Bacteroides uniformis (CCUG 4942, JCM 5828, CIP 103695)

Name: Bacteroides uniformis (CCUG 4942, JCM 5828, CIP 103695)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 1604

Type strain

Culture col. no. CCUG 4942 JCM 5828 CIP 103695 KCTC 5204 DSM 6597 4 more

NCBI tax ID(s) 411479 820

Special Collections DSMZ CCUG JCM KCTC CIP

History DSMZ <- ATCC <- A.H. Eggerth (Bacteroides thetaiotaomicron) KCTC <- JCM <- ATCC 8492 <- AH Eggerth, Bacteroides thetaiotaomicron` JCM <-- ATCC 8492 <-- A. H. Eggerth (Bacteroides thetaiotaomicron).

Links

Bacteroides uniformis CCUG 4942 is an anaerobe, rod-shaped bacterium that was isolated from human faeces.

rod-shaped anaerobe genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 34970

ATCC 8492,CCUG 4942,CIP 103695,DSM 6597,JCM 5828,NCTC 13054,KCTC 5204,LMG 28904,ATCC 8942

@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 uniformis

Full scientific name Bacteroides uniformis Eggerth and Gagnon 1933 (Approved Lists 1980)

BacDive ID	Other strains from **Bacteroides uniformis** (14)	Type strain
1605	B. uniformis mprl 1841, DSM 9672
147140	B. uniformis CCUG 32930
148471	B. uniformis CCUG 35501
150459	B. uniformis CCUG 39989
153424	B. uniformis CCUG 49527
156940	B. uniformis CCUG 67191
159170	B. uniformis H1_6, DSM 108145
159171	B. uniformis H4_4, DSM 108146
159172	B. uniformis H4_7, DSM 108147
159173	B. uniformis H5_2, DSM 108148
161337	B. uniformis JCM 13286
161338	B. uniformis JCM 13287
161339	B. uniformis JCM 13288
169338	B. uniformis CLA-AV-11, DSM 110080

Morphology

Cell morphology

@ref	Cell shape	Gram stain	Confidence
68367	rod-shaped			from API 20A
68367		negative		from API 20A
67771	rod-shaped
67771		negative
125439		negative	92.932
125438		negative	94.181

Colony morphology

@ref	Type of hemolysis	Hemolysis ability	Incubation period
2742	gamma	0	1-2 days

Culture and growth conditions

Culture medium

@ref	Name	Medium link	Composition
2742	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
2742	CHOPPED MEAT MEDIUM (DSMZ Medium 78)	Medium recipe at MediaDive	Name: CHOPPED MEAT MEDIUM (DSMZ Medium 78) Composition: Ground beef 500.0 g/l Casitone 30.0 g/l Agar 15.0 g/l Ethanol 9.5 g/l (optional) K2HPO4 5.0 g/l Yeast extract 5.0 g/l L-Cysteine HCl 0.5 g/l Haemin 0.005 g/l (optional) Resazurin 0.001 g/l Vitamin K3 0.0005 g/l (optional) Vitamin K1 (optional) NaOH (optional) Distilled water
32718	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)
2742	FASTIDIOUS ANAEROBE BROTH (DSMZ Medium 1203a)	Medium recipe at MediaDive	Name: FASTIDIOUS ANAEROBE BROTH (DSMZ Medium 1203a) Composition: Fastidious Anaerobe Basal Broth 35.4 g/l Distilled water

Culture temp

@ref	Growth	Type	Temperature (°C)
2742	positive	growth	37
32718	positive	growth	37
44812	positive	growth	37
67770	positive	growth	37
67771	positive	growth	37

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
2742	anaerobe
44812	anaerobe
44812	microaerophile
67771	anaerobe
125439	obligate anaerobe	97.674

Spore formation

@ref	Confidence
68367		from API 20A
67771
125438	91.478
125439	99.851

Observation

@ref	Observation
67770	quinones: MK-10, MK-11
67771	quinones: MK-10, MK-11

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
68380	29016 ChEBI	arginine	-	hydrolysis	from API rID32A
68367	17057 ChEBI	cellobiose	+	builds acid from	from API 20A
68367	17634 ChEBI	D-glucose	+	builds acid from	from API 20A
68367	16899 ChEBI	D-mannitol	-	builds acid from	from API 20A
68380	16024 ChEBI	D-mannose	+	fermentation	from API rID32A
68367	16024 ChEBI	D-mannose	+	builds acid from	from API 20A
68367	65327 ChEBI	D-xylose	+	builds acid from	from API 20A
68367	4853 ChEBI	esculin	+	hydrolysis	from API 20A
68367	5291 ChEBI	gelatin	-	hydrolysis	from API 20A
68367	17754 ChEBI	glycerol	-	builds acid from	from API 20A
68367	30849 ChEBI	L-arabinose	+	builds acid from	from API 20A
68380	29985 ChEBI	L-glutamate	+	degradation	from API rID32A
68367	17716 ChEBI	lactose	+	builds acid from	from API 20A
68367	17306 ChEBI	maltose	+	builds acid from	from API 20A
68367	6731 ChEBI	melezitose	-	builds acid from	from API 20A
68380	17632 ChEBI	nitrate	-	reduction	from API rID32A
68367	16634 ChEBI	raffinose	+	builds acid from	from API 20A
68367	17814 ChEBI	salicin	+	builds acid from	from API 20A
68367	30911 ChEBI	sorbitol	-	builds acid from	from API 20A
68367	17992 ChEBI	sucrose	+	builds acid from	from API 20A
68380	27897 ChEBI	tryptophan	+	energy source	from API rID32A
68367	27897 ChEBI	tryptophan	+	energy source	from API 20A
68380	16199 ChEBI	urea	-	hydrolysis	from API rID32A
68367	16199 ChEBI	urea	-	hydrolysis	from API 20A

Metabolite production

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

Metabolite tests

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

Enzymes

@ref	Value	Activity	Ec
68380	alanine arylamidase	+	3.4.11.2	from API rID32A
68380	alkaline phosphatase	+	3.1.3.1	from API rID32A
68380	alpha-arabinosidase	+	3.2.1.55	from API rID32A
68380	alpha-galactosidase	+	3.2.1.22	from API rID32A
68380	alpha-glucosidase	+	3.2.1.20	from API rID32A
68380	arginine dihydrolase	-	3.5.3.6	from API rID32A
68380	beta-galactosidase	+	3.2.1.23	from API rID32A
68380	beta-Galactosidase 6-phosphate	-		from API rID32A
68380	beta-glucosidase	+	3.2.1.21	from API rID32A
68367	beta-glucosidase	+	3.2.1.21	from API 20A
68380	beta-glucuronidase	-	3.2.1.31	from API rID32A
68367	catalase	-	1.11.1.6	from API 20A
68367	gelatinase	-		from API 20A
68380	glutamate decarboxylase	+	4.1.1.15	from API rID32A
68380	glutamyl-glutamate arylamidase	+		from API rID32A
68380	glycin arylamidase	-		from API rID32A
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
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
68367	urease	-	3.5.1.5	from API 20A

API 20A

@ref	IND	URE	GLU	MAN	LAC	SAC	MAL	SAL	XYL	ARA	GEL	ESC	GLY	CEL	MNE	MLZ	RAF	SOR	RHA	TRE	CAT	Spores presentSPOR	GramGRAM	Morphology coccus="+" rod="-"COCC
2742	+	-	+	-	+	+	+	+	+	+	-	+	-	+	+	-	+	-	-	-	-	-	-	-
2742	+	-	+	-	+	+	+	+	+	+	-	+	-	+	+	-	+	-	+/-	+	not determinedn.d.	not determinedn.d.	not determinedn.d.	not determinedn.d.

API rID32A

@ref	URE	ADH (Arg)	alpha GAL	beta GAL	beta-Galactosidase 6-phosphatebeta GP	alpha GLU	beta GLU	alpha ARA	beta GUR	beta-N-Acetyl-beta-glucosaminidasebeta NAG	MNE	RAF	GDC	alpha FUC	Reduction of nitrateNIT	IND	PAL	L-arginine arylamidaseArgA	ProA	LGA	Phenylalanine arylamidasePheA	Leucine arylamidaseLeuA	PyrA	Tyrosine arylamidaseTyrA	Alanine arylamidaseAlaA	Glycin arylamidaseGlyA	Histidine arylamidaseHisA	Glutamyl-glutamate arylamidaseGGA	Serine arylamidaseSerA
2742	-	-	+	+	-	+	+	+	-	+	+	-	+	+/-	-	+	+	-	-	+	-	-	-	-	+	-	-	+	-
2742	-	-	+	+	-	+	+	+	-	+	+	-	+	+	-	+	+	-	-	+	-	-	-	-	+	-	-	+	-
2742	-	-	+	+	-	+	+	+	-	+	+	+	+	+	-	+	+	-	-	+	-	-	-	-	+	-	-	+	-
2742	-	-	+	+	-	+	+	+	-	+	+	+	+	+	-	+	+	-	-	+	-	-	-	-	+	-	-	+	-
2742	-	-	+	+	-	+	+	+	-	+	+	-	+	+/-	-	+	+	-	-	+	-	-	-	-	+	-	-	+	-
2742	-	-	+	+	-	+	+	+	-	+	+	+	+	+	-	+	+	-	-	+	-	-	-	-	+	-	-	+	-
2742	-	-	+	+	-	+	+	+	-	+	+	-	+	+	-	+	+	-	-	+	-	-	-	-	+	-	-	+	-

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
2742	human faeces	Homo sapiens
67770	Human feces	Homo sapiens
67771	From human faeces	Homo sapiens

Taxonmaps

69479

Global distribution of 16S sequence AB510711 (>99% sequence identity) for Bacteroides uniformis from Microbeatlas

Aquatic Samples	15505
Soil Samples	4816
Animal Samples	363541
Plant Samples	1489
Total Samples	385351

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
2742	2	Risk group (German classification) According to TRBA 466

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
66792	ASM2514748v1 assembly for Bacteroides uniformis ATCC 8492	complete	GCA_025147485	820.5953	8119509655	820	97.91
124043	ASM1611781v1 assembly for Bacteroides uniformis FDAARGOS_901	chromosome	GCA_016117815	820.5080		820	88.45
124043	ASM5127483v1 assembly for Bacteroides uniformis DSM 6597	contig	GCA_051274835			820	77.29
67770	ASM295962v1 assembly for Phocaeicola vulgatus ATCC 8492	contig	GCA_002959625	821.336	2904834026	821	72.17
67770	IMG-taxon 2693429911 annotated assembly for Bacteroides uniformis DSM 6597	contig	GCA_900107315	820.37	2693429911	820	68.75
66792	ASM15420v1 assembly for Bacteroides uniformis ATCC 8492	scaffold	GCA_000154205	411479.10	641380447	411479	68.17
66792	ASM2853928v1 assembly for Bacteroides uniformis ATCC 8492	contig	GCA_028539285	820.6459		820	60.44
66792	81A2 assembly for Bacteroides uniformis ATCC 8492	contig	GCA_900624705	411479.31	2916274279	411479	58
66792	Bacteroides uniformis 82G1 assembly for Bacteroides uniformis ATCC 8492	contig	GCA_900896415	411479.32		411479	20.07

16S sequences

@ref	Description	Accession	Length	NCBI tax ID
20218	Bacteroides uniformis 16S-23S rDNA intergenic spacer region	AF176692	485	820
20218	Bacteroides uniformis ATCC 8492 16S ribosomal RNA gene, complete sequence	L16486	1469	820
2742	Bacteroides uniformis gene for 16S rRNA, partial sequence	AB050110	1425	820
67770	Bacteroides uniformis gene for 16S ribosomal RNA, partial sequence, strain: JCM 5828	AB510711	1477	820
124043	Bacteroides uniformis strain JCM5828 16S ribosomal RNA gene, partial sequence.	EU136680	2019	820

GC content

@ref	GC-content (mol%)	Method
2742	46.0	thermal denaturation, midpoint method (Tm)
2742	46.4	sequence analysis
67771	47.8	high performance liquid chromatography (HPLC)
67771	46.4	genome sequence analysis
67770	46	thermal denaturation, midpoint method (Tm)

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: ASM2514748v1 assembly for Bacteroides uniformis ATCC 8492
BV-BRC: 820.5953

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	oxygen_tolerance	BacteriaNetⓘ	obligate anaerobe	97.67	no
125439	gram_stain	BacteriaNetⓘ	negative	92.93	no
125439	motility	BacteriaNetⓘ	no	71.39	no
125439	spore_formation	BacteriaNetⓘ	no	99.85	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Bacteroides uniformis strain FDAARGOS_901 strain Not applicable
PATRIC: 820.5080

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	94.18	yes
125438	anaerobic	anaerobicⓘ	yes	88.00	no
125438	aerobic	aerobicⓘ	no	95.79	yes
125438	spore-forming	spore-formingⓘ	no	91.48	yes
125438	thermophilic	thermophileⓘ	no	96.97	yes
125438	flagellated	motile2+ⓘ	no	89.75	yes

Literature

Topic	Title	Authors	Journal	DOI	Year
Metabolism	Linear and branched beta-Glucans degrading enzymes from versatile Bacteroides uniformis JCM 13288^T and their roles in cooperation with gut bacteria.	Singh RP, Rajarammohan S, Thakur R, Hassan M.	Gut Microbes	10.1080/19490976.2020.1826761	2020
	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 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
Genetics	A simple method that enhances minority species detection in the microbiota: 16S metagenome-DRIP (Deeper Resolution using an Inhibitory Primer).	Nakajima A, Yoshida K, Gotoh A, Katoh T, Ojima MN, Sakanaka M, Xiao JZ, Odamaki T, Katayama T.	Microbiome Res Rep	10.20517/mrr.2022.08	2022
Genetics	The estrobolome: Estrogen-metabolizing pathways of the gut microbiome and their relation to breast cancer.	Larnder AH, Manges AR, Murphy RA.	Int J Cancer	10.1002/ijc.35427	2025
	Dissecting the role of the gut microbiome and fecal microbiota transplantation in radio- and immunotherapy treatment of colorectal cancer.	Van Dingenen L, Segers C, Wouters S, Mysara M, Leys N, Kumar-Singh S, Malhotra-Kumar S, Van Houdt R.	Front Cell Infect Microbiol	10.3389/fcimb.2023.1298264	2023
	Carotenoid productivity in human intestinal bacteria Eubacterium limosum and Leuconostoc mesenteroides with functional analysis of their carotenoid biosynthesis genes.	Matsumoto W, Takemura M, Nanaura H, Ami Y, Maoka T, Shindo K, Kurihara S, Misawa N.	Eng Microbiol	10.1016/j.engmic.2024.100147	2024
	The crosstalk between the gut microbiota and tumor immunity: Implications for cancer progression and treatment outcomes.	Wang M, Zhang L, Chang W, Zhang Y.	Front Immunol	10.3389/fimmu.2022.1096551	2022
Metabolism	Bacterial species involved in the conversion of dietary flavonoids in the human gut.	Braune A, Blaut M.	Gut Microbes	10.1080/19490976.2016.1158395	2016
	A review on the role of gut microbiota in immune checkpoint blockade therapy for cancer.	Kim E, Ahn H, Park H.	Mamm Genome	10.1007/s00335-021-09867-3	2021
Enzymology	Enzymatic Metabolism of Flavonoids by Gut Microbiota and Its Impact on Gastrointestinal Cancer.	Al-Ishaq RK, Liskova A, Kubatka P, Busselberg D.	Cancers (Basel)	10.3390/cancers13163934	2021
Metabolism	Probiotics in human gut microbiota can degrade host glycosaminoglycans.	Kawai K, Kamochi R, Oiki S, Murata K, Hashimoto W.	Sci Rep	10.1038/s41598-018-28886-w	2018
Metabolism	Glucuronides in the gut: Sugar-driven symbioses between microbe and host.	Pellock SJ, Redinbo MR.	J Biol Chem	10.1074/jbc.r116.767434	2017
	Next-generation prebiotic promotes selective growth of bifidobacteria, suppressing Clostridioides difficile.	Hirano R, Sakanaka M, Yoshimi K, Sugimoto N, Eguchi S, Yamauchi Y, Nara M, Maeda S, Ami Y, Gotoh A, Katayama T, Iida N, Kato T, Ohno H, Fukiya S, Yokota A, Nishimoto M, Kitaoka M, Nakai H, Kurihara S.	Gut Microbes	10.1080/19490976.2021.1973835	2021
	New Insights Into the Cancer-Microbiome-Immune Axis: Decrypting a Decade of Discoveries.	Jain T, Sharma P, Are AC, Vickers SM, Dudeja V.	Front Immunol	10.3389/fimmu.2021.622064	2021
Phylogeny	Age-related changes in gut microbiota composition from newborn to centenarian: a cross-sectional study.	Odamaki T, Kato K, Sugahara H, Hashikura N, Takahashi S, Xiao JZ, Abe F, Osawa R.	BMC Microbiol	10.1186/s12866-016-0708-5	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
Genetics	Gut bacterial profile in patients newly diagnosed with treatment-naïve Crohn's disease.	Ricanek P, Lothe SM, Frye SA, Rydning A, Vatn MH, Tonjum T.	Clin Exp Gastroenterol	10.2147/ceg.s33858	2012
Phylogeny	Molecular diversity of rumen bacterial communities from tannin-rich and fiber-rich forage fed domestic Sika deer (Cervus nippon) in China.	Li ZP, Liu HL, Li GY, Bao K, Wang KY, Xu C, Yang YF, Yang FH, Wright AD.	BMC Microbiol	10.1186/1471-2180-13-151	2013
	Comparative analysis of prebiotic effects of four oligosaccharides using in vitro gut model: digestibility, microbiome, and metabolome changes.	Cheon S, Kim G, Bae JH, Lee DH, Seong H, Kim DH, Han JS, Lim SY, Han NS.	FEMS Microbiol Ecol	10.1093/femsec/fiad002	2023
Genetics	A synthetic gut microbiota provides an understanding of the maintenance and functional impact of phage.	Koo H, Heber K, Tian S, Connolly ST, Hao F, Zhao J, Swencki-Underwood B, Patterson AD, Townsend GE, Bisanz JE.	mBio	10.1128/mbio.02341-25	2025
	Deciphering oxidative stress responses in human gut microbes and fecal microbiota: a cultivation-based approach.	Zund JN, Caflisch M, Mujezinovic D, Pluss S, Lacroix C, Pugin B.	FEMS Microbiol Ecol	10.1093/femsec/fiaf054	2025
	How Do Prebiotics Affect Human Intestinal Bacteria?-Assessment of Bacterial Growth with Inulin and XOS In Vitro.	Schropp N, Stanislas V, Michels KB, Thriene K.	Int J Mol Sci	10.3390/ijms241612796	2023
	GABA Production by Human Intestinal Bacteroides spp.: Prevalence, Regulation, and Role in Acid Stress Tolerance.	Otaru N, Ye K, Mujezinovic D, Berchtold L, Constancias F, Cornejo FA, Krzystek A, de Wouters T, Braegger C, Lacroix C, Pugin B.	Front Microbiol	10.3389/fmicb.2021.656895	2021
Metabolism	Sulfonolipids as novel metabolite markers of Alistipes and Odoribacter affected by high-fat diets.	Walker A, Pfitzner B, Harir M, Schaubeck M, Calasan J, Heinzmann SS, Turaev D, Rattei T, Endesfelder D, Castell WZ, Haller D, Schmid M, Hartmann A, Schmitt-Kopplin P.	Sci Rep	10.1038/s41598-017-10369-z	2017
Metabolism	Polysaccharide utilization loci in Bacteroides determine population fitness and community-level interactions.	Feng J, Qian Y, Zhou Z, Ertmer S, Vivas EI, Lan F, Hamilton JJ, Rey FE, Anantharaman K, Venturelli OS.	Cell Host Microbe	10.1016/j.chom.2021.12.006	2022
	Under-Oil Autonomously Regulated Oxygen Microenvironments: A Goldilocks Principle-Based Approach for Microscale Cell Culture.	Li C, Humayun M, Walker GM, Park KY, Connors B, Feng J, Pellitteri Hahn MC, Scarlett CO, Li J, Feng Y, Clark RL, Hefti H, Schrope J, Venturelli OS, Beebe DJ.	Adv Sci (Weinh)	10.1002/advs.202104510	2022
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	Paneth Cell-Derived Lysozyme Defines the Composition of Mucolytic Microbiota and the Inflammatory Tone of the Intestine.	Yu S, Balasubramanian I, Laubitz D, Tong K, Bandyopadhyay S, Lin X, Flores J, Singh R, Liu Y, Macazana C, Zhao Y, Beguet-Crespel F, Patil K, Midura-Kiela MT, Wang D, Yap GS, Ferraris RP, Wei Z, Bonder EM, Haggblom MM, Zhang L, Douard V, Verzi MP, Cadwell K, Kiela PR, Gao N.	Immunity	10.1016/j.immuni.2020.07.010	2020
	Quantification of Slackia and Eggerthella spp. in Human Feces and Adhesion of Representatives Strains to Caco-2 Cells.	Cho GS, Ritzmann F, Eckstein M, Huch M, Briviba K, Behsnilian D, Neve H, Franz CM.	Front Microbiol	10.3389/fmicb.2016.00658	2016
	Developing standards for the microbiome field.	Amos GCA, Logan A, Anwar S, Fritzsche M, Mate R, Bleazard T, Rijpkema S.	Microbiome	10.1186/s40168-020-00856-3	2020
	Deciphering microbial interactions in synthetic human gut microbiome communities.	Venturelli OS, Carr AC, Fisher G, Hsu RH, Lau R, Bowen BP, Hromada S, Northen T, Arkin AP.	Mol Syst Biol	10.15252/msb.20178157	2018
Pathogenicity	Procyanidin-Cell Wall Interactions within Apple Matrices Decrease the Metabolization of Procyanidins by the Human Gut Microbiota and the Anti-Inflammatory Effect of the Resulting Microbial Metabolome In Vitro.	Le Bourvellec C, Bagano Vilas Boas P, Lepercq P, Comtet-Marre S, Auffret P, Ruiz P, Bott R, Renard CMGC, Dufour C, Chatel JM, Mosoni P.	Nutrients	10.3390/nu11030664	2019
Metabolism	Diastereomer-specific quantification of bioactive hexosylceramides from bacteria and mammals.	von Gerichten J, Schlosser K, Lamprecht D, Morace I, Eckhardt M, Wachten D, Jennemann R, Grone HJ, Mack M, Sandhoff R.	J Lipid Res	10.1194/jlr.d076190	2017
Metabolism	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
Metabolism	Recurrent neural networks enable design of multifunctional synthetic human gut microbiome dynamics.	Baranwal M, Clark RL, Thompson J, Sun Z, Hero AO, Venturelli OS.	Elife	10.7554/elife.73870	2022
Enzymology	Phylogenetic analysis of faecal microbiota from captive cheetahs reveals underrepresentation of Bacteroidetes and Bifidobacteriaceae.	Becker AA, Hesta M, Hollants J, Janssens GP, Huys G.	BMC Microbiol	10.1186/1471-2180-14-43	2014
Metabolism	Intestinal integrity and Akkermansia muciniphila, a mucin-degrading member of the intestinal microbiota present in infants, adults, and the elderly.	Collado MC, Derrien M, Isolauri E, de Vos WM, Salminen S.	Appl Environ Microbiol	10.1128/aem.01477-07	2007
	Lacticaseibacillus rhamnosus LRJ-1 alleviates constipation through promoting gut Bacteroides-derived gamma-aminobutyric acid production.	Xia T, Huang F, Yun F, Liu Y, Wang T, Wang S, Jin S, Ma X, Wang W, He J, Teng K, Zhong J.	Curr Res Food Sci	10.1016/j.crfs.2024.100924	2024
	Protection against fibrosis by a bacterial consortium in metabolic dysfunction-associated steatohepatitis and the role of amino acid metabolism.	Kwan SY, Gonzales KA, Jamal MA, Stevenson HL, Tan L, Lorenzi PL, Futreal PA, Hawk ET, McCormick JB, Fisher-Hoch SP, Jenq RR, Beretta L.	Gut Microbes	10.1080/19490976.2024.2399260	2024
	Complete Genome Sequences of Two Bacteroides uniformis Bacteriophages.	Bean EM, Morella NM, Dey N.	Microbiol Resour Announc	10.1128/mra.00610-22	2022
	A combination of potential psychobiotics alleviates anxiety and depression behaviors induced by chronic unpredictable mild stress.	Meng C, Feng S, Hao Z, Liu H.	NPJ Biofilms Microbiomes	10.1038/s41522-025-00779-7	2025
	Xiaoyao San ameliorates maternal inflammation-induced neurobehavioral deficits by modulating the microbiota-gut-brain axis in offspring	Lin C, Zhu J, Zhang L, Shi L, Zhong Z, Xia X, Ding W, Yang Y.	Front Pharmacol		2025
	Artificial cellulose derivatives are metabolized by select human gut Bacteroidota upon priming with common plant beta-glucans.	Panwar D, Stewart WA, Rodd A, Brumer H.	J Bacteriol	10.1128/jb.00198-25	2025
	Gut microbiota aggravates neutrophil extracellular traps-induced pancreatic injury in hypertriglyceridemic pancreatitis.	Li G, Liu L, Lu T, Sui Y, Zhang C, Wang Y, Zhang T, Xie Y, Xiao P, Zhao Z, Cheng C, Hu J, Chen H, Xue D, Chen H, Wang G, Kong R, Tan H, Bai X, Li Z, McAllister F, Li L, Sun B.	Nat Commun	10.1038/s41467-023-41950-y	2023
	Discovery of Bacteroides uniformis F18-22 as a Safe and Novel Probiotic Bacterium for the Treatment of Ulcerative Colitis from the Healthy Human Colon.	Dai W, Zhang J, Chen L, Yu J, Zhang J, Yin H, Shang Q, Yu G.	Int J Mol Sci	10.3390/ijms241914669	2023
	Selective utilization of medicinal polysaccharides by human gut Bacteroides and Parabacteroides species.	Qu Z, Liu H, Yang J, Zheng L, Huang J, Wang Z, Xie C, Zuo W, Xia X, Sun L, Zhou Y, Xie Y, Lu J, Zhu Y, Yu L, Liu L, Zhou H, Dai L, Leung EL.	Nat Commun	10.1038/s41467-025-55845-7	2025
	A Gnotobiotic Mouse Model with Divergent Equol-Producing Phenotypes: Potential for Determining Microbial-Driven Health Impacts of Soy Isoflavone Daidzein.	Leonard LM, Simpson AMR, Li S, Reddivari L, Cross TL.	Nutrients	10.3390/nu16071079	2024
	Production of deoxycholic acid by low-abundant microbial species is associated with impaired glucose metabolism.	Wahlstrom A, Brumbaugh A, Sjoland W, Olsson L, Wu H, Henricsson M, Lundqvist A, Makki K, Hazen SL, Bergstrom G, Marschall HU, Fischbach MA, Backhed F.	Nat Commun	10.1038/s41467-024-48543-3	2024
	Diet-driven differential response of Akkermansia muciniphila modulates pathogen susceptibility.	Wolter M, Grant ET, Boudaud M, Pudlo NA, Pereira GV, Eaton KA, Martens EC, Desai MS.	Mol Syst Biol	10.1038/s44320-024-00036-7	2024
	Interbacterial warfare in the human gut: insights from Bacteroidales' perspective.	Jiang K, Pang X, Li W, Xu X, Yang Y, Shang C, Gao X.	Gut Microbes	10.1080/19490976.2025.2473522	2025
	Phylogenetic diversity of core rumen microbiota as described by cryo-ET.	Wimmer BH, Morais S, Zalk R, Mizrahi I, Medalia O.	Microlife	10.1093/femsml/uqad010	2023
	Fungal beta-glucan-facilitated cross-feeding activities between Bacteroides and Bifidobacterium species.	Fernandez-Julia P, Black GW, Cheung W, Van Sinderen D, Munoz-Munoz J.	Commun Biol	10.1038/s42003-023-04970-4	2023
Pathogenicity	Quantifying the varying harvest of fermentation products from the human gut microbiota.	Arnoldini M, Sharma R, Moresi C, Chure G, Chabbey J, Slack E, Cremer J.	Cell	10.1016/j.cell.2025.07.005	2025
	Serotonergic and immunomodulatory properties of the psychobiotic candidate Bacteroides finegoldii UO.H1052 and its extracellular vesicles.	Yousuf B, Esmail GA, Nazemof N, Bouhlel NE, Minic Z, Hammami R.	Appl Environ Microbiol	10.1128/aem.00891-25	2025
Metabolism	Synergy between Cell Surface Glycosidases and Glycan-Binding Proteins Dictates the Utilization of Specific Beta(1,3)-Glucans by Human Gut Bacteroides.	Dejean G, Tamura K, Cabrera A, Jain N, Pudlo NA, Pereira G, Viborg AH, Van Petegem F, Martens EC, Brumer H.	mBio	10.1128/mbio.00095-20	2020
Pathogenicity	A bacterial sialidase mediates early-life colonization by a pioneering gut commensal.	Buzun E, Hsu CY, Sejane K, Oles RE, Vasquez Ayala A, Loomis LR, Zhao J, Rossitto LA, McGrosso DM, Gonzalez DJ, Bode L, Chu H.	Cell Host Microbe	10.1016/j.chom.2023.12.014	2024
Enzymology	Cell Surface Xyloglucan Recognition and Hydrolysis by the Human Gut Commensal Bacteroides uniformis.	Grondin JM, Dejean G, Van Petegem F, Brumer H.	Appl Environ Microbiol	10.1128/aem.01566-21	2022
	Basis of narrow-spectrum activity of fidaxomicin on Clostridioides difficile.	Cao X, Boyaci H, Chen J, Bao Y, Landick R, Campbell EA.	Nature	10.1038/s41586-022-04545-z	2022
Genetics	Microbial characterization based on multifractal analysis of metagenomes.	Xie XH, Huang YJ, Han GS, Yu ZG, Ma YL.	Front Cell Infect Microbiol	10.3389/fcimb.2023.1117421	2023
Genetics	Discovery of antimicrobial peptides in the global microbiome with machine learning.	Santos-Junior CD, Torres MDT, Duan Y, Rodriguez Del Rio A, Schmidt TSB, Chong H, Fullam A, Kuhn M, Zhu C, Houseman A, Somborski J, Vines A, Zhao XM, Bork P, Huerta-Cepas J, de la Fuente-Nunez C, Coelho LP.	Cell	10.1016/j.cell.2024.05.013	2024
Pathogenicity	Oral Supplements of Combined Bacillus licheniformis Zhengchangsheng® and Xylooligosaccharides Improve High-Fat Diet-Induced Obesity and Modulate the Gut Microbiota in Rats.	Li Y, Liu M, Liu H, Wei X, Su X, Li M, Yuan J.	Biomed Res Int	10.1155/2020/9067821	2020
Metabolism	The Glycolytic Versatility of Bacteroides uniformis CECT 7771 and Its Genome Response to Oligo and Polysaccharides.	Benitez-Paez A, Gomez Del Pulgar EM, Sanz Y.	Front Cell Infect Microbiol	10.3389/fcimb.2017.00383	2017
	Cellular homologs of the double jelly-roll major capsid proteins clarify the origins of an ancient virus kingdom.	Krupovic M, Makarova KS, Koonin EV.	Proc Natl Acad Sci U S A	10.1073/pnas.2120620119	2022
	Scalable and cost-effective ribonuclease-based rRNA depletion for transcriptomics.	Huang Y, Sheth RU, Kaufman A, Wang HH.	Nucleic Acids Res	10.1093/nar/gkz1169	2020
Pathogenicity	Recovery of the Gut Microbiota after Antibiotics Depends on Host Diet, Community Context, and Environmental Reservoirs.	Ng KM, Aranda-Diaz A, Tropini C, Frankel MR, Van Treuren W, O'Loughlin CT, Merrill BD, Yu FB, Pruss KM, Oliveira RA, Higginbottom SK, Neff NF, Fischbach MA, Xavier KB, Sonnenburg JL, Huang KC.	Cell Host Microbe	10.1016/j.chom.2019.10.011	2019
Pathogenicity	Constructing a gnotobiotic mouse model with a synthetic human gut microbiome to study host-microbe cross talk.	Steimle A, De Sciscio A, Neumann M, Grant ET, Pereira GV, Ohno H, Martens EC, Desai MS.	STAR Protoc	10.1016/j.xpro.2021.100607	2021
Phylogeny	Berberine alters gut microbial function through modulation of bile acids.	Wolf PG, Devendran S, Doden HL, Ly LK, Moore T, Takei H, Nittono H, Murai T, Kurosawa T, Chlipala GE, Green SJ, Kakiyama G, Kashyap P, McCracken VJ, Gaskins HR, Gillevet PM, Ridlon JM.	BMC Microbiol	10.1186/s12866-020-02020-1	2021
Metabolism	Molecular basis of an agarose metabolic pathway acquired by a human intestinal symbiont.	Pluvinage B, Grondin JM, Amundsen C, Klassen L, Moote PE, Xiao Y, Thomas D, Pudlo NA, Anele A, Martens EC, Inglis GD, Uwiera RER, Boraston AB, Abbott DW.	Nat Commun	10.1038/s41467-018-03366-x	2018
Metabolism	Structural basis for tRNA methylthiolation by the radical SAM enzyme MiaB.	Esakova OA, Grove TL, Yennawar NH, Arcinas AJ, Wang B, Krebs C, Almo SC, Booker SJ.	Nature	10.1038/s41586-021-03904-6	2021
Enzymology	Structure and function of microbial alpha-l-fucosidases: a mini review.	Wu H, Owen CD, Juge N.	Essays Biochem	10.1042/ebc20220158	2023
	Strain-Level Analysis of Mother-to-Child Bacterial Transmission during the First Few Months of Life.	Yassour M, Jason E, Hogstrom LJ, Arthur TD, Tripathi S, Siljander H, Selvenius J, Oikarinen S, Hyoty H, Virtanen SM, Ilonen J, Ferretti P, Pasolli E, Tett A, Asnicar F, Segata N, Vlamakis H, Lander ES, Huttenhower C, Knip M, Xavier RJ.	Cell Host Microbe	10.1016/j.chom.2018.06.007	2018
Metabolism	Peptidoglycan synthesis in Tannerella forsythia: Scavenging is the modus operandi.	Ruscitto A, Sharma A.	Mol Oral Microbiol	10.1111/omi.12210	2018
Metabolism	Structure-guided functional characterization of DUF1460 reveals a highly specific NlpC/P60 amidase family.	Xu Q, Mengin-Lecreulx D, Patin D, Grant JC, Chiu HJ, Jaroszewski L, Knuth MW, Godzik A, Lesley SA, Elsliger MA, Deacon AM, Wilson IA.	Structure	10.1016/j.str.2014.09.018	2014
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
	Opposing diet, microbiome, and metabolite mechanisms regulate inflammatory bowel disease in a genetically susceptible host.	Pereira GV, Boudaud M, Wolter M, Alexander C, De Sciscio A, Grant ET, Trindade BC, Pudlo NA, Singh S, Campbell A, Shan M, Zhang L, Yang Q, Willieme S, Kim K, Denike-Duval T, Fuentes J, Bleich A, Schmidt TM, Kennedy L, Lyssiotis CA, Chen GY, Eaton KA, Desai MS, Martens EC.	Cell Host Microbe	10.1016/j.chom.2024.03.001	2024
	Gut Bacteroides act in a microbial consortium to cause susceptibility to severe malaria.	Mandal RK, Mandal A, Denny JE, Namazii R, John CC, Schmidt NW.	Nat Commun	10.1038/s41467-023-42235-0	2023
Enzymology	Two distinct gut microbial pathways contribute to meta-organismal production of phenylacetylglutamine with links to cardiovascular disease.	Zhu Y, Dwidar M, Nemet I, Buffa JA, Sangwan N, Li XS, Anderson JT, Romano KA, Fu X, Funabashi M, Wang Z, Keranahalli P, Battle S, Tittle AN, Hajjar AM, Gogonea V, Fischbach MA, DiDonato JA, Hazen SL.	Cell Host Microbe	10.1016/j.chom.2022.11.015	2023
	Gut microbiota from high-risk men who have sex with men drive immune activation in gnotobiotic mice and in vitro HIV infection.	Li SX, Sen S, Schneider JM, Xiong KN, Nusbacher NM, Moreno-Huizar N, Shaffer M, Armstrong AJS, Severs E, Kuhn K, Neff CP, McCarter M, Campbell T, Lozupone CA, Palmer BE.	PLoS Pathog	10.1371/journal.ppat.1007611	2019
	Project-based learning course on metabolic network modelling in computational systems biology.	Sauter T, Bintener T, Kishk A, Presta L, Prohaska T, Guignard D, Zeng N, Cipriani C, Arshad S, Pfau T, Martins Conde P, Pires Pacheco M.	PLoS Comput Biol	10.1371/journal.pcbi.1009711	2022
	Mucolytic bacteria license pathobionts to acquire host-derived nutrients during dietary nutrient restriction.	Sugihara K, Kitamoto S, Saraithong P, Nagao-Kitamoto H, Hoostal M, McCarthy C, Rosevelt A, Muraleedharan CK, Gillilland MG, Imai J, Omi M, Bishu S, Kao JY, Alteri CJ, Barnich N, Schmidt TM, Nusrat A, Inohara N, Golob JL, Kamada N.	Cell Rep	10.1016/j.celrep.2022.111093	2022
Metabolism	Structural and Functional Insights into PpgL, a Metal-Independent beta-Propeller Gluconolactonase That Contributes to Pseudomonas aeruginosa Virulence.	Song YJ, Wang KL, Shen YL, Gao J, Li T, Zhu YB, Li CC, He LH, Zhou QX, Zhao NL, Zhao C, Yang J, Huang Q, Mu XY, Li H, Dou DF, Liu C, He JH, Sun B, Bao R.	Infect Immun	10.1128/iai.00847-18	2019
	Collaborating genomic, transcriptomic and microbiomic alterations lead to canine extreme intestinal polyposis.	Wang J, Wang T, Bishop MA, Edwards JF, Yin H, Dalton S, Bryan LK, Bryan LK, Zhao S.	Oncotarget	10.18632/oncotarget.25646	2018
Proteome	Structures of single-layer beta-sheet proteins evolved from beta-hairpin repeats.	Xu Q, Biancalana M, Grant JC, Chiu HJ, Jaroszewski L, Knuth MW, Lesley SA, Godzik A, Elsliger MA, Deacon AM, Wilson IA.	Protein Sci	10.1002/pro.3683	2019
	Functional screening of a metagenomic library reveals operons responsible for enhanced intestinal colonization by gut commensal microbes.	Yoon MY, Lee KM, Yoon Y, Go J, Park Y, Cho YJ, Tannock GW, Yoon SS.	Appl Environ Microbiol	10.1128/aem.00581-13	2013
Enzymology	Identification of difructose dianhydride I synthase/hydrolase from an oral bacterium establishes a novel glycoside hydrolase family.	Kashima T, Okumura K, Ishiwata A, Kaieda M, Terada T, Arakawa T, Yamada C, Shimizu K, Tanaka K, Kitaoka M, Ito Y, Fujita K, Fushinobu S.	J Biol Chem	10.1016/j.jbc.2021.101324	2021
	A Bacteroides thetaiotaomicron genetic locus encodes activities consistent with mucin O-glycoprotein processing and N-acetylgalactosamine metabolism.	Ndeh DA, Nakjang S, Kwiatkowski KJ, Sawyers C, Koropatkin NM, Hirt RP, Bolam DN.	Nat Commun	10.1038/s41467-025-58660-2	2025
	Gut Microbiota Contributes to Spontaneous Colitis in E3 Ligase Itch-Deficient Mice.	Kathania M, Tsakem EL, Theiss AL, Venuprasad K.	J Immunol	10.4049/jimmunol.1701478	2020
	In silico identification of bacteriocin gene clusters in the gastrointestinal tract, based on the Human Microbiome Project's reference genome database.	Walsh CJ, Guinane CM, Hill C, Ross RP, O'Toole PW, Cotter PD.	BMC Microbiol	10.1186/s12866-015-0515-4	2015
	Maternal diet and gut microbiome composition modulate early-life immune development.	Grant ET, Boudaud M, Muller A, Muller A, Macpherson AJ, Desai MS.	EMBO Mol Med	10.15252/emmm.202217241	2023
Metabolism	Bacteroidales Secreted Antimicrobial Proteins Target Surface Molecules Necessary for Gut Colonization and Mediate Competition In Vivo.	Roelofs KG, Coyne MJ, Gentyala RR, Chatzidaki-Livanis M, Comstock LE.	mBio	10.1128/mbio.01055-16	2016
Metabolism	Discovery of alpha-l-arabinopyranosidases from human gut microbiome expands the diversity within glycoside hydrolase family 42.	Viborg AH, Katayama T, Arakawa T, Abou Hachem M, Lo Leggio L, Kitaoka M, Svensson B, Fushinobu S.	J Biol Chem	10.1074/jbc.m117.792598	2017
	Deep-learning-enabled antibiotic discovery through molecular de-extinction.	Wan F, Torres MDT, Peng J, de la Fuente-Nunez C.	Nat Biomed Eng	10.1038/s41551-024-01201-x	2024
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
	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
Metabolism	A fibrolytic potential in the human ileum mucosal microbiota revealed by functional metagenomic.	Patrascu O, Beguet-Crespel F, Marinelli L, Le Chatelier E, Abraham AL, Leclerc M, Klopp C, Terrapon N, Henrissat B, Blottiere HM, Dore J, Bera-Maillet C.	Sci Rep	10.1038/srep40248	2017
Pathogenicity	Microbiota-derived bile acids antagonize the host androgen receptor and drive anti-tumor immunity.	Jin WB, Xiao L, Jeong M, Han SJ, Zhang W, Yano H, Shi H, Arifuzzaman M, Lyu M, Wang D, Tang YA, Qiao S, JRI IBD Live Cell Bank Consortium, Yang X, Yang HS, Fu J, Sonnenberg GF, Collins N, Artis D, Guo CJ.	Cell	10.1016/j.cell.2025.02.029	2025
Metabolism	Extending the aerolysin family: from bacteria to vertebrates.	Szczesny P, Iacovache I, Muszewska A, Ginalski K, van der Goot FG, Grynberg M.	PLoS One	10.1371/journal.pone.0020349	2011
Genetics	Functional characterization of the antibiotic resistance reservoir in the human microflora.	Sommer MOA, Dantas G, Church GM.	Science	10.1126/science.1176950	2009
Metabolism	The Biosynthesis of Lipooligosaccharide from Bacteroides thetaiotaomicron.	Jacobson AN, Choudhury BP, Fischbach MA.	mBio	10.1128/mbio.02289-17	2018
Metabolism	Microbiota regulate innate immune signaling and protective immunity against cancer.	Xing C, Wang M, Ajibade AA, Tan P, Fu C, Chen L, Zhu M, Hao ZZ, Chu J, Yu X, Yin B, Zhu J, Shen WJ, Duan T, Wang HY, Wang RF.	Cell Host Microbe	10.1016/j.chom.2021.03.016	2021
Phylogeny	Imaging the in vivo growth patterns of bacteria in human gut Microbiota.	Lin L, Song J, Li J, Zuo X, Wei H, Yang C, Wang W.	Gut Microbes	10.1080/19490976.2021.1960134	2021
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
	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
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	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	Intestinal microbial communities and Holdemanella isolated from HIV+/- men who have sex with men increase frequencies of lamina propria CCR5⁺ CD4⁺ T cells.	Yamada E, Martin CG, Moreno-Huizar N, Fouquier J, Neff CP, Coleman SL, Schneider JM, Huber J, Nusbacher NM, McCarter M, Campbell TB, Lozupone CA, Palmer BE.	Gut Microbes	10.1080/19490976.2021.1997292	2021
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
Pathogenicity	The Use of Defined Microbial Communities To Model Host-Microbe Interactions in the Human Gut.	Elzinga J, van der Oost J, de Vos WM, Smidt H.	Microbiol Mol Biol Rev	10.1128/mmbr.00054-18	2019
	Polyphenols as Drivers of a Homeostatic Gut Microecology and Immuno-Metabolic Traits of Akkermansia muciniphila: From Mouse to Man.	Rodriguez-Daza MC, de Vos WM.	Int J Mol Sci	10.3390/ijms24010045	2022
Pathogenicity	Fish oil enhances recovery of intestinal microbiota and epithelial integrity in chronic rejection of intestinal transplant.	Li Q, Zhang Q, Wang C, Tang C, Zhang Y, Li N, Li J.	PLoS One	10.1371/journal.pone.0020460	2011
	gyrA mutations associated with quinolone resistance in Bacteroides fragilis group strains.	Oh H, El Amin N, Davies T, Appelbaum PC, Edlund C.	Antimicrob Agents Chemother	10.1128/aac.45.7.1977-1981.2001	2001
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
	Commensal Microbiota Modulation of Natural Resistance to Virus Infection.	Stefan KL, Kim MV, Iwasaki A, Kasper DL.	Cell	10.1016/j.cell.2020.10.047	2020
	Insights from Bacteroides Species in Children with Type 1 Diabetes.	Matos J, Matos I, Calha M, Santos P, Duarte I, Cardoso Y, Faleiro ML.	Microorganisms	10.3390/microorganisms9071436	2021
	A detailed analysis of 16S ribosomal RNA gene segments for the diagnosis of pathogenic bacteria.	Chakravorty S, Helb D, Burday M, Connell N, Alland D.	J Microbiol Methods	10.1016/j.mimet.2007.02.005	2007
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
	Autometa: automated extraction of microbial genomes from individual shotgun metagenomes.	Miller IJ, Rees ER, Ross J, Miller I, Baxa J, Lopera J, Kerby RL, Rey FE, Kwan JC.	Nucleic Acids Res	10.1093/nar/gkz148	2019
Metabolism	Dps and DpsL Mediate Survival In Vitro and In Vivo during the Prolonged Oxidative Stress Response in Bacteroides fragilis.	Betteken MI, Rocha ER, Smith CJ.	J Bacteriol	10.1128/jb.00342-15	2015
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
	Glycobiology Aspects of the Periodontal Pathogen Tannerella forsythia.	Posch G, Sekot G, Friedrich V, Megson ZA, Koerdt A, Messner P, Schaffer C.	Biomolecules	10.3390/biom2040467	2012
Enzymology	Taxonomic profiling and populational patterns of bacterial bile salt hydrolase (BSH) genes based on worldwide human gut microbiome.	Song Z, Cai Y, Lao X, Wang X, Lin X, Cui Y, Kalavagunta PK, Liao J, Jin L, Shang J, Li J.	Microbiome	10.1186/s40168-019-0628-3	2019
Metabolism	A Gut Commensal-Produced Metabolite Mediates Colonization Resistance to Salmonella Infection.	Jacobson A, Lam L, Rajendram M, Tamburini F, Honeycutt J, Pham T, Van Treuren W, Pruss K, Stabler SR, Lugo K, Bouley DM, Vilches-Moure JG, Smith M, Sonnenburg JL, Bhatt AS, Huang KC, Monack D.	Cell Host Microbe	10.1016/j.chom.2018.07.002	2018
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
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Pathogenicity	Compositional changes to the ileal microbiome precede the onset of spontaneous ileitis in SHIP deficient mice.	Dobranowski PA, Tang C, Sauve JP, Menzies SC, Sly LM.	Gut Microbes	10.1080/19490976.2018.1560767	2019
Metabolism	Prospecting for microbial alpha-N-acetylgalactosaminidases yields a new class of GH31 O-glycanase.	Rahfeld P, Wardman JF, Mehr K, Huff D, Morgan-Lang C, Chen HM, Hallam SJ, Withers SG.	J Biol Chem	10.1074/jbc.ra119.010628	2019
Phylogeny	PCR assay for species-specific identification of Bacteroides thetaiotaomicron.	Teng LJ, Hsueh PR, Tsai JC, Chiang FL, Chen CY, Ho SW, Luh KT.	J Clin Microbiol	10.1128/jcm.38.4.1672-1675.2000	2000
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Genetics	Assessment of k-mer spectrum applicability for metagenomic dissimilarity analysis.	Dubinkina VB, Ischenko DS, Ulyantsev VI, Tyakht AV, Alexeev DG.	BMC Bioinformatics	10.1186/s12859-015-0875-7	2016
Metabolism	Characterization and scope of S-layer protein O-glycosylation in Tannerella forsythia.	Posch G, Pabst M, Brecker L, Altmann F, Messner P, Schaffer C.	J Biol Chem	10.1074/jbc.m111.284893	2011
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Phylogeny	Tunable Expression Tools Enable Single-Cell Strain Distinction in the Gut Microbiome.	Whitaker WR, Shepherd ES, Sonnenburg JL.	Cell	10.1016/j.cell.2017.03.041	2017
Metabolism	A Metabolic Pathway for Activation of Dietary Glucosinolates by a Human Gut Symbiont.	Liou CS, Sirk SJ, Diaz CAC, Klein AP, Fischer CR, Higginbottom SK, Erez A, Donia MS, Sonnenburg JL, Sattely ES.	Cell	10.1016/j.cell.2020.01.023	2020
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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
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Phylogeny	Diet-induced metabolic improvements in a hamster model of hypercholesterolemia are strongly linked to alterations of the gut microbiota.	Martinez I, Wallace G, Zhang C, Legge R, Benson AK, Carr TP, Moriyama EN, Walter J.	Appl Environ Microbiol	10.1128/aem.00380-09	2009
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Metabolism	Role of glycoside phosphorylases in mannose foraging by human gut bacteria.	Ladeveze S, Tarquis L, Cecchini DA, Bercovici J, Andre I, Topham CM, Morel S, Laville E, Monsan P, Lombard V, Henrissat B, Potocki-Veronese G.	J Biol Chem	10.1074/jbc.m113.483628	2013
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	Antimicrobial activity of DU-6681a, a parent compound of novel oral carbapenem DZ-2640.	Tanaka M, Hohmura M, Nishi T, Sato K, Hayakawa I.	Antimicrob Agents Chemother	10.1128/aac.41.6.1260	1997
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	Microbiological toxicology of the new antibiotic aditoprim on human intestinal microbiota.	Wang J, Liu C, Gu F, Gu Y, Hao H.	Toxicol Lett	10.1016/j.toxlet.2025.111780	2025
	Gut microbiota composition and long-term physical activity in healthy older adults at high and low performance levels.	Fiorilli G, Medoro A, Viciani E, di Cagno A, Calcagno G, Di Costanzo A, Castagnetti A, Scapagnini G, Davinelli S.	Exp Gerontol	10.1016/j.exger.2025.112957	2025
	Changes in microbiota associated with the use of intragastric balloons.	Komorniak N, Cembrowska-Lech D, Wiechowska-Kozlowska A, Gawel K, Pawlus J, Skonieczna-Zydecka K, Sulikowski T, van Kley AM, Stachowska E.	Sci Rep	10.1038/s41598-025-27652-z	2025
	Gut microbiota modulation by polysaccharide from Aloe gel: Potential prebiotic and targeted regulatory effects.	Sun Y, Zhang S, Nie S.	Food Chem	10.1016/j.foodchem.2025.147049	2025
	Gut Microbiota Modulation by Lacticaseibacillus paracasei EFEL6501 Ameliorates Muscle Atrophy.	Pyeon GN, Seong H, Moon JS, Han NS.	J Microbiol Biotechnol	10.4014/jmb.2508.08024	2025
Genetics	Gut microbiota and bile acids changes in MASLD mice model with hepatic PLD1 knockout.	Zhao Y, Wang H, Lin W, Wang H, Cao LL.	Acta Biochim Biophys Sin (Shanghai)	10.3724/abbs.2025183	2025
	Gut microbiota dysbiosis and metabolic shifts in pediatric norovirus infection: a metagenomic study in Northeast China.	Wang Z, Wei X, Piao L, Zhang X, Wang H.	Front Cell Infect Microbiol	10.3389/fcimb.2025.1600470	2025
	Goat milk oligosaccharides improve growth and gut microbiota composition in stunted mice	Chen X, Zeng X, Xiang F, Li J, Li W, Cao T, Wang H, Li B, Wang J.	Food Research International.		2025
	The association between gut microbiota composition and cardiometabolic parameters in healthy adults.	Okalin SS, Arslan N, Demiray Gurbuz E, Arayici M, Kirca ND, Ozel Demiralp D, Dereli-Akdeniz D, Akan P, Ozkutuk AA.	BMC Microbiol	10.1186/s12866-025-04261-4	2025
	Synergistic effects of human-origin novel postbiotic Bacteroides & Phocaeicola on obesity and thermogenesis in high-fat diet-induced metabolic dysfunction.	Wu L, Wang JH, Park SH, Cui Y, Han K, Kim H.	Benef Microbes	10.1163/18762891-bja00080	2025
	Rotavirus gastroenteritis complicating meningitis caused by Bacteroides uniformis detected using mNGS: a case report and literature review.	Cai ZZ, Zeng DM, Lei LW, Xiao S.	Front Med (Lausanne)	10.3389/fmed.2025.1601953	2025
	Goat milk oligosaccharides improve growth and gut microbiota composition in stunted mice.	Chen X, Zeng X, Xiang F, Li J, Li W, Cao T, Wang H, Li B, Wang J.	Food Res Int	10.1016/j.foodres.2025.116640	2025
	Dietary Nutrition, Gut Microbiota, and Health Status Across Geographically Diverse Populations in Mongolia: A Cross-Sectional Study.	Zhao Z, Zhao F, Chimeddorj B, Sun Z, Tserenkhuu E, Ochirdanzan M, Ganpurev D, Fun W, Wusigale, Li W, Liu W, Yang S, Zhang M, Davaasambuu E, Talkhaa Y, Narankhuu Y, Bromage S, Warinner C, Menghe B, Ganmaa D.	Food Sci Nutr	10.1002/fsn3.70531	2025
Metabolism	Akkermansia muciniphila Growth Promoted by Lychee Major Flavonoid through Bacteroides uniformis Metabolism.	Tang S, Xu C, Zhou Y, Shen Y, Zeng Q, Su D.	J Agric Food Chem	10.1021/acs.jafc.4c07429	2024
Metabolism	Discovery of a Widespread Polyamine-Low-Molecular-Weight Thiol Hybrid Pathway in Clostridioides difficile.	Hunt RL, Oh J, Jain A, Kuo TH, Berardi D, Jian W, Song D, Wu Q, Goodman AL, Palm NW, Zimmermann M, Johnson CH, Crawford JM.	ACS Infect Dis	10.1021/acsinfecdis.5c00286	2025
	Protective Effect and Gut Microbiota Modulation of Grifola frondosa Antioxidant Peptides in Sodium Dextran Sulfate-Induced Ulcerative Colitis Mice.	Chen T, Hong L, Wang P, Teng Q, Fang F, Liu Q.	Biotechnol Appl Biochem	10.1002/bab.2734	2025
	Bacteroides uniformis ameliorates pro-inflammatory diet-exacerbated colitis by targeting endoplasmic reticulum stress-mediated ferroptosis.	Liu C, Liu L, Tian Z, Zhan S, Qiu Y, Li M, Li T, Mao R, Zhang S, Chen M, Zeng Z, Zhuang X.	J Adv Res	10.1016/j.jare.2024.11.025	2025
Genetics	Bile-processed Rhizoma Coptidis alleviates type 2 diabetes mellitus through modulating the gut microbiota and short-chain fatty acid metabolism.	Zhu Y, Tian Q, Huang Q, Wang J.	Int Immunopharmacol	10.1016/j.intimp.2025.114645	2025
	Gut microbiome and obesity in late adolescence: A case-control study in "Children of 1997" birth cohort.	He B, Xu S, Schooling CM, Leung GM, Ho JWK, Au Yeung SL.	Ann Epidemiol	10.1016/j.annepidem.2024.12.009	2025
	Association between Microbiome Dysbiosis and Postoperative Disorders before and after Gastrectomy.	Fujii T, Tanaka T, Fujii T, Takahashi H, Kuramitsu K, Funasaka K, Ohno E, Akimoto S, Nakauchi M, Shibasaki S, Uyama I, Hirooka Y, Suda K, Tochio T.	Digestion	10.1159/000545678	2025
	Effects of Traditional Asian Diet on dietary fibre requirement, gut microbiome composition, and faecal and urine metabolomes in healthy Asian women: a pilot study.	Sahran NF, Chong CW, Ismail IH, Taib F, Hoo PS, Palanisamy UD, Sundralingam U, Teh CSJ, Kong ZX, Ayub Q, Yoke Ling F, Hazlan SNH, Azlan M, Abdul Razak S, Tengku Din TADA, Abdullah N, Tagiling N, Tee V, Ehab Ayad M, Zheng FM, El-Omar E, Lee YY.	Benef Microbes	10.1163/18762891-bja00074	2025
	Investigating the relationship between intestinal microbiota and Th1/Th2/Th17 imbalance in subclinical hypothyroidism during the first half of pregnancy: a multi-omics approach.	Lin P, Xu Y, Sun Z, Li J, Ban Y, Zhang M, Wang Y, Zhang C.	Gut Pathog	10.1186/s13099-025-00743-y	2025
	Structural elucidation of a capsular polysaccharide from Bacteroides uniformis and its ameliorative impact on DSS-induced colitis in mice.	Ma C, Zhang S, Renaud SJ, Zhang Q, Qi H, Zhou H, Jin Y, Yu H, Xu Y, Huang H, Hong Y, Li H, Liao Q, Ding F, Qin M, Wang P, Xie Z.	Int J Biol Macromol	10.1016/j.ijbiomac.2024.135119	2024
	Antimicrobial resistance pattern of the Bacteroides fragilis group strains isolated at a teaching hospital in China.	Wu ZC, Feng HX, Wu L, Zhang M, Gu Z.	Acta Microbiol Immunol Hung	10.1556/030.2025.02400	2025
	Extracellular vesicles of Bacteroides uniformis induce M1 macrophage polarization and aggravate gut inflammation during weaning.	Tang W, Ni Z, Wei Y, Hou K, Valencak TG, Wang H.	Mucosal Immunol	10.1016/j.mucimm.2024.05.004	2024
Metabolism	Integrated Multi-Omics Analyses Reveal Lipid Metabolic Signature in Osteoarthritis.	Wang Y, Zeng T, Tang D, Cui H, Wan Y, Tang H.	J Mol Biol	10.1016/j.jmb.2024.168888	2025
	Exploring bacterial metabolites in microbe-human host dialogue and their therapeutic potential in Alzheimer's diseases.	Singh SD, Bharali P, Nagamani S.	Mol Divers	10.1007/s11030-024-11028-y	2025
Metabolism	3-O-acylated bile acids: disrupters or harmonizers of metabolism?	Chen R, Chen X, Gao J.	Trends Mol Med	10.1016/j.molmed.2024.06.003	2025
	The roles of different Bacteroides uniformis strains in alleviating DSS-induced ulcerative colitis and related functional genes.	Wang C, Guo H, Bai J, Yu L, Tian F, Zhao J, Zhang H, Chen W, Zhai Q.	Food Funct	10.1039/d3fo04863b	2024
	B.uniformis IM01-derived IAA alleviates asthma via AhR/NLRP3 pathways in mice.	He Y, Yang T, Mi J, He S, Yang Z, Lu S, Yue K, Huang Y, Song L, Xiao Y, Ren Z.	Cell Mol Life Sci	10.1007/s00018-025-05910-7	2025
	Comparison of different longan polysaccharides during gut Bacteroides fermentation.	Wang J, Ma Y, Xu X, Huang G, Zhang R, Jia X, Dong L, Deng M, Zhang M, Huang F.	Food Chem	10.1016/j.foodchem.2024.140840	2024
Transcriptome	Integration of microbiome, metabolomics and transcriptome for in-depth understanding of berberine attenuates AOM/DSS-induced colitis-associated colorectal cancer.	Wang M, Ma Y, Yu G, Zeng B, Yang W, Huang C, Dong Y, Tang B, Wu Z.	Biomed Pharmacother	10.1016/j.biopha.2024.117292	2024
Pathogenicity	IgA-mediated control of host-microbial interaction during weaning reaction influences gut inflammation.	Tang W, Wei Y, Ni Z, Hou K, Luo XM, Wang H.	Gut Microbes	10.1080/19490976.2024.2323220	2024
	Long-term dietary intervention of the hydrolyzed feather meal on microbiota composition of adult female dogs.	Balouei F, Armone R, Stefanon B, Randazzo A, Chiofalo B.	Res Vet Sci	10.1016/j.rvsc.2024.105340	2024
	Gut microbiota dysbiosis and metabolic shifts in pediatric norovirus infection: a metagenomic study in Northeast China	Wang Z, Wei X, Piao L, Zhang X, Wang H.	Front Cell Infect Microbiol		2025
	Sickle Cell Disease and Gut Health: The Influence of Intestinal Parasites and the Microbiome on Angolan Children.	Delgadinho M, Ginete C, Santos B, de Vasconcelos JN, Arez AP, Brito M.	Int J Mol Sci	10.3390/ijms25137258	2024
Genetics	Unveiling the causal effects of gut microbiome on trimethylamine N-oxide: evidence from Mendelian randomization.	Yu Y, Yin Y, Deng J, Yang X, Bai S, Yu R.	Front Microbiol	10.3389/fmicb.2024.1465455	2024
Genetics	MAGs-based genomic comparison of gut significantly enriched microbes in obese individuals pre- and post-bariatric surgery across diverse locations.	Shi H, Li J.	Front Cell Infect Microbiol	10.3389/fcimb.2025.1485048	2025
Enzymology	Levels of 5alpha-reductase gene in intestinal lavage fluid decrease with progression of colorectal cancer.	Fujii T, Nakagawa Y, Funasaka K, Hirooka Y, Tochio T.	J Med Microbiol	10.1099/jmm.0.001834	2024
	Bifidobacterium adolescentis CCFM1285 combined with yeast beta-glucan alleviates the gut microbiota and metabolic disturbances in mice with antibiotic-associated diarrhea.	Guo H, He X, Yu L, Tian F, Chen W, Zhai Q.	Food Funct	10.1039/d3fo05421g	2024
	The gut microbiota's role in bulimia nervosa and binge eating disorder: etiological insights and therapeutic implications from a scoping review.	Tempia Valenta S, Atti AR, Marcolini F, Rossi Grauenfels D, Giovannardi G, Fanelli G, De Ronchi D.	Neurosci Appl	10.1016/j.nsa.2025.105526	2025
	Mannan-oligosaccharides promote gut microecological recovery after antibiotic disturbance.	Chen J, Yin J, Xie H, Lu W, Wang H, Zhao J, Zhu J.	Food Funct	10.1039/d4fo00332b	2024
Phylogeny	A combined molecular approach utilizing microbial DNA and microRNAs in a qPCR multiplex for the classification of five forensically relevant body fluids.	Lewis CA, Seashols-Williams SJ.	J Forensic Sci	10.1111/1556-4029.15400	2024
Enzymology	The circulating dihydrotestosterone/testosterone ratio is increased by gut microbial 5alpha-reductase activity in females.	Ohlsson C, Li L, Horkeby K, Lawenius L, Collden H, Sjogren K, Baldanzi G, Engstrom G, Arnlov J, Orho-Melander M, Fall T, Grahnemo L.	EBioMedicine	10.1016/j.ebiom.2025.105978	2025
	The alteration of fecal microbial and metabolic profile of gallstone patients in Taiwan: Single-center study.	Chang TE, Huang KH, Luo JC, Huang YH, Lin HH, Fang WL, Hou MC.	J Chin Med Assoc	10.1097/jcma.0000000000001094	2024
	Impact of bacteroides uniformis on fatty liver hemorrhagic syndrome in dawu golden phoenix laying hens: modulation of gut microbiota and arachidonic acid metabolism.	Zhang Y, Ma R, Du X, He X, Zhang Y, Ma N, Liu H, Zhao X.	Front Microbiol	10.3389/fmicb.2025.1560887	2025
	Prioritizing gut microbial SNPs linked to immunotherapy outcomes in NSCLC patients by integrative bioinformatics analysis.	Raziq MF, Khan N, Manzoor H, Tariq HMA, Rafiq M, Rasool S, Kayani MUR, Huang L.	J Transl Med	10.1186/s12967-025-06370-0	2025
	Interactions between wheat germ polysaccharide and gut microbiota through in vitro batch fecal fermentation and an aging mice model: Targeting enrichment of Bacteroides uniformis and Bifidobacterium pseudocatenulatum.	Duan H, Yu Q, Ni Y, Li J, Yu L, Fan L.	Int J Biol Macromol	10.1016/j.ijbiomac.2023.127559	2023
	Treatment of Actinomyces europaeus and Clostridium innocuum necrotizing fasciitis: Case report and literature review.	Avery L, Kufel J, Rawlings R.	Am J Health Syst Pharm	10.1093/ajhp/zxaf190	2025
	Anti-Diabetic Potentials of Lactobacillus Strains by Modulating Gut Microbiota Structure and beta-Cells Regeneration in the Pancreatic Islets of Alloxan-Induced Diabetic Rats.	Kumar M, Muthurayar T, Karthika S, Gayathri S, Varalakshmi P, Ashokkumar B.	Probiotics Antimicrob Proteins	10.1007/s12602-024-10221-7	2025
	In vitro Effects of Cellulose Acetate on Fermentation Profiles, the Microbiome, and Gamma-aminobutyric Acid Production in Human Stool Cultures.	Yamada H, Miura H, Suzuki Y, Koike S, Shimamoto S, Kobayashi Y.	Curr Microbiol	10.1007/s00284-023-03383-0	2023
	Concentrations of ciprofloxacin in food defined as safe alter the gut microbiome and ciprofloxacin susceptibility in humans: an interventional clinical study.	Manoharan-Basil S, Gestels Z, Abdellati S, Vanbaelen T, Van Den Bossche D, van Alebeek L, Van Herrewege Y, Poppe L, Vandenhove L, Bracke S, Smekens B, Jacobs B, Genbrugge E, Kenyon C.	Sci Rep	10.1038/s41598-025-18714-3	2025
	[Buzhong Yiqi Decoction ameliorates spleen deficiency syndrome by regulating gut microbiota].	Yu HC, Meng YY, Wang EK, Yuan JY, Peng Y, Li XB.	Zhongguo Zhong Yao Za Zhi	10.19540/j.cnki.cjcmm.20231013.701	2024
	A blueprint of synergistic effect in Crataegus pinnatifida and obesity-related gut microbiota against obesity via systems biology concept.	Xie J, Guan H, Liu M, Ding W.	PLoS One	10.1371/journal.pone.0332038	2025
	Prebiotic Effect of Oxidized Hydroxypropyl Starch via In Vitro and In Vivo.	Zheng H, Xu Z, Fan Y, Han J, Zhou L, Li H, Pan X, Ma R, Liu C, Tian Y.	Foods	10.3390/foods14132217	2025
	Altered fecal microbial and metabolic profiles reveal potential mechanisms underlying anemia in patients with chronic renal failure.	Wang H, Xue W, Cheng J, He Y, Song Y, Hu D, Peng A, Li C, Bao H.	Microbiol Spectr	10.1128/spectrum.03166-24	2025
	Gut symbionts alleviate MASH through a secondary bile acid biosynthetic pathway.	Nie Q, Luo X, Wang K, Ding Y, Jia S, Zhao Q, Li M, Zhang J, Zhuo Y, Lin J, Guo C, Zhang Z, Liu H, Zeng G, You J, Sun L, Lu H, Ma M, Jia Y, Zheng MH, Pang Y, Qiao J, Jiang C.	Cell	10.1016/j.cell.2024.03.034	2024
	Divergent metabolism of two lychee (Litchi chinensis Sonn.) pulp flavonols and their modulatory effects on gut microbiota: Discovery of hydroxyethylation in vitro colonic fermentation.	Huang G, Zeng Q, Dong L, Zhang R, Zhang M, Huang F, Su D.	Food Chem	10.1016/j.foodchem.2023.136875	2023
	Study on characteristics of gut flora composition of pregnant women with preeclampsia	Li G, Niu H, Xie M, Yang M, Li M, Hao Y, Zhang J.	BMC Pregnancy Childbirth		2025
Metabolism	High Soluble Fiber Promotes Colorectal Tumorigenesis Through Modulating Gut Microbiota and Metabolites in Mice.	Yang J, Wei H, Lin Y, Chu ESH, Zhou Y, Gou H, Guo S, Lau HCH, Cheung AHK, Chen H, To KF, Sung JJY, Wang Y, Yu J.	Gastroenterology	10.1053/j.gastro.2023.10.012	2024
	Gut Microbiota in Adults with Chronic Widespread Pain: A Systematic Review.	Leong PY, Shi LH.	Diseases	10.3390/diseases13090299	2025
	Bacteroides uniformis-generated hexadecanedioic acid ameliorates metabolic-associated fatty liver disease.	Zhang DY, Li D, Chen SJ, Zhang LJ, Zhu XL, Chen FD, Chen C, Wang Q, Du Y, Xiong JX, Huang SM, Zhang XD, Lv YT, Zeng F, Chen RX, Huang X, Mao F, Zhou S, Yao Q, Huang Y, Chen R, Mo Y, Xie Y, Jiang YH, Chen Z, Mo CY, Chen JJ, Bai FH.	Gut Microbes	10.1080/19490976.2025.2508433	2025
	Bacteroides uniformis CECT 7771 requires adaptive immunity to improve glucose tolerance but not to prevent body weight gain in diet-induced obese mice.	Romani-Perez M, Lopez-Almela I, Bullich-Vilarrubias C, Evtoski Z, Benitez-Paez A, Sanz Y.	Microbiome	10.1186/s40168-024-01810-3	2024
	Sex-dependent modulation of T and NK cells and gut microbiome by low sodium diet in patients with primary aldosteronism.	Nowotny HF, Zheng T, Seiter TM, Ju J, Schneider H, Kroiss M, Sarkis AL, Sturm L, Britz V, Lechner A, Potzel AL, Kunz S, Bidlingmaier M, Neuhaus K, Gottschlich A, Kobold S, Reisch N, Schirmer M, Reincke M, Adolf C.	Front Immunol	10.3389/fimmu.2024.1428054	2024
	Bacteroidales-Specific Antimicrobial Genes Can Influence the Selection of the Dominant Fecal Strain of Bacteroides vulgatus and Bacteroides uniformis from the Gastrointestinal Tract Microbial Community.	Koo H, Morrow CD.	Life (Basel)	10.3390/life14050555	2024
	Effects of partially hydrolyzed guar gums of different molecular weights on a human intestinal in vitro fermentation model.	Sasaki D, Sasaki K, Abe A, Ozeki M, Kondo A.	J Biosci Bioeng	10.1016/j.jbiosc.2023.04.002	2023
Enzymology	A global perspective on microbial risk factors in effluents of wastewater treatment plants.	Chen K, Liang J, Wang Y, Tao Y, Lu Y, Wang A.	J Environ Sci (China)	10.1016/j.jes.2023.04.012	2024
	Metagenomic Characterization of Gut Microbiota in Individuals with Low Cardiovascular Risk.	Issilbayeva A, Kozhakhmetov S, Jarmukhanov Z, Vinogradova E, Mukhanbetzhanov N, Meiramova A, Rib Y, Ivanova-Razumova T, Myrzakhmetova G, Andossova S, Zeinoldina A, Kuantkhan M, Ainabekova B, Bekbossynova M, Kushugulova A.	J Clin Med	10.3390/jcm14145097	2025
	Correlation Between Gastroesophageal Reflux Disease and Small Intestinal Bacterial Overgrowth: Analysis of Intestinal Microbiome and Metabolic Characteristics.	Wang ZT, Tan WT, Huang JL, Zhang PF, Li Q, Wang MM, Meng MM, Su H, Guo CM, Liu H.	J Inflamm Res	10.2147/jir.s487185	2025
	Effects of Designed Herbal Formula on Growth Performance, Blood Indices, Organ Traits, and Cecum Microbiology in Broilers.	Sun Y, Zhang M, Shi D, Dai X, Li X.	Vet Sci	10.3390/vetsci11030107	2024
	The Effect of the Ideal Food Pyramid on Gut Microbiota in Rheumatoid Arthritis Patients.	Kacar Mutluturk U, Cicek B, Cengiz G.	Life (Basel)	10.3390/life15030463	2025
	Makgeolli Lees as a Novel Prebiotic Candidate: Effects on Human Gut Microbiota and Metabolites.	Kim JH, Kim HR, Seong H, Han SH, Kim G, Choi Y, Han NS.	J Microbiol Biotechnol	10.4014/jmb.2504.04020	2025
Phenotype	MetOrigin 2.0: Advancing the discovery of microbial metabolites and their origins.	Yu G, Xu C, Wang X, Ju F, Fu J, Ni Y.	Imeta	10.1002/imt2.246	2024
Genetics	High-altitude mountaineering induces adaptive gut microbiome shifts associated with dietary intake and performance markers.	Karpecka-Galka E, Zielinska K, Fraczek B, Labaj PP, Kosciolek T, Huminska-Lisowska K.	Sci Rep	10.1038/s41598-025-22848-9	2025
	Fecal microbiome composition in neonates with or without urinary tract infection.	Bahat H, Paret M, Uzan A, Klainer H, Sharon E, Turjeman S, Koren O, Goldman M, Youngster I.	Pediatr Nephrol	10.1007/s00467-024-06612-1	2025
	A rare case of Bilophila wadsworthia bacteremia presenting as multiple hepatic abscesses: A case report and literature review.	Han S, Krothapalli TR, Zafar SJ, Gautham S.	IDCases	10.1016/j.idcr.2025.e02342	2025
	Alterations in microbiome associated with acute pancreatitis.	Yazici C, Priyadarshini M, Boulay B, Dai Y, Layden BT.	Curr Opin Gastroenterol	10.1097/mog.0000000000001046	2024
	Dynamic Shifts in Antibiotic Residues and Gut Microbiome Following Tilmicosin Administration to Silkie Chickens.	Liang Q, Xie C, Gebreselase HB, Yuan Y, He J, Xie L, Luo C, Ji J.	Animals (Basel)	10.3390/ani14233428	2024
	Structural characterization on a beta-agarase Aga86A_Wa from Wenyingzhuangia aestuarii reveals the prevalent methyl-galactose accommodation capacity of GH86 enzymes at subsite -1.	Zhang Y, Dong S, Chen G, Cao S, Shen J, Mei X, Cui Q, Feng Y, Chang Y, Wang Y, Xue C.	Carbohydr Polym	10.1016/j.carbpol.2023.120594	2023
	Large Douglas Abscess with Distinctive Bilateral Salpingitis in a Young Virginal Woman 6 Months Following Small Bowel Perforation at the Level of the Jejunojejunostomy After Roux-en-Y Gastric Bypass: A Case Report.	Verta S, Brambs CE, Christmann C.	Int J Womens Health	10.2147/ijwh.s492026	2024
	Spraying compound probiotics improves growth performance and immunity and modulates gut microbiota and blood metabolites of suckling piglets.	Huang W, Ma T, Liu Y, Kwok LY, Li Y, Jin H, Zhao F, Shen X, Shi X, Sun Z, Zhang H.	Sci China Life Sci	10.1007/s11427-022-2229-1	2023
Phylogeny	Gut microbiota dysbiosis and short-chain fatty acid depletion in phlegm-dampness polycystic ovary syndrome: a cross-sectional 16S rRNA sequencing analysis.	Xia XY, Chen Y, Zhang XJ, Wang J, Xu HY, Zhao R.	BMC Endocr Disord	10.1186/s12902-025-02076-y	2025
	Gut microbiota profile in adults with abdominal obesity and non-abdominal obesity: links to body composition and macronutrient intake in Semarang, Indonesia-a brief research report.	Fadhillah FS, Arafat FB, Maharani N, Fadhilah J, Zariyah H, Sobirin MA, Tsutsui H, Wibowo A, Juniarto AZ, Pramono A.	Front Nutr	10.3389/fnut.2025.1648575	2025
	Water-soluble cellulose acetate attenuates glucose intolerance through GLP-1 and PYY signal upregulation.	Asaeda K, Takagi T, Murakami E, Hashimoto H, Yasuda T, Kajiwara-Kubota M, Sugaya T, Mizushima K, Higashimura Y, Ryuji OK, Kimura I, Inoue K, Uchiyama K, Shimamoto S, Ukawa Y, Kohara A, Kudoh M, Naito Y, Itoh Y.	NPJ Sci Food	10.1038/s41538-025-00505-9	2025
	Hindgut microbiota profiling and functional prediction of sheep (Ovis aries) fed with different dietary calcium levels.	Khan M, Zhao X, Ni X, Danzeng B, Ali S, Mushtaq M, Yang H, Liang J, Fareed SK, Xue B, Quan G.	Sci Rep	10.1038/s41598-025-11020-y	2025
	Baseline intestinal microbiota composition influences response to a real-world dietary fiber intervention.	Hoffmann Sarda FA, Giuntini EB, Oliveira A, Souza GS, Prado SBR, Taddei CR, Tadini CC, Bittinger K, Bushman FD, Menezes EW, Hoffmann C.	NPJ Biofilms Microbiomes	10.1038/s41522-025-00817-4	2025
Phylogeny	Gut Mucosal Microbiome of Patients With Low-Grade Adenomatous Bowel Polyps.	Welham Z, Li J, Tse B, Engel A, Molloy MP.	Gastro Hep Adv	10.1016/j.gastha.2025.100687	2025
	Ameliorating potential of Auricularia auricula-judae polysaccharides in mitigating hypercaloric diet-induced behavioral disorders through gut microbiota regulation.	Fei Y, Zhang J, Yuan S, Liu Y, Wang X, Wang M, Zhao H, Liu Q.	Front Nutr	10.3389/fnut.2025.1585778	2025
Phylogeny	Identifying fecal microbiota signatures of colorectal cancer in a Vietnamese cohort.	Nhung PTT, Le HTT, Nguyen QH, Huyen DT, Quyen DV, Song LH, Van Thuan T, Tran TTT.	Front Microbiol	10.3389/fmicb.2024.1388740	2024
	Identification of age-associated microbial changes via long-read 16S sequencing.	Toh KY, Toh TS, Chua KP, Rajakumar P, Lee JWJ, Chong CW.	Gut Pathog	10.1186/s13099-024-00650-8	2024
	Sickle Cell Disease and Gut Health: The Influence of Intestinal Parasites and the Microbiome on Angolan Children	Delgadinho M, Ginete C, Santos B, de Vasconcelos J, Arez A, Brito M.	Int J Mol Sci		2024
	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
	Bacteremia With Anaerobic Bacteria and Association With Colorectal Cancer: A Population-based Cohort Study.	Justesen US, Nielsen SL, Jensen TG, Dessau RB, Moller JK, Coia JE, Andersen SL, Pedersen C, Gradel KO.	Clin Infect Dis	10.1093/cid/ciac259	2022
	Astragalus polysaccharides-induced gut microbiota play a predominant role in enhancing of intestinal barrier function of broiler chickens.	Yang J, Sun Y, Wang Q, Yu S, Li Y, Yao B, Yang X.	J Anim Sci Biotechnol	10.1186/s40104-024-01060-1	2024
	The Emergence of Bacteroides pyogenes as a Human Pathogen of Animal Origin: A Narrative Review.	Mauri C, Giubbi C, Consonni A, Briozzo E, Meroni E, Luzzaro F, Tonolo S.	Microorganisms	10.3390/microorganisms13061200	2025
	alpha-Cyclodextrin supplementation improves endurance exercise performance and reduces post-exercise fatigue in human males: a randomized, double-blind, placebo-controlled, parallel-group study.	Onishi M, Nakamura T, Kano C, Hirota T, Fukuda S, Morita H.	Biosci Microbiota Food Health	10.12938/bmfh.2024-062	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
	Uncovering Predictive Factors and Interventions for Restoring Microecological Diversity after Antibiotic Disturbance.	Chen J, Zhu J, Lu W, Wang H, Pan M, Tian P, Zhao J, Zhang H, Chen W.	Nutrients	10.3390/nu15183925	2023
	Study of the Gut Microbiome in Patients with Psoriatic Arthritis.	Amorim GM, Ricardo Werner Castro G, Carneiro S.	Eur J Rheumatol	10.5152/eurjrheum.2024.23080	2024
	Bacteroides uniformis Ameliorates Carbohydrate and Lipid Metabolism Disorders in Diabetic Mice by Regulating Bile Acid Metabolism via the Gut-Liver Axis.	Zhu XX, Zhao CY, Meng XY, Yu XY, Ma LC, Chen TX, Chang C, Chen XY, Zhang Y, Hou B, Cai WW, Du B, Han ZJ, Qiu LY, Sun HJ.	Pharmaceuticals (Basel)	10.3390/ph17081015	2024
	Microbiome-Informed Dosing: Exploring Gut Microbial Communities Impact on Mycophenolate Enterohepatic Circulation and Therapeutic Target Achievement.	Saqr A, Cheng S, Al-Kofahi M, Staley C, Jacobson PA.	Clin Pharmacol Ther	10.1002/cpt.3740	2025
	[Correlation analysis of age and microbial characteristics in saliva and feces of high-risk population of upper gastrointestinal cancer].	Li MJ, Shao DT, Zhou JC, Gu JH, Fan ZY, Qin JJ, Li XQ, Hao CQ, Wei WW.	Zhonghua Yu Fang Yi Xue Za Zhi	10.3760/cma.j.cn112150-20220715-00720	2022
Phylogeny	BN-BacArena: Bayesian network extension of BacArena for the dynamic simulation of microbial communities.	Blasco T, Balzerani F, Valcarcel LV, Larranaga P, Bielza C, Francino MP, Rufian-Henares JA, Planes FJ, Perez-Burillo S.	Bioinformatics	10.1093/bioinformatics/btae266	2024
	Gut microbiome and metabolome to discover pathogenic bacteria and probiotics in ankylosing spondylitis.	Lai Y, Tang W, Luo X, Zheng H, Zhang Y, Wang M, Yu G, Yang M.	Front Immunol	10.3389/fimmu.2024.1369116	2024
	High-resolution analysis of the treated coeliac disease microbiome reveals strain-level variation.	Slager J, Simpson HL, Gacesa R, Chen L, Tan IL, Gelderloos J, Maatman A, Wijmenga C, Zhernakova A, Fu J, Weersma RK, Gonera G, Jonkers IH, Withoff S.	Gut Microbes	10.1080/19490976.2025.2489071	2025
	Dysbiosis in the Gut Microbiome of Pembrolizumab-Treated Non-Small Lung Cancer Patients Compared to Healthy Controls Characterized Through Opportunistic Sampling.	Charalambous H, Brown C, Vogazianos P, Katsaounou K, Nikolaou E, Stylianou I, Papageorgiou E, Vraxnos D, Aristodimou A, Chi J, Costeas P, Shammas C, Apidianakis Y, Antoniades A.	Thorac Cancer	10.1111/1759-7714.70075	2025
	Severe Cognitive Decline in Long-term Care Is Related to Gut Microbiome Production of Metabolites Involved in Neurotransmission, Immunomodulation, and Autophagy.	Shoubridge AP, Carpenter L, Flynn E, Papanicolas LE, Collins J, Gordon D, Lynn DJ, Whitehead C, Leong LEX, Cations M, De Souza DP, Narayana VK, Choo JM, Wesselingh SL, Crotty M, Inacio MC, Ivey K, Taylor SL, Rogers GB.	J Gerontol A Biol Sci Med Sci	10.1093/gerona/glaf053	2025
	Intestinal microbiota links to allograft stability after lung transplantation: a prospective cohort study.	Wu J, Li C, Gao P, Zhang C, Zhang P, Zhang L, Dai C, Zhang K, Shi B, Liu M, Zheng J, Pan B, Chen Z, Zhang C, Liao W, Pan W, Fang W, Chen C.	Signal Transduct Target Ther	10.1038/s41392-023-01515-3	2023
	Characteristics and function of the gut microbiota in patients with rectal neuroendocrine tumors.	Gao Y, Zheng H, Ye M, Zhou G, Chen J, Qiang X, Bai J, Lu X, Tang Q.	J Cancer	10.7150/jca.103297	2025
	Uncovering the complexity of childhood undernutrition through strain-level analysis of the gut microbiome.	Chang B, Zhang W, Wang Y, Zhang Y, Zhong S, Gao P, Wang L, Zhao Z.	BMC Microbiol	10.1186/s12866-024-03211-w	2024
	Intestinal Microbiota Composition in Patients with Type 2 Diabetes and Effects of Oral Antidiabetics.	Kalkan AT, Yorulmaz G, Akalin A, Dinleyici EC.	J Clin Med	10.3390/jcm14082786	2025
	Healthy Ageing and Gut Microbiota: A Study on Longevity in Adults.	Deng L, Xu J, Xue Q, Wei Y, Wang J.	Microorganisms	10.3390/microorganisms13071657	2025
	Straining to define a healthy microbiome.	Seekatz AM.	mSphere	10.1128/msphere.00797-24	2025
Genetics	Metagenomic analysis demonstrates distinct changes in the gut microbiome of Kawasaki diseases children.	Han L, Liu X, Lan Y, Hua Y, Fan Z, Li Y.	Front Immunol	10.3389/fimmu.2024.1416185	2024
	The Role of Gut Microbiota-Brain Axis in Pathophysiology of ADHD: A Systematic Review.	Shirvani-Rad S, Ejtahed HS, Ettehad Marvasti F, Taghavi M, Sharifi F, Arzaghi SM, Larijani B.	J Atten Disord	10.1177/10870547211073474	2022
	Role of Gut Microbiota and Metabolomics in Predicting Response to Vedolizumab in Inflammatory Bowel Disease: A Systematic Review.	Malinauskiene V, Cijauskaite E, Sadauskaite G, Stundiene I.	Pharmaceutics	10.3390/pharmaceutics17040476	2025
	Changes in Human Colonic Microbiota Promoted by Synbiotic Açai Juice Composed of Gluco-Oligosaccharides, Dextran, and Bifidobacterium breve NRRL B-41408.	Reges BM, da Silva Oliveira FA, Fonteles TV, Rodrigues S.	Foods	10.3390/foods13244121	2024
	Gut microbiome and attention deficit/hyperactivity disorder: a systematic review.	Gkougka D, Mitropoulos K, Tzanakaki G, Panagouli E, Psaltopoulou T, Thomaidis L, Tsolia M, Sergentanis TN, Tsitsika A.	Pediatr Res	10.1038/s41390-022-02027-6	2022
	A low-cost, easy-to-use prototype bioreactor model for the investigation of human gut microbiota: validation using a prebiotic treatment.	Agrinier AL, Pilon G, Marette A.	Front Microbiol	10.3389/fmicb.2024.1250366	2024
	Gut Dysbiosis Shaped by Cocoa Butter-Based Sucrose-Free HFD Leads to Steatohepatitis, and Insulin Resistance in Mice	Kochumon S, Malik M, Sindhu S, Arefanian H, Jacob T, Bahman F, Nizam R, Hasan A, Thomas R, Al-Rashed F, Shenouda S, Wilson A, Albeloushi S, Almansour N, Alhamar G, Al Madhoun A, Alzaid F, Thanaraj T, Koistinen H, Tuomilehto J, Al-Mulla F, Ahmad R.	Nutrients		2024
	Metabolism of a hybrid algal galactan by members of the human gut microbiome.	Robb CS, Hobbs JK, Pluvinage B, Reintjes G, Klassen L, Monteith S, Giljan G, Amundsen C, Vickers C, Hettle AG, Hills R, Nitin, Xing X, Montina T, Zandberg WF, Abbott DW, Boraston AB.	Nat Chem Biol	10.1038/s41589-022-00983-y	2022
	Anxiety-like behavior during protracted morphine withdrawal is driven by gut microbial dysbiosis and attenuated with probiotic treatment.	Oppenheimer M, Tao J, Moidunny S, Roy S.	Gut Microbes	10.1080/19490976.2025.2517838	2025
	Intestinal Barrier Impairment Induced by Gut Microbiome and Its Metabolites in School-Age Children with Zinc Deficiency.	Chai X, Chen X, Yan T, Zhao Q, Hu B, Jiang Z, Guo W, Zhang Y.	Nutrients	10.3390/nu16091289	2024
	Unraveling the links between estrogen and gut microbiota in sex-hormone driven cancers.	Tahri A, Amedei A.	World J Clin Oncol	10.5306/wjco.v16.i9.108819	2025
	Emphysematous gastritis: The silent storm within the stomach wall.	Aggarwal CS, Dahiya S, Kochhar S, Aggarwal K, Edgecombe L, Jeje T, Jain R.	J Int Med Res	10.1177/03000605251389384	2025
Pathogenicity	Sex-Specific Effect of a High-Energy Diet on Body Composition, Gut Microbiota, and Inflammatory Markers in Rats.	Minaya DM, Hoss A, Bhagat A, Guo TL, Czaja K.	Nutrients	10.3390/nu17071147	2025
	Lactobacillus rhamnosus GG Administration Is Associated with Stimulation of Vitamin D/VDR Pathway and Mucosal Microbiota Modulation in Ulcerative Colitis Patients: A Pilot Study.	Pagnini C, Gori M, Di Paolo MC, Urgesi R, Cicione C, Zingariello M, Arciprete F, Velardi V, Viciani E, Padella A, Castagnetti A, Graziani MG, Delle Fave G.	Pharmaceuticals (Basel)	10.3390/ph18111651	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
	Prophylactic treatment with Bacteroides uniformis and Bifidobacterium bifidum counteracts hepatic NK cell immune tolerance in nonalcoholic steatohepatitis induced by high fat diet.	Xu J, Xia Q, Wu T, Shao Y, Wang Y, Jin N, Tian P, Wu L, Lu X.	Gut Microbes	10.1080/19490976.2024.2302065	2024
	Types of fiber and gut microbiota composition and diversity among arab females.	Aljuraiban GS, Algabsani SS, Sabico S, AlShammari S, Aljazairy EA, Al-Musharaf S.	Saudi J Biol Sci	10.1016/j.sjbs.2023.103767	2023
	Impact of Blastocystis carriage and colonization intensity on gut microbiota composition in a non-westernized rural population from Colombia.	Castaneda S, Tomiak J, Andersen LO, Acosta CP, Vasquez-A LR, Stensvold CR, Ramirez JD.	PLoS Negl Trop Dis	10.1371/journal.pntd.0013111	2025
Genetics	CRISPR/Cas-Based Genome Editing for Human Gut Commensal Bacteroides Species.	Zheng L, Tan Y, Hu Y, Shen J, Qu Z, Chen X, Ho CL, Leung EL, Zhao W, Dai L.	ACS Synth Biol	10.1021/acssynbio.1c00543	2022
Genetics	Exploration of fecal microbiota in newly diagnosed patients with inflammatory bowel disease using shotgun metagenomics.	Orejudo M, Gomez MJ, Riestra S, Rivero M, Gutierrez A, Rodriguez-Lago I, Fernandez-Salazar L, Ceballos D, Benitez JM, Aguas M, Baston-Rey I, Bermejo F, Casanova MJ, Lorente-Poyatos RH, Ber Y, Ginard D, Esteve M, de Francisco R, Garcia MJ, Frances R, Rodriguez A, Alcaide Suarez N, Guerra Del Rio E, Soto P, Nos P, Barreiro-de Acosta M, Guerra I, Hervias Cruz D, Dominguez Cajal M, Royo V, Aceituno M, Aldars-Garcia L, Garre A, Ramirez C, Soleto I, Schuppe-Koistinen I, Engstrand L, Baldan-Martin M, Sanchez-Cabo F, Gisbert JP, Chaparro M.	Front Cell Infect Microbiol	10.3389/fcimb.2025.1595884	2025
	Predictive Role of Gut Microbiota in Weight Loss Achievement after Bariatric Surgery.	Gutierrez-Repiso C, Garrido-Sanchez L, Alcaide-Torres J, Cornejo-Pareja I, Ocana-Wilhelmi L, Garcia-Fuentes E, Moreno-Indias I, Tinahones FJ.	J Am Coll Surg	10.1097/xcs.0000000000000145	2022
Pathogenicity	Moderate altitude exposure impacts extensive host-microbiota multi-kingdom connectivity with serum metabolome and fasting blood glucose.	Huang X, Gao X, Fan Y, Wang D, Chen X, Qi X, Yang Z, Wang YE, Meng J, Zou G, Liu Z, Li X.	Virulence	10.1080/21505594.2025.2530660	2025
	Identification and characterization of two AA9 lytic polysaccharide monooxygenases isolated from the enzymatic arsenal in Phanerochaete chrysosporium.	Xu X, Chu CE, Li N, Sun XB, Han J, Xu Z, Liu Y, Wang JK, Zhang TT, Wang Q.	Bioresour Bioprocess	10.1186/s40643-025-00950-0	2025
Metabolism	A low molecular weight brown algae Laminaria japonica glycan modulation of gut microbiota and body weight in mice.	Jin Z, Fang Z, Pei Z, Wang H, Zhu J, Lee YK, Zhang H, Zhao J, Lu W, Chen W.	Food Funct	10.1039/d1fo03024h	2021
	Differences in tissue-associated bacteria between metastatic and non-metastatic colorectal cancer.	Zhou P, Dai Z, Xie Y, Li T, Xu Z, Huang Y, Sun D, Zhou Y.	Front Microbiol	10.3389/fmicb.2023.1133607	2023
	Gut microbes on the risk of advanced adenomas.	Jing Z, Zheng W, Jianwen S, Hong S, Xiaojian Y, Qiang W, Yunfeng Y, Xinyue W, Shuwen H, Feimin Z.	BMC Microbiol	10.1186/s12866-024-03416-z	2024
	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
	Bacteroides species differentially modulate depression-like behavior via gut-brain metabolic signaling.	Zhang Y, Fan Q, Hou Y, Zhang X, Yin Z, Cai X, Wei W, Wang J, He D, Wang G, Yuan Y, Hao H, Zheng X.	Brain Behav Immun	10.1016/j.bbi.2022.02.007	2022
	Effects of alcohol on gut microbiome in adolescent and adult MMTV-Wnt1 mice.	Li H, Meza LA, Shahi SK, Zhang Z, Wen W, Hu D, Lin H, Mangalam AK, Luo J.	Front Oncol	10.3389/fonc.2025.1557040	2025
	Triacetin and a Mushroom Blend Restore Butyrate Production by IBS Microbiomes Ex Vivo, Thus Promoting Barrier Integrity.	Van den Abbeele P, Poppe J, Baudot A, Vu LD.	Int J Mol Sci	10.3390/ijms26199388	2025
	MiMeJF: Application of Coupled Matrix and Tensor Factorization (CMTF) for Enhanced Microbiome-Metabolome Multi-Omic Analysis.	Ou Z, Fu X, Norback D, Lin R, Wen J, Sun Y.	Metabolites	10.3390/metabo15010051	2025
Genetics	Machine learning integrates region-specific microbial signatures to distinguish geographically adjacent populations within a province.	Luo L, Chen B, Zeng S, Li Y, Chen X, Zhang J, Guo X, Li S, Ruan L, Zhu S, Gao C, Zhang C, Li T.	Front Microbiol	10.3389/fmicb.2025.1586195	2025
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
	Lychee (Litchi chinensis Sonn.) Pulp Phenolics Activate the Short-Chain Fatty Acid-Free Fatty Acid Receptor Anti-inflammatory Pathway by Regulating Microbiota and Mitigate Intestinal Barrier Damage in Dextran Sulfate Sodium-Induced Colitis in Mice.	Huang G, Wang Z, Wu G, Zhang R, Dong L, Huang F, Zhang M, Su D.	J Agric Food Chem	10.1021/acs.jafc.0c07407	2021
Phenotype	Shared and Distinct Gut Microbial Profiles in Saudi Women with Metabolically Healthy and Unhealthy Obesity.	Aljuraiban GS, Alfhili MA, Aldhwayan MM, Aljazairy EA, Al-Musharaf S.	Microorganisms	10.3390/microorganisms11061430	2023
Genetics	Use of proximity ligation shotgun metagenomics to investigate the dynamics of plasmids and bacteriophages in the gut microbiome following fecal microbiota transplantation.	Bryson S, Sisson Z, Nelson B, Grove J, Reister E, Liachko I, Auch B, Graiziger C, Khoruts A.	Gut Microbes	10.1080/19490976.2025.2559019	2025
	The effect of culturing temperature on the growth of the most dominant bacterial species of human gut microbiota and harmful bacterial species.	Shimokawa H, Sakakibara H, Ami Y, Hirano R, Kurihara S.	Biosci Microbiota Food Health	10.12938/bmfh.2024-087	2025
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
Phylogeny	Gut microbial changes in a specialist blister beetle larvae and their nutritional metabolic characteristics.	Ma J, Fu Z, Yang X, Ming W, Song X, Du C.	Ecol Evol	10.1002/ece3.70184	2024
	Gut Microbiota-microRNA Interactions and Obesity Pathophysiology: A Systematic Review of Integrated Studies.	Azari H, George M, Albracht-Schulte K.	Int J Mol Sci	10.3390/ijms252312836	2024
	Eggerthella lenta down regulated flavone and flavonol biosynthesis promoted Kawasaki disease.	Yeh YT, Chen KD, Huang CH, Tsai JR, Kuo HC.	Virulence	10.1080/21505594.2025.2512401	2025
	Decoding IBD progression: a dynamic biomarker atlas for personalized disease stratification.	Tao Y, Wang LF, Li P, Sun R, Li YJ, Sun MH, Zhang LJ, Yang LH, Jin JJ, Zhong XN.	J Transl Med	10.1186/s12967-025-07024-x	2025
	Black rice diet alleviates colorectal cancer development through modulating tryptophan metabolism and activating AHR pathway.	Wang L, Tu YX, Chen L, Yu KC, Wang HK, Yang SQ, Zhang Y, Zhang SJ, Song S, Xu HL, Yin ZC, Feng MQ, Yue JQ, Huang XH, Tang T, Wei SZ, Liang XJ, Chen ZX.	Imeta	10.1002/imt2.165	2024
	Saliva-driven surface-engineered Bacteroides thetaiotaomicron alleviates hypertension.	Xu S, Luo H, Du LJ, Dong T, Zhou LJ, Chen BY, Li YL, Tian GC, Meng XQ, Bai XB, Ye HL, Zhang J, Lin WZ, Zhang WC, Liu J, Duan SZ.	Bioact Mater	10.1016/j.bioactmat.2025.11.007	2026
	Zearalenone-14-glucoside specifically promotes dysplasia of Gut-Associated Lymphoid Tissue: A natural product for constructing intestinal nodular lymphatic hyperplasia model.	Ruan H, Wang Y, Zhang J, Huang Y, Yang Y, Wu C, Guo M, Luo J, Yang M.	J Adv Res	10.1016/j.jare.2023.05.006	2023
	Colitis reduces active social engagement in mice and is ameliorated by supplementation with human microbiota members.	Brown DG, Murphy M, Cadeddu R, Bell R, Weis A, Chiaro T, Klag K, Morgan J, Coon H, Stephens WZ, Bortolato M, Round JL.	Nat Commun	10.1038/s41467-024-46733-7	2024
Genetics	Fecal Microbiota Composition, Their Interactions, and Metagenome Function in US Adults with Type 2 Diabetes According to Enterotypes.	Park S, Zhang T, Kang S.	Int J Mol Sci	10.3390/ijms24119533	2023
Phylogeny	Effect of aerobic exercise and particulate matter exposure duration on the diversity of gut microbiota.	Imdad S, Kim JH, So B, Jang J, Park J, Lim W, Lee YK, Shin WS, Hillyer T, Kang C.	Anim Cells Syst (Seoul)	10.1080/19768354.2024.2338855	2024
Pathogenicity	Baicalin-Aluminum Modulates the Broiler Gut Microbiome.	Guo L, He J, Zhang J, Zhang X, Zhang D, Zhou L, Yuan Y, Fu S, Qiu Y, Ye C, Liu Y, Wu Z, Hu CA.	DNA Cell Biol	10.1089/dna.2021.0080	2021
	Unhappy Triad: Infection with Leptospira spp. Escherichia coli and Bacteroides uniformis Associated with an Unusual Manifestation of Portal Vein Thrombosis.	Kalbitz S, Ermisch J, Schmidt JM, Wallstabe I, Lubbert C.	Case Rep Gastroenterol	10.1159/000517094	2021
	Comparative Binding Study of Gliptins to Bacterial DPP4-like Enzymes for the Treatment of Type 2 Diabetes Mellitus (T2DM).	Carpio LE, Olivares M, Benitez-Paez A, Serrano-Candelas E, Barigye SJ, Sanz Y, Gozalbes R.	Int J Mol Sci	10.3390/ijms25115744	2024
Genetics	Genomic Insights into Emerging Multidrug-Resistant Chryseobacterium indologenes Strains: First Report from Thailand.	Yinsai O, Yuantrakul S, Srisithan P, Zhou W, Chittaprapan S, Intajak N, Kruayoo T, Khamnoi P, Tongjai S, Duangsonk K.	Antibiotics (Basel)	10.3390/antibiotics14080746	2025
	Prolonged effect of antibiotic therapy on the gut microbiota composition, functionality, and antibiotic resistance genes' profiles in healthy stool donors.	Karimianghadim R, Satokari R, Yeo S, Arkkila P, Kao D, Pakpour S.	Front Microbiol	10.3389/fmicb.2025.1589704	2025
Genetics	Exploring the dynamics of gut microbiota, antibiotic resistance, and chemotherapy impact in acute leukemia patients: A comprehensive metagenomic analysis.	Luo Y, Sheikh TMM, Li X, Yuan Y, Yao F, Wang M, Guo X, Wu J, Shafiq M, Xie Q, Jiao X.	Virulence	10.1080/21505594.2024.2428843	2024
	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
Phylogeny	[Correlation between gut microbiota and liver biochemical indicators in patients with chronic hepatitis B].	Zhao Z, Qin S, Wang L, Li L, Liu Y, Deng L, Zou Z.	Sheng Wu Gong Cheng Xue Bao	10.13345/j.cjb.200279	2021
	Use of Deep Sequencing to Evaluate Transitions in Microbial Communities in Stranded Sargassum.	Abdool-Ghany AA, Babler KM, Bogumil D, Pollock S, Li J, Manning SR, Solo-Gabriele HM.	Int J Microbiol	10.1155/ijm/3915271	2025
	Positive Effects of Lycopene on Growth Performance, Hepatic Antioxidant Capacity, Intestinal Morphology, and Cecal Microflora of Yellow-Feather Broilers.	Cao G, Liu X, Wang H, Kang J, Wang F, Li M, Sun W, Lv X.	Animals (Basel)	10.3390/ani15142108	2025
Metabolism	Gut microbiota-mediated modulation of host amino acid availability and metabolism.	Han Z, Zhao L, Hu Q, Hung I, Liu C, Liu S, Mei X, Zeng X, Bin P, Wang J.	Gut Microbes	10.1080/19490976.2025.2552345	2025
Genetics	Impact of Limosilactobacillus fermentum probiotic treatment on gut microbiota composition in sahiwal calves with rotavirus diarrhea: A 16S metagenomic analysis study".	Murtaza N, Nawaz M, Yaqub T, Mehmood AK.	BMC Microbiol	10.1186/s12866-024-03254-z	2024
Genetics	Bacteraemia Associated with Bilophila wadsworthia: A Rare Case Presentation from Hungary.	Kovacs R, Arokszallasi T, Bozo A, Jakab A, Babel KS, Heja M, Kovacs KB, Balazs B, Vitalis E, Majoros L, Toth Z.	Pathogens	10.3390/pathogens13090749	2024
Phylogeny	Gut microbiome profile of Chinese hypertension patients with and without type 2 diabetes mellitus.	Ding H, Xu Y, Cheng Y, Zhou H, Dong S, Wu J, Lv J, Hu X, Tang O.	BMC Microbiol	10.1186/s12866-023-02967-x	2023
	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
	[Bacteremia due to strict anaerobes].	Pina Delgado C, Bolanos Rivero M, Carmona Tello MC, Ramirez Estupinan CJ, Hernandez Cabrera PM, de Miguel Martinez I.	Rev Esp Quimioter	10.37201/req/063.2024	2025
Metabolism	Ginseng Polysaccharides Inhibit Aspergillus sydowii-Driven Lung Adenocarcinoma via Modulating Gut Microbiota-Bile Acid Metabolism Axis.	He J, Shu X, Pan H, Wang M, Song Y, Zhou F, Lian L, Chen L, Ma G, Zhao Y, Li R, Liu L.	Cancers (Basel)	10.3390/cancers17193134	2025
	Inter-phylum circulation of a beta-lactamase-encoding gene: a rare but observable event.	Gschwind R, Petitjean M, Fournier C, Lao J, Clermont O, Nordmann P, Mellmann A, Denamur E, Poirel L, Ruppe E.	Antimicrob Agents Chemother	10.1128/aac.01459-23	2024
	Fecal microbiota transplantation significantly improved respiratory failure of amyotrophic lateral sclerosis.	Yan J, Chen H, Zhang Y, Peng L, Wang Z, Lan X, Yu S, Yang Y.	Gut Microbes	10.1080/19490976.2024.2353396	2024
Metabolism	Chemical and microbial characterization for fermentation of water-soluble cellulose acetate in human stool cultures.	Yamada H, Watabe Y, Suzuki Y, Koike S, Shimamoto S, Kobayashi Y.	J Sci Food Agric	10.1002/jsfa.10927	2021
Genetics	The mOTUs online database provides web-accessible genomic context to taxonomic profiling of microbial communities.	Dmitrijeva M, Ruscheweyh HJ, Feer L, Li K, Miravet-Verde S, Sintsova A, Mende DR, Zeller G, Sunagawa S.	Nucleic Acids Res	10.1093/nar/gkae1004	2025
	Modulation of the gut microbiome and Firmicutes phylum reduction by a nutraceutical blend in the obesity mouse model and overweight humans: A double-blind clinical trial.	Nehmi-Filho V, de Freitas JA, Franco LA, Martins RC, Turri JAO, Santamarina AB, Fonseca JVDS, Sabino EC, Moraes BC, Souza E, Murata GM, Costa SF, Alcantara PS, Otoch JP, Pessoa AFM.	Food Sci Nutr	10.1002/fsn3.3927	2024
	Exploring compositional and predicted functional alterations of gut microbiota in H. pylori infection.	Soliman NS, Soliman MS, Aziz HSA, El-Kholy AA.	Sci Rep	10.1038/s41598-025-22788-4	2025
	Temporal stability and lack of variance in microbiome composition and functionality in fit recreational athletes.	O' Donovan CM, Nori SRC, Shanahan F, Celentano G, Murphy TB, Cotter PD, Sullivan OO.	Sci Rep	10.1038/s41598-025-88723-9	2025
	Bacteroides uniformis degrades beta-glucan to promote Lactobacillus johnsonii improving indole-3-lactic acid levels in alleviating colitis.	Zhang S, Nie Q, Sun Y, Zuo S, Chen C, Li S, Yang J, Hu J, Zhou X, Yu Y, Huang P, Lian L, Xie M, Nie S.	Microbiome	10.1186/s40168-024-01896-9	2024
Phylogeny	Modulating the gut microbiota in Crohn's disease: a pilot study on the impact of a plant-based diet with DNA-based monitoring.	Ostergaard SK, Cetin Z, Rasmussen HH, Laerke HN, Holst M, Lauridsen C, Nielsen JL.	Front Nutr	10.3389/fnut.2024.1502967	2024
Genetics	Alterations of intestinal microbiota in liver cirrhosis with muscle wasting.	Ren X, Hao S, Yang C, Yuan L, Zhou X, Zhao H, Yao J.	Nutrition	10.1016/j.nut.2020.111081	2021
Genetics	Fecal microbiota transplantation restores normal fecal composition and delays malignant development of mild chronic kidney disease in rats.	Liu X, Zhang M, Wang X, Liu P, Wang L, Li Y, Wang X, Ren F.	Front Microbiol	10.3389/fmicb.2022.1037257	2022
	Human colitis-associated colorectal carcinoma progression is accompanied by dysbiosis with enriched pathobionts.	Masaadeh AH, Eletrebi M, Parajuli B, De Jager N, Bosch DE.	Gut Microbes	10.1080/19490976.2025.2479774	2025
	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
Transcriptome	Coordinated changes of gut microbiome and lipidome differentiates nonalcoholic steatohepatitis (NASH) from isolated steatosis.	Qian M, Hu H, Yao Y, Zhao D, Wang S, Pan C, Duan X, Gao Y, Liu J, Zhang Y, Yang S, Qi LW, Wang L.	Liver Int	10.1111/liv.14316	2020
	How is the human microbiome linked to kidney stones?	Pei X, Liu M, Yu S.	Front Cell Infect Microbiol	10.3389/fcimb.2025.1602413	2025
	Correlation study on gut microbiota and myosteatosis in patients with liver cirrhosis.	Zhao N, Bai J, Li X, Xu G, Fu X, Li J, Niu L, Yao J, Zhou X.	Front Nutr	10.3389/fnut.2025.1513973	2025
	Moderate altitude exposure induced gut microbiota enterotype shifts impacting host serum metabolome and phenome.	Ma Y, Wang D, Yu X, Fan Y, Yang Z, Gao X, Huang X, Meng J, Cheng P, Liu X, Liu Z, Li X.	BMC Microbiol	10.1186/s12866-025-04245-4	2025
	Integrative multiomics analysis reveals association of gut microbiota and its metabolites with susceptibility to keloids.	Li D, Li M, Gao H, Hu K, Xie R, Fan J, Huang M, Liao C, Han C, Guo Z, Chen X, Li M.	Front Microbiol	10.3389/fmicb.2024.1475984	2024
	Bite injuries at a level 1 trauma center in Germany.	Polan C, Kraus SC, Herten M, Meyer HL, Mester B, Hilken G, Dudda M, Kauther MD, Burggraf M.	Trauma Surg Acute Care Open	10.1136/tsaco-2024-001613	2025
Pathogenicity	Metabolic modeling links gut microbiota to metabolic markers of Parkinson's disease.	Hensen T, Thiele I.	Gut Microbes	10.1080/19490976.2025.2554195	2025
	Human Herpesvirus-6B Infection and Alterations of Gut Microbiome in Patients with Fibromyalgia: A Pilot Study.	Ievina L, Fomins N, Gudra D, Kenina V, Vilmane A, Gravelsina S, Rasa-Dzelzkaleja S, Murovska M, Fridmanis D, Nora-Krukle Z.	Biomolecules	10.3390/biom14101291	2024
Transcriptome	Multi-omics analysis reveals associations between gut microbiota and host transcriptome in colon cancer patients.	Qin Y, Wang Q, Lin Q, Liu F, Pan X, Wei C, Chen J, Huang T, Fang M, Yang W, Pan L.	mSystems	10.1128/msystems.00805-24	2025
Metabolism	Gut microbiome association with brain imaging markers, APOE genotype, calcium and vegetable intakes, and obesity in healthy aging adults.	Hammond TC, Green SJ, Jacobs Y, Chlipala GE, Xing X, Heil S, Chen A, Aware C, Flemister A, Stromberg A, Balchandani P, Lin AL.	Front Aging Neurosci	10.3389/fnagi.2023.1227203	2023
	Gut microbiome dynamics and predictive value in hospitalized COVID-19 patients: a comparative analysis of shallow and deep shotgun sequencing.	Kopera K, Gromowski T, Wydmanski W, Skonieczna-Zydecka K, Muszynska A, Zielinska K, Wierzbicka-Wos A, Kaczmarczyk M, Kadaj-Lipka R, Cembrowska-Lech D, Januszkiewicz K, Kotfis K, Witkiewicz W, Nalewajska M, Feret W, Marlicz W, Loniewski I, Labaj PP, Rydzewska G, Kosciolek T.	Front Microbiol	10.3389/fmicb.2024.1342749	2024
	Modulatory Role of Hesperetin-Copper(II) on Gut Microbiota in Type 2 Diabetes Mellitus Mice.	Peng X, Wei Y, Gong D, Zhang G.	Foods	10.3390/foods14132390	2025
	Exploring the Association between Anxiety, Depression, and Gut Microbiota during Pregnancy: Findings from a Pregnancy Cohort Study in Shijiazhuang, Hebei Province, China.	Chi R, Li M, Zhang M, Zhang N, Zhang G, Cui L, Ma G.	Nutrients	10.3390/nu16101460	2024
	Effects of a 217-km mountain ultramarathon on the gut microbiota of an obese runner: A case report.	Saragiotto GK, de Oliveira LFV, Scharlack NK, de Oliveira MM, Freire FC, Simabuco FM, Sivieri K, Sartoratto A, Belli T, Antunes AEC.	Physiol Rep	10.14814/phy2.70017	2024
	Gut Microbiota in Different Treatment Response Types of Crohn's Disease Patients Treated with Biologics over a Long Disease Course.	Zhao X, Xu J, Wu D, Chen N, Liu Y.	Biomedicines	10.3390/biomedicines13030708	2025
	Relationship between gut microbiota dysbiosis and immune indicator in children with sepsis.	Lin X, Abdalla M, Yang J, Liu L, Fu Y, Zhang Y, Yang S, Yu H, Ge Y, Zhang S, Kang G, Dang W, Jiang Q, Wang Y, Gai Z.	BMC Pediatr	10.1186/s12887-023-04349-8	2023
	Gut microbiome changes and cancer immunotherapy outcomes associated with dietary interventions: a systematic review of preclinical and clinical evidence.	Somodi C, Dora D, Horvath M, Szegvari G, Lohinai Z.	J Transl Med	10.1186/s12967-025-06586-0	2025
Genetics	Multi-omics study unravels gut microbiota and metabolites alteration in patients with Wilson's disease.	Cai X, Dai J, Xie Y, Xu S, Liu M.	Sci Rep	10.1038/s41598-024-71740-5	2024
	Impact of the gut microbiome on response and toxicity to chemotherapy in advanced esophageal cancer.	Li N, Gao L, Ge Y, Zhao L, Wang Y, Bai C.	Heliyon	10.1016/j.heliyon.2024.e32770	2024
Genetics	Structure-dependent degradation of milk oligosaccharides by newly isolated intestinal commensal bacterial strains from suckling piglets and rabbits.	Rumeau M, Chadi S, Pepke F, Beaumont M, Vicente CM, Juppeau A, Vandecasteele C, Cauquil L, Pascal G, Langella P, Knudsen C, Combes S, Martin R.	BMC Microbiol	10.1186/s12866-025-04205-y	2025
	The single degree of polymerization influences the efficacy of xylooligosaccharides in shaping microbial and metabolite profiles in chicken gut to combat avian pathogenic Escherichia coli.	Ren L, Cao Q, Ye H, Dong Z, Zhang C, Yan F, Zhou Y, Zhou H, Zuo J, Wang W.	BMC Microbiol	10.1186/s12866-025-03948-y	2025
Metabolism	In vitro fermentation outcomes of arabinoxylan and galactoxyloglucan depend on fecal inoculum more than substrate chemistry.	Feng G, Mikkelsen D, Hoedt EC, Williams BA, Flanagan BM, Morrison M, Gidley MJ.	Food Funct	10.1039/d0fo01103g	2020
Phylogeny	Diversity analysis of gut microbiota between healthy controls and those with atopic dermatitis in a Chinese population.	Ye S, Yan F, Wang H, Mo X, Liu J, Zhang Y, Li H, Chen D.	J Dermatol	10.1111/1346-8138.15530	2021
	Effects of Vegetable and Fruit Juicing on Gut and Oral Microbiome Composition.	Sardaro MLS, Grote V, Baik J, Atallah M, Amato KR, Ring M.	Nutrients	10.3390/nu17030458	2025
	Fermentation of Alginate and Its Oligosaccharides by the Human Gut Microbiota: Structure-Property Relationships and New Findings Focusing on Bacteroides xylanisolvens.	Li J, Lv Y, Shao M, Lv D, Fu Z, Guo P, Li Q, Shang Q.	Nutrients	10.3390/nu17091424	2025
Metabolism	Amelioration of Hepatic Steatosis in Mice through Bacteroides uniformis CBA7346-Mediated Regulation of High-Fat Diet-Induced Insulin Resistance and Lipogenesis.	Lee HB, Do MH, Jhun H, Ha SK, Song HS, Roh SW, Chung WH, Nam YD, Park HY.	Nutrients	10.3390/nu13092989	2021
Transcriptome	Combined Analysis of Transcriptomes and Metabolomes Reveals Key Genes and Substances That Affect the Formation of a Multi-Species Biofilm by Nine Gut Bacteria.	Zhang T, Pei Z, Wang H, Zhao J, Chen W, Lu W.	Microorganisms	10.3390/microorganisms13020234	2025
Genetics	New connections of medication use and polypharmacy with the gut microbiota composition and functional potential in a large population.	Larsson A, Ericson U, Jonsson D, Miari M, Athanasiadis P, Baldanzi G, Brunkwall L, Hellstrand S, Klinge B, Melander O, Nilsson PM, Fall T, Maziarz M, Orho-Melander M.	Sci Rep	10.1038/s41598-024-71571-4	2024
	Characteristics and Clinical Significance of Gut Microbiota in Patients with Invasive Pulmonary Aspergillosis.	Cao J, He Q, Zhang M, Zhou R, Feng C.	Pol J Microbiol	10.33073/pjm-2025-011	2025
Pathogenicity	Characterization of microbiota in acute leukemia patients following successful remission induction chemotherapy without antimicrobial prophylaxis.	Shen Z, Gu X, Cao H, Mao W, Yang L, He M, Zhang R, Zhou Y, Liu K, Wang L, Liu L, Yu J, Yin L.	Int Microbiol	10.1007/s10123-021-00163-3	2021
	Unraveling salivary microbiota diversity following kidney transplantation: insights from baseline peripheral blood lymphocyte subsets.	Xiang X, Wang T, Ding P, Zhu Y, Cheng K, Ming Y.	J Oral Microbiol	10.1080/20002297.2025.2490284	2025
	Spatial variations in intestinal skatole production and microbial composition in broilers	Yang G, Zhang P, Liu H, Zhu X, Dong W.	Animal Science Journal.		2019
Genetics	Characteristics of the gut virome in patients with premalignant colorectal adenoma.	Zhang P, Tuo X, Jiang J, Zhang Y, Zhao J, Deng C, Zhao G, Cheng Y, Song L, Yang Y, Guo R, Zhang H, Zhao H, Ma S, Li L, Shi H.	J Transl Med	10.1186/s12967-025-06404-7	2025
	Inter-species and individualized biotransformation of five saponins by human being- and mouse-derived fecal microbiota.	Wei W, Li M, Pan L, Shao M, He X, Li Y, Sheng L, Zheng N, Li H.	Chin Med	10.1186/s13020-025-01190-2	2025
	Quantification of Streptococcus salivarius using the digital polymerase chain reaction as a liver fibrosis marker.	Iwasaki S, Take A, Uojima H, Horio K, Sakaguchi Y, Gotoh K, Satoh T, Hidaka H, Tanaka Y, Hayashi S, Kusano C.	World J Hepatol	10.4254/wjh.v17.i4.102027	2025
	The association between gut microbiota composition and cardiometabolic parameters in healthy adults	Okalin S, Arslan N, Demiray Gurbuz E, Arayici M, Kirca N, Ozel Demiralp D, Dereli-Akdeniz D, Akan P, Ozkutuk A.	BMC Microbiol		2025
Phylogeny	Dynamic relationship between gut microbiota and post-necrotizing pancreatitis: insights from a multi-stage 16S rRNA sequencing study	Lu J, Wang Z, Cao F, Ji G, Li F.	Front Pharmacol		2025
Genetics	Growth phase estimation for abundant bacterial populations sampled longitudinally from human stool metagenomes.	Lim JJ, Diener C, Wilson J, Valenzuela JJ, Baliga NS, Gibbons SM.	Nat Commun	10.1038/s41467-023-41424-1	2023
Genetics	Association between the ABCC11 gene polymorphism-determined earwax properties and external auditory canal microbiota in healthy adults.	Amari Y, Hosonuma M, Mizukami T, Isobe J, Azetsu Y, Funayama E, Maruyama Y, Tsurui T, Tajima K, Sasaki A, Yamazaki Y, Nakano R, Sano Y, Ishida A, Nakanishi T, Mochizuki S, Yoshizawa Y, Kumagai S, Yasuhara S, Ryu K, Oguchi T, Kuramasu A, Yoshimura K, Sambe T, Kobayashi S, Uchida N.	Microbiol Spectr	10.1128/spectrum.01698-24	2025
	Co-variation of Host Gene Expression and Gut Microbiome in Intestine-Specific Spp1 Conditional Knockout Mice.	Li N, Gao G, Zhang T, Zhao C, Zhao Y, Zhang Y, Sun Z.	Curr Microbiol	10.1007/s00284-025-04246-6	2025
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
Pathogenicity	Bacteroides and NAFLD: pathophysiology and therapy.	Zhang J, Zhou J, He Z, Li H.	Front Microbiol	10.3389/fmicb.2024.1288856	2024
	Effects of Italian Mediterranean Organic Diet on the Gut Microbiota: A Pilot Comparative Study with Conventional Products and Free Diet.	Di Renzo L, Frank G, Pala B, Cianci R, La Placa G, Raffaelli G, Palma R, Peluso D, De Lorenzo A, Gualtieri P, On Behalf Of Clinical Nutrition And Nutrigenomics Project Group.	Microorganisms	10.3390/microorganisms13071694	2025
	Levofloxacin prophylaxis and parenteral nutrition have a detrimental effect on intestinal microbial networks in pediatric patients undergoing HSCT.	Fabbrini M, D'Amico F, Leardini D, Muratore E, Barone M, Belotti T, Forchielli ML, Zama D, Pession A, Prete A, Brigidi P, Rampelli S, Candela M, Turroni S, Masetti R.	Commun Biol	10.1038/s42003-023-04436-7	2023
	Relationships of the gut microbiome with cognitive development among healthy school-age children.	Lapidot Y, Maya M, Reshef L, Cohen D, Ornoy A, Gophna U, Muhsen K.	Front Pediatr	10.3389/fped.2023.1198792	2023
Metabolism	Activation of a Specific Gut Bacteroides-Folate-Liver Axis Benefits for the Alleviation of Nonalcoholic Hepatic Steatosis.	Qiao S, Bao L, Wang K, Sun S, Liao M, Liu C, Zhou N, Ma K, Zhang Y, Chen Y, Liu SJ, Liu H.	Cell Rep	10.1016/j.celrep.2020.108005	2020
Genetics	Metagenomic Analysis of Surface Waters and Wastewater in the Colombian Andean Highlands: Implications for Health and Disease.	Urrea V, Paez-Triana L, Velasquez-Ortiz N, Camargo M, Patino LH, Vega L, Ballesteros N, Hidalgo-Troya A, Galeano LA, Ramirez JD, Munoz M.	Curr Microbiol	10.1007/s00284-024-04019-7	2025
Genetics	StrainR2 accurately deconvolutes strain-level abundances in synthetic microbial communities.	Heber K, Tian S, Betancurt-Anzola D, Koo H, Bisanz JE.	Bioinformatics	10.1093/bioinformatics/btaf440	2025
	Changes in antioxidant capacity and gut microbiota in mice after intake of camel milk.	Wang J, Ren W, Liu S, Li Z, Zeng Y, Meng J, Yao X.	Front Cell Infect Microbiol	10.3389/fcimb.2025.1621031	2025
	mbSparse: an autoencoder-based imputation method to address sparsity in microbiome data.	Qi C, Cai Y, He G, Qian K, Guo M, Cheng L.	Gut Microbes	10.1080/19490976.2025.2552347	2025
	Butyricimonas is a key gut microbiome component for predicting postoperative recurrence of esophageal cancer.	Otsuka K, Isobe J, Asai Y, Nakano T, Hattori K, Ariyoshi T, Yamashita T, Motegi K, Saito A, Kohmoto M, Hosonuma M, Kuramasu A, Baba Y, Murayama M, Narikawa Y, Toyoda H, Funayama E, Tajima K, Shida M, Hirasawa Y, Tsurui T, Ariizumi H, Ishiguro T, Suzuki R, Ohkuma R, Kubota Y, Sambe T, Tsuji M, Wada S, Kiuchi Y, Kobayashi S, Horiike A, Goto S, Murakami M, Kim YG, Tsunoda T, Yoshimura K.	Cancer Immunol Immunother	10.1007/s00262-023-03608-y	2024
Metabolism	Spatial variations in intestinal skatole production and microbial composition in broilers.	Yang G, Zhang P, Liu H, Zhu X, Dong W.	Anim Sci J	10.1111/asj.13164	2019
	Bacteroidetes Species Are Correlated with Disease Activity in Ulcerative Colitis.	Nomura K, Ishikawa D, Okahara K, Ito S, Haga K, Takahashi M, Arakawa A, Shibuya T, Osada T, Kuwahara-Arai K, Kirikae T, Nagahara A.	J Clin Med	10.3390/jcm10081749	2021
Pathogenicity	Gut microbial dysbiosis correlates with stroke severity markers in aged rats.	Hammond TC, Messmer S, Frank JA, Lukins D, Colwell R, Lin AL, Pennypacker KR.	Front Stroke	10.3389/fstro.2022.1026066	2022
Phylogeny	The proteome landscape of the kingdoms of life.	Muller JB, Geyer PE, Colaco AR, Treit PV, Strauss MT, Oroshi M, Doll S, Virreira Winter S, Bader JM, Kohler N, Theis F, Santos A, Mann M.	Nature	10.1038/s41586-020-2402-x	2020
Phylogeny	A Comprehensive Metabolomic and Microbial Analysis Following Dietary Amino Acid Reduction in Mice.	Al-Ishaq RK, Ferrara CR, Stephan N, Krumsiek J, Suhre K, Montrose DC.	Metabolites	10.3390/metabo14120706	2024
	Fecal microbial marker panel for aiding diagnosis of autism spectrum disorders.	Wan Y, Wong OWH, Tun HM, Su Q, Xu Z, Tang W, Ma SL, Chan S, Chan FKL, Ng SC.	Gut Microbes	10.1080/19490976.2024.2418984	2024
	Ruptured isolated spinal artery aneurysms: a rare manifestation of an arterial dissecting disease.	Kee TP, Krings T, Pace J, Swaminathan SK, Orru' E.	Front Neurol	10.3389/fneur.2025.1567536	2025
	Effect of Lactobacillus rhamnosus AB-GG combined with phototherapy on neonatal jaundice indicators, intestinal microbiota and metabolism.	Yuan Y, Chen J, Liu T, Chen J, Zhang F, Shi Z, Zhang J.	Front Nutr	10.3389/fnut.2025.1581242	2025
	Fexofenadine HCl enhances growth, biofilm, and lactic acid production of Limosilactobacillus reuteri and Bifidobacterium longum: implications for allergy treatment.	Hammouda ZK, Wasfi R, Abdeltawab NF.	BMC Microbiol	10.1186/s12866-025-04130-0	2025
	LACC1 regulates changes in the intestinal flora in a mouse model of inflammatory bowel disease.	Xu ZY, Wang JC.	BMC Gastroenterol	10.1186/s12876-023-02971-5	2023
	Association between the Blautia/Bacteroides Ratio and Altered Body Mass Index after Bariatric Surgery.	Kim Y, Son D, Kim BK, Kim KH, Seo KW, Jung K, Park SJ, Lim S, Kim JH.	Endocrinol Metab (Seoul)	10.3803/enm.2022.1481	2022
	Association of the human gut microbiota with vascular stiffness.	Cuadrat RRC, Goris T, Birukov A, Eichelmann F, Andrade BGN, Bang C, Franke A, Wittenbecher C, Schulze MB.	Sci Rep	10.1038/s41598-023-40178-6	2023
Phylogeny	Altered gut microbiome profile in patients with knee osteoarthritis.	Wang X, Wu Y, Liu Y, Chen F, Chen S, Zhang F, Li S, Wang C, Gong Y, Huang R, Hu M, Ning Y, Zhao H, Guo X.	Front Microbiol	10.3389/fmicb.2023.1153424	2023
	Interplay of Lymphocytes with the Intestinal Microbiota in Children with Nonalcoholic Fatty Liver Disease.	Liang T, Li D, Zunong J, Li M, Amaerjiang N, Xiao H, Khattab NM, Vermund SH, Hu Y.	Nutrients	10.3390/nu14214641	2022
	Landscapes of gut microbiome and bile acid signatures and their interaction in HBV-associated acute-on-chronic liver failure.	Bao Z, Wei R, Zheng X, Zhang T, Bi Y, Shen S, Zou P, Zhang J, Yan H, Li MD, Yang Z, Gao H.	Front Microbiol	10.3389/fmicb.2023.1185993	2023
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
Metabolism	Integrated Multi-Omics Analysis Reveals the Regulatory Mechanism of Peanut Skin Procyanidins on Lipid Metabolism in High-Fat-Diet-Induced Obese Mice.	Shen J, Zhou Y, Yang D, Liu R, Zhu X, Liu R.	Nutrients	10.3390/nu17132228	2025
	Evaluating the prebiotic activity of arabinogalactan on the human gut microbiota using 16S rRNA gene sequencing and Raman-activated cell sorting.	Rasoulimehrabani H, Khadem S, Hodzic A, Philipp M, Gallo R, Nikolov G, Seneca J, Ramesmayer J, Sivulic P, Berry D.	Microbiome Res Rep	10.20517/mrr.2025.29	2025
	Metagenomic Comparison of Gut Microbes of Lemur catta in Captive and Semi-Free-Range Environments.	Xu C, Guo X, Li L.	Animals (Basel)	10.3390/ani15101442	2025
Metabolism	Kazak faecal microbiota transplantation induces short-chain fatty acids that promote glucagon-like peptide-1 secretion by regulating gut microbiota in db/db mice.	Han X, Wang Y, Zhang P, Zhu M, Li L, Mao X, Sha X, Li L.	Pharm Biol	10.1080/13880209.2021.1954667	2021
	Intestinal microbiota composition of children with infection with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and multisystem inflammatory syndrome (MIS-C).	Suskun C, Kilic O, Yilmaz Ciftdogan D, Guven S, Karbuz A, Ozkaya Parlakay A, Kara Y, Kacmaz E, Sahin A, Boga A, Kizmaz Isancli D, Gulhan B, Kanik-Yuksek S, Kiral E, Bozan G, Arslanoglu MO, Kizil MC, Dinleyici M, Us T, Varis A, Kaya M, Vandenplas Y, Dinleyici EC.	Eur J Pediatr	10.1007/s00431-022-04494-9	2022
Pathogenicity	Multiomics Integration Reveals Microbial Gene Interactions Shaping Host Responses in a DSS-Induced Colitis Mouse Model.	Hong HH, Lee SY, Jang DH, Ju SE, Shim JE, Kim TH, Kang HS, Kim SM.	J Microbiol Biotechnol	10.4014/jmb.2507.07010	2025
Phylogeny	Design and optimization of a 16S microbial qPCR multiplex for the presumptive identification of feces, saliva, vaginal and menstrual secretions.	Lewis C, Seashols-Williams SJ.	J Forensic Sci	10.1111/1556-4029.15029	2022
	Comprehensive insights from composition to functional microbe-based biodiversity of the infant human gut microbiota.	Lugli GA, Mancabelli L, Milani C, Fontana F, Tarracchini C, Alessandri G, van Sinderen D, Turroni F, Ventura M.	NPJ Biofilms Microbiomes	10.1038/s41522-023-00392-6	2023
	The role of microbiome dysbiosis in cardiovascular disease: Mechanisms and therapeutic implications.	Abdulaal R, Tlaiss Y, Jammal F, Moussbah TH, Tarchichi A, Hteit A, Tlais M, Nassif D.	Glob Cardiol Sci Pract	10.21542/gcsp.2025.3	2025
	Taking intestinal microbes and the immune system as opportunities to maintain the intestinal health of piglets: review.	Hou X, Chen Y, Chen F, Yin Y, Xu K.	Anim Biosci	10.5713/ab.25.0100	2025
	The impact of perinatal maternal stress on the maternal and infant gut and human milk microbiomes: A scoping review.	Ryan N, O'Mahony S, Leahy-Warren P, Philpott L, Mulcahy H.	PLoS One	10.1371/journal.pone.0318237	2025
Metabolism	Chemical Cross-Linking Controls in Vitro Fecal Fermentation Rate of High-Amylose Maize Starches and Regulates Gut Microbiota Composition.	Wang S, Zhang B, Chen T, Li C, Fu X, Huang Q.	J Agric Food Chem	10.1021/acs.jafc.9b04410	2019
	Sevoflurane-induced gut microbiota dysbiosis drives adolescent neurobehavioral deficits in neonatal rats: Protective role of eicosapentaenoic acid.	Fan P, Wang K, Wei H, Yang L, Zhang S, Cheng Y, Li C, Zhang Y, Jia P, Zhang Y, Xun Y, Wang Y, Yang P, Zhang P, Wang N.	iScience	10.1016/j.isci.2025.113657	2025
	Gut microbiota in the development and progression of chronic liver diseases: Gut microbiota-liver axis.	Yakut A.	World J Hepatol	10.4254/wjh.v17.i3.104167	2025
	Interactions between perceived stress and microbial-host immune components: two demographically and geographically distinct pregnancy cohorts.	Penalver Bernabe B, Maki PM, Cunningham JL, Eisenlohr-Moul T, Tussing-Humphreys L, Carroll IM, Meltzer-Brody S, Gilbert JA, Kimmel M.	Transl Psychiatry	10.1038/s41398-022-02276-3	2023
Phylogeny	Gut Microbiota Patterns in Patients with Non-Alcoholic Fatty Liver Disease: A Comprehensive Assessment Using Three Analysis Methods.	Korobeinikova AV, Zlobovskaya OA, Sheptulina AF, Ashniev GA, Bobrova MM, Yafarova AA, Akasheva DU, Kabieva SS, Bakoev SY, Zagaynova AV, Lukashina MV, Abramov IA, Pokrovskaya MS, Doludin YV, Tolkacheva LR, Kurnosov AS, Zyatenkova EV, Lavrenova EA, Efimova IA, Glazunova EV, Kiselev AR, Shipulin GA, Kontsevaya AV, Keskinov AA, Yudin VS, Makarov VV, Drapkina OM, Yudin SM.	Int J Mol Sci	10.3390/ijms242015272	2023
	Functional recovery outcomes following acute stroke is associated with abundance of gut microbiota related to inflammation, butyrate and secondary bile acid.	Hammond TC, Powell E, Green SJ, Chlipala G, Frank J, Yackzan AT, Yanckello LM, Chang YH, Xing X, Heil S, Springer JE, Pennypacker K, Stromberg A, Sawaki L, Lin AL.	Front Rehabil Sci	10.3389/fresc.2022.1017180	2022
Pathogenicity	Nutraceutical Capsules LL1 and Silymarin Supplementation Act on Mood and Sleep Quality Perception by Microbiota-Gut-Brain Axis: A Pilot Clinical Study.	Santamarina AB, Nehmi Filho V, Freitas JA, Franco LAM, Fonseca JV, Martins RC, Turri JAO, Silva BFRBD, Gusmao AF, Olivieri EHR, Otoch JP, Pessoa AFM.	Nutrients	10.3390/nu16183049	2024
	Antimicrobial Effects of Kelisha Capsule on Escherichia coli Induced Diarrhea in Mice.	Shi G, Lu X, Wang G, Qian K, Peng X, Zhu Y, Wu J, Ke H, Chen L, Zheng Y, Yang T, Shi X, Huang P.	Drug Des Devel Ther	10.2147/dddt.s511158	2025
Enzymology	Impact of ginsenoside Rb1 on gut microbiome and associated changes in pharmacokinetics in rats.	Chen Y, Zhang KX, Liu H, Zhu Y, Bu QY, Song SX, Li YC, Zou H, You XY, Zhao GP.	Sci Rep	10.1038/s41598-024-72225-1	2024
	The Role of Next-Generation Probiotics in Obesity and Obesity-Associated Disorders: Current Knowledge and Future Perspectives.	Vallianou NG, Kounatidis D, Tsilingiris D, Panagopoulos F, Christodoulatos GS, Evangelopoulos A, Karampela I, Dalamaga M.	Int J Mol Sci	10.3390/ijms24076755	2023
	Christensenella minuta interacts with multiple gut bacteria.	Xu C, Jiang H, Feng LJ, Jiang MZ, Wang YL, Liu SJ.	Front Microbiol	10.3389/fmicb.2024.1301073	2024
	Gut microbiome related to metabolic diseases after moderate-to-vigorous intensity exercise.	Yun S, Seo Y, Lee Y, Lee DT.	J Exerc Sci Fit	10.1016/j.jesf.2024.07.003	2024
	Multi-kingdom microbiota analysis reveals bacteria-viral interplay in IBS with depression and anxiety.	Liu Q, Fang W, Zheng P, Xie S, Jiang X, Luo W, Han L, Zhao L, Lu L, Zhai L, Yu DJ, Yang W, Lin C, Fang X, Bian Z.	NPJ Biofilms Microbiomes	10.1038/s41522-025-00760-4	2025
	Dietary fiber induces a fat preference associated with the gut microbiota.	Liow YJ, Kamimura I, Umezaki M, Suda W, Takayasu L.	PLoS One	10.1371/journal.pone.0305849	2024
	Identification of bacterial species in probiotic consortiums in selected commercial cleaning preparations.	Jezewska-Frackowiak J, Zebrowska J, Czajkowska E, Jasinska J, Peksa M, Jedrzejczak G, Skowron PM.	Acta Biochim Pol	10.18388/abp.2018_2782	2019
	Gut microbiota prevents small intestinal tumor formation due to bile acids in gnotobiotic mice.	Wortmann E, Wylensek D, Basic M, Hermeling S, Bleich A, Haller D, Tolba R, Liebisch G, Janssen KP, Clavel T.	Microbiome Res Rep	10.20517/mrr.2024.20	2024
Phenotype	Effects of Auricularia auricula Polysaccharides on Gut Microbiota and Metabolic Phenotype in Mice.	Liu Q, An X, Chen Y, Deng Y, Niu H, Ma R, Zhao H, Cao W, Wang X, Wang M.	Foods	10.3390/foods11172700	2022
	Persistent reduction of Bifidobacterium longum in the infant gut microbiome in the first year of age following intrapartum penicillin prophylaxis for maternal GBS colonization.	Teuscher JL, Lupatsii M, Graspeuntner S, Jonassen S, Bringewatt A, Herting E, Stichtenoth G, Bossung V, Rupp J, Hartel C, Demmert M.	Front Immunol	10.3389/fimmu.2025.1540979	2025
Metabolism	The Association Between Prevotella copri and Advanced Fibrosis in the Progression of Metabolic Dysfunction-Associated Steatotic Liver Disease.	Zhang D, Leitman M, Pawar S, Shera S, Hernandez L, Jacobs JP, Dong TS.	Nutrients	10.3390/nu17132145	2025
	Xylo-oligosaccharide-based prebiotics upregulate the proteins of the Sus-like system in caecal Bacteroidetes of the chicken: evidence of stimbiotic mechanism.	Amir SE, Naeem M, Boocock D, Coveney C, O'Neill HM, Bedford MR, Burton EJ.	Poult Sci	10.1016/j.psj.2023.103113	2023
	Gut Microbial Dysbiosis and Implications in Solid Organ Transplantation.	Medina CK, Aykut B.	Biomedicines	10.3390/biomedicines12122792	2024
	Assessing the Dark Field of Metaproteome.	Duan H, Cheng K, Ning Z, Li L, Mayne J, Sun Z, Figeys D.	Anal Chem	10.1021/acs.analchem.2c02452	2022
Phylogeny	The impact of different gastrointestinal reconstruction techniques on gut microbiota after gastric cancer surgery.	Yang Y, Zhou HY, Zhou GM, Chen J, Ming R, Zhang D, Jiang HW.	Front Microbiol	10.3389/fmicb.2024.1494049	2024
	Alterations in the Gut Microbiota in Pregnant Women with Pregestational Type 2 Diabetes Mellitus.	Ren Y, Hao L, Liu J, Wang P, Ding Q, Chen C, Song Y.	mSystems	10.1128/msystems.01146-22	2023
	In Vitro Fermentation of Polysaccharide from Edible Alga Enteromorpha clathrata by the Gut Microbiota of Patients with Ulcerative Colitis.	Ma M, Quan M, Zhang J, Zhang A, Gao P, Shang Q, Yu G.	Nutrients	10.3390/nu15194122	2023
Genetics	Characterization of gut microbiota and metabolites in individuals with constipation-predominant irritable bowel syndrome.	Wang YL, Xu XQ, Long YY, Cheng YL.	Front Microbiol	10.3389/fmicb.2025.1617288	2025
Pathogenicity	Glycerol-Monolaurate-Mediated Attenuation of Metabolic Syndrome is Associated with the Modulation of Gut Microbiota in High-Fat-Diet-Fed Mice.	Zhao M, Cai H, Jiang Z, Li Y, Zhong H, Zhang H, Feng F.	Mol Nutr Food Res	10.1002/mnfr.201801417	2019
Metabolism	Combined metagenomic and metabolomic analyses reveal gut microbiota dysbiosis and metabolic dysfunction in pediatric neurodevelopmental disorders.	Wang Q, Luo Y, Mao C, Xiang X, Chen J.	Front Immunol	10.3389/fimmu.2025.1645137	2025
Genetics	Prematurely delivering mothers show reductions of lachnospiraceae in their gut microbiomes.	Yang R, Li X, Ying Z, Zhao Z, Wang Y, Wang Q, Shen B, Peng W.	BMC Microbiol	10.1186/s12866-023-02892-z	2023
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
	Beneficial Effects of In Vitro Reconstructed Human Gut Microbiota by Ginseng Extract Fermentation on Intestinal Cell Lines.	Finazzi M, Bovio F, Forcella M, Lasagni M, Fusi P, Di Gennaro P.	Microorganisms	10.3390/microorganisms13010192	2025
	Exploring bacterial key genes and therapeutic agents for breast cancer among the Ghanaian female population: Insights from In Silico analyses.	Kibria MK, Ali MA, Mollah MNH.	PLoS One	10.1371/journal.pone.0312493	2024
	Exploring Next Generation Probiotics for Metabolic and Microbiota Dysbiosis Linked to Xenobiotic Exposure: Holistic Approach.	Torres-Sanchez A, Ruiz-Rodriguez A, Ortiz P, Moreno MA, Ampatzoglou A, Gruszecka-Kosowska A, Monteoliva-Sanchez M, Aguilera M.	Int J Mol Sci	10.3390/ijms232112917	2022
	Understanding the ADHD-Gut Axis by Metabolic Network Analysis.	Tas E, Ulgen KO.	Metabolites	10.3390/metabo13050592	2023
	Gut Microbiome Changes in Anorexia Nervosa: A Comprehensive Review.	Zhao W, Kodancha P, Das S.	Pathophysiology	10.3390/pathophysiology31010006	2024
	Immunotherapy-mediated modulation of the gut microbiota in multiple sclerosis and associations with diet and clinical response-the effect of dimethyl fumarate therapy.	Staun-Ram E, Volkowich A, Miller A.	Ther Adv Neurol Disord	10.1177/17562864241306565	2025
Genetics	Metagenomic Microbial Signatures for Noninvasive Detection of Pancreatic Cancer.	Chen Y, Nian F, Chen J, Jiang Q, Yuan T, Feng H, Shen X, Dong L.	Biomedicines	10.3390/biomedicines13041000	2025
Phylogeny	Characteristics of gut microbiota in people with obesity.	Duan M, Wang Y, Zhang Q, Zou R, Guo M, Zheng H.	PLoS One	10.1371/journal.pone.0255446	2021
	Human gut bacteria bioaccumulate per- and polyfluoroalkyl substances.	Lindell AE, Griesshammer A, Michaelis L, Papagiannidis D, Ochner H, Kamrad S, Guan R, Blasche S, Ventimiglia LN, Ramachandran B, Ozgur H, Zelezniak A, Beristain-Covarrubias N, Yam-Puc JC, Roux I, Barron LP, Richardson AK, Martin MG, Benes V, Morone N, Thaventhiran JED, Bharat TAM, Savitski MM, Maier L, Patil KR.	Nat Microbiol	10.1038/s41564-025-02032-5	2025
	Gallnut tannic acid alleviates gut damage induced by Salmonella pullorum in broilers by enhancing barrier function and modulating microbiota.	Zou J, Luan H, Xi P, Xue J, Fan J, Zhong X, Zhou X, Song X, Zhao X, Zou Y, Li L, Jia R, Fu Y, Liu Z, Yin Z.	Front Vet Sci	10.3389/fvets.2024.1382288	2024
Genetics	Effect of Palmitoylethanolamide Compared to a Placebo on the Gut Microbiome and Biochemistry in an Overweight Adult Population: A Randomised, Placebo Controlled, Double-Blind Study.	Batacan R, Briskey D, Bajagai YS, Smith C, Stanley D, Rao A.	Biomedicines	10.3390/biomedicines12071620	2024
	Microbiome signatures of virulence in the oral-gut-brain axis influence Parkinson's disease and cognitive decline pathophysiology.	Clasen F, Yildirim S, Arikan M, Garcia-Guevara F, Hanoglu L, Yilmaz NH, Sen A, Celik HK, Neslihan AA, Demir TK, Temel Z, Mardinoglu A, Moyes DL, Uhlen M, Shoaie S.	Gut Microbes	10.1080/19490976.2025.2506843	2025
	Fecal Bacterial Community and Metagenome Function in Asians with Type 2 Diabetes, According to Enterotypes.	Wu X, Park S.	Biomedicines	10.3390/biomedicines10112998	2022
Metabolism	Clinical study on the difference in intestinal microecology between patients with preeclampsia and pregnant women at different stages of pregnancy.	Xie F, Zhang H, Peng M, Jiang T.	Acta Biochim Pol	10.3389/abp.2024.12020	2024
Metabolism	Lipid alterations in acute myocardial infarction are associated with gut microbiota.	Zuo J, Wang P, Xue K, Tan Y, Zhang T, Li Y, He F, Wu W, Yan Z, Cong L, Li G.	Microbiol Spectr	10.1128/spectrum.02370-24	2025
	Bacteroides-derived isovaleric acid enhances mucosal immunity by facilitating intestinal IgA response in broilers.	Wang X, Hu Y, Zhu X, Cai L, Farooq MZ, Yan X.	J Anim Sci Biotechnol	10.1186/s40104-022-00807-y	2023
	cAMP-independent Crp homolog adds to the multi-layer regulatory network in Porphyromonas gingivalis.	Smiga M, Roszkiewicz E, Slezak P, Tracz M, Olczak T.	Front Cell Infect Microbiol	10.3389/fcimb.2025.1535009	2025
Genetics	Exploring the relationship between gut microbiota and breast cancer risk in European and East Asian populations using Mendelian randomization.	Lin W, Gu C, Chen Z, Xue S, Wu H, Zeng L.	BMC Cancer	10.1186/s12885-024-12721-9	2024
	Protocatechuic Acid, a Gut Bacterial Metabolite of Black Raspberries, Inhibits Adenoma Development and Alters Gut Microbiome Profiles in Apc ^Min/+ Mice.	Dong A, Lin CW, Echeveste CE, Huang YW, Oshima K, Yearsley M, Chen X, Yu J, Wang LS.	J Cancer Prev	10.15430/jcp.2022.27.1.50	2022
	Crosstalk between Helicobacter pylori and gastrointestinal microbiota in various gastroduodenal diseases-A systematic review.	Sharma P, Phatak SM, Warikoo P, Mathur A, Mahant S, Das K, Das R.	3 Biotech	10.1007/s13205-023-03734-5	2023
	De novo peptide databases enable protein-based stable isotope probing of microbial communities with up to species-level resolution.	Klaes S, White C, Alvarez-Cohen L, Adrian L, Ding C.	Environ Microbiome	10.1186/s40793-025-00767-6	2025
	MagMD: Database summarizing the metabolic action of gut microbiota to drugs.	Zhou J, Ouyang J, Gao Z, Qin H, Jun W, Shi T.	Comput Struct Biotechnol J	10.1016/j.csbj.2022.11.021	2022
	Enterotype-stratified gut microbial signatures in MASLD and cirrhosis based on integrated microbiome data.	Yuan H, Zhou J, Wu X, Wang S, Park S.	Front Microbiol	10.3389/fmicb.2025.1568672	2025
	Novel Catabolic Pathway of Quercetin-3-O-Rutinose-7-O-alpha-L-Rhamnoside by Lactobacillus plantarum GDMCC 1.140: The Direct Fission of C-Ring.	Huang G, Lai M, Xu C, He S, Dong L, Huang F, Zhang R, Young DJ, Liu H, Su D.	Front Nutr	10.3389/fnut.2022.849439	2022
Genetics	Alterations of the gut microbiome are associated with epigenetic age acceleration and physical fitness.	Torma F, Kerepesi C, Jokai M, Babszki G, Koltai E, Ligeti B, Kalcsevszki R, McGreevy KM, Horvath S, Radak Z.	Aging Cell	10.1111/acel.14101	2024
	Glucosylceramide Changes Bacterial Metabolism and Increases Gram-Positive Bacteria through Tolerance to Secondary Bile Acids In Vitro.	Dai H, Otsuka A, Tanabe K, Yanagita T, Nakayama J, Kitagaki H.	Int J Mol Sci	10.3390/ijms23105300	2022
	Positive mood-related gut microbiota in a long-term closed environment: a multiomics study based on the "Lunar Palace 365" experiment.	Hao Z, Meng C, Li L, Feng S, Zhu Y, Yang J, Han L, Sun L, Lv W, Figeys D, Liu H.	Microbiome	10.1186/s40168-023-01506-0	2023
	Ten-Week Sucralose Consumption Induces Gut Dysbiosis and Altered Glucose and Insulin Levels in Healthy Young Adults.	Mendez-Garcia LA, Bueno-Hernandez N, Cid-Soto MA, De Leon KL, Mendoza-Martinez VM, Espinosa-Flores AJ, Carrero-Aguirre M, Esquivel-Velazquez M, Leon-Hernandez M, Viurcos-Sanabria R, Ruiz-Barranco A, Cota-Arce JM, Alvarez-Lee A, De Leon-Nava MA, Melendez G, Escobedo G.	Microorganisms	10.3390/microorganisms10020434	2022
Phylogeny	First insights into microbial changes within an Inflammatory Bowel Disease Family Cohort study.	Rausch P, Ratjen I, Tittmann L, Enderle J, Wacker EM, Jaeger K, Ruhlemann MC, Franzpotter K, Ellul P, Kruse R, Halfvarson J, Roggenbuck D, Ellinghaus D, Jacobs G, Krawczak M, Schreiber S, Bang C, Lieb W, Franke A.	Gut Microbes	10.1080/19490976.2025.2559119	2025
	Symbiotic microbial population composition of Apolygus lucorum under temperature and pesticide pressures.	Ma M, Xue H, Zhu X, Wang L, Niu L, Luo J, Cui J, Gao X.	Front Microbiol	10.3389/fmicb.2024.1485708	2024
	Temporal variations in the gut microbial diversity in response to high-fat diet and exercise.	Imdad S, So B, Jang J, Park J, Lee SJ, Kim JH, Kang C.	Sci Rep	10.1038/s41598-024-52852-4	2024
	The convergent application of metabolites from Avena sativa and gut microbiota to ameliorate non-alcoholic fatty liver disease: a network pharmacology study.	Oh KK, Yoon SJ, Lee SB, Lee SY, Gupta H, Ganesan R, Sharma SP, Won SM, Jeong JJ, Kim DJ, Suk KT.	J Transl Med	10.1186/s12967-023-04122-6	2023
	Gut microbiome composition and metabolic activity in women with diverticulitis.	Ma W, Wang Y, Nguyen LH, Mehta RS, Ha J, Bhosle A, Mclver LJ, Song M, Clish CB, Strate LL, Huttenhower C, Chan AT.	Nat Commun	10.1038/s41467-024-47859-4	2024
Genetics	Integrating metagenomics and metabolomics to study the gut microbiome and host relationships in sports across different energy systems.	Aya V, Pardo-Rodriguez D, Vega LC, Cala MP, Ramirez JD.	Sci Rep	10.1038/s41598-025-98973-2	2025
	Intestinal iron bio-accessibility changes by Lignin and the subsequent impact on cell metabolism and intestinal microbiome communities.	Horniblow RD, Pathak P, Eshrati M, Latunde-Dada GO, Tselepis C.	Food Funct	10.1039/d2fo03807b	2023
	Maast: genotyping thousands of microbial strains efficiently.	Shi ZJ, Nayfach S, Pollard KS.	Genome Biol	10.1186/s13059-023-03030-8	2023
Pathogenicity	Metagenomic Analysis of the Gastrointestinal Phageome and Incorporated Dysbiosis in Children with Persistent Diarrhea of Unknown Etiology in Vietnam.	Dao TK, Pham TTN, Nguyen HD, Dam QT, Phung TBT, Nguyen TVH, Nguyen TQ, Hoang KC, Do TH.	Pathogens	10.3390/pathogens14100985	2025
	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
	Thick vs. thin tongue coatings in hemodialysis patients: unveiling gut microbiome dysregulation and systemic health implications.	Wang Y, Zeng X, Wu M, Lu B, Wang J, Chen S, Zhang A, Huang M, Zhu Y, Liu H, Zhu F, Chen S, Zhou X, Zhao L, Liu J, Lin R.	Front Cell Infect Microbiol	10.3389/fcimb.2025.1640429	2025
	Microbial Dysbiosis as an Emerging Pathology of Suicidal Behaviour? A Critical Review, Passing Through Depression to Chronic Pain.	Costanza A, Alexander J, Amerio A, Aguglia A, Magnani L, Parise A, Saverino D, Serafini G, Amore M, Nguyen KD.	Ann Neurosci	10.1177/09727531251349024	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
Genetics	Characteristics of intestinal flora in patients with cerebral infarction complicated with Type 2 diabetes mellitus.	Cheng X, Zhang Z, Dong W, Lun Y, Liu B.	Zhong Nan Da Xue Xue Bao Yi Xue Ban	10.11817/j.issn.1672-7347.2023.220558	2023
Genetics	Genetic insights into gut microbiota and risk of prostatitis: a Mendelian randomization study.	Qin P, He Y, Shao H, Jiang D.	Front Microbiol	10.3389/fmicb.2024.1389715	2024
	Coarse-grained model of serial dilution dynamics in synthetic human gut microbiome.	Mahajan T, Maslov S.	PLoS Comput Biol	10.1371/journal.pcbi.1013222	2025
Metabolism	Programmable probiotic consortium employ an oleic acid-inducible system to sense and degrade cholesterol in high-fat diet mice.	Yang Q, Xiang W, Khan A, Salama ES, Kulshreshtha S, Ji J, Wu Y, Li X.	Gut Microbes	10.1080/19490976.2025.2531198	2025
	A Clinical Outcome of the Anti-PD-1 Therapy of Melanoma in Polish Patients Is Mediated by Population-Specific Gut Microbiome Composition.	Pietrzak B, Tomela K, Olejnik-Schmidt A, Galus L, Mackiewicz J, Kaczmarek M, Mackiewicz A, Schmidt M.	Cancers (Basel)	10.3390/cancers14215369	2022
	Nutritional and Microbiome Effects of a Partial Substitution of Poultry Meat with Hydrolyzed Feather Meal in Dog Diets.	Balouei F, Stefanon B, Armone R, Randazzo A, Chiofalo B.	Microorganisms	10.3390/microorganisms13010121	2025
	Monascus red pigments alleviate high-fat and high-sugar diet-induced NAFLD in mice by modulating the gut microbiota and metabolites.	Gao W, Chen X, Wu S, Jin L, Chen X, Mao G, Wan X, Xing W.	Food Sci Nutr	10.1002/fsn3.4208	2024
Phylogeny	Identification of disease-specific gut microbial markers in vitiligo.	Dou Y, Niu Y, Shen H, Wang L, Lv Y, Liu S, Xie X, Feng A, Liu X.	Front Microbiol	10.3389/fmicb.2025.1499035	2025
	Adversarial regularized autoencoder graph neural network for microbe-disease associations prediction.	He L, Zou Q, Dai Q, Cheng S, Wang Y.	Brief Bioinform	10.1093/bib/bbae584	2024
	Effects of blackcurrant extract on indole and ammonia productions in an in vitro human fecal culture model.	Ishiguro N, Hayashi T, Okayama M, Yamaguchi T, Kohno M, Kawakami H, Mitsunaga T, Nakamura K, Inagaki M.	Biosci Microbiota Food Health	10.12938/bmfh.2022-094	2024
	Bacteroides salyersiae Is a Candidate Probiotic Species with Potential Anti-Colitis Properties in the Human Colon: First Evidence from an In Vivo Mouse Model.	Dai W, Lv Y, Quan M, Ma M, Shang Q, Yu G.	Nutrients	10.3390/nu16172918	2024
Phylogeny	Gut microbiota and dietary patterns in children with attention-deficit/hyperactivity disorder.	Wang LJ, Yang CY, Chou WJ, Lee MJ, Chou MC, Kuo HC, Yeh YM, Lee SY, Huang LH, Li SC.	Eur Child Adolesc Psychiatry	10.1007/s00787-019-01352-2	2020
	Cardiac function of colorectal cancer mice is remotely controlled by gut microbiota: regulating serum metabolites and myocardial cytokines	Gao Z, Fan C, Zhang B, Geng J, Han X, Xu D, Arshad M, Sun H, Li J, Jin X, Mu X.	Anim Microbiome		2025
	Bacteroides uniformis-induced perturbations in colonic microbiota and bile acid levels inhibit TH17 differentiation and ameliorate colitis developments.	Yan Y, Lei Y, Qu Y, Fan Z, Zhang T, Xu Y, Du Q, Brugger D, Chen Y, Zhang K, Zhang E.	NPJ Biofilms Microbiomes	10.1038/s41522-023-00420-5	2023
	Novel Siphoviridae Bacteriophages Infecting Bacteroides uniformis Contain Diversity Generating Retroelement.	Hedzet S, Rupnik M, Accetto T.	Microorganisms	10.3390/microorganisms9050892	2021
Pathogenicity	Rapid identification of antibiotic resistance gene hosts by prescreening ARG-like reads.	Su Z, Gu AZ, Wen D, Li F, Huang B, Mu Q, Chen L.	Environ Sci Ecotechnol	10.1016/j.ese.2024.100502	2025
Metabolism	In-depth multiomic characterization of the effects of obesity in high-fat diet-fed mice.	Li B, Chen J, Ou X, Liu X, Xu Z, Xiang X, Yang Y, Wang Q.	FEBS Open Bio	10.1002/2211-5463.13788	2024
	Effects of replacing soybean meal with cottonseed meal on growth performance, carcass trait, intestinal development and intestinal microbiota of broiler chickens.	Yan L, An S, Lv X, Lv Z, Zhang B, Choct M, Guo Y, Wang Z, Yan B, Li Y.	Poult Sci	10.1016/j.psj.2024.104653	2025
	Beyond the Brain: Attention Deficit/Hyperactivity Disorder and the Gut-Brain Axis.	Gandhi DN, Pande DN, Harikrishna A, Advilkar A, Basavan I, Ansari R.	Cureus	10.7759/cureus.76291	2024
	Dose-Responsive Effects of Iron Supplementation on the Gut Microbiota in Middle-Aged Women.	Shearer J, Shah S, MacInnis MJ, Shen-Tu G, Mu C.	Nutrients	10.3390/nu16060786	2024
Pathogenicity	Associations Between the Gut Microbiome, Inflammation, and Cardiovascular Profiles in People With Human Immunodeficiency Virus.	MacCann R, Li J, Leon AAG, Negi R, Alalwan D, Tinago W, McGettrick P, Cotter AG, Landay A, Sabin C, O'Toole PW, Mallon PWG, Understanding the Pathology of Comorbid Disease in HIV-Infected Individuals (HIV UPBEAT) Study Group .	J Infect Dis	10.1093/infdis/jiaf043	2025
	Microbial Intervention as a Novel Target in Treatment of Non-Alcoholic Fatty Liver Disease Progression.	Zhou Y, Zheng T, Chen H, Li Y, Huang H, Chen W, Du Y, He J, Li Y, Cao J, Nie Y, Zhou Y.	Cell Physiol Biochem	10.1159/000495830	2018
	Machine learning analysis of sex and menopausal differences in the gut microbiome in the HELIUS study.	Vriend EMC, Galenkamp H, Herrema H, Nieuwdorp M, van den Born BH, Verhaar BJH.	NPJ Biofilms Microbiomes	10.1038/s41522-024-00628-z	2024
	Sleep deprivation-induced anxiety-like behaviors are associated with alterations in the gut microbiota and metabolites.	Zhang N, Gao X, Li D, Xu L, Zhou G, Xu M, Peng L, Sun G, Pan F, Li Y, Ren R, Huang R, Yang Y, Wang Z.	Microbiol Spectr	10.1128/spectrum.01437-23	2024
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
	Gut microbiota-metabolome remodeling associated with low bone mass: an integrated multi-omics study in fracture patients.	Zhao X, Wu B, Han P, Wang Z, Cao R, Chen S, Cheng C, Lian H, Zha Y, Li M.	Front Mol Biosci	10.3389/fmolb.2025.1646361	2025
	Both viable Bifidobacterium longum subsp. infantis B8762 and heat-killed cells alleviate the intestinal inflammation of DSS-induced IBD rats.	Li Z, Peng C, Sun Y, Zhang T, Feng C, Zhang W, Huang T, Yao G, Zhang H, He Q.	Microbiol Spectr	10.1128/spectrum.03509-23	2024
Phylogeny	Phylum barrier and Escherichia coli intra-species phylogeny drive the acquisition of antibiotic-resistance genes.	Petitjean M, Condamine B, Burdet C, Denamur E, Ruppe E, Ruppe E.	Microb Genom	10.1099/mgen.0.000489	2021
	The Circadian Rhythm of the Behavior and Gut Microbiota in Dybowski's Frogs (Rana dybowskii) during the Autumn Migration Period.	Hu N, Li Y, Wang M, Ji H, Zhang X, San B, Shi H.	Life (Basel)	10.3390/life14030322	2024
	Horizontal gene transfer after faecal microbiota transplantation in adolescents with obesity.	Behling AH, Wilson BC, Ho D, Cutfield WS, Vatanen T, O'Sullivan JM.	Microbiome	10.1186/s40168-024-01748-6	2024
	Gut microbiota alterations are linked to COVID-19 severity in North African and European populations.	Bredon M, Hausfater P, Khalki L, Tijani Y, Cheikh A, Brot L, Creusot L, Rolhion N, Trottein F, Lambeau G, Georgin-Lavialle S, Bleibtreu A, Baudel JL, Lefevre A, Emond P, Tubach F, Simon-Tillaux N, Simon T, Gorochov G, Zaid Y, Sokol H.	NPJ Biofilms Microbiomes	10.1038/s41522-025-00733-7	2025
	Intestinal microbiota composition of children with glycogen storage Type I patients.	Gokalp S, Dinleyici EC, Muluk C, Inci A, Aktas E, Okur I, Ezgu F, Tumer L.	Eur J Clin Nutr	10.1038/s41430-024-01412-0	2024
	Evaluation of the therapeutic effect of pomegranate peel ginger ultrafine powder on chronic enteritis in mice by regulating intestinal microbiota.	Guo Z, Wang X, Li Y, Zhang Y, Guo P, Zhang J, Zhang Z, Ma X.	Front Immunol	10.3389/fimmu.2025.1563225	2025
Genetics	Genomic, Probiotic, and Functional Properties of Bacteroides dorei RX2020 Isolated from Gut Microbiota.	He S, Song L, Xiao Y, Huang Y, Ren Z.	Nutrients	10.3390/nu17061066	2025
	Role of the gut microbiome in psychological symptoms associated with inflammatory bowel diseases.	Atanasova K, Knodler LL, Reindl W, Ebert MP, Thomann AK.	Semin Immunopathol	10.1007/s00281-025-01036-x	2025
	The gut commensal Faecalibacterium hominis attenuates indole-AhR signaling and restores ASD-like behaviors with BTBR mice.	Yu Y, Wang Y, Zhang J, Li S, Wang Y, You X, Chen X, Du M, Xie L, Liu SJ.	Front Microbiol	10.3389/fmicb.2025.1640149	2025
Metabolism	Alterations in the Gut Microbiome and Metabolisms in Pregnancies with Fetal Growth Restriction.	Tao Z, Chen Y, He F, Tang J, Zhan L, Hu H, Ding Z, Ruan S, Chen Y, Chen B, Wang Y, Guo X, Xie L, Zhong M, Huang Q.	Microbiol Spectr	10.1128/spectrum.00076-23	2023
	Disturbances in the gut microbiota potentially associated with metabolic syndrome among patients living with HIV-1 and on antiretroviral therapy at Bafoussam Regional Hospital, Cameroon.	Diesse JM, Jadhav S, Tamekou SL, Simo G, Dzoyem JP, Souopgui J, Kuiate JR, Nema V.	Diabetol Metab Syndr	10.1186/s13098-025-01653-4	2025
	Impact of a defined bacterial community including and excluding Megamonas hypermegale on broiler cecal microbiota and resistance to Salmonella infection.	Schultz Marcolla C, Ju T, Ten K, Sivakumar Sharma U, Moeun L, Willing BP.	Appl Environ Microbiol	10.1128/aem.00948-25	2025
	Microbiota and metabolite-based prediction tool for colonic polyposis with and without a known genetic driver.	Katona BW, Shukla A, Hu W, Nyul T, Dudzik C, Arvanitis A, Clay D, Dungan M, Weber M, Tu V, Hao F, Gan S, Chau L, Buchner AM, Falk GW, Jaffe DL, Ginsberg G, Palmer SN, Zhan X, Patterson AD, Bittinger K, Ni J.	Gut Microbes	10.1080/19490976.2025.2474141	2025
	Systemic Granulomatosis in the Meagre Argyrosomus regius: Fishing for a Plausible Etiology.	Murgia C, Cubeddu T, Burrai GP, Alberti A, Bertolotti L, Colitti B, Prearo M, Pastorino P, Esposito G, Mandrioli L, Barbera G, Sanna MA, Polinas M, Soto E, Antuofermo E.	Vet Sci	10.3390/vetsci11120597	2024
	[Associations of Socioeconomic Factors,Nutrients Intake,and Gut Microbiota of Healthy Pregnant Women in the Third Trimester with Gestational Weight Gain].	Ma LK, Xue Y, He TC, Zhang YM.	Zhongguo Yi Xue Ke Xue Yuan Xue Bao	10.3881/j.issn.1000-503x.10505	2018
	Intestinal Dysbiosis Caused by Epithelial Fabp6 Gene Disruption Exacerbates Gut Inflammatory Disease.	Kwon K, Kim M, Jung Y, Yoon MY, Lee JY, Yoon SS, Rho M, Chung YW, Ryu JH.	Immune Netw	10.4110/in.2025.25.e35	2025
	Analysis of Serum Bile Acid Profile Characteristics and Identification of New Biomarkers in Lean Metabolic Dysfunction-Associated Fatty Liver Disease Based on LC-MS/MS.	Wang B, Zhang F, Qiu H, He Y, Shi H, Zhu Y.	Clin Med Insights Endocrinol Diabetes	10.1177/11795514241282253	2024
Genetics	Using gut microbiome metagenomic hypervariable features for diabetes screening and typing through supervised machine learning.	Chavarria X, Park HS, Oh S, Kang D, Choi JH, Kim M, Cho YH, Yi MH, Kim JY.	Microb Genom	10.1099/mgen.0.001365	2025
	New Insights into Porcine Milk N-Glycome and the Potential Relation with Offspring Gut Microbiome.	Mu C, Cai Z, Bian G, Du Y, Ma S, Su Y, Liu L, Voglmeir J, Huang R, Zhu W.	J Proteome Res	10.1021/acs.jproteome.8b00789	2019
	Breed-specific differences of gut microbiota and metabolomic insights into fat deposition and meat quality in Chinese Songliao Black Pig and Large White × Landrace Pig Breeds.	Kumar ST, Zhang Y, Zhang Q, Azeem RM, Jing Z, Pan L, Sun WS, Zhao Y, Zhang SM.	BMC Microbiol	10.1186/s12866-025-04051-y	2025
Pathogenicity	Chronic nonbacterial prostate inflammation in a rat model is associated with changes of gut microbiota that can be modified with a galactoglucomannan-rich hemicellulose extract in the diet.	Konkol Y, Keskitalo A, Vuorikoski H, Pietila S, Elo LL, Munukka E, Bernoulli J, Tuomela J.	BJU Int	10.1111/bju.14553	2019
	Sex-specific gut microbiome dynamics in Labeo catla: links to reproductive hormones, metabolic dimorphism, and environmental factors	Sundaray J, Mohapatra M, Rasal A, Udit U, Mohanty S, Mohanty D, Das I, Sahoo L, Sahoo P.	Front Microbiol
Genetics	The impact of antibiotic exposure on antibiotic resistance gene dynamics in the gut microbiota of inflammatory bowel disease patients.	Zhang Y, Xue G, Wang F, Zhang J, Xu L, Yu C.	Front Microbiol	10.3389/fmicb.2024.1382332	2024
	Bariatric surgery drives major rearrangements of the intestinal microbiota including the biofilm composition.	Campisciano G, Cason C, Palmisano S, Giuricin M, Rizzardi A, Croce LS, De Manzini N, Comar M.	Front Biosci (Elite Ed)	10.2741/e836	2018
	The Prebiotic Effect of Kaempferol in Regulating Bile Acid Metabolism.	Li X, Huang G, Khan I, Ding Z, Hsiao WLW, Liu Z.	Food Sci Nutr	10.1002/fsn3.70023	2025
	Gestational exposure to HIV drugs alters intestinal mucosa-associated microbial diversity in adult rat offspring	Yanamadala Y, Muthumula C, Gokulan K, Karn K, Sutherland V, Cunny H, Santos J, Khare S.	Exp Biol Med (Maywood)		2025
Phylogeny	Analysis of early childhood intestinal microbial dynamics in a continuous-flow bioreactor.	Granato A, Renwick S, Yau C, Kong T, Daigneault MC, Knip M, DIABIMMUNE Study Group, Allen-Vercoe E, Danska JS.	Microbiome	10.1186/s40168-024-01976-w	2024
	Dietary Milk or Isolated Legume Proteins Modulate Intestinal Microbiota Composition in Rats.	Rubio LA.	Nutrients	10.3390/nu16010149	2024
Pathogenicity	Virulence Factors of the Gut Microbiome Are Associated with BMI and Metabolic Blood Parameters in Children with Obesity.	Murga-Garrido SM, Ulloa-Perez EJ, Diaz-Benitez CE, Orbe-Orihuela YC, Cornejo-Granados F, Ochoa-Leyva A, Sanchez-Flores A, Cruz M, Castaneda-Marquez AC, Plett-Torres T, Burguete Garcia AI, Lagunas-Martinez A.	Microbiol Spectr	10.1128/spectrum.03382-22	2023
	Associations between Dietary Fiber, the Fecal Microbiota and Estrogen Metabolism in Postmenopausal Women with Breast Cancer.	Zengul AG, Demark-Wahnefried W, Barnes S, Morrow CD, Bertrand B, Berryhill TF, Fruge AD.	Nutr Cancer	10.1080/01635581.2020.1784444	2021
	Iatrogenic rectal injury associated with fleet enema administration masquerading as Fournier's Gangrene.	Liang Y, Di Re A, Ctercteko G.	J Surg Case Rep	10.1093/jscr/rjz414	2020
	Gut-derived Faecalibaculum rodentium exerts anti-cancer effects on colorectal cancer by modulating PDPN-CLEC-2 signaling pathway.	Yang X, Liu M, Wang T, Ma X, Guan Z, Ma B, Duan X, Su C.	mSystems	10.1128/msystems.00148-25	2025
	May Sulfites in Wine Affect Gut Microbiota? An In Vitro Study of Their Digestion and Interplay with Wine Polyphenols.	Relano de la Guia E, Cueva C, Molinero N, Ruano A, Motilva MJ, Bartolome B, Moreno-Arribas MV.	J Agric Food Chem	10.1021/acs.jafc.5c02710	2025
Metabolism	Association of Subjective and Objective Measures of Sleep With Gut Microbiota Composition and Diversity in Older Men: The Osteoporotic Fractures in Men Study.	Estaki M, Langsetmo L, Shardell M, Mischel A, Jiang L, Zhong Y, Kaufmann C, Knight R, Stone K, Kado D.	J Gerontol A Biol Sci Med Sci	10.1093/gerona/glad011	2023
Pathogenicity	Targeting IL-23 for the interception of obesity-associated colorectal cancer.	Madka V, Chiliveru S, Panneerselvam J, Pathuri G, Zhang Y, Stratton N, Kumar N, Sanghera DK, Rao CV.	Neoplasia	10.1016/j.neo.2023.100939	2023
Metabolism	Evaluation of a Plant-Based Infant Formula Containing Almonds and Buckwheat on Gut Microbiota Composition, Intestine Morphology, Metabolic and Immune Markers in a Neonatal Piglet Model.	Gurung M, Rosa F, Yelvington B, Terry N, Read QD, Piccolo BD, Moody B, Tripp P, Pittman HE, Fay BL, Ross TJ, Sikes JD, Flowers JB, Fox R, LeRoith T, Talatala R, Bar-Yoseph F, Yeruva L.	Nutrients	10.3390/nu15020383	2023
	The Role of a Spinning Top Urethra in the Development of Pyosalpinx in a Precoital Female.	Andrews TJ, Hicar M, Islam S.	Cureus	10.7759/cureus.27099	2022
Genetics	Metagenomics reveals an increased proportion of an Escherichia coli-dominated enterotype in elderly Chinese people.	Li J, Wu Y, Yang Y, Chen L, He C, Zhou S, Huang S, Zhang X, Wang Y, Gui Q, Lu H, Zhang Q, Yang Y.	J Zhejiang Univ Sci B	10.1631/jzus.b2400341	2025
	The interaction of gut microbiota, genetic variation, and diet in autism spectrum disorder.	Liu X.	mLife	10.1002/mlf2.12024	2022
Genetics	Impact of Baizhu, Daqingye, and Hehuanhua extracts on the human gut microbiome.	Lemons JMS, Narrowe AB, Liu L, Firrman J, Mahalak KK, Van den Abbeele P, Baudot A, Deyaert S, Li Y, Yu LL.	Front Cell Infect Microbiol	10.3389/fcimb.2023.1298392	2023
Genetics	Insights into gut microbiomes in stem cell transplantation by comprehensive shotgun long-read sequencing.	Spohr P, Scharf S, Rommerskirchen A, Henrich B, Jager P, Klau GW, Haas R, Dilthey A, Pfeffer K.	Sci Rep	10.1038/s41598-024-53506-1	2024
	Research status and development trends of probiotics in clinical applications.	Li Y, Yao Y, Zhang Z, Gan Y.	Front Nutr	10.3389/fnut.2025.1650883	2025
	Dynamic Alteration of the Gut Microbiota Associated with Obesity and Intestinal Inflammation in Ovariectomy C57BL/6 Mice.	Zhao H, Wang Q, Wang Q, Hu L, Xing S, Gong H, Liu Z, Qin P, Xu J, Du J, Ai W, Peng S, Li Y.	Int J Endocrinol	10.1155/2022/6600158	2022
	Altered gut microbial profile accompanied by abnormal short chain fatty acid metabolism exacerbates nonalcoholic fatty liver disease progression.	Yang C, Wu J, Yang L, Hu Q, Li L, Yang Y, Hu J, Pan D, Zhao Q.	Sci Rep	10.1038/s41598-024-72909-8	2024
	Alteration of the Fecal but Not Salivary Microbiome in Patients with Behçet's Disease According to Disease Activity Shift.	Kim JC, Park MJ, Park S, Lee ES.	Microorganisms	10.3390/microorganisms9071449	2021
Metabolism	Parabacteroides johnsonii inhibits the onset and progression of colorectal cancer by modulating the gut microbiota.	Liu J, Zhang Y, Xu L, Gu G, Dong Z.	J Transl Med	10.1186/s12967-025-06675-0	2025
	Modeling the effects of prebiotic interventions on luminal and mucosa-associated gut microbiota without and with Clostridium difficile challenge in vitro.	Wiese M, van der Wurff M, Ouwens A, van Leijden B, Verheij ER, Heerikhuisen M, van der Vossen JMBM.	Front Nutr	10.3389/fnut.2024.1403007	2024
	The gut-brain-axis: A positive relationship between gut microbial dysbiosis and glioblastoma brain tumour.	Ishaq HM, Yasin R, Mohammad IS, Fan Y, Li H, Shahzad M, Xu J.	Heliyon	10.1016/j.heliyon.2024.e30494	2024
	Effects of GLP-1 Analogues and Agonists on the Gut Microbiota: A Systematic Review.	Gofron KK, Wasilewski A, Malgorzewicz S.	Nutrients	10.3390/nu17081303	2025
	Maternal and placental microbiome and immune crosstalk in pregnancies with small-for-gestational-age fetuses - a pilot case-control study.	Kosinska-Kaczynska K, Krawczyk D, Bednorz M, Chaberek K, Czapska A, Zgliczynska M, Goryca K, Piatkowska M, Balabas A, Czarnowski P, Zeber-Lubecka N.	Front Cell Infect Microbiol	10.3389/fcimb.2025.1596588	2025
	Integrating 16S rDNA and metabolomics to uncover the therapeutic mechanism of electroacupuncture in type 2 diabetic rats.	Yue Z, Xiang W, Duping D, Yuanyuan G, Xuanyi C, Juan L, Xiaojuan H.	Front Microbiol	10.3389/fmicb.2024.1436911	2024
Pathogenicity	In vitro fermentation of Cookeina speciosa glucans stimulates the growth of the butyrogenic Clostridium cluster XIVa in a targeted way.	Cantu-Jungles TM, Ruthes AC, El-Hindawy M, Moreno RB, Zhang X, Cordeiro LMC, Hamaker BR, Iacomini M.	Carbohydr Polym	10.1016/j.carbpol.2017.12.020	2018
	Gut microbiota of children with autism spectrum disorder and healthy siblings: A comparative study.	Abuljadayel D, Alotibi A, Algothmi K, Basingab F, Alhazmi S, Almuhammadi A, Alharthi A, Alyoubi R, Bahieldin A.	Exp Ther Med	10.3892/etm.2024.12719	2024
Genetics	Effects of data transformation and model selection on feature importance in microbiome classification data.	Karwowska Z, Aasmets O, Estonian Biobank research team, Kosciolek T, Org E.	Microbiome	10.1186/s40168-024-01996-6	2025
	Different intestinal ecological niches drive the divergent evolution of probiotics in the gut.	Han Z, Huang D, Liu X, Ma W, Cui W, Jiang S, Zhen D, Zhang J.	ISME Commun	10.1093/ismeco/ycaf023	2025
Enzymology	Structural and Functional Alterations of Gut Microbiota in Males With Hyperuricemia and High Levels of Liver Enzymes.	Sheng S, Chen J, Zhang Y, Qin Q, Li W, Yan S, Wang Y, Li T, Gao X, Tang L, Li A, Ding S.	Front Med (Lausanne)	10.3389/fmed.2021.779994	2021
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
	Conditional Vitamin D Receptor Deletion Induces Fungal and Archaeal Dysbiosis and Altered Metabolites.	Claypool DJ, Zhang YG, Xia Y, Sun J.	Metabolites	10.3390/metabo14010032	2024
Phylogeny	Optimizing Akkermansia muciniphila Isolation and Cultivation: Insights into Gut Microbiota Composition and Potential Growth Promoters in a Chinese Cohort.	Meng X, Xv C, Lv J, Zhang S, Ma C, Pang X.	Microorganisms	10.3390/microorganisms12050881	2024
Genetics	Exploring fecal microbiota signatures associated with immune response and antibiotic impact in NSCLC: insights from metagenomic and machine learning approaches	Han W, Zhou Y, Wang Y, Liu X, Sun T, Xu J.	Front Cell Infect Microbiol		2025
	The Impact of Akkermansia muciniphila on Mouse Models of Depression, Anxiety, and Stress: A Systematic Review and Meta-Analysis.	Khalili L, Park G, Nagpal R, Bhide P, Salazar G.	Curr Neuropharmacol	10.2174/011570159x360149250225041829	2025
	Quantitative Analysis and Visualization of the Interaction Between Intestinal Microbiota and Type 1 Diabetes in Children Based on Multi-Databases.	Zhao M, Xu S, Cavagnaro MJ, Zhang W, Shi J.	Front Pediatr	10.3389/fped.2021.752250	2021
Genetics	The genetic diversity and populational specificity of the human gut virome at single-nucleotide resolution.	Wang X, Dong Q, Huang P, Yang S, Gao M, Zhang C, Zhang C, Deng Y, Huang Z, Ma B, Jiao Y, Zhou Y, Wu T, Zou H, Shi J, Sheng Y, Wang Y, Consortium C, Tang L, Hu S, Duan Y, Sun W, Chen W, Zhai Q, Kong X, Chen L.	Microbiome	10.1186/s40168-025-02185-9	2025
Phylogeny	Mucosal Microbiome in Patients with Early Bowel Polyps: Inferences from Short-Read and Long-Read 16S rRNA Sequencing.	Welham Z, Li J, Engel AF, Molloy MP.	Cancers (Basel)	10.3390/cancers15205045	2023
	Triple-Probiotic-Fermented Goji (Lycium barbarum L.) Ameliorates Metabolic Disorders Associated with Hyperuricemia in Mice.	Ren L, Li Y, Liu S, Jia X, He H, Zhong F, Lu F, Luo X.	Microorganisms	10.3390/microorganisms13061367	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
	Synthetic beta-d-Glucuronides: Substrates for Exploring Glucuronide Degradation by Human Gut Bacteria.	Gorecka A, Schacht H, Fraser MK, Teriosina A, London JA, Barsukov IL, Powell AK, Cartmell A, Stachulski AV, Yates EA.	ACS Omega	10.1021/acsomega.4c09036	2025
Genetics	Probing the "Dark Matter" of the Human Gut Phageome: Culture Assisted Metagenomics Enables Rapid Discovery and Host-Linking for Novel Bacteriophages.	Fitzgerald CB, Shkoporov AN, Upadrasta A, Khokhlova EV, Ross RP, Hill C.	Front Cell Infect Microbiol	10.3389/fcimb.2021.616918	2021
	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
	Integrated Microbiome and Metabolome Analysis Reveals Hypothalamic-Comorbidities Related Signatures in Craniopharyngioma.	Lin B, Ye Z, Cao Z, Ye Z, Yu Y, Jiang W, Guo S, Melnikov V, Zhou P, Ji C, Shi C, Wu Z, Chen Z, Xu Y, Zhang Q, Ma Z, Qiao N, Chen L, Shou X, Cao X, Zhou X, Zhang L, He M, Wang Y, Ye H, Li Y, Zhang Z, Wang M, Gao R, Zhang Y.	Adv Sci (Weinh)	10.1002/advs.202400684	2024
	Early indicators of microbial strain dysbiosis in the human gastrointestinal microbial community of certain healthy humans and hospitalized COVID-19 patients.	Koo H, Morrow CD.	Sci Rep	10.1038/s41598-022-10472-w	2022
	Elucidating the gut microbiome alterations of tribal community of Arunachal Pradesh: perspectives on their lifestyle or food habits.	Hazarika P, Chattopadhyay I, Umpo M, Choudhury Y, Sharma I.	Sci Rep	10.1038/s41598-022-23124-w	2022
	Bacteroides uniformis combined with fiber amplifies metabolic and immune benefits in obese mice.	Lopez-Almela I, Romani-Perez M, Bullich-Vilarrubias C, Benitez-Paez A, Gomez Del Pulgar EM, Frances R, Liebisch G, Sanz Y.	Gut Microbes	10.1080/19490976.2020.1865706	2021
	Characterization of the gut microbiota and fecal and blood metabolomes under various factors in urban children from Northwest China.	Yang Y, Chen J, Gao H, Cui M, Zhu M, Xiang X, Wang Q.	Front Cell Infect Microbiol	10.3389/fcimb.2024.1374544	2024
Proteome	Fibromyalgia diagnosis from a multi-omics approach: a gut feeling.	Duran-Gonzalez E, Ramirez-Tejero JA, Perez-Sanchez M, Morales-Torres C, Gomez-Morano R, Diaz-Lopez C, Martinez-Lara A, Cotan D.	Front Microbiol	10.3389/fmicb.2025.1641185	2025
	Boolean implication analysis unveils candidate universal relationships in microbiome data.	Vo D, Singh SC, Safa S, Sahoo D.	BMC Bioinformatics	10.1186/s12859-020-03941-4	2021
Pathogenicity	The Reduced Gut Lachnospira Species Is Linked to Liver Enzyme Elevation and Insulin Resistance in Pediatric Fatty Liver Disease.	Tsai CC, Chiu MH, Kek HP, Yang MC, Su YT, Liu HK, Wu MS, Yeh YT.	Int J Mol Sci	10.3390/ijms25073640	2024
	Comprehensive analysis of vaginal microbiota, metabolites, and inflammatory factors in preterm and term pregnancies.	Shen LP, Cai BJ, Guan JX, Peng T, Jin L.	Front Microbiol	10.3389/fmicb.2025.1689494	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
Metabolism	A Cross Talking between the Gut Microbiota and Metabolites of Participants in a Confined Environment.	Song X, Wang Z, Xia Y, Chen Z, Wang G, Yang Y, Zhu B, Ai L, Xu H, Wang C.	Nutrients	10.3390/nu16111761	2024
	Carotenoids from Halophilic Archaea: A Novel Approach to Improve Egg Quality and Cecal Microbiota in Laying Hens.	Dou X, Zhang G, Tang H, Chen X, Chen B, Mei Y, Jiao H, Ren M.	Animals (Basel)	10.3390/ani14233470	2024
	Altered skin microbiome, inflammation, and JAK/STAT signaling in Southeast Asian ichthyosis patients.	Ho M, Nguyen HN, Van Hoang M, Bui TTT, Vu BQ, Dinh THT, Vo HTM, Blaydon DC, Eldirany SA, Bunick CG, Bui CB.	Hum Genomics	10.1186/s40246-024-00603-x	2024
	Probiotic lactic acid bacteria alleviate pediatric IBD and remodel gut microbiota by modulating macrophage polarization and suppressing epithelial apoptosis.	Hua H, Pan C, Chen X, Jing M, Xie J, Gao Y, Huang J, Chen X, Gao Y, Xu C, Li P.	Front Microbiol	10.3389/fmicb.2023.1168924	2023
	Multi-omic profiling reveals distinct gut microbial and metabolic landscapes in golden snub-nosed monkeys under contrasting conservation strategies.	Zhang D, Hu Q, Zhou Y, Yu H, Cong W, Cheng M, Wang J, Liu X, Zou K, Long S, Zhao C, Jiang J, Zhang Y.	NPJ Biofilms Microbiomes	10.1038/s41522-025-00836-1	2025
Metabolism	Composition and functional profiles of gut microbiota reflect the treatment stage, severity, and etiology of acute pancreatitis.	Wang Z, Guo M, Li J, Jiang C, Yang S, Zheng S, Li M, Ai X, Xu X, Zhang W, He X, Wang Y, Chen Y.	Microbiol Spectr	10.1128/spectrum.00829-23	2023
	Heterocyclic Antidepressants with Antimicrobial and Fungicide Activity.	Zolotareva D, Zazybin A, Belyankova Y, Bayazit S, Dauletbakov A, Seilkhanov T, Kemelbekov U, Aydemir M.	Molecules	10.3390/molecules30051102	2025
	A Prebiotic Diet Containing Galactooligosaccharides and Polydextrose Produces Dynamic and Reproducible Changes in the Gut Microbial Ecosystem in Male Rats.	Thompson RS, Bowers SJ, Vargas F, Hopkins S, Kelley T, Gonzalez A, Lowry CA, Dorrestein PC, Vitaterna MH, Turek FW, Knight R, Wright KP, Fleshner M.	Nutrients	10.3390/nu16111790	2024
	Extreme drought shapes the gut microbiota composition and function of common cranes (Grus grus) wintering in Poyang Lake.	Wang C, Zhang C, Cai H, Zhu Y, Sun J, Liu W, Wang Z, Li Y.	Front Microbiol	10.3389/fmicb.2024.1489906	2024
	Fecal short-chain fatty acids in non-constipated irritable bowel syndrome: a potential clinically relevant stratification factor based on catabotyping analysis.	Gargari G, Mantegazza G, Taverniti V, Gardana C, Valenza A, Rossignoli F, Barbaro MR, Marasco G, Cremon C, Barbara G, Guglielmetti S.	Gut Microbes	10.1080/19490976.2023.2274128	2023
	Alteration of the gut microbiome and correlated metabolism in a rat model of long-term depression.	Li Y, Li J, Cheng R, Liu H, Zhao Y, Liu Y, Chen Y, Sun Z, Zhai Z, Wu M, Yan Y, Sun Y, Zhang Z.	Front Cell Infect Microbiol	10.3389/fcimb.2023.1116277	2023
	Fecal microbiota transplantation treatment for type 1 diabetes mellitus with malnutrition: a case report.	Xie YC, Jing XB, Chen X, Chen LZ, Zhang SH, Cai XB.	Ther Adv Chronic Dis	10.1177/20406223221117449	2022
	Vaping-Induced Sepsis and Rapidly Evolving Pleural Effusion in a Young, Otherwise Healthy Male.	Malik B, Kalantary A, Ghatol A, Kunadi A.	Cureus	10.7759/cureus.25327	2022
	Cannabidiol reshapes the gut microbiome to promote endurance exercise in mice.	Chen S, Lee YB, Song MY, Lim C, Cho H, Shim HJ, Kim JS, Park BH, Kim JK, Bae EJ.	Exp Mol Med	10.1038/s12276-025-01404-5	2025
	Microbiome features associated with performance measures in athletic and non-athletic individuals: A case-control study.	Huminska-Lisowska K, Zielinska K, Mieszkowski J, Michalowska-Sawczyn M, Cieszczyk P, Labaj PP, Wasag B, Fraczek B, Grzywacz A, Kochanowicz A, Kosciolek T.	PLoS One	10.1371/journal.pone.0297858	2024
	Plant-based dietary index in relation to gut microbiota in Arab women.	Aljuraiban GS, Aljazairy EA, Alsahli AS, Sabico S, Al-Musharaf S.	Medicine (Baltimore)	10.1097/md.0000000000035262	2023
Genetics	Early-life and concurrent predictors of the healthy adolescent microbiome in a cohort study.	Laue HE, Willis AD, Wang F, MacDougall MC, Xu Y, Karagas MR, Madan JC, Fleisch AF, Lanphear BP, Cecil KM, Yolton K, Chen A, Buckley JP, Braun JM.	Genome Med	10.1186/s13073-025-01481-1	2025
Pathogenicity	In vitro effects of inulin and soya bean oligosaccharide on skatole production and the intestinal microbiota in broilers.	Liu HY, Hou R, Yang GQ, Zhao F, Dong WG.	J Anim Physiol Anim Nutr (Berl)	10.1111/jpn.12830	2018
	Effects of systemic Bifidobacterium longum and Lactobacillus rhamnosus probiotics on the ligature-induced periodontitis in rat.	Chen YW, Lee ML, Chiang CY, Fu E.	J Dent Sci	10.1016/j.jds.2023.04.013	2023
	Functional Muffins Exert Bifidogenic Effects along with Highly Product-Specific Effects on the Human Gut Microbiota Ex Vivo.	Deyaert S, Poppe J, Dai Vu L, Baudot A, Bubeck S, Bayne T, Krishnan K, Giusto M, Moltz S, Van den Abbeele P.	Metabolites	10.3390/metabo14090497	2024
	Mendelian randomization analysis revealed a gut microbiota-mammary axis in breast cancer.	Zhang S, Zhang W, Ren H, Xue R, Wang Z, Wang Z, Lv Q.	Front Microbiol	10.3389/fmicb.2023.1193725	2023
	Disruption of Genes Encoding Putative Zwitterionic Capsular Polysaccharides of Diverse Intestinal Bacteroides Reduces the Induction of Host Anti-Inflammatory Factors.	Arnolds KL, Yamada E, Neff CP, Schneider JM, Palmer BE, Lozupone CA.	Microb Ecol	10.1007/s00248-022-02037-1	2023
	From Upper Respiratory Symptoms to Hemophagocytic Lymphohistiocytosis: Case Report of a Human Adenovirus Infection in Haploidentical Hematopoietic Stem Cell Transplant Recipient.	Demey B, Brault C, Maizel J, Francois C.	Pathogens	10.3390/pathogens10030340	2021
	Huaier Polysaccharide Alleviates Dextran Sulphate Sodium Salt-Induced Colitis by Inhibiting Inflammation and Oxidative Stress, Maintaining the Intestinal Barrier, and Modulating Gut Microbiota.	Tang YF, Xie WY, Wu HY, Guo HX, Wei FH, Ren WZ, Gao W, Yuan B.	Nutrients	10.3390/nu16091368	2024
Genetics	Expanded gut microbial genomes from Chinese populations reveal population-specific genomic features related to human physiological traits.	Dong Q, Ma B, Zhou X, Huang P, Gao M, Yang S, Jiao Y, Zhou Y, Shi Z, Deng Q, Hua D, Wang X, Liu L, Zhang C, Zhang C, Kong M, He C, Wu T, Zou H, Shi J, Sheng Y, Wang Y, GMR Consortium, Tang L, Hu S, Zhong H, Sun W, Chen W, Zhai Q, Kong X, Zheng Y, Chen L.	Genome Med	10.1186/s13073-025-01566-x	2025
	Amoxicillin Increased Functional Pathway Genes and Beta-Lactam Resistance Genes by Pathogens Bloomed in Intestinal Microbiota Using a Simulator of the Human Intestinal Microbial Ecosystem.	Liu L, Wang Q, Lin H, Das R, Wang S, Qi H, Yang J, Xue Y, Mao D, Luo Y.	Front Microbiol	10.3389/fmicb.2020.01213	2020
	Exploring the Association between Citrus Nutraceutical Eriocitrin and Metformin for Improving Pre-Diabetes in a Dynamic Microbiome Model.	Cesar T, Salgaco MK, Mesa V, Sartoratto A, Sivieri K.	Pharmaceuticals (Basel)	10.3390/ph16050650	2023
	Multi-omics unveils strain-specific neuroactive metabolite production linked to inflammation modulation by Bacteroides and their extracellular vesicles.	Yousuf B, Mottawea W, Esmail GA, Nazemof N, Bouhlel NE, Njoku E, Li Y, Zhang X, Minic Z, Hammami R.	Curr Res Microb Sci	10.1016/j.crmicr.2025.100358	2025
	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
	Key Stratification of Microbiota Taxa and Metabolites in the Host Metabolic Health-Disease Balance.	Torres-Sanchez A, Ruiz-Rodriguez A, Ortiz P, Aguilera M.	Int J Mol Sci	10.3390/ijms24054519	2023
	Neurodevelopmental functions of CHD8: new insights and questions.	Basson MA.	Biochem Soc Trans	10.1042/bst20220926	2024
	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
	Brain abscess due to Aggregatibacter aphrophilus and Bacteroides uniformis.	Bogdan M, Zujic Atalic V, Hecimovic I, Vukovic D.	Acta Med Acad	10.5644/ama2006-124.144	2015
Phylogeny	Gut Microbiota Signatures in Gestational Anemia.	Long Y, Liang F, Guo R, Zhu C, Zhao X, Wang X, Liu F, Jiang M, Liang Q, Zeng S, Han M, Qin J, Li S, Li S, Yang H.	Front Cell Infect Microbiol	10.3389/fcimb.2021.549678	2021
Phylogeny	Gut Microbiota Profiles in Myopes and Nonmyopes.	Omar WEW, Singh G, McBain AJ, Cruickshank F, Radhakrishnan H.	Invest Ophthalmol Vis Sci	10.1167/iovs.65.5.2	2024
	Fermentation characteristics of Megasphaera elsdenii J6 derived from pig feces on different lactate isomers	JIANG Xl, Wei-yun ZHU, Yong SU.	Journal of integrative agriculture.	10.1016/s2095-3119(15)61236-9	2016
	Cow, yak, and camel milk diets differentially modulated the systemic immunity and fecal microbiota of rats.	Wen Y, He Q, Ding J, Wang H, Hou Q, Zheng Y, Li C, Ma Y, Zhang H, Kwok LY.	Sci Bull (Beijing)	10.1016/j.scib.2017.01.027	2017
	Gut microbiota interplay with autophagy-EMT dynamics in colorectal cancer.	Vescovo T, Bontempi G, Bayat M, Piredda L, Fidaleo M, Strippoli R, Antonioli M.	Front Cell Dev Biol	10.3389/fcell.2025.1608248	2025
	Time series strain tracking analysis post fecal transplantation identifies individual specific patterns of fecal dominant donor, recipient, and unrelated microbial strains.	Koo H, Morrow CD.	PLoS One	10.1371/journal.pone.0274633	2022
	Metabolomics and metagenomics in mice reveal the role of the gut microbiota in tryptophan metabolism.	Leve M, Manghi P, Bredon M, Lefevre A, Manara S, Armanini F, Emond P, Planchais J, Rolhion N, Segata N, Sokol H.	iScience	10.1016/j.isci.2025.113751	2025
	Intestinal Bacteroides sp. Imbalance Associated With the Occurrence of Childhood Undernutrition in China.	Li D, Li Y, Dai W, Wang H, Qiu C, Feng S, Zhou Q, Wang W, Feng X, Yao K, Liu Y, Yang Y, Yang Z, Xu X, Li S, Wei J, Zhou K.	Front Microbiol	10.3389/fmicb.2019.02635	2019
	Bridging preclinical and clinical gut microbiota research using the ex vivo SIFR^® technology.	Van den Abbeele P, Deyaert S, Thabuis C, Perreau C, Bajic D, Wintergerst E, Joossens M, Firrman J, Walsh D, Baudot A.	Front Microbiol	10.3389/fmicb.2023.1131662	2023
	Microbial Species that Initially Colonize the Human Gut at Birth or in Early Childhood Can Stay in Human Body for Lifetime.	Li W, Nelson KE.	Microb Ecol	10.1007/s00248-020-01636-0	2021
	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
	Age-related changes in the gut microbiota and the core gut microbiome of healthy Thai humans.	La-Ongkham O, Nakphaichit M, Nakayama J, Keawsompong S, Nitisinprasert S.	3 Biotech	10.1007/s13205-020-02265-7	2020
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
	Stage-specific roles of microbial dysbiosis and metabolic disorders in rheumatoid arthritis.	Cheng M, Zhao Y, Cui Y, Zhong C, Zha Y, Li S, Cao G, Li M, Zhang L, Ning K, Han J.	Ann Rheum Dis	10.1136/ard-2022-222871	2022
	Cell free supernatants of Bifidobacterium adolescentis and Bifidobacterium longum suppress the tumor growth in colorectal cancer organoid model.	Kim MJ, Song MH, Ji YS, Park JW, Shin YK, Kim SC, Kim G, Cho B, Park H, Ku JL, Jeong SY.	Sci Rep	10.1038/s41598-024-83048-5	2025
Pathogenicity	Human gut commensal Alistipes timonensis modulates the host lipidome and delivers anti-inflammatory outer membrane vesicles to suppress colitis in an Il10-deficient mouse model.	Older EA, Mitchell MK, Campbell A, Lian X, Madden M, Wang Y, van de Wal LE, Zaw T, VanderVeen BN, Tatum R, Murphy EA, Chen YH, Fan D, Ellermann M, Li J.	Gut Microbes	10.1080/19490976.2025.2517380	2025
	Integrated multi-omics analysis reveals the functional signature of microbes and metabolomics in pre-diabetes individuals.	Liu Y, Qiu Q, Chen Y, Deng Y, Huang W, Sun C, Shang X, Chen X, Wang C, Han L, Chen S, Yuan J, Xu F, Yang Z, Fang X, Huang L.	Microbiol Spectr	10.1128/spectrum.01459-24	2025
	Exposure to environmental pollutants selects for xenobiotic-degrading functions in the human gut microbiome.	De Filippis F, Valentino V, Sequino G, Borriello G, Riccardi MG, Pierri B, Cerino P, Pizzolante A, Pasolli E, Esposito M, Limone A, Ercolini D.	Nat Commun	10.1038/s41467-024-48739-7	2024
Genetics	A cross-sectional comparison of gut metagenomes between dairy workers and community controls.	Trinh P, Teichman S, Roberts MC, Rabinowitz PM, Willis AD.	BMC Genomics	10.1186/s12864-024-10562-1	2024
	Disentangling the age-related manner in the associations between gut microbiome and women's health: a multi-cohort microbiome study.	Dong C, Guan Q, Xu W, Zhang X, Jin B, Yu S, Xu X, Xia Y.	Gut Microbes	10.1080/19490976.2023.2290320	2023
Transcriptome	The altered TBI fecal microbiome is stable and functionally distinct.	Pyles RB, Miller AL, Urban RJ, Sheffield-Moore M, Wright TJ, Maxwell CA, Randolph KM, Danesi CP, McGovern KA, Vargas J, Armstrong P, Kreber L, Cumpa G, Randall K, Morrison M, Masel BE.	Front Mol Neurosci	10.3389/fnmol.2024.1341808	2024
Genetics	Prediction of BMI traits in the Chinese population based on the gut metagenome.	Liang Y, Dou S, Zhao G, Shen J, Fu G, Fu L, Li S, Cong B, Dong C.	Microb Cell Fact	10.1186/s12934-023-02255-3	2023
	Evidences and perspectives on the association between gut microbiota and sepsis: A bibliometric analysis from 2003 to 2023.	Hu J, Yao Q, Zhao L.	Heliyon	10.1016/j.heliyon.2024.e37921	2024
	Plant-Based Diet Index and Metabolic Risk in Men: Exploring the Role of the Gut Microbiome.	Li Y, Wang DD, Satija A, Ivey KL, Li J, Wilkinson JE, Li R, Baden M, Chan AT, Huttenhower C, Rimm EB, Hu FB, Sun Q.	J Nutr	10.1093/jn/nxab175	2021
	Altered Gut Microbiota Contributes to Acute-Respiratory-Distress-Syndrome-Related Depression through Microglial Neuroinflammation.	Zhu B, Gu Z, Hu H, Huang J, Zeng Z, Liang H, Yuan Z, Huang S, Qiu Y, Sun XD, Liu Y.	Research (Wash D C)	10.34133/research.0636	2025
	The porphyran degradation system is complete, phylogenetically and geographically diverse across the gut microbiota of East Asian populations.	Segurel L, Ulaganathan TS, Mathieu S, Loiodice M, Poulet L, Drouillard S, Cygler M, Helbert W.	PLoS One	10.1371/journal.pone.0329457	2025
Genetics	The gut microbiome and HLA-B27-associated anterior uveitis: a case-control study.	Morandi SC, Herzog EL, Munk M, Kreuzer M, Largiader CR, Wolf S, Zinkernagel M, Zysset-Burri DC.	J Neuroinflammation	10.1186/s12974-024-03109-4	2024
Phylogeny	Development of a Novel Metagenomic Biomarker for Prediction of Upper Gastrointestinal Tract Involvement in Patients With Crohn's Disease.	Kwak MS, Cha JM, Shin HP, Jeon JW, Yoon JY.	Front Microbiol	10.3389/fmicb.2020.01162	2020
	The Maternal Microbiome as a Map to Understanding the Impact of Prenatal Stress on Offspring Psychiatric Health.	Kimmel MC, Verosky B, Chen HJ, Davis O, Gur TL.	Biol Psychiatry	10.1016/j.biopsych.2023.11.014	2024
Pathogenicity	Intestinal Microbiota Influence Doxorubicin Responsiveness in Triple-Negative Breast Cancer.	Bawaneh A, Wilson AS, Levi N, Howard-McNatt MM, Chiba A, Soto-Pantoja DR, Cook KL.	Cancers (Basel)	10.3390/cancers14194849	2022
Phylogeny	Comparative analysis of gut microbiota in children with obstructive sleep apnea: assessing the efficacy of 16S rRNA gene sequencing in metabolic function prediction based on weight status.	Chuang HH, Huang CG, Chou SH, Li HY, Lee CC, Lee LA.	Front Endocrinol (Lausanne)	10.3389/fendo.2024.1344152	2024
Genetics	Integration analysis of tumor metagenome and peripheral immunity data of diffuse large-B cell lymphoma.	Zhang Y, Han S, Xiao X, Zheng L, Chen Y, Zhang Z, Gao X, Zhou S, Yu K, Huang L, Fu J, Hong Y, Jiang J, Qian W, Yang H, Shen J.	Front Immunol	10.3389/fimmu.2023.1146861	2023
Phylogeny	The influence of blood on the human gut microbiome.	Chenard T, Malick M, Dube J, Masse E.	BMC Microbiol	10.1186/s12866-020-01724-8	2020
	Rumen fermentation and bacterial communities in weaned Chahaer lambs on diets with different protein levels	YANG Ct, Bing-wen SI, Hai JIN, Qi-yu DIAO, Shu-qin ZENG, Yan TU.	Journal of integrative agriculture.	10.1016/s2095-3119(15)61217-5	2016
	Infusion of donor feces affects the gut-brain axis in humans with metabolic syndrome.	Hartstra AV, Schuppel V, Imangaliyev S, Schrantee A, Prodan A, Collard D, Levin E, Dallinga-Thie G, Ackermans MT, Winkelmeijer M, Havik SR, Metwaly A, Lagkouvardos I, Nier A, Bergheim I, Heikenwalder M, Dunkel A, Nederveen AJ, Liebisch G, Mancano G, Claus SP, Benitez-Paez A, la Fleur SE, Bergman JJ, Gerdes V, Sanz Y, Booij J, Kemper E, Groen AK, Serlie MJ, Haller D, Nieuwdorp M.	Mol Metab	10.1016/j.molmet.2020.101076	2020
	Bifidobacterium species serve as key gut microbiome regulators after intervention in gestational diabetes mellitus.	Cui Z, Wang S, Niu J, Ma J, Yang H.	BMC Microbiol	10.1186/s12866-024-03680-z	2024
	Deep metagenomic characterization of gut microbial community and function in preeclampsia.	Lv LJ, Li SH, Wen JY, Wang GY, Li H, He TW, Lv QB, Xiao MC, Duan HL, Chen MC, Yi ZT, Yan QL, Yin AH.	Front Cell Infect Microbiol	10.3389/fcimb.2022.933523	2022
	Hyperglycemia is associated with duodenal dysbiosis and altered duodenal microenvironment.	Darra A, Singh V, Jena A, Popli P, Nada R, Gupta P, Bhadada SK, Singh AK, Sharma V, Bhattacharya A, Agrawal A, Dutta U.	Sci Rep	10.1038/s41598-023-37720-x	2023
	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
	Gut resistome profiling reveals high diversity and fluctuations in pancreatic cancer cohorts.	Liu X, Li K, Yang Y, Cao D, Xu X, He Z, Wu W.	Front Cell Infect Microbiol	10.3389/fcimb.2024.1354234	2024
	The Dose-Response Effect of Fluoride Exposure on the Gut Microbiome and Its Functional Pathways in Rats.	Mo Z, Wang J, Meng X, Li A, Li Z, Que W, Wang T, Tarnue KF, Ma X, Liu Y, Yan S, Wu L, Zhang R, Pei J, Wang X.	Metabolites	10.3390/metabo13111159	2023
	Integrated microbiome and metabolome analysis reveals the interaction between intestinal flora and serum metabolites as potential biomarkers in hepatocellular carcinoma patients.	Li X, Yi Y, Wu T, Chen N, Gu X, Xiang L, Jiang Z, Li J, Jin H.	Front Cell Infect Microbiol	10.3389/fcimb.2023.1170748	2023
	Socioeconomic disparities and household crowding in association with the fecal microbiome of school-age children.	Lapidot Y, Reshef L, Maya M, Cohen D, Gophna U, Muhsen K.	NPJ Biofilms Microbiomes	10.1038/s41522-022-00271-6	2022
	Gut microbiota response to in vitro transit time variation is mediated by microbial growth rates, nutrient use efficiency and adaptation to in vivo transit time.	Minnebo Y, Delbaere K, Goethals V, Raes J, Van de Wiele T, De Paepe K.	Microbiome	10.1186/s40168-023-01691-y	2023
Phylogeny	Improved Equine Fecal Microbiome Characterization Using Target Enrichment by Hybridization Capture.	Alvarez Narvaez S, Beaudry MS, Norris CG, Bartlett PB, Glenn TC, Sanchez S.	Animals (Basel)	10.3390/ani14030445	2024
	The gut microbiota modulates responses to anti-PD-1 and chemotherapy combination therapy and related adverse events in patients with advanced solid tumors.	Wu Z, Zhang S, Li L, Huang Z, Huang D, Hu Y.	Front Oncol	10.3389/fonc.2022.887383	2022
	Matching between Donors and Ulcerative Colitis Patients Is Important for Long-Term Maintenance after Fecal Microbiota Transplantation.	Okahara K, Ishikawa D, Nomura K, Ito S, Haga K, Takahashi M, Shibuya T, Osada T, Nagahara A.	J Clin Med	10.3390/jcm9061650	2020
	Fecal Microbiota Alterations and Small Intestinal Bacterial Overgrowth in Functional Abdominal Bloating/Distention.	Noh CK, Lee KJ.	J Neurogastroenterol Motil	10.5056/jnm20080	2020
Enzymology	The Role of Gut Microbiome in Psoriasis: Oral Administration of Staphylococcus aureus and Streptococcus danieliae Exacerbates Skin Inflammation of Imiquimod-Induced Psoriasis-Like Dermatitis.	Okada K, Matsushima Y, Mizutani K, Yamanaka K.	Int J Mol Sci	10.3390/ijms21093303	2020
	Microbial Community of Healthy Thai Vegetarians and Non-Vegetarians, Their Core Gut Microbiota, and Pathogen Risk.	Ruengsomwong S, La-Ongkham O, Jiang J, Wannissorn B, Nakayama J, Nitisinprasert S.	J Microbiol Biotechnol	10.4014/jmb.1603.03057	2016
	Uric acid, high density lipoprotein cholesterol levels and their ratio are related to microbial enterotypes and serum metabolites in females with a blood stasis constitution.	Sun C, Liu Y, Huang W, Chen Y, Deng Y, Yuan J, Deng L, Xu N, Shang X, Wang C, Yang Z, Huang L, Qiu Q.	Lipids Health Dis	10.1186/s12944-024-02066-4	2024
	Metagenomic analysis of the interaction between the gut microbiota and colorectal cancer: a paired-sample study based on the GMrepo database.	Chen H, Jiao J, Wei M, Jiang X, Yang R, Yu X, Zhang G, Zhou X.	Gut Pathog	10.1186/s13099-022-00527-8	2022
	Intermittent supplementation with Akkermansia muciniphila and galactooligosaccharides modulates Alzheimer's disease progression, gut microbiota, and colon short-chain fatty acid profiles in mice.	Kunevicius A, Vijaya AK, Atzeni A, Mingaila J, Simoliune I, Jamontas R, Kezeviciute E, Gueimonde M, Meskys R, Baltriukiene D, Arboleya S, Burokas A.	Front Aging Neurosci	10.3389/fnagi.2025.1617980	2025
	Native microbiome dominates over host factors in shaping the probiotic genetic evolution in the gut.	Jiang S, Zhang C, Han Z, Ma W, Wang S, Huo D, Cui W, Zhai Q, Huang S, Zhang J.	NPJ Biofilms Microbiomes	10.1038/s41522-023-00447-8	2023
	Acarbose impairs gut Bacteroides growth by targeting intracellular glucosidases.	Brown HA, Morris AL, Pudlo NA, Hopkins AE, Martens EC, Golob JL, Koropatkin NM.	mBio	10.1128/mbio.01506-24	2024
	Population-level gut microbiome and its associations with environmental factors and metabolic disorders in Southwest China.	Qu Q, Dou Q, Xiang Z, Yu B, Chen L, Fan Z, Zhao X, Yang S, Zeng P.	NPJ Biofilms Microbiomes	10.1038/s41522-025-00661-6	2025
Genetics	Metagenomic Analysis of Microbial Contamination in the U.S. Portion of the Tijuana River Watershed.	Allsing N, Kelley ST, Fox AN, Sant KE.	Int J Environ Res Public Health	10.3390/ijerph20010600	2022
Phylogeny	Lower Genital Tract Microbiome in Early Pregnancy in the Eastern European Population.	Gryaznova M, Lebedeva O, Kozarenko O, Smirnova Y, Burakova I, Syromyatnikov M, Maslov A, Popov V.	Microorganisms	10.3390/microorganisms10122368	2022
	Utilizing kombucha culture for coffee fermentation and biochemical characteristic analysis.	Kim H, Jeon J, Lee J, Song C, Gu B, Kim NM, Yang TH, Oh S, Park S, Pal K, Kim GJ, Kim D.	Curr Res Food Sci	10.1016/j.crfs.2025.100996	2025
	Differential network connectivity analysis for microbiome data adjusted for clinical covariates using jackknife pseudo-values.	Ahn S, Datta S.	BMC Bioinformatics	10.1186/s12859-024-05689-7	2024
Genetics	Unraveling the microbial diversity of bovine liver abscesses: isolation, identification, and genomic characterization of the Bacteroides found in hepatic lesions.	Gruninger RJ, McCormack ML, Chomistek NC, Zaheer R, McAllister TA.	Microbiol Spectr	10.1128/spectrum.00423-25	2025
	Risk Factors Associated with Severe Clostridioides difficile Infection in Patients with Cancer.	Francisco DMA, Zhang L, Jiang Y, Olvera A, Adachi J, Guevara EY, Aitken SL, Garey KW, Peterson CB, Do KA, Dillon R, Obi EN, Jenq R, Okhuysen PC.	Infect Dis Ther	10.1007/s40121-022-00722-9	2023
	Effect of Bovine Milk Fat Globule Membrane and Lactoferrin in Infant Formula on Gut Microbiome and Metabolome at 4 Months of Age.	Chichlowski M, Bokulich N, Harris CL, Wampler JL, Li F, Berseth CL, Rudolph C, Wu SS.	Curr Dev Nutr	10.1093/cdn/nzab027	2021
	Gut Microbial Species and Endotypes Associate with Remission in Ulcerative Colitis Patients Treated with Anti-TNF or Anti-integrin Therapy.	Tamburini FB, Tripathi A, Gold MP, Yang JC, Biancalani T, McBride JM, Keir ME, Gardenia Study Group.	J Crohns Colitis	10.1093/ecco-jcc/jjae084	2024
	Proof of Concept of Culturomics Use of Time of Care.	Naud S, Khelaifia S, Mbogning Fonkou MD, Dione N, Lagier JC, Raoult D.	Front Cell Infect Microbiol	10.3389/fcimb.2020.524769	2020
	Proton-pump inhibitors increase C. difficile infection risk by altering pH rather than by affecting the gut microbiome based on a bioreactor model.	Schumacher J, Muller P, Sulzer J, Faber F, Molitor B, Maier L.	Gut Microbes	10.1080/19490976.2025.2519697	2025
Phylogeny	Fecal Microbiota Characteristics in Constipation-Predominant and Mixed-Type Irritable Bowel Syndrome.	Gryaznova M, Smirnova Y, Burakova I, Morozova P, Lagutina S, Chizhkov P, Korneeva O, Syromyatnikov M.	Microorganisms	10.3390/microorganisms12071414	2024
	Gut Microbiome and Metabolome Modulation by High-Hydrostatic-Pressure-Processed Tomato Juice.	Wang X, Li D, Ma C, Hu X, Chen F.	Nutrients	10.3390/nu16050710	2024
Phylogeny	16S rRNA gene sequencing reveals the correlation between the gut microbiota and the susceptibility to pathological scars.	Li M, Li M, Dai Y, Li D, Yu H, Liu J, Gao H, Zhong Y, Huang M, Lin J, Xie Y, Guo Z, Chen X.	Front Microbiol	10.3389/fmicb.2023.1215884	2023
	Mapping human pathogens in wastewater using a metatranscriptomic approach.	Carneiro J, Pascoal F, Semedo M, Pratas D, Tomasino MP, Rego A, Carvalho MF, Mucha AP, Magalhaes C.	Environ Res	10.1016/j.envres.2023.116040	2023
	Lactobacillus reuteri ZJ617 attenuates metabolic syndrome via microbiota-derived spermidine.	Ma Y, Zhong Y, Tang W, Valencak TG, Liu J, Deng Z, Mao J, Liu D, Wang S, Wang Y, Wang H.	Nat Commun	10.1038/s41467-025-56105-4	2025
Pathogenicity	Integrating multi-omics data to reveal the host-microbiota interactome in inflammatory bowel disease.	Su F, Su M, Wei W, Wu J, Chen L, Sun X, Liu M, Sun S, Mao R, Bourgonje AR, Hu S.	Gut Microbes	10.1080/19490976.2025.2476570	2025
	Distinct Plasma Metabolomic and Gut Microbiome Profiles after Gestational Diabetes Mellitus Diet Treatment: Implications for Personalized Dietary Interventions.	Sugino KY, Hernandez TL, Barbour LA, Kofonow JM, Frank DN, Friedman JE.	Microorganisms	10.3390/microorganisms12071369	2024
Pathogenicity	Signature changes in gut microbiome are associated with increased susceptibility to HIV-1 infection in MSM.	Chen Y, Lin H, Cole M, Morris A, Martinson J, Mckay H, Mimiaga M, Margolick J, Fitch A, Methe B, Srinivas VR, Peddada S, Rinaldo CR.	Microbiome	10.1186/s40168-021-01168-w	2021
	Region-Specific Effects of Metformin on Gut Microbiome and Metabolome in High-Fat Diet-Induced Type 2 Diabetes Mouse Model.	Cheng M, Jia X, Ren L, Chen S, Wang W, Wang J, Cong B.	Int J Mol Sci	10.3390/ijms25137250	2024
	Reduced Abundance of Butyrate-Producing Bacteria Species in the Fecal Microbial Community in Crohn's Disease.	Takahashi K, Nishida A, Fujimoto T, Fujii M, Shioya M, Imaeda H, Inatomi O, Bamba S, Sugimoto M, Andoh A.	Digestion	10.1159/000441768	2016
	Islet autoantibody seroconversion in type-1 diabetes is associated with metagenome-assembled genomes in infant gut microbiomes.	Zhang L, Jonscher KR, Zhang Z, Xiong Y, Mueller RS, Friedman JE, Pan C.	Nat Commun	10.1038/s41467-022-31227-1	2022
Pathogenicity	Gut microbiota intervention alleviates pulmonary inflammation in broilers exposed to fine particulate matter from broiler house.	Liu J, Li Y, Shen D, Li X, Wang K, Nagaoka K, Li C.	Appl Environ Microbiol	10.1128/aem.02174-23	2024
	Gut Microbiota Alteration Influences Colorectal Cancer Metastasis to the Liver by Remodeling the Liver Immune Microenvironment.	Yuan N, Li X, Wang M, Zhang Z, Qiao L, Gao Y, Xu X, Zhi J, Li Y, Li Z, Jia Y.	Gut Liver	10.5009/gnl210177	2022
	Sugar lowering in fermented apple-pear juice orchestrates a promising metabolic answer in the gut microbiome and intestinal integrity.	Tlais AZA, Polo A, Granehall L, Filannino P, Vincentini O, De Battistis F, Di Cagno R, Gobbetti M.	Curr Res Food Sci	10.1016/j.crfs.2024.100833	2024
	Clinico-microbiological profile of Bacteroides fragilis with focus on molecular detection of emerging resistance.	Gupta A, Shenoy PA, Kumar A, Chawla K.	Indian J Med Res	10.4103/ijmr.ijmr_2568_19	2021
	The impact of gut microbiome enterotypes on ulcerative colitis: identifying key bacterial species and revealing species co-occurrence networks using machine learning.	Wu X, Zhang T, Zhang T, Park S.	Gut Microbes	10.1080/19490976.2023.2292254	2024
	Fecal microbiota transplantation from patients with rheumatoid arthritis causes depression-like behaviors in mice through abnormal T cells activation.	Pu Y, Zhang Q, Tang Z, Lu C, Wu L, Zhong Y, Chen Y, Hashimoto K, Luo Y, Liu Y.	Transl Psychiatry	10.1038/s41398-022-01993-z	2022
	Association of gut microbiome and metabolites with onset and treatment response of patients with pemphigus vulgaris.	Wang Y, Xia X, Zhou X, Zhan T, Dai Q, Zhang Y, Zhang W, Shu Y, Li W, Xu H.	Front Immunol	10.3389/fimmu.2023.1114586	2023
	Chitosan Oligosaccharide Ameliorates Metabolic Syndrome Induced by Overnutrition via Altering Intestinal Microbiota.	Wang Y, Liu S, Tang D, Dong R, Feng Q.	Front Nutr	10.3389/fnut.2021.743492	2021
Pathogenicity	Potassium Alginate Oligosaccharides Alter Gut Microbiota, and Have Potential to Prevent the Development of Hypertension and Heart Failure in Spontaneously Hypertensive Rats.	Han ZL, Chen M, Fu XD, Yang M, Hrmova M, Zhao YH, Mou HJ.	Int J Mol Sci	10.3390/ijms22189823	2021
	The role of non-Helicobacter pylori bacteria in the pathogenesis of gastroduodenal diseases.	Waskito LA, Rezkitha YAA, Vilaichone RK, Sugihartono T, Mustika S, Dewa Nyoman Wibawa I, Yamaoka Y, Miftahussurur M.	Gut Pathog	10.1186/s13099-022-00494-0	2022
	Chronic intestinal pseudo-obstruction: associations with gut microbiota and genes expression of intestinal serotonergic pathway.	Radocchia G, Marazzato M, Harbi KB, Capuzzo E, Pantanella F, De Giorgio R, Guarino M, Costanzini A, Zenzeri L, Parisi P, Ferretti A, Felici E, Palamara AT, Di Nardo G, Schippa S.	BMC Microbiol	10.1186/s12866-024-03200-z	2024
	Attenuation of allergen-specific immunotherapy for atopic dermatitis by ectopic colonization of Brevundimonas vesicularis in the intestine.	Liu X, Xu B, Xu X, Wang Z, Luo Y, Gao Y, Ling S, Wang A, Zhou Y, Wang X, Leng SX, Li W, Yao X.	Cell Rep Med	10.1016/j.xcrm.2023.101340	2023
	Microbially-produced folate forms support the growth of Roseburia intestinalis but not its competitive fitness in fecal batch fermentations.	Kundra P, Geirnaert A, Pugin B, Pluss S, Kariluoto S, Lacroix C, Greppi A.	BMC Microbiol	10.1186/s12866-024-03528-6	2024
	Systemic metabolic depletion of gut microbiome undermines responsiveness to melanoma immunotherapy.	Zakharevich NV, Morozov MD, Kanaeva VA, Filippov MS, Zyubko TI, Ivanov AB, Ulyantsev VI, Klimina KM, Olekhnovich EI.	Life Sci Alliance	10.26508/lsa.202302480	2024
	Dietary Clostridium butyricum and 25-Hydroxyvitamin D₃ modulate bone metabolism of broilers through the gut-brain axis.	Cao G, Yu Y, Wang H, Yang H, Tao F, Yang S, Liu J, Li Z, Yang C.	Poult Sci	10.1016/j.psj.2024.103966	2024
	High Diversity but Monodominance of Multidrug-Resistant Bacteria in Immunocompromised Pediatric Patients with Acute Lymphoblastic Leukemia Developing GVHD Are Not Associated with Changes in Gut Mycobiome.	Sardzikova S, Andrijkova K, Svec P, Beke G, Klucar L, Minarik G, Bielik V, Kolenova A, Soltys K.	Antibiotics (Basel)	10.3390/antibiotics12121667	2023
	In Vitro Human Gastrointestinal Digestibility and Colonic Fermentation of Wheat Sourdough and Yeast Breads.	Martinez Tuppia C, Rezaei MN, Machuron F, Duysburgh C, Ghyselinck J, Marzorati M, Koper JEB, Monnet C, Bosco N.	Foods	10.3390/foods13183014	2024
	Diversification and deleterious role of microbiome in gastric cancer.	Chattopadhyay I, Gundamaraju R, Rajeev A.	Cancer Rep (Hoboken)	10.1002/cnr2.1878	2023
	Biodegradable Electrospun PLGA Nanofibers-Encapsulated Trichinella Spiralis Antigens Protect from Relapsing Experimental Autoimmune Encephalomyelitis and Related Gut Microbiota Dysbiosis.	Sabljic L, Radulovic N, Dokic J, Stojanovic DB, Radojevic D, Glamoclija S, Dinic M, Golic N, Vasilev S, Uskokovic P, Sofronic-Milosavljevic L, Gruden-Movsesijan A, Tomic S.	Int J Nanomedicine	10.2147/ijn.s499161	2025
	The diagnostic and prognostic potential of gut bacteria in inflammatory bowel disease.	Wiredu Ocansey DK, Hang S, Yuan X, Qian H, Zhou M, Valerie Olovo C, Zhang X, Mao F.	Gut Microbes	10.1080/19490976.2023.2176118	2023
	Exploring the vitamin biosynthesis landscape of the human gut microbiota.	Tarracchini C, Lugli GA, Mancabelli L, van Sinderen D, Turroni F, Ventura M, Milani C.	mSystems	10.1128/msystems.00929-24	2024
Genetics	Dynamics of gut resistome and mobilome in early life: a meta-analysis.	Bargheet A, Noordzij HT, Ponsero AJ, Jian C, Korpela K, Valles-Colomer M, Debelius J, Kurilshikov A, Pettersen VK.	EBioMedicine	10.1016/j.ebiom.2025.105630	2025
Genetics	The Effect of a Planetary Health Diet on the Human Gut Microbiome: A Descriptive Analysis.	Rehner J, Schmartz GP, Kramer T, Keller V, Keller A, Becker SL.	Nutrients	10.3390/nu15081924	2023
	Abundance and prevalence of ESBL coding genes in patients undergoing first line eradication therapy for Helicobacter pylori.	Gudra D, Silamikelis I, Pjalkovskis J, Danenberga I, Pupola D, Skenders G, Ustinova M, Megnis K, Leja M, Vangravs R, Fridmanis D.	PLoS One	10.1371/journal.pone.0289879	2023
	Bacteroides thetaiotaomicron enhances oxidative stress tolerance through rhamnose-dependent mechanisms.	Xie S, Ma J, Lu Z.	Front Microbiol	10.3389/fmicb.2024.1505218	2024
	Nutraceutical blends predict enhanced health via microbiota reshaping improving cytokines and life quality: a Brazilian double-blind randomized trial.	Santamarina AB, de Freitas JA, Franco LAM, Nehmi-Filho V, Fonseca JV, Martins RC, Turri JA, da Silva BFRB, Fugi BEI, da Fonseca SS, Gusmao AF, Olivieri EHR, de Souza E, Costa S, Sabino EC, Otoch JP, Pessoa AFM.	Sci Rep	10.1038/s41598-024-61909-3	2024
	Multicenter Evaluation of the FilmArray Blood Culture Identification 2 Panel for Pathogen Detection in Bloodstream Infections.	Camelena F, Pean de Ponfilly G, Pailhories H, Bonzon L, Alanio A, Poncin T, Lafaurie M, Depret F, Cambau E, Godreuil S, Chenouard R, Le Monnier A, Jacquier H, Bercot B.	Microbiol Spectr	10.1128/spectrum.02547-22	2023
	Modeling spatial interaction networks of the gut microbiota.	Cao X, Dong A, Kang G, Wang X, Duan L, Hou H, Zhao T, Wu S, Liu X, Huang H, Wu R.	Gut Microbes	10.1080/19490976.2022.2106103	2022
	Integrated analysis of the microbiome and transcriptome in stomach adenocarcinoma.	Zhou D, Xiong S, Xiong J, Deng X, Long Q, Li Y.	Open Life Sci	10.1515/biol-2022-0528	2023
Genetics	Anti-Hyperuricemic Effect of Anserine Based on the Gut-Kidney Axis: Integrated Analysis of Metagenomics and Metabolomics.	Halimulati M, Wang R, Aihemaitijiang S, Huang X, Ye C, Zhang Z, Li L, Zhu W, Zhang Z, He L.	Nutrients	10.3390/nu15040969	2023
	Identification of vaginal fluid, saliva, and feces using microbial signatures in a Han Chinese population.	Zou KN, Ren LJ, Ping Y, Ma K, Li H, Cao Y, Zhou HG, Wei YL.	J Forensic Leg Med	10.1016/j.jflm.2016.08.003	2016
	Cross-cohort single-nucleotide-variant profiling of gut microbiota suggests a novel gut-health assessment approach.	Ma C, Zhang Y, Jiang S, Teng F, Huang S, Zhang J.	mSystems	10.1128/msystems.00828-23	2023
	In Vitro Activity of Tedizolid Compared to Linezolid and Five Other Antimicrobial Agents against 332 Anaerobic Isolates, Including Bacteroides fragilis Group, Prevotella, Porphyromonas, and Veillonella Species.	Goldstein EJC, Merriam CV, Citron DM.	Antimicrob Agents Chemother	10.1128/aac.01088-20	2020
Metabolism	Exploring potential polysaccharide utilization loci involved in the degradation of typical marine seaweed polysaccharides by Bacteroides thetaiotaomicron.	Yu B, Lu Z, Zhong S, Cheong KL.	Front Microbiol	10.3389/fmicb.2024.1332105	2024
Genetics	Alterations of the Gut Microbiome in Patients With Pituitary Adenoma.	Hu J, Yang J, Chen L, Meng X, Zhang X, Li W, Li Z, Huang G.	Pathol Oncol Res	10.3389/pore.2022.1610402	2022
Pathogenicity	Diet, obesity, and the gut microbiome as determinants modulating metabolic outcomes in a non-human primate model.	Newman TM, Shively CA, Register TC, Appt SE, Yadav H, Colwell RR, Fanelli B, Dadlani M, Graubics K, Nguyen UT, Ramamoorthy S, Uberseder B, Clear KYJ, Wilson AS, Reeves KD, Chappell MC, Tooze JA, Cook KL.	Microbiome	10.1186/s40168-021-01069-y	2021
Phylogeny	Metagenomic insights into the relationship between intestinal flora and residual feed intake of meat ducks.	Yang C, Dong B, Chen A, Jiang Y, Bai H, Chen G, Chang G, Wang Z.	Poult Sci	10.1016/j.psj.2024.103836	2024
Phylogeny	Composition of the intestinal microbiota in extended-spectrum beta-lactamase-producing Enterobacteriaceae carriers and non-carriers in Thailand.	Piewngam P, Quinones M, Thirakittiwatthana W, Yungyuen T, Otto M, Kiratisin P.	Int J Antimicrob Agents	10.1016/j.ijantimicag.2018.12.006	2019
	Ex Vivo Colonic Fermentation of NUTRIOSE^® Exerts Immuno-Modulatory Properties and Strong Anti-Inflammatory Effects.	Perreau C, Thabuis C, Verstrepen L, Ghyselinck J, Marzorati M.	Nutrients	10.3390/nu15194229	2023
Genetics	Precision probiotics supplement strategy in aging population based on gut microbiome composition.	Chuang YF, Fan KC, Su YY, Wu MF, Chiu YL, Liu YC, Lin CC.	Brief Bioinform	10.1093/bib/bbae351	2024
	Vascular Graft Infection After Aneurysm Repair: A Population-Based Study.	Tabaja H, Baddour LM, Chesdachai S, DeMartino RR, Lahr BD, DeSimone DC.	Mayo Clin Proc	10.1016/j.mayocp.2023.02.027	2023
	Changes in the Intestinal Microbiota of Patients with Inflammatory Bowel Disease with Clinical Remission during an 8-Week Infliximab Infusion Cycle.	Seong G, Kim N, Joung JG, Kim ER, Chang DK, Chun J, Hong SN, Kim YH.	Microorganisms	10.3390/microorganisms8060874	2020
	Characteristics of putative keystones in the healthy adult human gut microbiota as determined by correlation network analysis.	Bauchinger F, Seki D, Berry D.	Front Microbiol	10.3389/fmicb.2024.1454634	2024
Phylogeny	Gut Microbiota Composition in Prediabetes and Newly Diagnosed Type 2 Diabetes: A Systematic Review of Observational Studies.	Letchumanan G, Abdullah N, Marlini M, Baharom N, Lawley B, Omar MR, Mohideen FBS, Addnan FH, Nur Fariha MM, Ismail Z, Pathmanathan SG.	Front Cell Infect Microbiol	10.3389/fcimb.2022.943427	2022
	The impact of antibiotics on the gut microbiota of children recovering from watery diarrhoea.	Le SH, Nguyen Ngoc Minh C, de Sessions PF, Jie S, Tran Thi Hong C, Thwaites GE, Baker S, Pham DT, Chung The H.	NPJ Antimicrob Resist	10.1038/s44259-024-00030-x	2024
	Gut Microbiota Analysis and In Silico Biomarker Detection of Children with Autism Spectrum Disorder across Cohorts.	Wang W, Fu P.	Microorganisms	10.3390/microorganisms11020291	2023
	Methotrexate promotes recovery of arthritis-induced alveolar bone loss and modifies the composition of the oral-gut microbiota.	de Arruda JAA, Correa JD, Singh Y, Oliveira SR, Machado CC, Schneider AH, Medeiros JD, Fernandes GR, Macari S, Barrioni BR, Santos MS, Duffles LF, Nakaya HTI, Fukada SY, Graves DT, Cunha FQ, Silva TA.	Anaerobe	10.1016/j.anaerobe.2022.102577	2022
Pathogenicity	Colonic Transendoscopic Enteral Tubing Is a New Pathway to Microbial Therapy, Colonic Drainage, and Host-Microbiota Interaction Research.	Wang W, Lu G, Wu X, Wen Q, Zhang F.	J Clin Med	10.3390/jcm12030780	2023
	Grain, Gluten, and Dietary Fiber Intake Influence Gut Microbial Diversity: Data from the Food and Microbiome Longitudinal Investigation.	Um CY, Peters BA, Choi HS, Oberstein P, Beggs DB, Usyk M, Wu F, Hayes RB, Gapstur SM, McCullough ML, Ahn J.	Cancer Res Commun	10.1158/2767-9764.crc-22-0154	2023
	Immunoglobulin-coating patterns reveal altered humoral responses to gut bacteria in pediatric cow milk allergies.	Augustine T, Murugesan S, Badri F, Gentilcore G, Grivel JC, Akobeng A, Elawad M, Adeli M, Al Khodor S, van Panhuys N.	J Transl Med	10.1186/s12967-024-05850-z	2024
Metabolism	Changes in Intestinal Flora Structure and Metabolites Are Associated With Myocardial Fibrosis in Patients With Persistent Atrial Fibrillation.	Liu L, Su J, Li R, Luo F.	Front Nutr	10.3389/fnut.2021.702085	2021
Genetics	Metagenomic analysis reveals distinct changes in the gut microbiome of obese Chinese children.	Li P, Jiang J, Li Y, Lan Y, Yang F, Wang J, Xie Y, Xiong F, Wu J, Liu H, Fan Z.	BMC Genomics	10.1186/s12864-023-09805-4	2023
	Microbial signature of plaque and gut in acute coronary syndrome.	Pisano E, Bugli F, Severino A, Pedicino D, Paroni Sterbini F, Martini C, De Maio F, Vinci R, Sacconi A, Canonico F, D'Aiello A, Bonanni A, Proto L, Ciampi P, Ponzo M, Grimaldi MC, Urbani A, Primiano A, Gervasoni J, Montone R, Crea F, Sanguinetti M, Liuzzo G.	Sci Rep	10.1038/s41598-023-41867-y	2023
	Immunogenic peptides putatively from intratumor microbes: Opportunities for colorectal cancer treatment.	Guan X, Bu F, Fu Y, Zhang H, Xiang H, Chen X, Chen T, Wu X, Wu K, Liu L, Dong X.	iScience	10.1016/j.isci.2024.111338	2024
Genetics	Novel Insights into the Pig Gut Microbiome Using Metagenome-Assembled Genomes.	Holman DB, Kommadath A, Tingley JP, Abbott DW.	Microbiol Spectr	10.1128/spectrum.02380-22	2022
Genetics	Gut microbiota and blood biomarkers in IBD-Related arthritis: insights from mendelian randomization.	Yang W, Cui M, Yang P, Liu C, Han X, Yao W, Li Z.	Sci Rep	10.1038/s41598-024-84116-6	2025
Genetics	Multi-kingdom gut microbiota dysbiosis is associated with the development of pulmonary arterial hypertension.	Chen Y, Chen Z, Liang L, Li J, Meng L, Yuan W, Xie B, Zhang X, Feng L, Jia Y, Fu Z, Su P, Tong Z, Zhong J, Liu X.	EBioMedicine	10.1016/j.ebiom.2025.105686	2025
	Chronic oral exposure to glycated whey proteins increases survival of aged male NOD mice with autoimmune prostatitis by regulating the gut microbiome and anti-inflammatory responses.	Chen Y, Guo KM, Nagy T, Guo TL.	Food Funct	10.1039/c9fo01740b	2020
	Microbial ecology between Clostridioides difficile and gut microbiota.	Kamiya S.	Biosci Microbiota Food Health	10.12938/bmfh.2023-033	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
Genetics	Targeted remodeling of the human gut microbiome using Juemingzi (Senna seed extracts).	Narrowe AB, Lemons JMS, Mahalak KK, Firrman J, den Abbeele PV, Baudot A, Deyaert S, Li Y, Yu LL, Liu L.	Front Cell Infect Microbiol	10.3389/fcimb.2024.1296619	2024
Metabolism	Bacteroides thetaiotaomicron ameliorates mouse hepatic steatosis through regulating gut microbial composition, gut-liver folate and unsaturated fatty acids metabolism.	Li H, Wang XK, Tang M, Lei L, Li JR, Sun H, Jiang J, Dong B, Li HY, Jiang JD, Peng ZG.	Gut Microbes	10.1080/19490976.2024.2304159	2024
	Study of Correlation between Intestinal Microbiota and Traditional Chinese Medicine Syndrome of Patients with Colon Cancer.	Tuo LY, Zhang ZR, Xin H, Chu X, Xu W.	Evid Based Complement Alternat Med	10.1155/2022/2989456	2022
	Characteristics of Intestinal Barrier State and Immunoglobulin-Bound Fraction of Stool Microbiota in Advanced Melanoma Patients Undergoing Anti-PD-1 Therapy	Drymel B, Tomela K, Galus L, Olejnik-Schmidt A, Mackiewicz J, Kaczmarek M, Mackiewicz A, Schmidt M.	Int J Mol Sci		2025
	The role of gut microbiota in diarrhea and its alleviation through microbiota-targeted interventions.	Tian R, Chong CJ, Bai YY, Chen N, Qiao RR, Wang K, Wang YW, Zhao P, Zhao CB, Tang YP, Zhang L, Zhang Q.	Front Microbiol	10.3389/fmicb.2025.1630823	2025
Metabolism	The Interplay between Gut Microbiota and Oral Medications and Its Impact on Advancing Precision Medicine.	Mousa S, Sarfraz M, Mousa WK.	Metabolites	10.3390/metabo13050674	2023
	Correlation of distribution characteristics and dynamic changes of gut microbiota with the efficacy of immunotherapy in EGFR-mutated non-small cell lung cancer.	Luo WC, Mei SQ, Huang ZJ, Chen ZH, Zhang YC, Yang MY, Liu JQ, Xu JY, Yang XR, Zhong RW, Tang LB, Yin LX, Deng Y, Peng YL, Lu C, Chen BL, Ke DX, Tu HY, Yang JJ, Xu CR, Wu YL, Zhou Q.	J Transl Med	10.1186/s12967-024-05135-5	2024
	Insight into gut dysbiosis of patients with inflammatory bowel disease and ischemic colitis.	Dahal RH, Kim S, Kim YK, Kim ES, Kim J.	Front Microbiol	10.3389/fmicb.2023.1174832	2023
	The Role of Gut Microbiota in Various Neurological and Psychiatric Disorders-An Evidence Mapping Based on Quantified Evidence.	Zang Y, Lai X, Li C, Ding D, Wang Y, Zhu Y.	Mediators Inflamm	10.1155/2023/5127157	2023
	Bile Acids in Inflammatory Bowel Disease: From Pathophysiology to Treatment.	Bai SH, Chandnani A, Cao S.	Biomedicines	10.3390/biomedicines12122910	2024
	Advancements in gene editing technologies for probiotic-enabled disease therapy.	Wang L, Hu J, Li K, Zhao Y, Zhu M.	iScience	10.1016/j.isci.2024.110791	2024
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
	A Long-Chain Dextran Produced by Weissella cibaria Boosts the Diversity of Health-Related Gut Microbes Ex Vivo.	Tintore M, Cune J, Vu LD, Poppe J, Van den Abbeele P, Baudot A, de Lecea C.	Biology (Basel)	10.3390/biology13010051	2024
	Intestinal microbiome characterization of adult Brazilian men with psoriasis compared to omnivore and vegetarian controls.	Polo TCF, Lai MRR, Miot LDB, Bento GFC, Silva MGD, Marques SA, Miot HA.	An Bras Dermatol	10.1016/j.abd.2022.08.008	2023
	Next generation probiotics for human health: An emerging perspective.	Jan T, Negi R, Sharma B, Kumar S, Singh S, Rai AK, Shreaz S, Rustagi S, Chaudhary N, Kaur T, Kour D, Sheikh MA, Kumar K, Yadav AN, Ahmed N.	Heliyon	10.1016/j.heliyon.2024.e35980	2024
Metabolism	Microbiota modulation by teriflunomide therapy in people with multiple sclerosis: An observational case-control study.	Moles L, Otaegui-Chivite A, Gorostidi-Aicua M, Romarate L, Mendiburu I, Crespillo-Velasco H, Alvarez de Arcaya A, Ferreira E, Arruti M, Castillo-Trivino T, Otaegui D.	Neurotherapeutics	10.1016/j.neurot.2024.e00457	2024
Phylogeny	Senior Thai fecal microbiota comparison between vegetarians and non-vegetarians using PCR-DGGE and real-time PCR.	Ruengsomwong S, Korenori Y, Sakamoto N, Wannissorn B, Nakayama J, Nitisinprasert S.	J Microbiol Biotechnol	10.4014/jmb.1310.10043	2014
	mNFE: microbiome network flow entropy for detecting pre-disease states of type 1 diabetes.	Gao R, Li P, Ni Y, Peng X, Ren J, Chen L.	Gut Microbes	10.1080/19490976.2024.2327349	2024
Genetics	Study of the intestinal microbiota composition and the effect of treatment with intensive chemotherapy in patients recovered from acute leukemia.	Vazquez X, Lumbreras-Iglesias P, Rodicio MR, Fernandez J, Bernal T, Moreno AF, de Ugarriza PL, Fernandez-Verdugo A, Margolles A, Sabater C.	Sci Rep	10.1038/s41598-024-56054-w	2024
	Quantifying the impact of ecological memory on the dynamics of interacting communities.	Khalighi M, Sommeria-Klein G, Gonze D, Faust K, Lahti L.	PLoS Comput Biol	10.1371/journal.pcbi.1009396	2022
Genetics	Taxonomic and metabolic development of the human gut microbiome across life stages: a worldwide metagenomic investigation.	Mancabelli L, Milani C, De Biase R, Bocchio F, Fontana F, Lugli GA, Alessandri G, Tarracchini C, Viappiani A, De Conto F, Nouvenne A, Ticinesi A, Bussolati O, Meschi T, Cecchi R, Turroni F, Ventura M.	mSystems	10.1128/msystems.01294-23	2024
	Colonic in vitro fermentation of mycoprotein promotes shifts in gut microbiota, with enrichment of Bacteroides species.	Colosimo R, Harris HC, Ahn-Jarvis J, Troncoso-Rey P, Finnigan TJA, Wilde PJ, Warren FJ.	Commun Biol	10.1038/s42003-024-05893-4	2024
	Multiomics Revealed the Multi-Dimensional Effects of Late Sleep on Gut Microbiota and Metabolites in Children in Northwest China.	Xiang X, Chen J, Zhu M, Gao H, Liu X, Wang Q, Wang Q.	Nutrients	10.3390/nu15204315	2023
	Gut fungi differentially response to the antipyretic (heat-clearing) and diaphoretic (exterior-releasing) traditional Chinese medicines in Coptis chinensis-conditioned gut microbiota.	Yang Y, Lu W, Zhang X, Wu C.	Front Pharmacol	10.3389/fphar.2022.1032919	2022
	Alteration in the gut microbiome is associated with changes in bone metabolism after laparoscopic sleeve gastrectomy.	Wu KC, McCauley KE, Lynch SV, Nayak RR, King NJ, Patel S, Kim TY, Condra K, Fadrosh D, Nguyen D, Lin DL, Lynch K, Rogers SJ, Carter JT, Posselt AM, Stewart L, Schafer AL.	J Bone Miner Res	10.1093/jbmr/zjad017	2024
	Microbiome insights into pediatric familial adenomatous polyposis.	Attard TM, Septer S, Lawson CE, Attard MI, Lee STM, Umar S.	Orphanet J Rare Dis	10.1186/s13023-022-02569-2	2022
	Gut dysbiosis in Thai intrahepatic cholangiocarcinoma and hepatocellular carcinoma.	Pomyen Y, Chaisaingmongkol J, Rabibhadana S, Pupacdi B, Sripan D, Chornkrathok C, Budhu A, Budhisawasdi V, Lertprasertsuke N, Chotirosniramit A, Pairojkul C, Auewarakul CU, Ungtrakul T, Sricharunrat T, Phornphutkul K, Sangrajang S, Loffredo CA, Harris CC, Mahidol C, Wang XW, Ruchirawat M, TIGER-LC Consortium.	Sci Rep	10.1038/s41598-023-38307-2	2023
Genetics	Dynamical alterations of brain function and gut microbiome in weight loss.	Zhou J, Wu X, Xiang T, Liu F, Gao H, Tong L, Yan B, Li Z, Zhang C, Wang L, Ou L, Li Z, Wang W, Yang T, Li F, Ma H, Zhao X, Mi N, Yu Z, Lan C, Wang Q, Li H, Wang L, Wang X, Li Y, Zeng Q.	Front Cell Infect Microbiol	10.3389/fcimb.2023.1269548	2023
	Differences in gut microbiota between Dutch and South-Asian Surinamese: potential implications for type 2 diabetes mellitus.	Nayman EI, Schwartz BA, Polmann M, Gumabong AC, Nieuwdorp M, Cickovski T, Mathee K.	Sci Rep	10.1038/s41598-024-54769-4	2024
	Ecological Structuring of Temperate Bacteriophages in the Inflammatory Bowel Disease-Affected Gut.	Nishiyama H, Endo H, Blanc-Mathieu R, Ogata H.	Microorganisms	10.3390/microorganisms8111663	2020
	Analysis of a novel 8.9kb cryptic plasmid from Bacteroides uniformis, its long-term stability and spread within human microbiota.	Shkoporov AN, Khokhlova EV, Kulagina EV, Smeianov VV, Kuchmiy AA, Kafarskaya LI, Efimov BA.	Plasmid	10.1016/j.plasmid.2012.11.002	2013
	The gut-brain axis in individuals with alcohol use disorder: An exploratory study of associations among clinical symptoms, brain morphometry, and the gut microbiome.	Maki KA, Wallen GR, Bastiaanssen TFS, Hsu LY, Valencia ME, Ramchandani VA, Schwandt ML, Diazgranados N, Cryan JF, Momenan R, Barb JJ.	Alcohol Clin Exp Res (Hoboken)	10.1111/acer.15346	2024
	Temporal response patterns of human gut microbiota to dietary fiber.	Lin X, Wang C, Liu B, Zhu Y, Zhai R, Zhang C.	Imeta	10.1002/imt2.70046	2025
	Modulation of the Gut Microbiota in Memory Impairment and Alzheimer's Disease via the Inhibition of the Parasympathetic Nervous System.	Park S, Wu X.	Int J Mol Sci	10.3390/ijms232113574	2022
Genetics	Differential Effects of Western and Mediterranean-Type Diets on Gut Microbiota: A Metagenomics and Metabolomics Approach.	Barber C, Mego M, Sabater C, Vallejo F, Bendezu RA, Masihy M, Guarner F, Espin JC, Margolles A, Azpiroz F.	Nutrients	10.3390/nu13082638	2021
Genetics	Investigation of the Ecological Link between Recurrent Microbial Human Gut Communities and Physical Activity.	Tarracchini C, Fontana F, Lugli GA, Mancabelli L, Alessandri G, Turroni F, Ventura M, Milani C.	Microbiol Spectr	10.1128/spectrum.00420-22	2022
Genetics	An integrated strain-level analytic pipeline utilizing longitudinal metagenomic data.	Zhou B, Wang C, Putzel G, Hu J, Liu M, Wu F, Chen Y, Pironti A, Li H.	Microbiol Spectr	10.1128/spectrum.01431-24	2024
	Amoxicillin impact on pathophysiology induced by short term high salt diet in mice.	Kumar S, Perumal N, Yadav PK, Pandey RP, Chang CM, Raj VS.	Sci Rep	10.1038/s41598-022-21270-9	2022
	Case report: Meningitis and intracranial aneurysm caused by mixed infection of oral microflora dominated by anaerobes.	Cheng H, Xu L, Yang F, Jia L, Zhao D, Li H, Liu W, Li Y, Liu X, Geng X, Guo J, Ling C, Zhang J.	Front Neurol	10.3389/fneur.2022.889838	2022
	Short-chain fatty acids of various lengths differentially inhibit Klebsiella pneumoniae and Enterobacteriaceae species.	Chang KC, Nagarajan N, Gan Y-H.	mSphere	10.1128/msphere.00781-23	2024
	Spatial recovery of the murine gut microbiota after antibiotics perturbation.	Taguer M, Xiao J, Crawford R, Shi H, Cheng MP, Citron M, Hannigan GD, Kasper SH.	mBio	10.1128/mbio.00707-24	2024
	Amoxicillin modulates gut microbiota to improve short-term high-fat diet induced pathophysiology in mice.	Kumar S, Raj VS, Ahmad A, Saini V.	Gut Pathog	10.1186/s13099-022-00513-0	2022
	Metagenomics analysis reveals universal signatures of the intestinal microbiota in colorectal cancer, regardless of regional differences.	Berbert L, Santos A, Magro DO, Guadagnini D, Assalin HB, Lourenco LH, Martinez CAR, Saad MJA, Coy CSR.	Braz J Med Biol Res	10.1590/1414-431x2022e11832	2022
	Circulating Cell-Free Microbial DNA Signatures and Plasma Soluble CD14 Level Are Associated with Clinical Outcomes of Anti-PD-1 Therapy in Advanced Melanoma Patients.	Drymel B, Tomela K, Galus L, Olejnik-Schmidt A, Mackiewicz J, Kaczmarek M, Mackiewicz A, Schmidt M.	Int J Mol Sci	10.3390/ijms252312982	2024
	The Gut Microbiome May Help Address Mental Health Disparities in Hispanics: A Narrative Review.	Vera-Urbina F, Dos Santos-Torres MF, Godoy-Vitorino F, Torres-Hernandez BA.	Microorganisms	10.3390/microorganisms10040763	2022
	Total Astragalus saponins can reverse type 2 diabetes mellitus-related intestinal dysbiosis and hepatic insulin resistance in vivo.	Ma L, La X, Zhang B, Xu W, Tian C, Fu Q, Wang M, Wu C, Chen Z, Chang H, Li JA.	Front Endocrinol (Lausanne)	10.3389/fendo.2023.1190827	2023
	Gut Microbial Characterization of Melon-Headed Whales (Peponocephala electra) Stranded in China.	Bai S, Zhang P, Zhang X, Yang Z, Li S.	Microorganisms	10.3390/microorganisms10030572	2022
	The inconsistent pathogenesis of endometriosis and adenomyosis: insights from endometrial metabolome and microbiome.	Li C, Xu X, Zhao X, Du B.	mSystems	10.1128/msystems.00202-25	2025
	Gastrointestinal Microbiota and Breast Cancer Chemotherapy Interactions: A Systematic Review.	Csendes D, Gutlapalli SD, Prakash K, Swarnakari KM, Bai M, Manoharan MP, Raja R, Jamil A, Desai A, Desai DM, Khan S.	Cureus	10.7759/cureus.31648	2022
Metabolism	Cutting Edge: Intestinal IL-17A Receptor Signaling Specifically Regulates High-Fat Diet-Mediated, Microbiota-Driven Metabolic Disorders.	Gaudino SJ, Huang H, Jean-Pierre M, Joshi P, Beaupre M, Kempen C, Wong HT, Kumar P.	J Immunol	10.4049/jimmunol.2000986	2021
Genetics	Bifidobacterium lactis Probio-M8 Adjuvant Treatment Confers Added Benefits to Patients with Coronary Artery Disease via Target Modulation of the Gut-Heart/-Brain Axes.	Sun B, Ma T, Li Y, Yang N, Li B, Zhou X, Guo S, Zhang S, Kwok LY, Sun Z, Zhang H.	mSystems	10.1128/msystems.00100-22	2022
	Bacterial targets of fecal host miRNAs in high-fat diet-fed mice.	Silamikele L, Silamikelis I, Kotovica PP, Klovins J.	PLoS One	10.1371/journal.pone.0315871	2025
Genetics	The Trajectory of Successful Aging: Insights from Metagenome and Cytokine Profiling.	Chulenbayeva L, Ganzhula Y, Kozhakhmetov S, Jarmukhanov Z, Nurgaziyev M, Nurgozhina A, Muhanbetzhanov N, Sergazy S, Zhetkenev S, Borykbay Z, Tkachev V, Urazova S, Vinogradova E, Kushugulova A.	Gerontology	10.1159/000536082	2024
	Commensal antimicrobial resistance mediates microbiome resilience to antibiotic disruption.	Bhattarai SK, Du M, Zeamer AL, M Morzfeld B, Kellogg TD, Firat K, Benjamin A, Bean JM, Zimmerman M, Mardi G, Vilbrun SC, Walsh KF, Fitzgerald DW, Glickman MS, Bucci V.	Sci Transl Med	10.1126/scitranslmed.adi9711	2024
	Probiotics maintain the gut microbiome homeostasis during Indian Antarctic expedition by ship.	Srivastava AK, Rohil V, Bhushan B, Eslavath MR, Gupta H, Chanda S, Kumar B, Varshney R, Ganju L.	Sci Rep	10.1038/s41598-021-97890-4	2021
Genetics	The human gut microbiome of athletes: metagenomic and metabolic insights.	Fontana F, Longhi G, Tarracchini C, Mancabelli L, Lugli GA, Alessandri G, Turroni F, Milani C, Ventura M.	Microbiome	10.1186/s40168-023-01470-9	2023
	"Trust your gut": exploring the connection between gut microbiome dysbiosis and the advancement of Metabolic Associated Steatosis Liver Disease (MASLD)/Metabolic Associated Steatohepatitis (MASH): a systematic review of animal and human studies.	Bahitham W, Banoun Y, Aljahdali M, Almuaiqly G, Bahshwan SM, Aljahdali L, Sanai FM, Rosado AS, Sergi CM.	Front Nutr	10.3389/fnut.2025.1637071	2025
	Functional diversification despite structural congruence in the HipBST toxin-antitoxin system of Legionella pneumophila.	Lin JD, Stogios PJ, Abe KT, Wang A, MacPherson J, Skarina T, Gingras A-C, Savchenko A, Ensminger AW.	mBio	10.1128/mbio.01510-23	2023
	Systematic review of donor and recipient predictive biomarkers of response to faecal microbiota transplantation in patients with ulcerative colitis.	Rees NP, Shaheen W, Quince C, Tselepis C, Horniblow RD, Sharma N, Beggs AD, Iqbal TH, Quraishi MN.	EBioMedicine	10.1016/j.ebiom.2022.104088	2022
	The effects of antibiotic exposures on the gut resistome during hematopoietic cell transplantation in children.	Heston SM, Young RR, Jenkins K, Martin PL, Stokhuyzen A, Ward DV, Bhattarai SK, Bucci V, Arshad M, Chao NJ, Seed PC, Kelly MS.	Gut Microbes	10.1080/19490976.2024.2333748	2024
Phylogeny	Association of dietary fibre intake and gut microbiota in adults.	Lin D, Peters BA, Friedlander C, Freiman HJ, Goedert JJ, Sinha R, Miller G, Bernstein MA, Hayes RB, Ahn J.	Br J Nutr	10.1017/s0007114518002465	2018
	Longitudinal phage-bacteria dynamics in the early life gut microbiome.	Tisza MJ, Lloyd RE, Hoffman K, Smith DP, Rewers M, Javornik Cregeen SJ, Petrosino JF.	Nat Microbiol	10.1038/s41564-024-01906-4	2025
Genetics	miMatch: a microbial metabolic background matching tool for mitigating host confounding in metagenomics research.	Liu L, Cao S, Lin W, Gao Z, Yang L, Zhu L, Yang B, Zhang G, Zhu R, Wu D.	Gut Microbes	10.1080/19490976.2024.2434029	2024
Phylogeny	Gut Microbial Profile in Asymptomatic Gallstones.	Song ST, Cai LY, Zeng X, Xie WF.	Front Microbiol	10.3389/fmicb.2022.882265	2022
	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
	Selecting a Single Stereocenter: The Molecular Nuances That Differentiate beta-Hexuronidases in the Human Gut Microbiome.	Pellock SJ, Walton WG, Redinbo MR.	Biochemistry	10.1021/acs.biochem.8b01285	2019
Metabolism	Comprehensive metagenomic and lipidomic analysis showed that baicalin could improve depressive behaviour in atherosclerotic mice by inhibiting nerve cell ferroptosis.	Ren P, Zhao Y, Li X, Xie J, Liao X, Luo Q, Liu X, Li J, Fan Y, Cheng X, Fu X, Zhou J, Wu X.	Front Immunol	10.3389/fimmu.2025.1599570	2025
	Future for probiotic science in functional food and dietary supplement development.	Neef A, Sanz Y.	Curr Opin Clin Nutr Metab Care	10.1097/mco.0b013e328365c258	2013
	The gut microbiome is associated with susceptibility to febrile malaria in Malian children.	Van Den Ham KM, Bower LK, Li S, Lorenzi H, Doumbo S, Doumtabe D, Kayentao K, Ongoiba A, Traore B, Crompton PD, Schmidt NW.	Nat Commun	10.1038/s41467-024-52953-8	2024
	Comparative time-series analyses of gut microbiome profiles in genetically and chemically induced lupus-prone mice and the impacts of fecal transplantation.	Chatthanathon P, Leelahavanichkul A, Cheibchalard T, Wilantho A, Hirankarn N, Somboonna N.	Sci Rep	10.1038/s41598-024-77672-4	2024
	Rapid design of bacteriophage cocktails to suppress the burden and virulence of gut-resident carbapenem-resistant Klebsiella pneumoniae.	Rotman E, McClure S, Glazier J, Fuerte-Stone J, Foldi J, Erani A, McGann R, Arnold J, Lin H, Valaitis S, Mimee M.	Cell Host Microbe	10.1016/j.chom.2024.09.004	2024
	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
	Characterisation of Indian gut microbiome for B-vitamin production and its comparison with Chinese cohort.	Chandel N, Somvanshi PR, Thakur V.	Br J Nutr	10.1017/s0007114523002179	2024
	Bacterial pathogens in pediatric appendicitis: a comprehensive retrospective study.	Felber J, Gross B, Rahrisch A, Waltersbacher E, Trips E, Schrottner P, Fitze G, Schultz J.	Front Cell Infect Microbiol	10.3389/fcimb.2023.1027769	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
Genetics	Virome and metagenomic analysis reveal the distinct distribution of microbiota in human fetal gut during gestation.	Liu X, He G, Lan Y, Guo W, Liu X, Li J, Liu A, He M, Liu X, Fan Z, Zhang Y.	Front Immunol	10.3389/fimmu.2022.1079294	2022
Pathogenicity	Field evaluation of the gut microbiome composition of pre-school and school-aged children in Tha Song Yang, Thailand, following oral MDA for STH infections.	Stracke K, Adisakwattana P, Phuanukoonnon S, Yoonuan T, Poodeepiyasawat A, Dekumyoy P, Chaisiri K, Roth Schulze A, Wilcox S, Karunajeewa H, Traub RJ, Jex AR.	PLoS Negl Trop Dis	10.1371/journal.pntd.0009597	2021
	Elucidating Sequence and Structural Determinants of Carbohydrate Esterases for Complete Deacetylation of Substituted Xylans.	Penttinen L, Kouhi V, Faure R, Skarina T, Stogios P, Master E, Jurak E.	Molecules	10.3390/molecules27092655	2022
	Diabetes and gut microbiota.	Xi Y, Xu PF.	World J Diabetes	10.4239/wjd.v12.i10.1693	2021
	Associations of Childhood and Perinatal Blood Metals with Children's Gut Microbiomes in a Canadian Gestation Cohort.	Shen Y, Laue HE, Shrubsole MJ, Wu H, Bloomquist TR, Larouche A, Zhao K, Gao F, Boivin A, Prada D, Hunting DJ, Gillet V, Takser L, Baccarelli AA.	Environ Health Perspect	10.1289/ehp9674	2022
	Effects of Bacillus licheniformis on the Growth Performance, Antioxidant Capacity, Ileal Morphology, Intestinal Short Chain Fatty Acids, and Colonic Microflora in Piglets Challenged with Lipopolysaccharide.	Cao G, Yang S, Wang H, Zhang R, Wu Y, Liu J, Qiu K, Dong Y, Yue M.	Animals (Basel)	10.3390/ani13132172	2023
Genetics	Integrative metagenomic analysis reveals distinct gut microbial signatures related to obesity.	Hu X, Yu C, He Y, Zhu S, Wang S, Xu Z, You S, Jiao Y, Liu SL, Bao H.	BMC Microbiol	10.1186/s12866-024-03278-5	2024
Genetics	Combined analysis of cross-population healthy adult human microbiome reveals consistent differences in gut microbial characteristics between Western and non-Western countries.	Sheng Y, Wang J, Gao Y, Peng Y, Li X, Huang W, Zhou H, Liu R, Zhang W.	Comput Struct Biotechnol J	10.1016/j.csbj.2023.11.047	2024
	Bacteroides fragilis participates in the therapeutic effect of methotrexate on arthritis through metabolite regulation.	Zhou B, Dong C, Zhao B, Lin K, Tian Y, Zhang R, Zhu L, Xu H, Yang L.	Front Microbiol	10.3389/fmicb.2022.1015130	2022
Genetics	Characterization of Fecal Microbiomes of Osteoporotic Patients in Korea.	Ul-Haq A, Seo H, Jo S, Park H, Kim S, Lee Y, Lee S, Jeong JH, Song HY.	Pol J Microbiol	10.33073/pjm-2022-045	2022
	Multi-omic analysis reveals transkingdom gut dysbiosis in metabolic dysfunction-associated steatotic liver disease.	Kim H, Nelson P, Nzabarushimana E, Shen J, Jensen J, Bhosle A, Li C, Lee N, Everett C, Berdy B, Frongillo G, Livny J, Hu FB, Simon TG, McIver L, Franzosa EA, Chan AT, Hayete B, Thompson KN, Huttenhower C, Nguyen LH.	Nat Metab	10.1038/s42255-025-01318-6	2025
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
	Human Fecal Contamination Corresponds to Changes in the Freshwater Bacterial Communities of a Large River Basin.	McClary-Gutierrez JS, Driscoll Z, Nenn C, Newton RJ.	Microbiol Spectr	10.1128/spectrum.01200-21	2021
	Gut commensal Kineothrix alysoides mitigates liver dysfunction by restoring lipid metabolism and gut microbial balance.	Choi KJ, Yoon MY, Kim JE, Yoon SS.	Sci Rep	10.1038/s41598-023-41160-y	2023
	Hybrid metagenome assemblies link carbohydrate structure with function in the human gut microbiome.	Ravi A, Troncoso-Rey P, Ahn-Jarvis J, Corbin KR, Harris S, Harris H, Aydin A, Kay GL, Le Viet T, Gilroy R, Pallen MJ, Page AJ, O'Grady J, Warren FJ.	Commun Biol	10.1038/s42003-022-03865-0	2022
Enzymology	The gut microbiome in dogs with congestive heart failure: a pilot study.	Seo J, Matthewman L, Xia D, Wilshaw J, Chang YM, Connolly DJ.	Sci Rep	10.1038/s41598-020-70826-0	2020
Metabolism	Dietary Fiber Hierarchical Specificity: the Missing Link for Predictable and Strong Shifts in Gut Bacterial Communities.	Cantu-Jungles TM, Bulut N, Chambry E, Ruthes A, Iacomini M, Keshavarzian A, Johnson TA, Hamaker BR.	mBio	10.1128/mbio.01028-21	2021
	Multi-omic integration of microbiome data for identifying disease-associated modules.	Muller E, Shiryan I, Borenstein E.	Nat Commun	10.1038/s41467-024-46888-3	2024
	Diet replacement with whole insect larvae affects intestinal morphology and microbiota of broiler chickens.	Vasilopoulos S, Giannenas I, Mellidou I, Stylianaki I, Antonopoulou E, Tzora A, Skoufos I, Athanassiou CG, Papadopoulos E, Fortomaris P.	Sci Rep	10.1038/s41598-024-54184-9	2024
Phylogeny	The effect of antibiotics on the intestinal microbiota in children - a systematic review.	Wurm J, Curtis N, Zimmermann P.	Front Allergy	10.3389/falgy.2024.1458688	2024
	Alteration of the fecal microbiome in patients with cholecystectomy: potential relationship with postcholecystectomy diarrhea - before and after study.	Noh CK, Jung W, Yang MJ, Kim WH, Hwang JC.	Int J Surg	10.1097/js9.0000000000000518	2023
Enzymology	Bacteroides uniformis is a putative bacterial species associated with the degradation of the isoflavone genistein in human feces.	Renouf M, Hendrich S.	J Nutr	10.3945/jn.111.140988	2011
	Nutraceuticals and Herbal Food Supplements for Weight Loss: Is There a Prebiotic Role in the Mechanism of Action?	Bertuccioli A, Cardinali M, Biagi M, Moricoli S, Morganti I, Zonzini GB, Rigillo G.	Microorganisms	10.3390/microorganisms9122427	2021
	Inflammatory bowel disease biomarkers revealed by the human gut microbiome network.	Hu M, Caldarelli G, Gili T.	Sci Rep	10.1038/s41598-023-46184-y	2023
Phylogeny	Can longer lifespan be associated with gut microbiota involvement in lipid metabolism?	Sardzikova S, Gajewska M, Galka N, Stefanek M, Balaz A, Garaiova M, Holic R, Swiderek W, Soltys K.	FEMS Microbiol Ecol	10.1093/femsec/fiae135	2024
Genetics	Ectopic gut colonization: a metagenomic study of the oral and gut microbiome in Crohn's disease.	Hu S, Png E, Gowans M, Ong DEH, de Sessions PF, Song J, Nagarajan N.	Gut Pathog	10.1186/s13099-021-00409-5	2021
	Composition of the gut microbiota in patients with inflammatory bowel disease in Saudi Arabia: A pilot study.	Al-Amrah H, Saadah OI, Mosli M, Annese V, Al-Hindi R, Edris S, Alshehri D, Alatawi H, Alatawy M, Bahieldin A.	Saudi J Gastroenterol	10.4103/sjg.sjg_368_22	2023
	Association Studies on Gut and Lung Microbiomes in Patients with Lung Adenocarcinoma.	Guo Y, Yuan W, Lyu N, Pan Y, Cao X, Wang Y, Han Y, Zhu B.	Microorganisms	10.3390/microorganisms11030546	2023
Pathogenicity	Microbial-Based Bioactive Compounds to Alleviate Inflammation in Obesity.	Apalowo OE, Adegoye GA, Obuotor TM.	Curr Issues Mol Biol	10.3390/cimb46030119	2024
	Orally administrated Lactobacillus gasseri TM13 and Lactobacillus crispatus LG55 can restore the vaginal health of patients recovering from bacterial vaginosis.	Qi F, Fan S, Fang C, Ge L, Lyu J, Huang Z, Zhao S, Zou Y, Huang L, Liu X, Liang Y, Zhang Y, Zhong Y, Zhang H, Xiao L, Zhang X.	Front Immunol	10.3389/fimmu.2023.1125239	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
	Transmission and dynamics of mother-infant gut viruses during pregnancy and early life.	Garmaeva S, Sinha T, Gulyaeva A, Kuzub N, Spreckels JE, Andreu-Sanchez S, Gacesa R, Vich Vila A, Brushett S, Kruk M, Lifelines NEXT cohort study, Dekens J, Sikkema J, Kuipers F, Shkoporov AN, Hill C, Scherjon S, Wijmenga C, Fu J, Kurilshikov A, Zhernakova A.	Nat Commun	10.1038/s41467-024-45257-4	2024
	The Impact of Air Pollution on Intestinal Microbiome of Asthmatic Children: A Panel Study.	Zheng P, Zhang B, Zhang K, Lv X, Wang Q, Bai X.	Biomed Res Int	10.1155/2020/5753427	2020
Phylogeny	Multi-centre evaluation of mass spectrometric identification of anaerobic bacteria using the VITEK® MS system.	Garner O, Mochon A, Branda J, Burnham CA, Bythrow M, Ferraro M, Ginocchio C, Jennemann R, Manji R, Procop GW, Richter S, Rychert J, Sercia L, Westblade L, Lewinski M.	Clin Microbiol Infect	10.1111/1469-0691.12317	2014
	Genome-centric analysis of short and long read metagenomes reveals uncharacterized microbiome diversity in Southeast Asians.	Gounot JS, Chia M, Bertrand D, Saw WY, Ravikrishnan A, Low A, Low A, Ding Y, Ng AHQ, Tan LWL, Teo YY, Seedorf H, Nagarajan N.	Nat Commun	10.1038/s41467-022-33782-z	2022
	Creation of a non-Western humanized gnotobiotic mouse model through the transplantation of rural African fecal microbiota.	Van Den Ham KM, Little MR, Bednarski OJ, Fusco EM, Mandal RK, Mitra R, Li S, Doumbo S, Doumtabe D, Kayentao K, Ongoiba A, Traore B, Crompton PD, Schmidt NW.	Microbiol Spectr	10.1128/spectrum.01554-23	2023
	Dietary Impacts on Changes in Diversity and Abundance of the Murine Microbiome during Progression and Treatment of Cancer.	Paden H, Kurbatfinski N, Poelstra JW, Ormiston K, Orchard T, Ilic S.	Nutrients	10.3390/nu15030724	2023
	Prediction of Pathogenic Factors in Dysbiotic Gut Microbiomes of Colorectal Cancer Patients Using Reverse Microbiomics.	Wang H, Zhang K, Wu L, Qin Q, He Y.	Front Oncol	10.3389/fonc.2022.882874	2022
	Diagnostic, Prognostic, and Therapeutic Roles of Gut Microbiota in COVID-19: A Comprehensive Systematic Review.	Farsi Y, Tahvildari A, Arbabi M, Vazife F, Sechi LA, Shahidi Bonjar AH, Jamshidi P, Nasiri MJ, Mirsaeidi M.	Front Cell Infect Microbiol	10.3389/fcimb.2022.804644	2022
Enzymology	Ethnic diversity of gut microbiota: species characterization of Bacteroides fragilis group and genus Bifidobacterium in healthy Belgian adults, and comparison with data from Japanese subjects.	Ishikawa E, Matsuki T, Kubota H, Makino H, Sakai T, Oishi K, Kushiro A, Fujimoto J, Watanabe K, Watanuki M, Tanaka R.	J Biosci Bioeng	10.1016/j.jbiosc.2013.02.010	2013
	From Microbes to Metabolites: Advances in Gut Microbiome Research in Type 1 Diabetes.	Blok L, Hanssen N, Nieuwdorp M, Rampanelli E.	Metabolites	10.3390/metabo15020138	2025
Metabolism	Therapeutic Potential of Metabolites from Lactobacillus rhamnosus and Mare's Milk in the Treatment of Dysbiosis.	Kozhakhmetov S, Babenko D, Kozhakhmetova S, Tuyakova A, Nurgaziyev M, Nurgozhina A, Muhanbetganov N, Chulenbayeva L, Sergazy S, Gulyayev A, Aljofan M, Kushugulova A.	Biomed Res Int	10.1155/2022/3851478	2022
	A comparative analysis of lipoprotein transport proteins: LolA and LolB from Vibrio cholerae and LolA from Porphyromonas gingivalis.	Jaiman D, Nagampalli R, Persson K.	Sci Rep	10.1038/s41598-023-33705-y	2023
Pathogenicity	Human-derived microRNA 21 regulates indole and L-tryptophan biosynthesis transcripts in the gut commensal Bacteroides thetaiotaomicron.	Flanagan K, Gassner K, Lang M, Ozelyte J, Hausmann B, Crepaz D, Pjevac P, Gasche C, Berry D, Vesely C, Pereira FC.	mBio	10.1128/mbio.03928-24	2025
	Cranberry polyphenols and agave agavins impact gut immune response and microbiota composition while improving gut barrier function, inflammation, and glucose metabolism in mice fed an obesogenic diet.	Medina-Larque AS, Rodriguez-Daza MC, Roquim M, Dudonne S, Pilon G, Levy E, Marette A, Roy D, Jacques H, Desjardins Y.	Front Immunol	10.3389/fimmu.2022.871080	2022
	Gut dysbiosis and inflammatory blood markers precede HIV with limited changes after early seroconversion.	Fulcher JA, Li F, Tobin NH, Zabih S, Elliott J, Clark JL, D'Aquila R, Mustanski B, Kipke MD, Shoptaw S, Gorbach PM, Aldrovandi GM.	EBioMedicine	10.1016/j.ebiom.2022.104286	2022
	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
	High-fat diet feeding exacerbates HIV-1 rectal transmission.	Lohani SC, Ramer-Tait AE, Li Q.	mSystems	10.1128/msystems.01322-23	2024
Metabolism	Understanding the Role of the Gut Microbiome in Diabetes and Therapeutics Targeting Leaky Gut: A Systematic Review.	Sadagopan A, Mahmoud A, Begg M, Tarhuni M, Fotso M, Gonzalez NA, Sanivarapu RR, Osman U, Latha Kumar A, Mohammed L.	Cureus	10.7759/cureus.41559	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
Genetics	Multi-omics analysis reveals the influence of genetic and environmental risk factors on developing gut microbiota in infants at risk of celiac disease.	Leonard MM, Karathia H, Pujolassos M, Troisi J, Valitutti F, Subramanian P, Camhi S, Kenyon V, Colucci A, Serena G, Cucchiara S, Montuori M, Malamisura B, Francavilla R, Elli L, Fanelli B, Colwell R, Hasan N, Zomorrodi AR, Fasano A, CD-GEMM Team.	Microbiome	10.1186/s40168-020-00906-w	2020
	Gut microbiota markers associated with obesity and overweight in Italian adults.	Palmas V, Pisanu S, Madau V, Casula E, Deledda A, Cusano R, Uva P, Vascellari S, Loviselli A, Manzin A, Velluzzi F.	Sci Rep	10.1038/s41598-021-84928-w	2021
	Intermittent fasting modulates the intestinal microbiota and improves obesity and host energy metabolism.	Hu X, Xia K, Dai M, Han X, Yuan P, Liu J, Liu S, Jia F, Chen J, Jiang F, Yu J, Yang H, Wang J, Xu X, Jin X, Kristiansen K, Xiao L, Chen W, Han M, Duan S.	NPJ Biofilms Microbiomes	10.1038/s41522-023-00386-4	2023
Metabolism	Products of gut microbial Toll/interleukin-1 receptor domain NADase activities in gnotobiotic mice and Bangladeshi children with malnutrition.	Weagley JS, Zaydman M, Venkatesh S, Sasaki Y, Damaraju N, Yenkin A, Buchser W, Rodionov DA, Osterman A, Ahmed T, Barratt MJ, DiAntonio A, Milbrandt J, Gordon JI.	Cell Rep	10.1016/j.celrep.2022.110738	2022
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
	Exploring Novel Antimalarial Compounds Targeting Plasmodium falciparum Enoyl-ACP Reductase: Computational and Experimental Insights.	A R Oliveira G, G D V Morales B, M O Sousa R, S Pereira S, Antunes D, Caffarena ER, Zanchi FB.	ACS Omega	10.1021/acsomega.3c09893	2024
	Microbial succinate promotes the response to metformin by upregulating secretory immunoglobulin a in intestinal immunity.	Zhang Y, Wang A, Zhao W, Qin J, Zhang Y, Liu B, Yao C, Long J, Yuan M, Yan D.	Gut Microbes	10.1080/19490976.2025.2450871	2025
	Exploring the presence of oral bacteria in non-oral sites of patients with cardiovascular diseases using whole metagenomic data.	Chopra A, Franco-Duarte R, Rajagopal A, Choowong P, Soares P, Rito T, Eberhard J, Jayasinghe TN.	Sci Rep	10.1038/s41598-023-50891-x	2024
	Strain-level profiling of viable microbial community by selective single-cell genome sequencing.	Hosokawa M, Endoh T, Kamata K, Arikawa K, Nishikawa Y, Kogawa M, Saeki T, Yoda T, Takeyama H.	Sci Rep	10.1038/s41598-022-08401-y	2022
Genetics	Transmission of the gut microbiome in cohousing goats and pigs.	Zhang T, Li M, Shi T, Yan Y, Niyazbekova Z, Wang X, Li Z, Jiang Y.	Front Microbiol	10.3389/fmicb.2022.948617	2022
	Eubacterium siraeum suppresses fat deposition via decreasing the tyrosine-mediated PI3K/AKT signaling pathway in high-fat diet-induced obesity.	Lai X, Liu S, Miao J, Shen R, Wang Z, Zhang Z, Gong H, Li M, Pan Y, Wang Q.	Microbiome	10.1186/s40168-024-01944-4	2024
	Strain-Level Dynamics Reveal Regulatory Roles in Atopic Eczema by Gut Bacterial Phages.	Chu Y, Meng Q, Yu J, Zhang J, Chen J, Kang Y.	Microbiol Spectr	10.1128/spectrum.04551-22	2023
	The Mediterranean Diet, Its Microbiome Connections, and Cardiovascular Health: A Narrative Review.	Abrignani V, Salvo A, Pacinella G, Tuttolomondo A.	Int J Mol Sci	10.3390/ijms25094942	2024
	A Method for Isolation and Proteomic Analysis of Outer Membrane Vesicles from Fecal Samples by LC-MS/MS.	Wu J, An M, Zhu J, Tan Z, Chen GY, Stidham RW, Lubman DM.	J Proteomics Bioinform	10.4172/0974-276x.1000494	2019
	Soy Metabolism by Gut Microbiota from Patients with Precancerous Intestinal Lesions.	Polimeno L, Barone M, Mosca A, Viggiani MT, Joukar F, Mansour-Ghanaei F, Mavaddati S, Daniele A, Debellis L, Bilancia M, Santacroce L, Di Leo A.	Microorganisms	10.3390/microorganisms8040469	2020
	Novel Bacteroides Vulgatus strain protects against gluten-induced break of human celiac gut epithelial homeostasis: a pre-clinical proof-of-concept study.	Tran T, Senger S, Baldassarre M, Brosnan RA, Cristofori F, Crocco M, De Santis S, Elli L, Faherty CS, Francavilla R, Goodchild-Michelman I, Kenyon VA, Leonard MM, Lima RS, Malerba F, Montuori M, Morelli A, Norsa L, Passaro T, Piemontese P, Reed JC, Sansotta N, Valitutti F, Zomorrodi AR, Fasano A, CDGEMM Team.	Pediatr Res	10.1038/s41390-023-02960-0	2024
Metabolism	Role of intestinal flora in the development of nonalcoholic fatty liver disease in children.	Zhang J, Shi M, Zhao C, Liang G, Li C, Ge X, Pei C, Kong Y, Li D, Yang W, Cao B, Fu L, Yan Y, Wu J, Zhou J, Fang Y, Meng X, Li Y, Wang L, Wang L.	Microbiol Spectr	10.1128/spectrum.01006-23	2024
Metabolism	Bacteroides acidifaciens in the gut plays a protective role against CD95-mediated liver injury.	Wang H, Wang Q, Yang C, Guo M, Cui X, Jing Z, Liu Y, Qiao W, Qi H, Zhang H, Zhang X, Zhao N, Zhang M, Chen M, Zhang S, Xu H, Zhao L, Qiao M, Wu Z.	Gut Microbes	10.1080/19490976.2022.2027853	2022
	Microbiome Analysis of Mucosal Ileoanal Pouch in Ulcerative Colitis Patients Revealed Impairment of the Pouches Immunometabolites.	Palmieri O, Castellana S, Biscaglia G, Panza A, Latiano A, Fontana R, Guerra M, Corritore G, Latiano T, Martino G, Mazza T, Andriulli A, Perri F, Bossa F.	Cells	10.3390/cells10113243	2021
	Ecological niches and assembly dynamics of diverse microbial consortia in the gastrointestine of goat kids.	Jiao J, Wu J, Zhou C, He Z, Tan Z, Wang M.	ISME J	10.1093/ismejo/wrae002	2024
Genetics	Temporal colonization and metabolic regulation of the gut microbiome in neonatal oxen at single nucleotide resolution.	Dong Q, Hua D, Wang X, Jiao Y, Liu L, Deng Q, Wu T, Zou H, Zhao C, Wang C, Reng J, Ding L, Hu S, Shi J, Wang Y, Zhang H, Sheng Y, Sun W, Shen Y, Tang L, Kong X, Chen L.	ISME J	10.1093/ismejo/wrad022	2024
Metabolism	Interactions Between Antidepressants and Intestinal Microbiota.	Xu F, Xie Q, Kuang W, Dong Z.	Neurotherapeutics	10.1007/s13311-023-01362-8	2023
	The specific hallmarks, emerging roles, key mechanisms, and clinical applications of intra-tumoral microbiota in human cancers.	Zhao T, Sun N, Ding J, Peng Z, Han F, Qi X.	Genes Dis	10.1016/j.gendis.2025.101733	2026
Phylogeny	Gut Microbiome Changes Associated With HIV Infection and Sexual Orientation.	Zhou J, Zhang Y, Cui P, Luo L, Chen H, Liang B, Jiang J, Ning C, Tian L, Zhong X, Ye L, Liang H, Huang J.	Front Cell Infect Microbiol	10.3389/fcimb.2020.00434	2020
	Temporal change in the gut community of rats fed high amylose cornstarch is driven by endogenous urea rather than strictly on carbohydrate availability.	Kalmokoff M, Zwicker B, O'Hara M, Matias F, Green J, Shastri P, Green-Johnson J, Brooks SP.	J Appl Microbiol	10.1111/jam.12157	2013
	Gut Microbiota Composition Can Predict Colonization by Multidrug-Resistant Bacteria in SARS-CoV-2 Patients in Intensive Care Unit: A Pilot Study.	Garcia-Garcia J, Diez-Echave P, Yuste ME, Chueca N, Garcia F, Garcia F, Cabeza-Barrera J, Fernandez-Varon E, Galvez J, Colmenero M, Rodriguez-Cabezas ME, Rodriguez-Nogales A, Moron R.	Antibiotics (Basel)	10.3390/antibiotics12030498	2023
	Multi-omics analysis reveals gut microbiota-induced intramuscular fat deposition via regulating expression of lipogenesis-associated genes.	Xie C, Teng J, Wang X, Xu B, Niu Y, Ma L, Yan X.	Anim Nutr	10.1016/j.aninu.2021.10.010	2022
	The Role of the Gut Microbiota in Anorexia Nervosa in Children and Adults-Systematic Review.	Anton-Paduraru DT, Trofin F, Nastase EV, Miftode RS, Miftode IL, Trandafirescu MF, Cojocaru E, Tarca E, Mindru DE, Dorneanu OS.	Int J Mol Sci	10.3390/ijms25010041	2023
	A functionally augmented carbohydrate utilization locus from herbivore gut microbiota fueled by dietary beta-glucans.	Mandelli F, Martins MP, Chinaglia M, Lima EA, Morais MAB, Lima TB, Cabral L, Pirolla RAS, Fuzita FJ, Paixao DAA, Andrade MO, Wolf LD, Vieira PS, Persinoti GF, Murakami MT.	NPJ Biofilms Microbiomes	10.1038/s41522-024-00578-6	2024
	Key Bacteria in the Gut Microbiota Network for the Transition between Sedentary and Active Lifestyle.	Castellanos N, Diez GG, Antunez-Almagro C, Bressa C, Bailen M, Gonzalez-Soltero R, Perez M, Larrosa M.	Microorganisms	10.3390/microorganisms8050785	2020
Genetics	Neuroblastoma is associated with alterations in gut microbiome composition subsequent to maternal microbial seeding.	Valles-Colomer M, Manghi P, Cumbo F, Masetti G, Armanini F, Asnicar F, Blanco-Miguez A, Pinto F, Puncochar M, Garaventa A, Amoroso L, Ponzoni M, Corrias MV, Segata N.	EBioMedicine	10.1016/j.ebiom.2023.104917	2024
Metabolism	Alterations in Metabolome and Microbiome Associated with an Early Stress Stage in Male Wistar Rats: A Multi-Omics Approach.	Hernandez-Baixauli J, Puigbo P, Abasolo N, Palacios-Jordan H, Foguet-Romero E, Sunol D, Galofre M, Caimari A, Baselga-Escudero L, Bas JMD, Mulero M.	Int J Mol Sci	10.3390/ijms222312931	2021
Enzymology	[Bacteria isolated from surgical infections and its susceptibilities to antimicrobial agents - Special references to bacteria isolated between April 2011 and March 2012].	Shinagawa N, Taniguchi M, Hirata K, Furuhata T, Mizuguchi T, Osanai H, Yanai Y, Hata F, Kihara C, Sasaki K, Oono K, Nakamura M, Shibuya H, Hasegawa I, Kimura M, Watabe K, Hoshikawa T, Oshima H, Aikawa N, Sasaki J, Suzuki M, Sekine K, Abe S, Takeyama H, Wakasugi T, Mashita K, Tanaka M, Mizuno A, Ishikawa M, Iwai A, Saito T, Muramoto M, Kubo S, Lee S, Fukuhara K, Kobayashi Y, Yamaue H, Hirono S, Takesue Y, Fujiwara T, Shinoura S, Kimura H, Iwagaki H, Tokunaga N, Sueda T, Hiyama E, Murakami Y, Ohge H, Uemura K, Tsumura H, Kanehiro T, Takeuchi H, Tanakaya K, Iwasaki M.	Jpn J Antibiot		2014
Metabolism	Production of secoisolariciresinol from defatted flaxseed by bacterial biotransformation.	Li MX, Zhu HY, Yang DH, Ma XQ, Wang CZ, Cai SQ, Liu GR, Ku BS, Liu SL.	J Appl Microbiol	10.1111/j.1365-2672.2012.05436.x	2012
	Lactobacillus rhamnosus GG induces cGAS/STING- dependent type I interferon and improves response to immune checkpoint blockade.	Si W, Liang H, Bugno J, Xu Q, Ding X, Yang K, Fu Y, Weichselbaum RR, Zhao X, Wang L.	Gut	10.1136/gutjnl-2020-323426	2022
	Distinct gut flora profile induced by postnatal trans-fat diet in gestationally bisphenol A-exposed rats.	Zulkifli S, Mohd Nor NS, Sheikh Abdul Kadir SH, Mohd Ranai N, Abdul Khalil K.	PLoS One	10.1371/journal.pone.0306741	2024
	Identification of feces by detection of Bacteroides genes.	Nakanishi H, Shojo H, Ohmori T, Hara M, Takada A, Adachi N, Saito K.	Forensic Sci Int Genet	10.1016/j.fsigen.2012.09.006	2013
	Attention Deficit Hyperactivity Disorder (ADHD) and the gut microbiome: An ecological perspective.	Cickovski T, Mathee K, Aguirre G, Tatke G, Hermida A, Narasimhan G, Stollstorff M.	PLoS One	10.1371/journal.pone.0273890	2023
	Two-sample Mendelian randomization analysis investigates causal associations between gut microbiota and attention deficit hyperactivity disorder.	Wang L, Xie Z, Xie Z, Li G, Li G, Liang J.	Front Microbiol	10.3389/fmicb.2023.1144851	2023
	Design of a proteolytic module for improved metabolic modeling of Bacteroides caccae.	Paulay A, Grimaud GM, Caballero R, Laroche B, Leclerc M, Labarthe S, Maguin E.	mSystems	10.1128/msystems.00153-24	2024
	Revolutionizing gastroenterology and hepatology with artificial intelligence: From precision diagnosis to equitable healthcare through interdisciplinary practice.	Chen ZL, Wang C, Wang F.	World J Gastroenterol	10.3748/wjg.v31.i24.108021	2025
Metabolism	Exploring Metabolic and Gut Microbiome Responses to Paraquat Administration in Male Wistar Rats: Implications for Oxidative Stress.	Hernandez-Baixauli J, Chomiciute G, Tracey H, Mora I, Cortes-Espinar AJ, Avila-Roman J, Abasolo N, Palacios-Jordan H, Foguet-Romero E, Sunol D, Galofre M, Alcaide-Hidalgo JM, Baselga-Escudero L, Del Bas JM, Mulero M.	Antioxidants (Basel)	10.3390/antiox13010067	2024
	Bacteriophages playing nice: Lysogenic bacteriophage replication stable in the human gut microbiota.	Sutcliffe SG, Reyes A, Maurice CF.	iScience	10.1016/j.isci.2023.106007	2023
	Influence of structural features and feruloylation on fermentability and ability to modulate gut microbiota of arabinoxylan in in vitro fermentation.	Li Z, Zhang H, He L, Hou Y, Che Y, Liu T, Xiong S, Zhang X, Luo S, Liu C, Chen T.	Front Microbiol	10.3389/fmicb.2022.1113601	2022
	[Clinical analysis of 11 cases of otogenic intracranial complications treated by multidisciplinary collaboration].	Song Z, Liu W, Wang N, Fu Y, Li Z, Wang C, Sun Y.	Lin Chuang Er Bi Yan Hou Tou Jing Wai Ke Za Zhi	10.13201/j.issn.2096-7993.2023.10.011	2023
	Enhancing therapeutic effects of murine cancer vaccine by reshaping gut microbiota with Lactobacillus rhamnosus GG and jujube powder.	Jing N, Wang L, Zhuang H, Jiang G, Liu Z.	Front Immunol	10.3389/fimmu.2023.1195075	2023
	Marine Chitooligosaccharide Alters Intestinal Flora Structure and Regulates Hepatic Inflammatory Response to Influence Nonalcoholic Fatty Liver Disease.	Feng J, Liu Y, Chen J, Bai Y, He J, Cao H, Che Q, Guo J, Su Z.	Mar Drugs	10.3390/md20060383	2022
	Pea hull fiber supplementation does not modulate uremic metabolites in adults receiving hemodialysis: a randomized, double-blind, controlled trial.	Fatani AMN, Suh JH, Auger J, Alabasi KM, Wang Y, Segal MS, Dahl WJ.	Front Nutr	10.3389/fnut.2023.1179295	2023
Pathogenicity	Supplementation with Lactobacillus helveticus NS8 alleviated behavioral, neural, endocrine, and microbiota abnormalities in an endogenous rat model of depression.	Alatan H, Liang S, Shimodaira Y, Wu X, Hu X, Wang T, Luo J, Iijima K, Jin F.	Front Immunol	10.3389/fimmu.2024.1407620	2024
	Bridging gut microbiota composition with extended-spectrum beta-lactamase Enterobacteriales faecal carriage in critically ill patients (microbe cohort study).	Prevel R, Enaud R, Orieux A, Camino A, Sioniac P, M'Zali F, Dubois V, Berger P, Boyer A, Delhaes L, Gruson D.	Ann Intensive Care	10.1186/s13613-023-01121-0	2023
	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
	Microbiome modulation in inflammatory diseases: Progress to microbiome genetic engineering.	Mousavinasab F, Karimi R, Taheri S, Ahmadvand F, Sanaaee S, Najafi S, Halvaii MS, Haghgoo A, Zamany M, Majidpoor J, Khosravifar M, Baniasadi M, Talebi M, Movafagh A, Aghaei-Zarch SM, Khorram N, Farnia P, Kalhor K.	Cancer Cell Int	10.1186/s12935-023-03095-2	2023
Phylogeny	Effect of Bifidobacterium bifidum on Clinical Characteristics and Gut Microbiota in Attention-Deficit/Hyperactivity Disorder.	Wang LJ, Yang CY, Kuo HC, Chou WJ, Tsai CS, Lee SY.	J Pers Med	10.3390/jpm12020227	2022
	Short term supplementation with cranberry extract modulates gut microbiota in human and displays a bifidogenic effect.	Lessard-Lord J, Roussel C, Lupien-Meilleur J, Genereux P, Richard V, Guay V, Roy D, Desjardins Y.	NPJ Biofilms Microbiomes	10.1038/s41522-024-00493-w	2024
	Probable Clostridium septicum pneumocephalus in a user of natural remedies with newly diagnosed diabetes mellitus type 1.	Mirzai S, Rifai AO, Webb S, Rifai K, Reiner A.	IDCases	10.1016/j.idcr.2019.e00581	2019
	Health-Related Composition and Bioactivity of an Agave Sap/Prickly Pear Juice Beverage.	Duque-Buitrago LF, Solorzano-Lugo IE, Gonzalez-Vazquez M, Jimenez-Martinez C, Hernandez-Aguirre MA, Osorio-Diaz P, Calderon-Dominguez G, Loera-Castaneda V, Mora-Escobedo R.	Molecules	10.3390/molecules29122742	2024
Phylogeny	Gut Microbiota Signature of Obese Adults Across Different Classifications.	Hu J, Guo P, Mao R, Ren Z, Wen J, Yang Q, Yan T, Yu J, Zhang T, Liu Y.	Diabetes Metab Syndr Obes	10.2147/dmso.s387523	2022
Pathogenicity	Two intestinal microbiota-derived metabolites, deoxycholic acid and butyrate, synergize to enhance host defense peptide synthesis and alleviate necrotic enteritis.	Kim DM, Liu J, Whitmore MA, Tobin I, Zhao Z, Zhang G.	J Anim Sci Biotechnol	10.1186/s40104-024-00995-9	2024
	The Effect of Human Milk Oligosaccharides and Bifidobacterium longum subspecies infantis Bi-26 on Simulated Infant Gut Microbiome and Metabolites.	Salli K, Hirvonen J, Anglenius H, Hibberd AA, Ahonen I, Saarinen MT, Maukonen J, Ouwehand AC.	Microorganisms	10.3390/microorganisms11061553	2023
	Gut microbe metabolism of small molecules supports human development across the early stages of life.	Tarracchini C, Fontana F, Mancabelli L, Lugli GA, Alessandri G, Turroni F, Ventura M, Milani C.	Front Microbiol	10.3389/fmicb.2022.1006721	2022
Pathogenicity	Detection of Dysbiosis and Increased Intestinal Permeability in Brazilian Patients with Relapsing-Remitting Multiple Sclerosis.	Pellizoni FP, Leite AZ, Rodrigues NC, Ubaiz MJ, Gonzaga MI, Takaoka NNC, Mariano VS, Omori WP, Pinheiro DG, Matheucci Junior E, Gomes E, de Oliveira GLV.	Int J Environ Res Public Health	10.3390/ijerph18094621	2021
Phylogeny	Nutritional Effects of the Enteral Nutritional Formula on Regulation of Gut Microbiota and Metabolic Level in Type 2 Diabetes Mellitus Mice.	Wei T, Jia Y, Xue W, Ma M, Wu W.	Diabetes Metab Syndr Obes	10.2147/dmso.s301454	2021
	Pharmacomicrobiomics: Immunosuppressive Drugs and Microbiome Interactions in Transplantation.	Mohamed ME, Saqr A, Staley C, Onyeaghala G, Teigen L, Dorr CR, Remmel RP, Guan W, Oetting WS, Matas AJ, Israni AK, Jacobson PA.	Transplantation	10.1097/tp.0000000000004926	2024
	Delivery mode and maternal gestational diabetes are important factors in shaping the neonatal initial gut microbiota.	Shi X, Liu Y, Ma T, Jin H, Zhao F, Sun Z.	Front Cell Infect Microbiol	10.3389/fcimb.2024.1397675	2024
	Impact of cryoprotective agents on human gut microbes and in vitro stabilized artificial gut microbiota communities.	Alessandri G, Rizzo SM, Mancabelli L, Fontana F, Longhi G, Turroni F, van Sinderen D, Ventura M.	Microb Biotechnol	10.1111/1751-7915.14509	2024
Phylogeny	Subspecies phylogeny in the human gut revealed by co-evolutionary constraints across the bacterial kingdom.	Doran BA, Chen RY, Giba H, Behera V, Barat B, Sundararajan A, Lin H, Sidebottom A, Pamer EG, Raman AS.	Cell Syst	10.1016/j.cels.2024.12.008	2025
Pathogenicity	Antioxidant Vitamins and Prebiotic FOS and XOS Differentially Shift Microbiota Composition and Function and Improve Intestinal Epithelial Barrier In Vitro.	Pham VT, Calatayud M, Rotsaert C, Seifert N, Richard N, Van den Abbeele P, Marzorati M, Steinert RE.	Nutrients	10.3390/nu13041125	2021
	Non-absorbable antibiotic treatment inhibits colorectal cancer liver metastasis by modulating deoxycholic acid metabolism by intestinal microbes.	Deng J, Yuan W, Tan Q, Wei X, Ma J.	J Cancer	10.7150/jca.63490	2022
Pathogenicity	Gut Dysbiosis and Neurobehavioral Alterations in Rats Exposed to Silver Nanoparticles.	Javurek AB, Suresh D, Spollen WG, Hart ML, Hansen SA, Ellersieck MR, Bivens NJ, Givan SA, Upendran A, Kannan R, Rosenfeld CS.	Sci Rep	10.1038/s41598-017-02880-0	2017
Phylogeny	Gut-microbiome-based predictive model for ST-elevation myocardial infarction in young male patients.	Liu M, Wang M, Peng T, Ma W, Wang Q, Niu X, Hu L, Qi B, Guo D, Ren G, Geng J, Wang D, Song L, Hu J, Li Y.	Front Microbiol	10.3389/fmicb.2022.1031878	2022
	The science behind TCM and Gut microbiota interaction-their combinatorial approach holds promising therapeutic applications.	Xia W, Liu B, Tang S, Yasir M, Khan I.	Front Cell Infect Microbiol	10.3389/fcimb.2022.875513	2022
	Gut Microbiome-Based Analysis of Lipid A Biosynthesis in Individuals with Autism Spectrum Disorder: An In Silico Evaluation.	Maigoro AY, Lee S.	Nutrients	10.3390/nu13020688	2021
	The prebiotic and anti-fatigue effects of hyaluronan.	Huang G, Su L, Zhang N, Han R, Leong WK, Li X, Ren X, Hsiao WLW.	Front Nutr	10.3389/fnut.2022.977556	2022
	The global RNA-binding protein RbpB is a regulator of polysaccharide utilization in Bacteroides thetaiotaomicron.	Ruttiger AS, Ryan D, Spiga L, Lamm-Schmidt V, Prezza G, Reichardt S, Langford M, Barquist L, Faber F, Zhu W, Westermann AJ.	Nat Commun	10.1038/s41467-024-55383-8	2025
	Faecal microbiome-based machine learning for multi-class disease diagnosis.	Su Q, Liu Q, Lau RI, Zhang J, Xu Z, Yeoh YK, Leung TWH, Tang W, Zhang L, Liang JQY, Yau YK, Zheng J, Liu C, Zhang M, Cheung CP, Ching JYL, Tun HM, Yu J, Chan FKL, Ng SC.	Nat Commun	10.1038/s41467-022-34405-3	2022
	The gut microbial diversity of colon cancer patients and the clinical significance.	He T, Cheng X, Xing C.	Bioengineered	10.1080/21655979.2021.1972077	2021
	Antimicrobial Resistance Profile and Nim Gene Detection among Bacteroides fragilis Group Isolates in a University Hospital in South India.	Vishwanath S, Shenoy PA, Chawla K.	J Glob Infect Dis	10.4103/jgid.jgid_116_18	2019
Genetics	Weight Loss Promotion in Individuals with Obesity through Gut Microbiota Alterations with a Multiphase Modified Ketogenic Diet.	Wang H, Lv X, Zhao S, Yuan W, Zhou Q, Sadiq FA, Zhao J, Lu W, Wu W.	Nutrients	10.3390/nu15194163	2023
	Investigating the cecal microbiota of broilers raised in extensive and intensive production systems.	Marcolla CS, Ju T, Lantz HL, Willing BP.	Microbiol Spectr	10.1128/spectrum.02352-23	2023
	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
	Bacterial and Fungal Adaptations in Cecum and Distal Colon of Piglets Fed With Dairy-Based Milk Formula in Comparison With Human Milk.	Elolimy A, Rosa F, Tripp P, Zeineldin M, Bowlin AK, Randolph C, Robeson MS, Yeruva L.	Front Microbiol	10.3389/fmicb.2022.801854	2022
Genetics	Comparison of gene clustering criteria reveals intrinsic uncertainty in pangenome analyses.	Manzano-Morales S, Liu Y, Gonzalez-Bodi S, Huerta-Cepas J, Iranzo J.	Genome Biol	10.1186/s13059-023-03089-3	2023
	Neonatal Diet and Gut Microbiome Development After C-Section During the First Three Months After Birth: A Systematic Review.	Pivrncova E, Kotaskova I, Thon V.	Front Nutr	10.3389/fnut.2022.941549	2022
Phylogeny	Comparison between 16S rRNA and shotgun sequencing in colorectal cancer, advanced colorectal lesions, and healthy human gut microbiota.	Bars-Cortina D, Ramon E, Rius-Sansalvador B, Guino E, Garcia-Serrano A, Mach N, Khannous-Lleiffe O, Saus E, Gabaldon T, Ibanez-Sanz G, Rodriguez-Alonso L, Mata A, Garcia-Rodriguez A, Obon-Santacana M, Moreno V.	BMC Genomics	10.1186/s12864-024-10621-7	2024
Metabolism	Stratification of Volunteers According to Flavanone Metabolite Excretion and Phase II Metabolism Profile after Single Doses of 'Pera' Orange and 'Moro' Blood Orange Juices.	Nishioka A, Tobaruela EC, Fraga LN, Tomas-Barberan FA, Lajolo FM, Hassimotto NMA.	Nutrients	10.3390/nu13020473	2021
Pathogenicity	Protein Intake, Metabolic Status and the Gut Microbiota in Different Ethnicities: Results from Two Independent Cohorts.	Bel Lassen P, Attaye I, Adriouch S, Nicolaou M, Aron-Wisnewsky J, Nielsen T, Chakaroun R, Le Chatelier E, Forslund S, Belda E, Bork P, Backhed F, Stumvoll M, Pedersen O, Herrema H, Groen AK, Pinto-Sietsma SJ, Zwinderman AH, Nieuwdorp M, Clement K, On Behalf Of Metacardis Consortium.	Nutrients	10.3390/nu13093159	2021
	Preliminary evidence for an influence of exposure to polycyclic aromatic hydrocarbons on the composition of the gut microbiota and neurodevelopment in three-year-old healthy children.	Zhang W, Sun Z, Zhang Q, Sun Z, Su Y, Song J, Wang B, Gao R.	BMC Pediatr	10.1186/s12887-021-02539-w	2021
	Sharing of gut microbial strains between selected individual sets of twins cohabitating for decades.	Koo H, Hakim JA, Crossman DK, Lefkowitz EJ, Morrow CD.	PLoS One	10.1371/journal.pone.0226111	2019
Pathogenicity	Influence of red wine polyphenols and ethanol on the gut microbiota ecology and biochemical biomarkers.	Queipo-Ortuno MI, Boto-Ordonez M, Murri M, Gomez-Zumaquero JM, Clemente-Postigo M, Estruch R, Cardona Diaz F, Andres-Lacueva C, Tinahones FJ.	Am J Clin Nutr	10.3945/ajcn.111.027847	2012
	Microbial Composition and Co-occurrence Patterns in the Gut Microbial Community of Normal and Obese Mice in Response to Astaxanthin.	Gao Y, Liu F, Li RW, Li C, Xue C, Tang Q.	Front Microbiol	10.3389/fmicb.2021.671271	2021
	Inulin diet uncovers complex diet-microbiota-immune cell interactions remodeling the gut epithelium.	Correa RO, Castro PR, Fachi JL, Nirello VD, El-Sahhar S, Imada S, Pereira GV, Pral LP, Araujo NVP, Fernandes MF, Matheus VA, de Souza Felipe J, Dos Santos Pereira Gomes AB, de Oliveira S, de Rezende Rodovalho V, de Oliveira SRM, de Assis HC, Oliveira SC, Dos Santos Martins F, Martens E, Colonna M, Varga-Weisz P, Vinolo MAR.	Microbiome	10.1186/s40168-023-01520-2	2023
	Short- and Branched-Chain Fatty Acids as Fecal Markers for Microbiota Activity in Vegans and Omnivores.	Trefflich I, Dietrich S, Braune A, Abraham K, Weikert C.	Nutrients	10.3390/nu13061808	2021
Genetics	An extended catalog of integrated prophages in the infant and adult fecal microbiome shows high prevalence of lysogeny.	Dikareva E, Matharu D, Lahtinen E, Kolho KL, De Vos WM, Salonen A, Ponsero AJ.	Front Microbiol	10.3389/fmicb.2023.1254535	2023
	Symbiotic biofilms formed by Clostridioides difficile and bacteroides thetaiotaomicron in the presence of vancomycin.	Yang J, Rui W, Zhong S, Li X, Liu W, Meng L, Li Y, Huang H.	Gut Microbes	10.1080/19490976.2024.2390133	2024
	Commensal Intestinal Protozoa-Underestimated Members of the Gut Microbial Community.	Dubik M, Pilecki B, Moeller JB.	Biology (Basel)	10.3390/biology11121742	2022
	Diet-microbiota associations in gastrointestinal research: a systematic review.	Duncanson K, Williams G, Hoedt EC, Collins CE, Keely S, Talley NJ.	Gut Microbes	10.1080/19490976.2024.2350785	2024
	Hypervirulent Klebsiella pneumoniae employs genomic island encoded toxins against bacterial competitors in the gut.	Tan YH, Arros P, Berrios-Pasten C, Wijaya I, Chu WHW, Chen Y, Cheam G, Mohamed Naim AN, Marcoleta AE, Ravikrishnan A, Nagarajan N, Lagos R, Gan YH.	ISME J	10.1093/ismejo/wrae054	2024
	At-hatch administration of probiotic to chickens can introduce beneficial changes in gut microbiota.	Baldwin S, Hughes RJ, Hao Van TT, Moore RJ, Stanley D.	PLoS One	10.1371/journal.pone.0194825	2018
	Metabolic disorder and intestinal microflora dysbiosis in chronic inflammatory demyelinating polyradiculoneuropathy.	Fu J, Shan J, Cui Y, Yan C, Wang Q, Han J, Cao G.	Cell Biosci	10.1186/s13578-023-00956-1	2023
	The gut microbiota contributes to the pathogenesis of anorexia nervosa in humans and mice.	Fan Y, Stoving RK, Berreira Ibraim S, Hyotylainen T, Thirion F, Arora T, Lyu L, Stankevic E, Hansen TH, Dechelotte P, Sinioja T, Ragnarsdottir O, Pons N, Galleron N, Quinquis B, Levenez F, Roume H, Falony G, Vieira-Silva S, Raes J, Clausen L, Telleus GK, Backhed F, Oresic M, Ehrlich SD, Pedersen O.	Nat Microbiol	10.1038/s41564-023-01355-5	2023
	Identification and structural basis of an enzyme that degrades oligosaccharides in caramel.	Kashima T, Ishiwata A, Fujita K, Fushinobu S.	Biophys Physicobiol	10.2142/biophysico.bppb-v20.0017	2023
	Agarolytic Pathway in the Newly Isolated Aquimarina sp. Bacterial Strain ERC-38 and Characterization of a Putative beta-agarase.	Kang JY, Song HY, Kim JM.	Mar Biotechnol (NY)	10.1007/s10126-023-10206-7	2023
	HMOs Exert Marked Bifidogenic Effects on Children's Gut Microbiota Ex Vivo, Due to Age-Related Bifidobacterium Species Composition.	Bajic D, Wiens F, Wintergerst E, Deyaert S, Baudot A, Van den Abbeele P.	Nutrients	10.3390/nu15071701	2023
	Helicobacter pylori infection altered gastric microbiota in patients with chronic gastritis.	Hua Z, Xu L, Zhu J, Xiao L, Lu B, Wu J, Wu Z, Zhou Q, Zhang J.	Front Cell Infect Microbiol	10.3389/fcimb.2023.1221433	2023
	Lactobacillus sp. for the Attenuation of Metabolic Dysfunction-Associated Steatotic Liver Disease in Mice.	Olotu T, Ferrell JM.	Microorganisms	10.3390/microorganisms12122488	2024
Genetics	Characterization and Demonstration of Mock Communities as Control Reagents for Accurate Human Microbiome Community Measurements.	Tourlousse DM, Narita K, Miura T, Ohashi A, Matsuda M, Ohyama Y, Shimamura M, Furukawa M, Kasahara K, Kameyama K, Saito S, Goto M, Shimizu R, Mishima R, Nakayama J, Hosomi K, Kunisawa J, Terauchi J, Sekiguchi Y, Kawasaki H.	Microbiol Spectr	10.1128/spectrum.01915-21	2022
	Gut microbiota contributes to the methionine metabolism in host.	Wu X, Han Z, Liu B, Yu D, Sun J, Ge L, Tang W, Liu S.	Front Microbiol	10.3389/fmicb.2022.1065668	2022
	Evaluation of the contribution of gut microbiome dysbiosis to cardiac surgery-associated acute kidney injury by comparative metagenome analysis.	Li Y, Jiang X, Chen J, Hu Y, Bai Y, Xu W, He L, Wang Y, Chen C, Chen J.	Front Microbiol	10.3389/fmicb.2023.1119959	2023
	Yoyo Dieting, Post-Obesity Weight Loss, and Their Relationship with Gut Health.	Phuong-Nguyen K, McGee SL, Aston-Mourney K, Mcneill BA, Mahmood MQ, Rivera LR.	Nutrients	10.3390/nu16183170	2024
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
	Bioaccessibility of Phenolic Compounds, Resistant Starch, and Dietary Fibers from Australian Green Banana during In Vitro Digestion and Colonic Fermentation.	Bashmil YM, Dunshea FR, Appels R, Suleria HAR.	Molecules	10.3390/molecules29071535	2024
	Exploring the Ecological Effects of Naturally Antibiotic-Insensitive Bifidobacteria in the Recovery of the Resilience of the Gut Microbiota during and after Antibiotic Treatment.	Argentini C, Mancabelli L, Alessandri G, Tarracchini C, Barbetti M, Carnevali L, Longhi G, Viappiani A, Anzalone R, Milani C, Sgoifo A, van Sinderen D, Ventura M, Turroni F.	Appl Environ Microbiol	10.1128/aem.00522-22	2022
	Helicobacter pylori antibiotic eradication coupled with a chemically defined diet in INS-GAS mice triggers dysbiosis and vitamin K deficiency resulting in gastric hemorrhage.	Quinn L, Sheh A, Ellis JL, Smith DE, Booth SL, Fu X, Muthupalani S, Ge Z, Puglisi DA, Wang TC, Gonda TA, Holcombe H, Fox JG.	Gut Microbes	10.1080/19490976.2019.1710092	2020
Genetics	A bacterial sensor taxonomy across earth ecosystems for machine learning applications.	Park H, Joachimiak MP, Jungbluth SP, Yang Z, Riehl WJ, Canon RS, Arkin AP, Dehal PS.	mSystems	10.1128/msystems.00026-23	2024
	A systematic review on the impact of gastrointestinal microbiota composition and function on cognition in healthy infants and children.	McMath AL, Aguilar-Lopez M, Cannavale CN, Khan NA, Donovan SM.	Front Neurosci	10.3389/fnins.2023.1171970	2023
	Microbiota Phenotype Promotes Anastomotic Leakage in a Model of Rats with Ischemic Colon Resection.	Zamorano D, Ivulic D, Viver T, Morales F, Lopez-Kostner F, Vidal RM.	Microorganisms	10.3390/microorganisms11030680	2023
	Lactiplantibacillus plantarum, lactiplantibacillus pentosus and inulin meal inclusion boost the metagenomic function of broiler chickens.	Ferrocino I, Biasato I, Dabbou S, Colombino E, Rantsiou K, Squara S, Gariglio M, Capucchio MT, Gasco L, Cordero CE, Liberto E, Schiavone A, Cocolin L.	Anim Microbiome	10.1186/s42523-023-00257-5	2023
	Effects of anthropogenic habitat disturbance and Giardia duodenalis infection on a sentinel species' gut bacteria.	Kuthyar S, Kowalewski MM, Roellig DM, Mallott EK, Zeng Y, Gillespie TR, Amato KR.	Ecol Evol	10.1002/ece3.6910	2021
	Targeting gut microbiota: new therapeutic opportunities in multiple sclerosis.	Kujawa D, Laczmanski L, Budrewicz S, Pokryszko-Dragan A, Podbielska M.	Gut Microbes	10.1080/19490976.2023.2274126	2023
	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
Pathogenicity	Investigation of the relationship between inflammation and microbiota in the intestinal tissue of female and male rats fed with fructose: Modulatory role of metformin.	Yalcin Bugdayci A, Akarca Dizakar SO, Demirel MA, Omeroglu S, Akar F, Uludag MO.	Daru	10.1007/s40199-024-00521-2	2024
Pathogenicity	Broad host range may be a key to long-term persistence of bacteriophages infecting intestinal Bacteroidaceae species.	Hedzet S, Rupnik M, Accetto T.	Sci Rep	10.1038/s41598-022-25636-x	2022
Genetics	Multiomics Analysis Reveals the Impact of Microbiota on Host Metabolism in Hepatic Steatosis.	Zeybel M, Arif M, Li X, Altay O, Yang H, Shi M, Akyildiz M, Saglam B, Gonenli MG, Yigit B, Ulukan B, Ural D, Shoaie S, Turkez H, Nielsen J, Zhang C, Uhlen M, Boren J, Mardinoglu A.	Adv Sci (Weinh)	10.1002/advs.202104373	2022
	In-Silico Characterization of Estrogen Reactivating beta-Glucuronidase Enzyme in GIT Associated Microbiota of Normal Human and Breast Cancer Patients.	Muccee F, Ghazanfar S, Ajmal W, Al-Zahrani M.	Genes (Basel)	10.3390/genes13091545	2022
Metabolism	Immune System, Microbiota, and Microbial Metabolites: The Unresolved Triad in Colorectal Cancer Microenvironment.	Hanus M, Parada-Venegas D, Landskron G, Wielandt AM, Hurtado C, Alvarez K, Hermoso MA, Lopez-Kostner F, De la Fuente M.	Front Immunol	10.3389/fimmu.2021.612826	2021
Metabolism	Microbial vitamin production mediates dietary effects on diabetic risk.	Wang D, Pham VT, Steinert RE, Zhernakova A, Fu J.	Gut Microbes	10.1080/19490976.2022.2154550	2022
	Celastrol-regulated gut microbiota and bile acid metabolism alleviate hepatocellular carcinoma proliferation by regulating the interaction between FXR and RXRalpha in vivo and in vitro.	Zeng D, Zhang L, Luo Q.	Front Pharmacol	10.3389/fphar.2023.1124240	2023
	Molecular Alteration Analysis of Human Gut Microbial Composition in Graves' disease Patients.	Ishaq HM, Mohammad IS, Shahzad M, Ma C, Raza MA, Wu X, Guo H, Shi P, Xu J.	Int J Biol Sci	10.7150/ijbs.24151	2018
	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
	Stronger gut microbiome modulatory effects by postbiotics than probiotics in a mouse colitis model.	Zhang T, Zhang W, Feng C, Kwok LY, He Q, Sun Z.	NPJ Sci Food	10.1038/s41538-022-00169-9	2022
	Intratumoral microorganisms in tumors of the digestive system.	Xuan M, Gu X, Liu Y, Yang L, Li Y, Huang D, Li J, Xue C.	Cell Commun Signal	10.1186/s12964-023-01425-5	2024
	Immune-Related Colitis Is Associated with Fecal Microbial Dysbiosis and Can Be Mitigated by Fecal Microbiota Transplantation.	Elkrief A, Waters NR, Smith N, Dai A, Slingerland J, Aleynick N, Febles B, Gogia P, Socci ND, Lumish M, Giardina PA, Chaft JE, Eng J, Motzer RJ, Mendelsohn RB, Markey KA, Zhuang M, Li Y, Yang Z, Hollmann TJ, Rudin CM, van den Brink MRM, Shia J, DeWolf S, Schoenfeld AJ, Hellmann MD, Babady NE, Faleck DM, Peled JU.	Cancer Immunol Res	10.1158/2326-6066.cir-23-0498	2024
	Capturing the dynamics of microbial interactions through individual-specific networks.	Yousefi B, Melograna F, Galazzo G, van Best N, Mommers M, Penders J, Schwikowski B, Van Steen K.	Front Microbiol	10.3389/fmicb.2023.1170391	2023
	Restructuring the Gut Microbiota by Intermittent Fasting Lowers Blood Pressure.	Shi H, Zhang B, Abo-Hamzy T, Nelson JW, Ambati CSR, Petrosino JF, Bryan RM, Durgan DJ.	Circ Res	10.1161/circresaha.120.318155	2021
Phylogeny	Timing of complementary feeding is associated with gut microbiota diversity and composition and short chain fatty acid concentrations over the first year of life.	Differding MK, Benjamin-Neelon SE, Hoyo C, Ostbye T, Mueller NT.	BMC Microbiol	10.1186/s12866-020-01723-9	2020
	Gut microbiome of captive wolves is more similar to domestic dogs than wild wolves indicated by metagenomics study.	Chen L, Sun M, Xu D, Gao Z, Shi Y, Wang S, Zhou Y.	Front Microbiol	10.3389/fmicb.2022.1027188	2022
	Uterine Sarcoma Presenting with Sepsis from Clostridium perfringens Endometritis in a Postmenopausal Woman.	Kao MJ, Roy M, Harter J, Spencer RJ.	Case Rep Obstet Gynecol	10.1155/2018/8217296	2018
Genetics	Exclusive enteral nutrition initiates individual protective microbiome changes to induce remission in pediatric Crohn's disease.	Hacker D, Siebert K, Smith BJ, Kohler N, Riva A, Mahapatra A, Heimes H, Nie J, Metwaly A, Holz H, Manz Q, De Zen F, Heetmeyer J, Socas K, Le Thi G, Meng C, Kleigrewe K, Pauling JK, Neuhaus K, List M, Pollard KS, Schwerd T, Haller D.	Cell Host Microbe	10.1016/j.chom.2024.10.001	2024
	1,25(OH)₂D₃ deficiency-induced gut microbial dysbiosis degrades the colonic mucus barrier in Cyp27b1 knockout mouse model.	Zhu W, Yan J, Zhi C, Zhou Q, Yuan X.	Gut Pathog	10.1186/s13099-019-0291-z	2019
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
	The Microbiome Modulates the Immune System to Influence Cancer Therapy.	Roy R, Singh SK.	Cancers (Basel)	10.3390/cancers16040779	2024
Phylogeny	Intestinal Bacteroides species associated with coeliac disease.	Sanchez E, Donat E, Ribes-Koninckx C, Calabuig M, Sanz Y.	J Clin Pathol	10.1136/jcp.2010.076950	2010
	Protective Effect of Vegan Microbiota on Liver Steatosis Is Conveyed by Dietary Fiber: Implications for Fecal Microbiota Transfer Therapy.	Daskova N, Heczkova M, Modos I, Hradecky J, Hudcovic T, Kuzma M, Pelantova H, Buskova I, Sticova E, Funda D, Golias J, Drabonova B, Jarkovska J, Kralova M, Cibulkova I, Gojda J, Cahova M.	Nutrients	10.3390/nu15020454	2023
Metabolism	Insights into the interplay between gut microbiota and lipid metabolism in the obesity management of canines and felines.	Li K, Xiao X, Li Y, Lu S, Zi J, Sun X, Xu J, Liu HY, Li X, Song T, Cai D.	J Anim Sci Biotechnol	10.1186/s40104-024-01073-w	2024
	A bacterial spermidine biosynthetic pathway via carboxyaminopropylagmatine.	Xi H, Nie X, Gao F, Liang X, Li H, Zhou H, Cai Y, Yang C.	Sci Adv	10.1126/sciadv.adj9075	2023
	A pilot study of dietary fibres on pathogen growth in an ex vivo colonic model reveals their potential ability to limit vancomycin-resistant Enterococcus expansion.	Strain R, Tran TTT, Mills S, Stanton C, Ross RP.	Microbiome Res Rep	10.20517/mrr.2022.14	2023
Pathogenicity	Targeted inhibition of Gus-expressing Enterococcus faecalis to promote intestinal stem cell and epithelial renovation contributes to the relief of irinotecan chemotoxicity by dehydrodiisoeugenol.	Gao R, Yue B, Lv C, Geng X, Yu Z, Wang H, Zhang B, Ai F, Wang Z, Liu D, Wang Z, Chen K, Dou W.	Acta Pharm Sin B	10.1016/j.apsb.2024.09.018	2024
	Nutritional composition, heavy metal content and in vitro effect on the human gut microbiota of Talitrus saltator, an underutilized crustacean from the Atlantic coast.	Lopez-Santamarina A, Cardelle-Cobas A, Lamas A, Mondragon-Portocarrero A, Cepeda A, Miranda JM.	Front Nutr	10.3389/fnut.2022.943133	2022
	Multi-angle meta-analysis of the gut microbiome in Autism Spectrum Disorder: a step toward understanding patient subgroups.	West KA, Yin X, Rutherford EM, Wee B, Choi J, Chrisman BS, Dunlap KL, Hannibal RL, Hartono W, Lin M, Raack E, Sabino K, Wu Y, Wall DP, David MM, Dabbagh K, DeSantis TZ, Iwai S.	Sci Rep	10.1038/s41598-022-21327-9	2022
	Investigating Antibody Reactivity to the Intestinal Microbiome in Severe Myalgic Encephalomyelitis/Chronic Fatigue Syndrome (ME/CFS): A Feasibility Study.	Seton KA, Defernez M, Telatin A, Tiwari SK, Savva GM, Hayhoe A, Noble A, de Carvalho-KoK ALS, James SA, Bansal A, Wileman T, Carding SR.	Int J Mol Sci	10.3390/ijms242015316	2023
	Lactulose Suppresses Osteoclastogenesis and Ameliorates Estrogen Deficiency-Induced Bone Loss in Mice.	Chen X, Zhang Z, Hu Y, Cui J, Zhi X, Li X, Jiang H, Wang Y, Gu Z, Qiu Z, Dong X, Li Y, Su J.	Aging Dis	10.14336/ad.2019.0613	2020
	D-methionine alleviates cisplatin-induced mucositis by restoring the gut microbiota structure and improving intestinal inflammation.	Wu CH, Ko JL, Liao JM, Huang SS, Lin MY, Lee LH, Chang LY, Ou CC.	Ther Adv Med Oncol	10.1177/1758835918821021	2019
Metabolism	The 'in vivo lifestyle' of bile acid 7alpha-dehydroxylating bacteria: comparative genomics, metatranscriptomic, and bile acid metabolomics analysis of a defined microbial community in gnotobiotic mice.	Ridlon JM, Devendran S, Alves JM, Doden H, Wolf PG, Pereira GV, Ly L, Volland A, Takei H, Nittono H, Murai T, Kurosawa T, Chlipala GE, Green SJ, Hernandez AG, Fields CJ, Wright CL, Kakiyama G, Cann I, Kashyap P, McCracken V, Gaskins HR	Gut Microbes	10.1080/19490976.2019.1618173	2019
Enzymology	Cloning, expression, and characterization of the beta-glucosidase hydrolyzing secoisolariciresinol diglucoside to secoisolariciresinol from Bacteroides uniformis ZL1.	Tao YL, Yang DH, Zhang YT, Zhang Y, Wang ZQ, Wang YS, Cai SQ, Liu SL	Appl Microbiol Biotechnol	10.1007/s00253-013-5111-7	2013
Phylogeny	Bacteroides rhinocerotis sp. nov., isolated from the fresh feces of rhinoceros in Beijing Zoo.	Li X, Sun P, Gong L, Shi W, Xiang Z, Li M, Su L, Qin C.	Arch Microbiol	10.1007/s00203-023-03513-z	2023
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 humanifaecis sp. nov., isolated from faeces of healthy Korean.	Kim HS, Kim JS, Suh MK, Eom MK, Lee JH, Park SH, Kang SW, Lee DH, Yoon H, Lee JH, Lee JS	Arch Microbiol	10.1007/s00203-022-02967-x	2022
Phylogeny	Bacteroides chinchillae sp. nov. and Bacteroides rodentium sp. nov., isolated from chinchilla (Chinchilla lanigera) faeces.	Kitahara M, Tsuchida S, Kawasumi K, Amao H, Sakamoto M, Benno Y, Ohkuma M	Int J Syst Evol Microbiol	10.1099/ijs.0.024026-0	2010
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
Phylogeny	Bacteroides muris sp. nov. isolated from the cecum of wild-derived house mice.	Fokt H, Unni R, Repnik U, Schmitz RA, Bramkamp M, Baines JF, Unterweger D	Arch Microbiol	10.1007/s00203-022-03148-6	2022

References

#2742	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 6597
#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 )
#32718	; Curators of the CIP;
#44812	Culture Collection University of Gothenburg (CCUG) ; Curators of the CCUG; CCUG 4942
#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;
#67771	Korean Collection for Type Cultures (KCTC) ; Curators of the KCTC;
#68367	Automatically annotated from API 20A .
#68380	Automatically annotated from API rID32A .
#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 .
#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 )

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Bacteroides uniformis (CCUG 4942, JCM 5828, CIP 103695)

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