg (CCUG) ; Curators of the CCUG; CCUG 9559
#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;
#68380	Automatically annotated from API rID32A .
#68381	Automatically annotated from API rID32STR .
#69479	João F Matias Rodrigues, Janko Tackmann,Gregor Rot, Thomas SB Schmidt, Lukas Malfertheiner, Mihai Danaila,Marija Dmitrijeva, Daniela Gaio, Nicolas Näpflin and Christian von Mering. University of Zurich.: MicrobeAtlas 1.0 beta .
#118999	Collection of Institut Pasteur ; Curators of the CIP; CIP 104285
#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 eggerthii (DSM 20697, ATCC 27754, NCTC 11155)

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 rID32A

API rID32STR

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_025146565

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

Help

Social Media