Bacteroides caccae (DSM 19024, ATCC 43185, CCUG 38735)

Name: Bacteroides caccae (DSM 19024, ATCC 43185, CCUG 38735)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 1617

Type strain

Strain Designation 3452A

Culture col. no. DSM 19024 ATCC 43185 CCUG 38735 CIP 104201 JCM 9498 3 more

NCBI tax ID(s) 411901 47678

Special Collections DSMZ CCUG JCM CIP

History DSMZ <- CIP <- ATCC <- W. E. C. Moore JCM <-- ATCC 43185 <-- L. V. Holdeman VPI 3452A. CIP <- 1994, ATCC <- L.V. Moore, VPI: strain 3452A <- W.E.C. Moore

Links

Bacteroides caccae 3452A 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 41699

ATCC 43185,CIP 104201,JCM 9498,CCUG 38735,NCTC 13051,KCTC 5132,DSM 19024,VTT E-062952

@ref 20215

Last LPSN update 2026-05-29 08:25:18

Domain Bacteria

Phylum Bacteroidota

Class Bacteroidia

Order Bacteroidales

Family Bacteroidaceae

Genus Bacteroides

Species Bacteroides caccae

Full scientific name Bacteroides caccae Johnson et al. 1986

BacDive ID	Other strains from **Bacteroides caccae** (4)	Type strain
142386	B. caccae CCUG 12221
143032	B. caccae CCUG 16431
159505	B. caccae H6_7, DSM 108144
159506	B. caccae H1_3, DSM 108159

Morphology

Cell morphology

@ref	Gram stain	Cell shape	Confidence
68367		rod-shaped		from API 20A
68367	negative			from API 20A
117087	negative	rod-shaped
125439	negative		95.025

Colony morphology

@ref	Incubation period
7844	1-2 days
54426	2 days

Culture and growth conditions

Culture medium

@ref	Name	Medium link	Composition
7844	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
7844	CHOPPED MEAT MEDIUM (DSMZ Medium 78)	Medium recipe at MediaDive	Name: CHOPPED MEAT MEDIUM (DSMZ Medium 78; with strain-specific modifications) 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 Resazurin 0.001 g/l Vitamin K3 0.0005 g/l (optional) Vitamin K1 (optional) NaOH (optional) Distilled water
34561	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)
7844	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
117087	CIP Medium 20	Medium recipe at CIP

Culture temp

@ref	Growth	Type	Temperature (°C)
7844	positive	growth	37
34561	positive	growth	37
54426	positive	growth	37
67770	positive	growth	37

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance
7844	anaerobe
54426	obligate anaerobe
117087	obligate aerobe

Spore formation

@ref	Spore formation	Confidence
68367			from API 20A
125439		99.24

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	62345 ChEBI	L-rhamnose	+	builds acid from	from API 20A
68367	17716 ChEBI	lactose	+	builds acid from	from API 20A
68367	17306 ChEBI	maltose	-	builds acid from	from API 20A
68367	6731 ChEBI	melezitose	-	builds acid from	from API 20A
68380	17632 ChEBI	nitrate	-	reduction	from API rID32A
117087	17632 ChEBI	nitrate	-	reduction
117087	16301 ChEBI	nitrite	-	reduction
68380	16634 ChEBI	raffinose	+	fermentation	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
68367	27082 ChEBI	trehalose	+	builds acid from	from API 20A
68380	27897 ChEBI	tryptophan	-	energy source	from API rID32A
68367	27897 ChEBI	tryptophan	-	energy source	from API 20A
68380	16199 ChEBI	urea	-	hydrolysis	from API rID32A
68367	16199 ChEBI	urea	-	hydrolysis	from API 20A

Metabolite production

@ref	Chebi-ID	Metabolite
68380	35581 ChEBI	indole	from API rID32A
117087	35581 ChEBI	indole
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
68382	acid phosphatase	-	3.1.3.2	from API zym
68380	alanine arylamidase	+	3.4.11.2	from API rID32A
68382	alkaline phosphatase	+	3.1.3.1	from API zym
68380	alkaline phosphatase	+	3.1.3.1	from API rID32A
68382	alpha-chymotrypsin	-	3.4.21.1	from API zym
68382	alpha-fucosidase	-	3.2.1.51	from API zym
68380	alpha-fucosidase	+	3.2.1.51	from API rID32A
68382	alpha-galactosidase	-	3.2.1.22	from API zym
68380	alpha-galactosidase	+	3.2.1.22	from API rID32A
68382	alpha-glucosidase	-	3.2.1.20	from API zym
68382	alpha-mannosidase	-	3.2.1.24	from API zym
68380	arginine dihydrolase	-	3.5.3.6	from API rID32A
68382	beta-galactosidase	+	3.2.1.23	from API zym
68380	beta-galactosidase	+	3.2.1.23	from API rID32A
68380	beta-Galactosidase 6-phosphate	-		from API rID32A
68382	beta-glucosidase	-	3.2.1.21	from API zym
68367	beta-glucosidase	+	3.2.1.21	from API 20A
68382	beta-glucuronidase	-	3.2.1.31	from API zym
117087	catalase	-	1.11.1.6
68367	catalase	-	1.11.1.6	from API 20A
68382	cystine arylamidase	-	3.4.11.3	from API zym
68382	esterase (C 4)	-		from API zym
68382	esterase lipase (C 8)	+		from API zym
68367	gelatinase	-		from API 20A
68380	glutamate decarboxylase	+	4.1.1.15	from API rID32A
68380	L-arginine arylamidase	+		from API rID32A
68382	leucine arylamidase	-	3.4.11.1	from API zym
68380	leucine arylamidase	+	3.4.11.1	from API rID32A
68380	leucyl glycin arylamidase	+	3.4.11.1	from API rID32A
68382	lipase (C 14)	-		from API zym
68382	N-acetyl-beta-glucosaminidase	-	3.2.1.52	from API zym
68382	naphthol-AS-BI-phosphohydrolase	-		from API zym
117087	oxidase	-
68380	proline-arylamidase	-	3.4.11.5	from API rID32A
68380	pyrrolidonyl arylamidase	-	3.4.19.3	from API rID32A
68382	trypsin	-	3.4.21.4	from API zym
68380	tryptophan deaminase	-	4.1.99.1	from API rID32A
117087	urease	-	3.5.1.5
68380	urease	-	3.5.1.5	from API rID32A
68367	urease	-	3.5.1.5	from API 20A
68382	valine arylamidase	-		from API zym

Pathway annotation

Computationally determined by

@ref	pathway	enzyme coverage	annotated reactions
66794	coenzyme A metabolism	100	4 of 4
66794	gluconeogenesis	100	8 of 8
66794	C4 and CAM-carbon fixation	100	8 of 8
66794	L-lactaldehyde degradation	100	3 of 3
66794	ppGpp biosynthesis	100	4 of 4
66794	O-antigen biosynthesis	100	5 of 5
66794	palmitate biosynthesis	100	22 of 22
66794	cis-vaccenate biosynthesis	100	2 of 2
66794	acetate fermentation	100	4 of 4
66794	glycogen metabolism	100	5 of 5
66794	formaldehyde oxidation	100	3 of 3
66794	biotin biosynthesis	100	4 of 4
66794	anapleurotic synthesis of oxalacetate	100	1 of 1
66794	folate polyglutamylation	100	1 of 1
66794	suberin monomers biosynthesis	100	2 of 2
66794	sulfopterin metabolism	100	4 of 4
66794	CDP-diacylglycerol biosynthesis	100	2 of 2
66794	teichoic acid biosynthesis	100	1 of 1
66794	tetrahydrofolate metabolism	92.86	13 of 14
66794	vitamin B6 metabolism	90.91	10 of 11
66794	chorismate metabolism	88.89	8 of 9
66794	lipid A biosynthesis	88.89	8 of 9
66794	aspartate and asparagine metabolism	88.89	8 of 9
66794	propanol degradation	85.71	6 of 7
66794	vitamin B1 metabolism	84.62	11 of 13
66794	pyrimidine metabolism	84.44	38 of 45
66794	pentose phosphate pathway	81.82	9 of 11
66794	metabolism of amino sugars and derivatives	80	4 of 5
66794	peptidoglycan biosynthesis	80	12 of 15
66794	glycine betaine biosynthesis	80	4 of 5
66794	starch degradation	80	8 of 10
66794	lipoate biosynthesis	80	4 of 5
66794	threonine metabolism	80	8 of 10
66794	vitamin K metabolism	80	4 of 5
66794	photosynthesis	78.57	11 of 14
66794	NAD metabolism	77.78	14 of 18
66794	valine metabolism	77.78	7 of 9
66794	d-mannose degradation	77.78	7 of 9
66794	serine metabolism	77.78	7 of 9
66794	phenylalanine metabolism	76.92	10 of 13
66794	alanine metabolism	75.86	22 of 29
66794	purine metabolism	75.53	71 of 94
66794	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	75	6 of 8
66794	glycogen biosynthesis	75	3 of 4
66794	CMP-KDO biosynthesis	75	3 of 4
66794	glutamate and glutamine metabolism	75	21 of 28
66794	isoleucine metabolism	75	6 of 8
66794	flavin biosynthesis	73.33	11 of 15
66794	degradation of hexoses	72.22	13 of 18
66794	cardiolipin biosynthesis	71.43	5 of 7
66794	citric acid cycle	71.43	10 of 14
66794	propionate fermentation	70	7 of 10
66794	myo-inositol biosynthesis	70	7 of 10
66794	Entner Doudoroff pathway	70	7 of 10
66794	acetoin degradation	66.67	2 of 3
66794	octane oxidation	66.67	2 of 3
66794	UDP-GlcNAc biosynthesis	66.67	2 of 3
66794	CO2 fixation in Crenarchaeota	66.67	6 of 9
66794	glycolysis	64.71	11 of 17
66794	proline metabolism	63.64	7 of 11
66794	d-xylose degradation	63.64	7 of 11
66794	degradation of sugar alcohols	62.5	10 of 16
66794	degradation of pentoses	60.71	17 of 28
66794	hydrogen production	60	3 of 5
66794	cellulose degradation	60	3 of 5
66794	non-pathway related	57.89	22 of 38
66794	isoprenoid biosynthesis	57.69	15 of 26
66794	ubiquinone biosynthesis	57.14	4 of 7
66794	lysine metabolism	54.76	23 of 42
66794	metabolism of disaccharids	54.55	6 of 11
66794	methionine metabolism	53.85	14 of 26
66794	leucine metabolism	53.85	7 of 13
66794	histidine metabolism	51.72	15 of 29
66794	lipid metabolism	51.61	16 of 31
66794	ketogluconate metabolism	50	4 of 8
66794	dTDPLrhamnose biosynthesis	50	4 of 8
66794	ethanol fermentation	50	1 of 2
66794	pantothenate biosynthesis	50	3 of 6
66794	adipate degradation	50	1 of 2
66794	phenylmercury acetate degradation	50	1 of 2
66794	butanoate fermentation	50	2 of 4
66794	degradation of sugar acids	48	12 of 25
66794	tryptophan metabolism	47.37	18 of 38
66794	oxidative phosphorylation	46.15	42 of 91
66794	arginine metabolism	45.83	11 of 24
66794	cysteine metabolism	44.44	8 of 18
66794	polyamine pathway	43.48	10 of 23
66794	reductive acetyl coenzyme A pathway	42.86	3 of 7
66794	degradation of aromatic, nitrogen containing compounds	41.67	5 of 12
66794	bacilysin biosynthesis	40	2 of 5
66794	methylglyoxal degradation	40	2 of 5
66794	glycine metabolism	40	4 of 10
66794	factor 420 biosynthesis	40	2 of 5
66794	arachidonate biosynthesis	40	2 of 5
66794	coenzyme M biosynthesis	40	4 of 10
66794	sulfate reduction	38.46	5 of 13
66794	phenylpropanoid biosynthesis	38.46	5 of 13
66794	ascorbate metabolism	36.36	8 of 22
66794	tyrosine metabolism	35.71	5 of 14
66794	selenocysteine biosynthesis	33.33	2 of 6
66794	nitrate assimilation	33.33	3 of 9
66794	acetyl CoA biosynthesis	33.33	1 of 3
66794	cyanate degradation	33.33	1 of 3
66794	molybdenum cofactor biosynthesis	33.33	3 of 9
66794	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
66794	IAA biosynthesis	33.33	1 of 3
66794	glycolate and glyoxylate degradation	33.33	2 of 6
66794	androgen and estrogen metabolism	31.25	5 of 16
66794	urea cycle	30.77	4 of 13
66794	glutathione metabolism	28.57	4 of 14
66794	dolichyl-diphosphooligosaccharide biosynthesis	27.27	3 of 11
66794	vitamin E metabolism	25	1 of 4
66794	alginate biosynthesis	25	1 of 4
66794	lactate fermentation	25	1 of 4
66794	cyclohexanol degradation	25	1 of 4
66794	toluene degradation	25	1 of 4
66794	phosphatidylethanolamine bioynthesis	23.08	3 of 13
66794	arachidonic acid metabolism	22.22	4 of 18

API zym

@ref	Control	Alkaline phosphatase	Esterase (C 4)	2-naphtyl caprylateEsterase Lipase (C 8)	Lipase (C 14)	L-leucyl-2-naphthylamideLeucine arylamidase	L-valyl-2-naphthylamideValine arylamidase	L-cystyl-2-naphthylamideCystine arylamidase	Trypsin	alpha- Chymotrypsin	Acid phosphatase	Naphthol-AS-BI-phosphateNaphthol-AS-BI-phosphohydrolase	alpha- Galactosidase	beta- Galactosidase	beta- Glucuronidase	alpha- Glucosidase	beta- Glucosidase	N-acetyl-beta- glucosaminidase	alpha- Mannosidase	alpha- Fucosidase
117087	-	+	-	+	-	-	-	-	-	-	-	-	-	+	-	-	-	-	-	-

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
7844	-	-	+	-	+	+	-	-	+	+	-	+	-	-	+	-	+	-	+	+	-	-	-	-
7844	not determinedn.d.	-	+	-	+	+	-	-	+	+	-	+	-	-	+	-	+	-	+	+	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
7844	-	-	+	+	-	+	+	+	+/-	+	+	+	+	+	-	-	+	+	-	+	+	+	-	+	+	+	+	+	+
7844	-	-	+	+	-	+	+	+	-	+	+	+	+	+	-	-	+	+	-	+	+	+	-	+	+	+/-	+	+	+
7844	-	-	+	+	-	+	+	+	-	+	+	+	+	+	-	-	+	+	-	+	+/-	+	-	+/-	+	-	+/-	+	-
7844	-	-	+	+	-	+	+	+	+	+	+	+	+	+	-	-	+	+	-	+	-	+	-	-	+	-	+	+	-
7844	-	-	+	+	-	+/-	+/-	+/-	-	+/-	+	+	+	+	-	-	+	+	-	+	+/-	+	-	+/-	+	-	+/-	+/-	-

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	Geographic location	Country	Country ISO 3 Code	Continent	Isolation date
7844	human faeces	Homo sapiens	Texas	USA	USA	North America
54426	Human feces	Homo sapiens	Texas	USA	USA	North America
67770	Human feces	Homo sapiens
117087	Human, Feces	Homo sapiens	Texas	United States of America	USA	North America	1968

Taxonmaps

69479

Global distribution of 16S sequence AB510697 (>99% sequence identity) for Bacteroides from Microbeatlas

Aquatic Samples	5702
Soil Samples	1566
Animal Samples	215810
Plant Samples	469
Total Samples	223547

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
7844	2	Risk group (German classification) According to TRBA 466
117087	2	Risk group (French classification) According to TRBA 466

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
66792	ASM222261v2 assembly for Bacteroides caccae ATCC 43185	complete	GCA_002222615	47678.18	2806310690	47678	98.11
124043	ASM1672630v1 assembly for Bacteroides caccae FDAARGOS_1097	complete	GCA_016726305	47678.1024		47678	97.49
66792	ASM2514631v1 assembly for Bacteroides caccae ATCC 43185	complete	GCA_025146315	47678.1222	8119486686	47678	97.31
67770	ASM295971v1 assembly for Bacteroides caccae ATCC 43185	contig	GCA_002959715	47678.99	2806310790	47678	77.71
67770	ASM16901v1 assembly for Bacteroides caccae ATCC 43185	contig	GCA_000169015	411901.7	640963023	411901	73.78
66792	ASM2853953v1 assembly for Bacteroides caccae DSM 19024	contig	GCA_028539535	47678.1314	8118303482	47678	67.55

16S sequences

@ref	Description	Accession	Length	NCBI tax ID
20218	Bacteroides caccae 16S ribosomal RNA gene, partial sequence; 16S-23S ribosomal RNA intergenic spacer region, complete sequence; and 23S ribosomal RNA gene, partial sequence	AY153428	676	47678
20218	Bacteroides caccae strain JCM9498 16S ribosomal RNA gene, partial sequence	EU136686	1972	47678
7844	Bacteroides caccae gene for 16S ribosomal RNA, partial sequence, strain: JCM 9498	AB510697	1478	47678
124043	Bacteroides caccae strain ATCC 43185 16S ribosomal RNA gene, partial sequence.	MN326670	1336	47678

GC content

@ref	GC-content (mol%)	Method
7844	40
7844	41.9	sequence analysis
67770	40	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: ASM222261v2 assembly for Bacteroides caccae ATCC 43185
BV-BRC: 47678.18

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	oxygen_tolerance	BacteriaNetⓘ	obligate anaerobe	66.13	no
125439	gram_stain	BacteriaNetⓘ	negative	95.03	no
125439	motility	BacteriaNetⓘ	no	68.86	no
125439	spore_formation	BacteriaNetⓘ	no	99.24	no

Literature

Topic	Title	Authors	Journal	DOI	Year
	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
	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
	Environmental factors drive bacterial degradation of gastrointestinal mucus.	Arias SL, van Wijngaarden EW, Balint D, Jones J, Crawford CC, Shukla PJ, Silberstein M, Brito IL.	NPJ Biofilms Microbiomes	10.1038/s41522-025-00741-7	2025
	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
	Distinct in vitro utilization and degradation of porcine gastric mucin glycans by human intestinal bacteria.	de Ram C, Berkhout MD, O Pandeirada C, Vincken JP, Hooiveld GJEJ, Belzer C, Schols HA.	FEMS Microbiol Ecol	10.1093/femsec/fiaf066	2025
	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
	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
	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
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
	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	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	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
	Development of an in vitro Model of Human Gut Microbiota for Screening the Reciprocal Interactions With Antibiotics, Drugs, and Xenobiotics.	El Houari A, Ecale F, Mercier A, Crapart S, Laparre J, Soulard B, Ramnath M, Berjeaud JM, Rodier MH, Crepin A.	Front Microbiol	10.3389/fmicb.2022.828359	2022
	Preliminary safety evaluation of a new Bacteroides xylanisolvens isolate.	Ulsemer P, Toutounian K, Schmidt J, Karsten U, Goletz S.	Appl Environ Microbiol	10.1128/aem.06641-11	2012
Pathogenicity	The Use of Defined Microbial Communities To Model Host-Microbe Interactions in the Human Gut.	Elzinga J, van der Oost J, de Vos WM, Smidt H.	Microbiol Mol Biol Rev	10.1128/mmbr.00054-18	2019
Metabolism	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
	A Dietary Fiber-Deprived Gut Microbiota Degrades the Colonic Mucus Barrier and Enhances Pathogen Susceptibility.	Desai MS, Seekatz AM, Koropatkin NM, Kamada N, Hickey CA, Wolter M, Pudlo NA, Kitamoto S, Terrapon N, Muller A, Young VB, Henrissat B, Wilmes P, Stappenbeck TS, Nunez G, Martens EC.	Cell	10.1016/j.cell.2016.10.043	2016
	Analysis of chondroitin degradation by components of a Bacteroides caccae polysaccharide utilization locus.	Alvarez B, Canil OF, Low KE, Hettle AG, Abbott DW, Boraston AB.	J Biol Chem	10.1016/j.jbc.2025.110354	2025
	A Globally Distributed Bacteroides caccae Strain Is the Most Prevalent Mother-Child Shared Bacteroidaceae Strain in a Large Scandinavian Cohort.	Nilsen M, Rehbinder EM, Lodrup Carlsen KC, Haugen G, Hedlin G, Jonassen CM, Killingstad ME, Nordlund B, Ormaasen I, Skjerven HO, Snipen L, Staff AC, Soderhall C, Sorensen R, Vettukattil R, Wilborn LM, Rudi K.	Appl Environ Microbiol	10.1128/aem.00789-23	2023
	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
	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
	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
	Comprehensive profiling of genomic invertons in defined gut microbial community reveals associations with intestinal colonization and surface adhesion.	Jin X, Cheng AG, Chanin RB, Yu FB, Dimas A, Jasper M, Weakley A, Yan J, Bhatt AS, Pollard KS.	Microbiome	10.1186/s40168-025-02052-7	2025
	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
	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
	Hadza Prevotella require diet-derived microbiota-accessible carbohydrates to persist in mice.	Gellman RH, Olm MR, Terrapon N, Enam F, Higginbottom SK, Sonnenburg JL, Sonnenburg ED.	Cell Rep	10.1016/j.celrep.2023.113233	2023
	Cross-feeding of bifidobacteria promotes intestinal homeostasis: a lifelong perspective on the host health.	Xiao M, Zhang C, Duan H, Narbad A, Zhao J, Chen W, Zhai Q, Yu L, Tian F.	NPJ Biofilms Microbiomes	10.1038/s41522-024-00524-6	2024
	Culturing of a complex gut microbial community in mucin-hydrogel carriers reveals strain- and gene-associated spatial organization.	Jin X, Yu FB, Yan J, Weakley AM, Dubinkina V, Meng X, Pollard KS.	Nat Commun	10.1038/s41467-023-39121-0	2023
	A Bacteroides thetaiotaomicron genetic locus encodes activities consistent with mucin O-glycoprotein processing and N-acetylgalactosamine metabolism.	Ndeh DA, Nakjang S, Kwiatkowski KJ, Sawyers C, Koropatkin NM, Hirt RP, Bolam DN.	Nat Commun	10.1038/s41467-025-58660-2	2025
	GH20 and GH84 beta-N-acetylglucosaminidases with different linkage specificities underpin mucin O-glycan breakdown capability of Bifidobacterium bifidum.	Takada H, Katoh T, Sakanaka M, Odamaki T, Katayama T.	J Biol Chem	10.1016/j.jbc.2023.104781	2023
Pathogenicity	Common Oral Medications Lead to Prophage Induction in Bacterial Isolates from the Human Gut.	Sutcliffe SG, Shamash M, Hynes AP, Maurice CF.	Viruses	10.3390/v13030455	2021
Phylogeny	Multiple classes and isoforms of the RNA polymerase recycling motor protein HelD.	Larsen JS, Miller M, Oakley AJ, Dixon NE, Lewis PJ.	Microbiologyopen	10.1002/mbo3.1251	2021
Genetics	O-Mucin-degrading carbohydrate-active enzymes and their possible implication in inflammatory bowel diseases.	Labourel A, Parrou JL, Deraison C, Mercier-Bonin M, Lajus S, Potocki-Veronese G.	Essays Biochem	10.1042/ebc20220153	2023
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
	Actively replicating gut bacteria identified by 5-ethynyl-2'-deoxyuridine (EdU) click chemistry and cell sorting.	Beauchemin ET, Hunter C, Maurice CF.	Gut Microbes	10.1080/19490976.2023.2180317	2023
	Proteomic insight into arabinogalactan utilization by particle-associated Maribacter sp. MAR_2009_72.	Kalenborn S, Zuhlke D, Riedel K, Amann RI, Harder J.	FEMS Microbiol Ecol	10.1093/femsec/fiae045	2024
Phylogeny	Identifying Group-Specific Sequences for Microbial Communities Using Long k-mer Sequence Signatures.	Wang Y, Fu L, Ren J, Yu Z, Chen T, Sun F.	Front Microbiol	10.3389/fmicb.2018.00872	2018
	Toward FAIR Representations of Microbial Interactions.	Pacheco AR, Pauvert C, Kishore D, Segre D.	mSystems	10.1128/msystems.00659-22	2022
	How microbial glycosyl hydrolase activity in the gut mucosa initiates microbial cross-feeding.	Berkhout MD, Plugge CM, Belzer C.	Glycobiology	10.1093/glycob/cwab105	2022
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 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
	Microbiome-encoded bile acid metabolism modulates colonic transit times.	Li N, Koester ST, Lachance DM, Dutta M, Cui JY, Dey N.	iScience	10.1016/j.isci.2021.102508	2021
Metabolism	Genetic Variation of the SusC/SusD Homologs from a Polysaccharide Utilization Locus Underlies Divergent Fructan Specificities and Functional Adaptation in Bacteroides thetaiotaomicron Strains.	Joglekar P, Sonnenburg ED, Higginbottom SK, Earle KA, Morland C, Shapiro-Ward S, Bolam DN, Sonnenburg JL.	mSphere	10.1128/mspheredirect.00185-18	2018
Pathogenicity	Recovery of the Gut Microbiota after Antibiotics Depends on Host Diet, Community Context, and Environmental Reservoirs.	Ng KM, Aranda-Diaz A, Tropini C, Frankel MR, Van Treuren W, O'Loughlin CT, Merrill BD, Yu FB, Pruss KM, Oliveira RA, Higginbottom SK, Neff NF, Fischbach MA, Xavier KB, Sonnenburg JL, Huang KC.	Cell Host Microbe	10.1016/j.chom.2019.10.011	2019
Metabolism	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
	Immunoglobulin A antibody composition is sculpted to bind the self gut microbiome.	Yang C, Chen-Liaw A, Spindler MP, Tortorella D, Moran TM, Cerutti A, Faith JJ.	Sci Immunol	10.1126/sciimmunol.abg3208	2022
	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
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
Genetics	Strain/species identification in metagenomes using genome-specific markers.	Tu Q, He Z, Zhou J.	Nucleic Acids Res	10.1093/nar/gku138	2014
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
	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
	Identification of D-arabinan-degrading enzymes in mycobacteria.	Al-Jourani O, Benedict ST, Ross J, Layton AJ, van der Peet P, Marando VM, Bailey NP, Heunis T, Manion J, Mensitieri F, Franklin A, Abellon-Ruiz J, Oram SL, Parsons L, Cartmell A, Wright GSA, Basle A, Trost M, Henrissat B, Munoz-Munoz J, Hirt RP, Kiessling LL, Lovering AL, Williams SJ, Lowe EC, Moynihan PJ.	Nat Commun	10.1038/s41467-023-37839-5	2023
Metabolism	Intestinal microbiota composition modulates choline bioavailability from diet and accumulation of the proatherogenic metabolite trimethylamine-N-oxide.	Romano KA, Vivas EI, Amador-Noguez D, Rey FE.	mBio	10.1128/mbio.02481-14	2015
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
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
	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
Metabolism	Dps and DpsL Mediate Survival In Vitro and In Vivo during the Prolonged Oxidative Stress Response in Bacteroides fragilis.	Betteken MI, Rocha ER, Smith CJ.	J Bacteriol	10.1128/jb.00342-15	2015
Metabolism	Mobilization of vitamin B₁₂ transporters alters competitive dynamics in a human gut microbe.	Frye KA, Piamthai V, Hsiao A, Degnan PH.	Cell Rep	10.1016/j.celrep.2021.110164	2021
Metabolism	Slimy partners: the mucus barrier and gut microbiome in ulcerative colitis.	Fang J, Wang H, Zhou Y, Zhang H, Zhou H, Zhang X.	Exp Mol Med	10.1038/s12276-021-00617-8	2021
	The prevalence of species and strains in the human microbiome: a resource for experimental efforts.	Kraal L, Abubucker S, Kota K, Fischbach MA, Mitreva M.	PLoS One	10.1371/journal.pone.0097279	2014
Metabolism	The microbial gbu gene cluster links cardiovascular disease risk associated with red meat consumption to microbiota L-carnitine catabolism.	Buffa JA, Romano KA, Copeland MF, Cody DB, Zhu W, Galvez R, Fu X, Ward K, Ferrell M, Dai HJ, Skye S, Hu P, Li L, Parlov M, McMillan A, Wei X, Nemet I, Koeth RA, Li XS, Wang Z, Sangwan N, Hajjar AM, Dwidar M, Weeks TL, Bergeron N, Krauss RM, Tang WHW, Rey FE, DiDonato JA, Gogonea V, Gerberick GF, Garcia-Garcia JC, Hazen SL.	Nat Microbiol	10.1038/s41564-021-01010-x	2022
Metabolism	Metabolic, Epigenetic, and Transgenerational Effects of Gut Bacterial Choline Consumption.	Romano KA, Martinez-Del Campo A, Kasahara K, Chittim CL, Vivas EI, Amador-Noguez D, Balskus EP, Rey FE.	Cell Host Microbe	10.1016/j.chom.2017.07.021	2017
Metabolism	Two new families of the FtsZ-tubulin protein superfamily implicated in membrane remodeling in diverse bacteria and archaea.	Makarova KS, Koonin EV.	Biol Direct	10.1186/1745-6150-5-33	2010
Metabolism	An ecological network of polysaccharide utilization among human intestinal symbionts.	Rakoff-Nahoum S, Coyne MJ, Comstock LE.	Curr Biol	10.1016/j.cub.2013.10.077	2014
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
Phylogeny	Combining 16S rRNA gene variable regions enables high-resolution microbial community profiling.	Fuks G, Elgart M, Amir A, Zeisel A, Turnbaugh PJ, Soen Y, Shental N.	Microbiome	10.1186/s40168-017-0396-x	2018
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
Genetics	Metagenomic binning and association of plasmids with bacterial host genomes using DNA methylation.	Beaulaurier J, Zhu S, Deikus G, Mogno I, Zhang XS, Davis-Richardson A, Canepa R, Triplett EW, Faith JJ, Sebra R, Schadt EE, Fang G.	Nat Biotechnol	10.1038/nbt.4037	2018
	A nested leucine rich repeat (LRR) domain: the precursor of LRRs is a ten or eleven residue motif.	Matsushima N, Miyashita H, Mikami T, Kuroki Y.	BMC Microbiol	10.1186/1471-2180-10-235	2010
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
Pathogenicity	In vitro activities of gatifloxacin, two other quinolones, and five nonquinolone antimicrobials against obligately anaerobic bacteria.	Schaumann R, Ackermann G, Pless B, Claros MC, Rodloff AC.	Antimicrob Agents Chemother	10.1128/aac.43.11.2783	1999
	Defined microbiota transplant restores Th17/RORgammat⁺ regulatory T cell balance in mice colonized with inflammatory bowel disease microbiotas.	Britton GJ, Contijoch EJ, Spindler MP, Aggarwala V, Dogan B, Bongers G, San Mateo L, Baltus A, Das A, Gevers D, Borody TJ, Kaakoush NO, Kamm MA, Mitchell H, Paramsothy S, Clemente JC, Colombel JF, Simpson KW, Dubinsky MC, Grinspan A, Faith JJ.	Proc Natl Acad Sci U S A	10.1073/pnas.1922189117	2020
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
	Longitudinal analysis of the prevalence, maintenance, and IgA response to species of the order Bacteroidales in the human gut.	Zitomersky NL, Coyne MJ, Comstock LE.	Infect Immun	10.1128/iai.01348-10	2011
	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 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
Metabolism	Biological systems discovery in silico: radical S-adenosylmethionine protein families and their target peptides for posttranslational modification.	Haft DH, Basu MK.	J Bacteriol	10.1128/jb.00040-11	2011
	Spatial organization of a model 15-member human gut microbiota established in gnotobiotic mice.	Mark Welch JL, Hasegawa Y, McNulty NP, Gordon JI, Borisy GG.	Proc Natl Acad Sci U S A	10.1073/pnas.1711596114	2017
Metabolism	The Stringent Response Determines the Ability of a Commensal Bacterium to Survive Starvation and to Persist in the Gut.	Schofield WB, Zimmermann-Kogadeeva M, Zimmermann M, Barry NA, Goodman AL.	Cell Host Microbe	10.1016/j.chom.2018.06.002	2018
	Top-down proteomic identification of furin-cleaved alpha-subunit of Shiga toxin 2 from Escherichia coli O157:H7 using MALDI-TOF-TOF-MS/MS.	Fagerquist CK, Sultan O.	J Biomed Biotechnol	10.1155/2010/123460	2010
	Deciphering interactions between the gut microbiota and the immune system via microbial cultivation and minimal microbiomes.	Clavel T, Gomes-Neto JC, Lagkouvardos I, Ramer-Tait AE.	Immunol Rev	10.1111/imr.12578	2017
Genetics	Analysis of the genome sequence of Lactobacillus gasseri ATCC 33323 reveals the molecular basis of an autochthonous intestinal organism.	Azcarate-Peril MA, Altermann E, Goh YJ, Tallon R, Sanozky-Dawes RB, Pfeiler EA, O'Flaherty S, Buck BL, Dobson A, Duong T, Miller MJ, Barrangou R, Klaenhammer TR.	Appl Environ Microbiol	10.1128/aem.00054-08	2008
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
	A novel extracellular metallopeptidase domain shared by animal host-associated mutualistic and pathogenic microbes.	Nakjang S, Ndeh DA, Wipat A, Bolam DN, Hirt RP.	PLoS One	10.1371/journal.pone.0030287	2012
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
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
	Analysis of rRNA restriction fragment length polymorphisms from Bacteroides spp. and Bacteroides fragilis isolates associated with diarrhea in humans and animals.	Smith CJ, Callihan DR.	J Clin Microbiol	10.1128/jcm.30.4.806-812.1992	1992
Metabolism	Evolutionary primacy of sodium bioenergetics.	Mulkidjanian AY, Galperin MY, Makarova KS, Wolf YI, Koonin EV.	Biol Direct	10.1186/1745-6150-3-13	2008
Phylogeny	High-resolution microbial community reconstruction by integrating short reads from multiple 16S rRNA regions.	Amir A, Zeisel A, Zuk O, Elgart M, Stern S, Shamir O, Turnbaugh PJ, Soen Y, Shental N.	Nucleic Acids Res	10.1093/nar/gkt1070	2013
	A score of the ability of a three-dimensional protein model to retrieve its own sequence as a quantitative measure of its quality and appropriateness.	Martinez-Castilla LP, Rodriguez-Sotres R.	PLoS One	10.1371/journal.pone.0012483	2010
Phylogeny	Web-based software for rapid top-down proteomic identification of protein biomarkers, with implications for bacterial identification.	Fagerquist CK, Garbus BR, Williams KE, Bates AH, Boyle S, Harden LA.	Appl Environ Microbiol	10.1128/aem.00079-09	2009
	Noncellulosomal cohesin- and dockerin-like modules in the three domains of life.	Peer A, Smith SP, Bayer EA, Lamed R, Borovok I.	FEMS Microbiol Lett	10.1111/j.1574-6968.2008.01420.x	2009
Phylogeny	Rapid and correct identification of intestinal Bacteroides spp. with chromosomal DNA probes by whole-cell dot blot hybridization.	Morotomi M, Ohno T, Mutai M.	Appl Environ Microbiol	10.1128/aem.54.5.1158-1162.1988	1988
Phylogeny	Systematic analysis of compositional order of proteins reveals new characteristics of biological functions and a universal correlate of macroevolution.	Persi E, Horn D.	PLoS Comput Biol	10.1371/journal.pcbi.1003346	2013
Metabolism	Effects of diet on resource utilization by a model human gut microbiota containing Bacteroides cellulosilyticus WH2, a symbiont with an extensive glycobiome.	McNulty NP, Wu M, Erickson AR, Pan C, Erickson BK, Martens EC, Pudlo NA, Muegge BD, Henrissat B, Hettich RL, Gordon JI.	PLoS Biol	10.1371/journal.pbio.1001637	2013
	Heterologous Expression and Characterization of Cellouronate (beta-1,4-Glucuronan) Lyase from a Human Intestinal Bacterium Bacteroides luhongzhouii.	Tanaka Y, Matsumura K, Ariga M, Konno N, Ogata M, Habu N.	J Appl Glycosci (1999)	10.5458/jag.7203102	2025
	Development of culture methods capable of culturing a wide range of predominant species of intestinal bacteria.	Hirano R, Nishita I, Nakai R, Bito A, Sasabe R, Kurihara S.	Front Cell Infect Microbiol	10.3389/fcimb.2023.1056866	2023
	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
	Gut butyrate-producers confer post-infarction cardiac protection.	Chen HC, Liu YW, Chang KC, Wu YW, Chen YM, Chao YK, You MY, Lundy DJ, Lin CJ, Hsieh ML, Cheng YC, Prajnamitra RP, Lin PJ, Ruan SC, Chen DH, Shih ESC, Chen KW, Chang SS, Chang CMC, Puntney R, Moy AW, Cheng YY, Chien HY, Lee JJ, Wu DC, Hwang MJ, Coonen J, Hacker TA, Yen CE, Rey FE, Kamp TJ, Hsieh PCH.	Nat Commun	10.1038/s41467-023-43167-5	2023
Metabolism	Gut microbial carbohydrate metabolism contributes to insulin resistance.	Takeuchi T, Kubota T, Nakanishi Y, Tsugawa H, Suda W, Kwon AT, Yazaki J, Ikeda K, Nemoto S, Mochizuki Y, Kitami T, Yugi K, Mizuno Y, Yamamichi N, Yamazaki T, Takamoto I, Kubota N, Kadowaki T, Arner E, Carninci P, Ohara O, Arita M, Hattori M, Koyasu S, Ohno H.	Nature	10.1038/s41586-023-06466-x	2023
	Analysis of a new anti-depression mechanism of Chaigui granules based on multi-omics integration: In-depth mining of intestinal microbiota-metabolite interaction network.	Wu ZN, Zhao HL, Wang Q, Chen JL, Ren Y, Qin XM, Tian JS.	J Affect Disord	10.1016/j.jad.2025.120319	2026
	Association between the gut microbiotic composition and dietary patterns in hypertensive elderly patients: a cross-sectional study.	Hung HC, Lin YY, Tien WJ, Chen YY, Yang SC.	Nutr Metab (Lond)	10.1186/s12986-025-00963-8	2025
	Association between sphingomyelin levels and gut microbiota abundance in Alzheimer's disease: a two-sample Mendelian randomization study.	Wang L, Ding Y, Tang Y, Yang M, Yang Z, Yang X, Xia J.	BMC Neurol	10.1186/s12883-025-04207-3	2025
	Intestinal Energy Harvest Mediates Gut Microbiota-Associated Weight Loss Following Bariatric Surgery.	Qian Y, Sorgen AA, Steffen KJ, Heinberg LJ, Reed K, Carroll IM.	Obes Surg	10.1007/s11695-024-07467-z	2024
	The role of monoammonium glycyrrhizinate as a methane inhibitor to limit the rumen methane emissions of Karakul sheep.	Bai T, Jiang C, Wang J, E G, Guo X, Liu J, Le VH, Cheng L.	Animal	10.1016/j.animal.2024.101293	2024
Genetics	Metagenome-informed metaproteomics methodology: a new breakthrough in revealing the mechanisms of host-microbiota-diet interactions in inflammatory bowel disease.	Zhang S, Xu Q.	Front Cell Dev Biol	10.3389/fcell.2025.1634974	2025
	Maternal dietary intervention during lactation impacts the maternal faecal and human milk microbiota.	Sindi AS, Stinson LF, Gridneva Z, Leghi GE, Netting MJ, Wlodek ME, Muhlhausler BS, Rea A, Trevenen ML, Geddes DT, Payne MS.	J Appl Microbiol	10.1093/jambio/lxae024	2024
	Clinical and Gut Microbiome Characteristics of Medically Complex Patients Receiving Blenderized Tube Feeds vs. Standard Enteral Feeds.	Ferrer MF, Retuerto M, Thavamani A, San Valentin EM, Sferra TJ, Ghannoum M, Sankararaman S.	Nutrients	10.3390/nu17122018	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
	Probiotic Engraftment of Akkermansia muciniphila in an In Vitro Synthetic Microbial Community.	Berkhout MD, de Ram C, Boeren S, Plugge CM, Belzer C.	Microb Ecol	10.1007/s00248-025-02605-1	2025
	Gut Colonization With Vancomycin-Resistant Enterococcus Shapes the Gut Microbiome in the Intensive Care Unit.	Park H, Abrams JA, Uhlemann AC, Freedberg DE.	J Infect Dis	10.1093/infdis/jiaf194	2025
	Associations between the gut microbiota, immune cells, and different subtypes of epilepsy: A Mendelian randomization study.	Zhang X, Yang Z, Guo J, Wei Y, Li J.	Epilepsia Open	10.1002/epi4.70072	2025
	Associations Between the Gut Microbiota and Its Related Metabolic Pathways and Uveitis: A Bidirectional Two-Sample Mendelian Randomization Study.	Luo M, Xing Z, Gou Y, Yang X, Zhang X, Yu W, Lv H.	Transl Vis Sci Technol	10.1167/tvst.14.5.15	2025
	Interaction between Bacteroidetes species in the fermentation of Lycium barbarum arabinogalactan.	Cao C, Wang L, Zhang X, Ai C, Wang Z, Huang L, Song S, Zhu B.	Food Chem	10.1016/j.foodchem.2022.135288	2023
	Analysis of Gut Microbiota and Their Metabolites in CADASIL Patients.	Watanabe-Hosomi A, Inoue R, Mizuta I, Matsuura J, Matsuura H, Fukunaga D, Ohara T, Naito Y, Mizuno T.	J Clin Neurol	10.3988/jcn.2025.0231	2025
	Parity influences postpartum adaptations in the maternal gut microbiota.	Jarmukhanov Z, Vinogradova E, Mukhanbetzhanov N, Kozhakhmetov S, Khassenbekova D, Kushugulova A.	Sci Rep	10.1038/s41598-025-02013-y	2025
Phylogeny	Alterations in the gut microbiome and metabolism with doxorubicin-induced heart failure severity.	Wang Q, Liu M, Liu T, Li L, Wang C, Wang X, Rong S, Zhou X.	Front Microbiol	10.3389/fmicb.2024.1348403	2024
Genetics	Intestinal Microbial Profiles of Wild Zobaidy (Pampus argenteus) Fish Characterized by 16S rRNA Next Generation Sequencing.	Albaijan D, Albaijan D, Akbar A.	Curr Issues Mol Biol	10.3390/cimb47110890	2025
	Red meat consumption in higher healthy eating index diets is associated with brain health critical nutritional adequacy, and fecal microbial diversity.	Dhakal S, Hossain M, Parajuli S.	Sci Rep	10.1038/s41598-025-18907-w	2025
	Distinctions Between Fecal and Intestinal Mucosal Microbiota in Subgroups of Irritable Bowel Syndrome.	Hou Y, Dong L, Lu X, Shi H, Xu B, Zhong W, Ma L, Wang S, Yang C, He X, Zhao Y, Wang S.	Dig Dis Sci	10.1007/s10620-022-07588-4	2022
	The Influence of Seasonal Variations in Clinical Trials Based on Gut Microbiota Studies.	Cocomazzi G, Panebianco C, Vallelunga A, De Ruvo D, Del Pup L, Smeazzetto S, Antinori M, Chimienti V, Maggio G, Finocchiaro C, Contu V, Pazienza V.	Microorganisms	10.3390/microorganisms13102386	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
	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
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
	Immune cells appraising the causal effect of gut microbiota on endometrial cancer: A Mendelian randomization analysis.	Liu L, Wu S, Lai X, Jin Q.	Medicine (Baltimore)	10.1097/md.0000000000045088	2025
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
Enzymology	Novel Endo-beta-N-Acetylglucosaminidases Derived from Human Fecal Samples Selectively Release N-Glycans from Model Glycoproteins.	Bolino M, Haththotuwe Gamage N, Duman H, Abiodun O, De Mello AS, Karav S, Frese SA.	Foods	10.3390/foods14081288	2025
	Comparative Analysis of Bacteriome in Hair Follicle Layers of Patients with Female Pattern Androgenic Alopecia.	Park Y, Kyung S, Mun S, Yu BS, Yun K, Baek C, Lee DG, Kang S, Kim SR, Kim JH, Lee Y, Park BC, Han K.	Microorganisms	10.3390/microorganisms13061365	2025
Pathogenicity	Eurotium cristatum, a Probiotic Fungus from Fuzhuan Brick Tea, and Its Polysaccharides Ameliorated DSS-Induced Ulcerative Colitis in Mice by Modulating the Gut Microbiota.	Lu X, Jing Y, Zhang N, Cao Y.	J Agric Food Chem	10.1021/acs.jafc.1c08301	2022
Genetics	Machine learning-based investigation of the relationship between gut microbiome and obesity status.	Liu W, Fang X, Zhou Y, Dou L, Dou T.	Microbes Infect	10.1016/j.micinf.2021.104892	2022
	Impact of Gut Dysbiosis on the Risk of Non-Small-Cell Lung Cancer.	Wei YF, Huang MS, Huang CH, Yeh YT, Hung CH.	Int J Environ Res Public Health	10.3390/ijerph192315991	2022
Phylogeny	Evaluation of the gastric microbiota based on body mass index using 16S rRNA gene sequencing.	Lee SH, Kim EB, Park SC, Nam SJ, Cho H, Jeon HJ, Lee SP.	Front Cell Infect Microbiol	10.3389/fcimb.2025.1651316	2025
	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
	Prebiotic, probiotic, and postbiotic properties of fermented corn starch and their application in type 2 diabetes management.	Gumenku L, Erukainure OL, Islam MS, Olaniran AO.	World J Diabetes	10.4239/wjd.v16.i8.107775	2025
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
	Gut microbiota predicts the diagnosis of ulcerative colitis in Saudi children.	El Mouzan M, Al Sarkhy A, Assiri A.	World J Clin Pediatr	10.5409/wjcp.v13.i1.90755	2024
	Oral, not gut microbiota diversity, reflects the inflammation and neoplasia in patients with uveitis and vitreoretinal lymphoma.	Brichova M, Dlouha L, Tenglerova M, Rehakova J, Kostovcik M, Benesova K, Coufal S, Pivrncova E, Jiraskova Zakostelska Z, Kverka M, Skrlova E, Svozilkova P, Klimova A, Kostovcikova K, Trneny M, Heissigerova J.	J Ophthalmic Inflamm Infect	10.1186/s12348-025-00517-2	2025
	Altered gut microbiota and metabolite profiles in community-acquired pneumonia: a metagenomic and metabolomic study.	Zhang F, Luan J, Suo L, Wang H, Zhao Y, Sun T, Ni Y, Cao H, Zou X, Liu B.	Microbiol Spectr	10.1128/spectrum.02639-24	2025
	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
	Major heavy metals and human gut microbiota composition: a systematic review with nutritional approach.	Rezazadegan M, Forootani B, Hoveyda Y, Rezazadegan N, Amani R.	J Health Popul Nutr	10.1186/s41043-025-00750-4	2025
Pathogenicity	Association Between the Inflammatory Potential of Diet and Constipation Among Adults in the United States: A Cross-sectional Study.	Lu WF, Liu L, Zhang YH, Liu H.	J Clin Gastroenterol	10.1097/mcg.0000000000002060	2025
	Coleus forskohlii and Garcinia indica extracts attenuated lipid accumulation by regulating energy metabolism and modulating gut microbiota in obese mice.	Tung YC, Shih YA, Nagabhushanam K, Ho CT, Cheng AC, Pan MH.	Food Res Int	10.1016/j.foodres.2021.110143	2021
Pathogenicity	Fecal microbiota signatures of insulin resistance, inflammation, and metabolic syndrome in youth with obesity: a pilot study.	Del Chierico F, Manco M, Gardini S, Guarrasi V, Russo A, Bianchi M, Tortosa V, Quagliariello A, Shashaj B, Fintini D, Putignani L.	Acta Diabetol	10.1007/s00592-020-01669-4	2021
	Bloodstream Infection Caused by Bacteroides caccae in a Diabetic Patient: a Case Report and Review of the Literature.	Cheng Z, Huang Y, Wie W, Wang Y, Wang Z.	Clin Lab	10.7754/clin.lab.2019.190534	2019
	Gut microbiota profiles associated with persistent anal HPV infection in men who have sex with men.	Yang H, Bian J, Yu W, Asilibieke S, Tian T, Zhang W, Lynn HS, He J, Dai J, Zhang G.	BMC Infect Dis	10.1186/s12879-025-11624-9	2025
Genetics	Metagenomic profiling of gut microbiome in early chronic kidney disease.	Sato N, Kakuta M, Hasegawa T, Yamaguchi R, Uchino E, Murashita K, Nakaji S, Imoto S, Yanagita M, Okuno Y.	Nephrol Dial Transplant	10.1093/ndt/gfaa122	2021
	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
	Comparative analysis of dietary fiber impact on bile acid metabolism and gut microbiota composition in mice.	Zochling A, Seneca J, Pjevac P, Aunon-Lopez A, Zebeli Q, Pignitter M, Duszka K.	NPJ Gut Liver	10.1038/s44355-025-00041-z	2025
	Bloodstream infection caused by Bacteroides caccae in a patient with renal hypertension: a case report.	Yang Y, Zhang Q, Hu H, Zhang W, Lu T.	J Int Med Res	10.1177/03000605211047277	2021
	Dietary inflammatory index and its relationship with gut microbiota in individuals with intestinal constipation: a cross-sectional study.	Costa LM, Mendes MM, Oliveira AC, Magalhaes KG, Shivappa N, Hebert JR, da Costa THM, Botelho PB.	Eur J Nutr	10.1007/s00394-021-02649-2	2022
	CO₂ Is Beneficial to Gut Microbiota Homeostasis during Colonoscopy: Randomized Controlled Trial.	Yang X, Xiu WB, Wang JX, Li LP, He C, Gao CP.	J Clin Med	10.3390/jcm11185281	2022
	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
	The Accumulation of Gut Microbiome-derived Indoxyl Sulfate and P-Cresyl Sulfate in Patients With End-stage Renal Disease.	Lin X, Liang W, Li L, Xiong Q, He S, Zhao J, Guo X, Xiang S, Zhang P, Wang H, Ying C, Yao Y, Zuo X.	J Ren Nutr	10.1053/j.jrn.2021.09.007	2022
	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
	Two-Decade Retrospective Analysis of Endogenous Endophthalmitis in Spain and Mexico: A Comprehensive Study.	de Esteban Macineira E, Bande MF, Soberanes-Perez JI, Paniagua L, Golzarri MF, Fromow-Guerra J, Blanco Teijeiro MJ, Tourino Peralba R.	J Clin Med	10.3390/jcm13174990	2024
Genetics	Investigating gut microbiota-blood and urine metabolite correlations in early sepsis-induced acute kidney injury: insights from targeted KEGG analyses.	Xu Y, Xu J, Zhu Y, Mao H, Li J, Kong X, Zhu X, Zhang J.	Front Cell Infect Microbiol	10.3389/fcimb.2024.1375874	2024
	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
Metabolism	Methanogenesis associated with altered microbial production of short-chain fatty acids and human-host metabolizable energy.	Dirks B, Davis TL, Carnero EA, Corbin KD, Smith SR, Rittmann BE, Krajmalnik-Brown R.	ISME J	10.1093/ismejo/wraf103	2025
	Combining Bifidobacterium longum subsp. infantis and human milk oligosaccharides synergistically increases short chain fatty acid production ex vivo.	De Bruyn F, James K, Cottenet G, Dominick M, Katja J.	Commun Biol	10.1038/s42003-024-06628-1	2024
	Prognostic value of 24-hour cultivation of peritoneal fluid to distinguish complicated from uncomplicated acute appendicitis: a prospective cohort study.	Mark-Christensen A, Bro Sorensen D, Qvist N, Justesen US, Moller S, Ellebaek MB.	Langenbecks Arch Surg	10.1007/s00423-024-03428-3	2024
Phylogeny	Full-length 16S rRNA Sequencing Reveals Gut Microbiome Signatures Predictive of MASLD in children with obesity.	Lin YC, Wu CC, Li YE, Chen CL, Lin CR, Ni YH.	BMC Microbiol	10.1186/s12866-025-03849-0	2025
	Disruption and adaptation: infant gut microbiota's dynamic response to SARS-CoV-2 infection.	Zhu LT, Zhao L, Zhu Y, Xu XL, Lin JJ, Duan YF, Long L, Wu YY, Xu WJ, Chen JY, Yin YH, Obeten AU, Huang Q.	Microbiome	10.1186/s40168-025-02029-6	2025
	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
	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
Genetics	Infant Gut Microbial Metagenome Mining of alpha-l-Fucosidases with Activity on Fucosylated Human Milk Oligosaccharides and Glycoconjugates.	Moya-Gonzalvez EM, Pena-Gil N, Rubio-Del-Campo A, Coll-Marques JM, Gozalbo-Rovira R, Monedero V, Rodriguez-Diaz J, Yebra MJ.	Microbiol Spectr	10.1128/spectrum.01775-22	2022
	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
	Investigating the causal relationship of gut microbiota with GERD and BE: a bidirectional mendelian randomization.	Liu Y, Yu J, Yang Y, Han B, Wang Q, Du S.	BMC Genomics	10.1186/s12864-024-10377-0	2024
	Consumption of Limosilactobacillus fermentum Inhibits Corneal Damage and Inflammation in Dry Eye Disease Mouse Model through Regulating the Gut Microbiome.	Lee K, Gwon H, Shim JJ, Kim JY, Lee JH.	Int J Mol Sci	10.3390/ijms25063528	2024
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
	Assessing the gut microbiota composition in older adults: connections to physical activity and healthy ageing.	Ramos C, Magistro D, Walton GE, Whitham A, Camp N, Poveda C, Gibson GR, Hough J, Kinnear W, Hunter K.	Geroscience	10.1007/s11357-025-01605-w	2025
Genetics	Structural and functional characterization of gut microbiota in dyslipidemic patients from high-altitude Tibetan pastoral areas.	Chen J, Luo Y, Hao Y, Wang Q, Wang Q.	Front Nutr	10.3389/fnut.2025.1676238	2025
	Comprehensive microbial and clinical profiling of functional constipation: A stratified comparative study of age and constipation subtype.	Zhu HT, Wang HF, Zhang Q, Bai JF, Wang M, Du SY, Zhang YL.	World J Gastroenterol	10.3748/wjg.v31.i40.112637	2025
	Fecal Microbiota Transplant in Immunotherapy-Resistant Melanoma: What Can We Expect in the Near Future?	Ferreira A, Neves MT, Baleiras A, Malheiro M, Martins A.	Cureus	10.7759/cureus.32586	2022
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
	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
	Bacterial dysbiosis in newly diagnosed treatment naïve pediatric ulcerative colitis in Saudi Arabia.	El Mouzan M, Al Mofarreh M, Alsaleem B, Al Sarkhy A, Alanazi A, Khormi M, Almasoud A, Assiri A.	Saudi J Gastroenterol	10.4103/sjg.sjg_66_24	2025
Pathogenicity	Effect of Sodium Butyrate Supplementation on Type 2 Diabetes-Literature Review.	Krauze W, Busz N, Pikula W, Maternowska M, Prowans P, Maciejewska-Markiewicz D.	Nutrients	10.3390/nu17111753	2025
Pathogenicity	Spatial host-microbiome profiling demonstrates bacterial-associated host transcriptional alterations in pediatric ileal Crohn's disease.	Jang S, Lee EJ, Park S, Lim H, Ahn B, Huh Y, Koh H, Park YR.	Microbiome	10.1186/s40168-025-02178-8	2025
Phylogeny	Microbiome metabolic capacity is buffered against phylotype losses by functional redundancy.	Cross K, Beckman N, Jahnes B, Sabree ZL.	Appl Environ Microbiol	10.1128/aem.02368-24	2025
	Benefits, side effects, and uses of Hericium erinaceus as a supplement: a systematic review.	Menon A, Jalal A, Arshad Z, Nawaz FA, Kashyap R.	Front Nutr	10.3389/fnut.2025.1641246	2025
	Gut microbial structural variation associates with immune checkpoint inhibitor response.	Liu R, Zou Y, Wang WQ, Chen JH, Zhang L, Feng J, Yin JY, Mao XY, Li Q, Luo ZY, Zhang W, Wang DM.	Nat Commun	10.1038/s41467-023-42997-7	2023
Transcriptome	The fecal microbiota of patients with primary biliary cholangitis (PBC) causes PBC-like liver lesions in mice and exacerbates liver damage in a mouse model of PBC.	Jiang H, Yu Y, Hu X, Du B, Shao Y, Wang F, Chen L, Yan R, Li L, Lv L.	Gut Microbes	10.1080/19490976.2024.2383353	2024
	Detrimental effect of an early exposure to antibiotics on the outcomes of immunotherapy in a multi-tumor cohort of patients.	Guerrero P, Albarran V, Gonzalez-Merino C, Garcia de Quevedo C, Sotoca P, Chamorro J, Rosero DI, Barrill A, Alia V, Calvo JC, Moreno J, Perez de Aguado P, Alvarez-Ballesteros P, San Roman M, Serrano JJ, Soria A, Olmedo ME, Saavedra C, Cortes A, Gomez A, Lage Y, Ruiz A, Ferreiro MR, Longo F, Guerra E, Martinez-Delfrade I, Garrido P, Gajate P.	Oncologist	10.1093/oncolo/oyae284	2025
	Metagenomic analysis of fecal samples in colorectal cancer Egyptians patients post colectomy: A pilot study.	Abo-Hammam RH, Salah M, Shabayek S, Hanora A, Zakeer S, Khattab RH.	AIMS Microbiol	10.3934/microbiol.2024008	2024
Metabolism	Effects of modified corn straw supplementation on laying performance, egg quality, immune response, antioxidant capacity, lipid metabolism and intestinal microbiota of post-peak laying hens.	Wang P, Chu Y, Fan X, Qin Y, Wang H, Chang J, Wang L, Jin S, Li X, Yuan L, Yin Q, Zuo R, Dang X, Lu F, Liu C, Chen J.	Poult Sci	10.1016/j.psj.2025.105579	2025
	Prenatal lead exposure is negatively associated with the gut microbiome in childhood.	Eggers S, Midya V, Bixby M, Gennings C, Torres-Olascoaga LA, Walker RW, Wright RO, Arora M, Tellez-Rojo MM.	Front Microbiol	10.3389/fmicb.2023.1193919	2023
	Assessing Gut Microbiome Alterations in Children With Allergic Rhinitis: Associations With Allergen-Specific IgE Levels and Sensitization Patterns.	Li J, Shi Y, Hu L, He W, Li Y.	J Asthma Allergy	10.2147/jaa.s496477	2025
	Mucin-driven ecological interactions in an in vitro synthetic community of human gut microbes.	Berkhout MD, Ioannou A, de Ram C, Boeren S, Plugge CM, Belzer C.	Glycobiology	10.1093/glycob/cwae085	2024
	A taxon-specific measurement of disruption in a multi-modal study of microbiomes and metabolomes reveals system-wide dysbiosis preceding HIV-1 infection.	Fouladi F, Chen Y, Bera S, Jarmusch AK, Van Tyne D, Palella FJ, Margolick JB, Chew KW, Sun J, Martinson J, Rinaldo CR, Peddada SD.	Nat Commun	10.1038/s41467-025-64822-z	2025
Metabolism	Gut microbiome alterations and hepatic encephalopathy post-TIPS in liver cirrhosis patients.	Li S, Xu Z, Diao H, Zhou A, Tu D, Wang S, Feng Y, Feng X, Lai Y, Yang S, Tang B.	J Transl Med	10.1186/s12967-025-06774-y	2025
	Optimizing microbiome reference databases with PacBio full-length 16S rRNA sequencing for enhanced taxonomic classification and biomarker discovery.	Han H, Choi YH, Kim SY, Park JH, Chung J, Na HS.	Front Microbiol	10.3389/fmicb.2024.1485073	2024
	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
	Checkpoint inhibitor responses can be regulated by the gut microbiota - A systematic review.	Zeriouh M, Raskov H, Kvich L, Gogenur I, Bennedsen ALB.	Neoplasia	10.1016/j.neo.2023.100923	2023
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
	The Association Between Maternal Diet and the Human Milk Microbiome: A Review of Evidence and Methodological Challenges.	Sindi AS.	Microorganisms	10.3390/microorganisms13102347	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
	Gut microbiome links obesity to type 2 diabetes: insights from Mendelian randomization.	Fu L, Baranova A, Cao H, Zhang F.	BMC Microbiol	10.1186/s12866-025-03968-8	2025
	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
	Multimodal approach in a patient with Fournier's gangrene during the coronavirus pandemic.	Trama F, Illiano E, Bertuzzi G, Chiummariello S, Costantini E.	Urol Case Rep	10.1016/j.eucr.2021.101825	2021
	Intermittent fasting and metabolic dysfunction-associated steatotic liver disease: the potential role of the gut-liver axis.	Zhang Z, Kong AP, Wong VW, Hui HX.	Cell Biosci	10.1186/s13578-025-01406-w	2025
Pathogenicity	Comparative study of adenosine 3'-pyrophosphokinase domains of MuF polymorphic toxins.	Paulet EM, Bartoli J, Kabtan A, Piras CM, Tempier AC, Cascales E, Viala JP.	FEBS Open Bio	10.1002/2211-5463.70038	2025
	Gut Microbiota Patterns Predicting Long-Term Weight Loss Success in Individuals with Obesity Undergoing Nonsurgical Therapy.	Bischoff SC, Nguyen NK, Seethaler B, Beisner J, Kugler P, Stefan T.	Nutrients	10.3390/nu14153182	2022
	The Role of Gut Microbiota in Pediatric Obesity and Metabolic Disorders: Insights from a Comprehensive Review.	Koller AM, Sasaran MO, Marginean CO.	Nutrients	10.3390/nu17111883	2025
	Gut Microbiota and Bile Acids Mediate the Clinical Benefits of YH1 in Male Patients with Type 2 Diabetes Mellitus: A Pilot Observational Study.	Huang YH, Wu YH, Tang HY, Chen ST, Wang CC, Ho WJ, Lin YH, Liu GH, Lin PY, Lo CJ, Yeh YM, Cheng ML.	Pharmaceutics	10.3390/pharmaceutics14091857	2022
Pathogenicity	Development of the Gut Microbial Immune and Epithelial Cellular System (GutMICS) to Investigate the Immunological Role of Gut Anaerobes.	Kwon SY, Jo SH, Park J, Park JH, Kim YR, Baek JH, Kim MG, Choi BG, Hong NY, Jung HK, Ryu HW, Jeon JS, Kim YG.	Biotechnol Bioeng	10.1002/bit.29031	2025
	Systematic review: The gut microbiota as a link between colorectal cancer and obesity.	Ruiz-Malagon AJ, Rodriguez-Sojo MJ, Redondo E, Rodriguez-Cabezas ME, Galvez J, Rodriguez-Nogales A.	Obes Rev	10.1111/obr.13872	2025
	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
	Microbial Biomarkers in Patients with Nonresponsive Celiac Disease.	Viitasalo L, Kurppa K, Ashorn M, Saavalainen P, Huhtala H, Ashorn S, Maki M, Ilus T, Kaukinen K, Iltanen S.	Dig Dis Sci	10.1007/s10620-018-5285-z	2018
Genetics	Association between gut microbiota and central retinal artery occlusion: A two-sample Mendelian randomization study.	Chen J, Wang X, Yang J, Huang J, Xie M, Su Z, Jiang F.	Indian J Ophthalmol	10.4103/ijo.ijo_3304_23	2024
Genetics	Metabolic response of intestinal microbiota to guar gum consumption.	Barber C, Sabater C, Guarner F, Margolles A, Azpiroz F.	Front Nutr	10.3389/fnut.2023.1160694	2023
	Discitis due to late-onset mesh infection 14 years after inguinal hernia repair: a case report.	Maeda C, Kato K, Yamada S, Tanaka M, Sujishi K, Sato R, Takanashi S, Waseda M, Suzuki T, Ishida Y, Kasahara F.	Surg Case Rep	10.1186/s40792-022-01449-y	2022
	Associations between gut microbiota and sarcopenia or its defining parameters in older adults: A systematic review.	Lapauw L, Rutten A, Dupont J, Amini N, Vercauteren L, Derrien M, Raes J, Raes J, Gielen E.	J Cachexia Sarcopenia Muscle	10.1002/jcsm.13569	2024
	Does seasonality of the microbiota contribute to the seasonality of acute gout flare?	Schlesinger N, Brunetti L, Androulakis IP.	Clin Exp Rheumatol	10.55563/clinexprheumatol/hdtge7	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
	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
	Gut microbiota differences in five-year-old children that were born preterm with a history of necrotizing enterocolitis: A pilot trial.	Magnusson A, Jabbari Shiadeh SM, Ardalan M, Swolin-Eide D, Elfvin A.	iScience	10.1016/j.isci.2024.110325	2024
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
	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
	Dissecting the molecular interactions between botanical extracts and the human gut microbiota.	Mancabelli L, Tarracchini C, Longhi G, Alessandri G, Ventura M, Turroni F.	Front Microbiol	10.3389/fmicb.2025.1610170	2025
	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
Phylogeny	Alterations of ileal mucosa-associated microbiota in hypercholesterolemia patients.	Li J, Ma J, Wang W, Du H, Tang S, Li Y, Zhu W, Zhang R, Wan J.	Heliyon	10.1016/j.heliyon.2023.e22116	2023
Pathogenicity	Could dysbiosis of inflammatory and anti-inflammatory gut bacteria have an implications in the development of type 2 diabetes? A pilot investigation.	Kulkarni P, Devkumar P, Chattopadhyay I.	BMC Res Notes	10.1186/s13104-021-05466-2	2021
	The release patterns and potential prebiotic characteristics of soluble and insoluble dietary fiber-bound polyphenols from pinot noir grape pomace in vitro digestion and fermentation.	Li Y, Chen X, Wang G, Xu L, Liu Y, Yuan C, Li J.	Food Chem X	10.1016/j.fochx.2025.102694	2025
	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
	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
	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
	The gut microbiota and diabetic nephropathy: an observational study review and bidirectional Mendelian randomization study.	Han YZ, Wang YZY, Zhu XY, Du BX, Wang YX, Zhang XQ, Jia JM, Liu WJ, Zheng HJ.	Trials	10.1186/s13063-025-08755-4	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
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
	Fiber Intervention Study in Prader-Willi Syndrome: Insights into Metabolic and Microbiota Shifts.	Tan Q, Peng Y, Deehan EC, Vieira FT, Ho BWP, Afhami S, Wine E, Madsen KL, Field CJ, Pakseresht M, Ilkayeva O, Newgard CB, Walter J, Tun HM, Haqq AM.	J Clin Endocrinol Metab	10.1210/clinem/dgaf142	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
	Oral administration of pioglitazone inhibits pulmonary hypertension by regulating the gut microbiome and plasma metabolome in male rats.	Zhang Z, Liang Y, Mo S, Zhao M, Li Y, Zhang C, Shan X, Liu S, Liao J, Luo X, Zhu J, Wang C, Jiang Q, Hou C, Hong W, Lai N, Chen Y, Xu L, Lu W, Wang J, Wang Z, Yang K.	Physiol Rep	10.14814/phy2.70174	2025
	Gut Microbiota Changes by an SGLT2 Inhibitor, Luseogliflozin, Alters Metabolites Compared with Those in a Low Carbohydrate Diet in db/db Mice.	Hata S, Okamura T, Kobayashi A, Bamba R, Miyoshi T, Nakajima H, Kitagawa N, Hashimoto Y, Majima S, Senmaru T, Okada H, Ushigome E, Nakanishi N, Takakuwa H, Sasano R, Hamaguchi M, Fukui M.	Nutrients	10.3390/nu14173531	2022
Genetics	Next-generation sequencing of the athletic gut microbiota: a systematic review.	Sabater C, Iglesias-Gutierrez E, Ruiz L, Margolles A.	Microbiome Res Rep	10.20517/mrr.2022.16	2023
	Observational study protocol: the faecal microbiome in the acute stage of new-onset paediatric type 1 diabetes in an Irish cohort.	Kennedy EC, Ross FC, O'Shea CA, Lavelle A, Ross P, Dempsey E, Stanton C, Hawkes CP.	BMJ Open	10.1136/bmjopen-2024-089206	2025
Phylogeny	PhyloFunc: phylogeny-informed functional distance as a new ecological metric for metaproteomic data analysis.	Wang L, Simopoulos CMA, Serrana JM, Ning Z, Li Y, Sun B, Yuan J, Figeys D, Li L.	Microbiome	10.1186/s40168-024-02015-4	2025
	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
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
Pathogenicity	Association of gut microbiota and inflammatory markers in obese patients with type 2 diabetes mellitus: post hoc analysis of a synbiotic interventional study.	Sugawara Y, Kanazawa A, Aida M, Yoshida Y, Yamashiro Y, Watada H.	Biosci Microbiota Food Health	10.12938/bmfh.2021-081	2022
	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
	Integrated analysis of microbiota with bile acids for the phototherapy treatment of neonatal jaundice.	Zhang K, Fan S, Lv A, Ma Y, Fang X, Zhang J.	Arch Med Sci	10.5114/aoms/134023	2023
	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
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
	Early infancy dysbiosis in food protein-induced enterocolitis syndrome: A prospective cohort study.	Su KW, Cetinbas M, Martin VM, Virkud YV, Seay H, Ndahayo R, Rosow R, Elkort M, Gupta B, Kramer E, Pronchick T, Reuter S, Sadreyev RI, Huang JL, Shreffler WG, Yuan Q.	Allergy	10.1111/all.15644	2023
Genetics	Impact of dietary fructooligosaccharides (FOS) on murine gut microbiota and intestinal IgA secretion.	Jangid A, Fukuda S, Kato T, Seki M, Suzuki Y, Taylor TD, Ohno H, Prakash T.	3 Biotech	10.1007/s13205-022-03116-3	2022
	Bariatric Surgery Is Associated with Lower Concentrations of Fecal Secondary Bile Acids and Their Metabolizing Microbial Enzymes: A Pilot Study.	Hussan H, Ali MR, Lyo V, Webb A, Pietrzak M, Zhu J, Choueiry F, Li H, Cummings BP, Marco ML, Medici V, Clinton SK.	Obes Surg	10.1007/s11695-024-07420-0	2024
Pathogenicity	Gut Microbiome dysbiosis and immune activation correlate with somatic and neuropsychiatric symptoms in COVID-19 patients.	Scalzo PL, Marshall AG, Soriano S, Curry K, Dulay M, Hodics T, Quigley EMM, Treangen TJ, Piskorz MM, Villapol S.	J Transl Med	10.1186/s12967-025-06348-y	2025
Phylogeny	Probiotic administration correlated with reduced diarrheal incidence and improved gut microbiota diversity in young goats	Essa M, Cheng C, Li J, Han X, Wei Z, Abdelhadi L, Hassan H, Adam S, Husien H, Saleh A, Cheng D.	Front Vet Sci		2025
	Hyperuricemia and the gut microbiota: current research hotspots and future trends.	Yang J, Chen J, Li D, Wu Q, Zhang Y, Li Y, Deng Y.	Front Microbiol	10.3389/fmicb.2025.1620561	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
	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
	Apigenin protects ischemic stroke by regulating intestinal microbiota homeostasis, regulates brain metabolic profile.	Li J, Xu Q, Xu X, He W, Zhang H, Ren H, Wang Y, Wang X, Zhao D.	Front Pharmacol	10.3389/fphar.2025.1553081	2025
	First-degree Relatives of Celiac Disease Patients Have Increased Seroreactivity to Serum Microbial Markers.	Viitasalo L, Iltanen S, Huhtala H, Saavalainen P, Kaukinen K, Lindfors K, Kurppa K.	Nutrients	10.3390/nu12041073	2020
	Safety evaluation of Balanced Health Care Dan-A medicinal formulation containing traditional edible ingredients in lung tumor-loaded mice.	Dong F, Zhao C, He X, Dong Y, Liu H, Yao P, Xu W.	Food Sci Nutr	10.1002/fsn3.3195	2023
Pathogenicity	Influence of Short-Term Consumption of Hericium erinaceus on Serum Biochemical Markers and the Changes of the Gut Microbiota: A Pilot Study.	Xie XQ, Geng Y, Guan Q, Ren Y, Guo L, Lv Q, Lu ZM, Shi JS, Xu ZH.	Nutrients	10.3390/nu13031008	2021
	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	Complex Probiotics Ameliorate Fecal Microbiota Transplantation-Induced IBS in Mice via Gut Microbiota and Metabolite Modulation.	Gao Y, Borjihan Q, Zhang W, Li L, Wang D, Bai L, Zhu S, Chen Y.	Nutrients	10.3390/nu17050801	2025
	Generation of genome-scale metabolic reconstructions for 773 members of the human gut microbiota.	Magnusdottir S, Heinken A, Kutt L, Ravcheev DA, Bauer E, Noronha A, Greenhalgh K, Jager C, Baginska J, Wilmes P, Fleming RM, Thiele I.	Nat Biotechnol	10.1038/nbt.3703	2017
	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
Proteome	Proteogenomic annotation of T6SS components identified in Bacteroides fragilis secretome.	Zakharzhevskaya NB, Shagaleeva OY, Kashatnikova DA, Goncharov AO, Evsyutina DV, Kardonsky DA, Vorobeva EA, Silantiev AS, Kazakova VD, Kolesnikova IV, Butenko IO, Vanyushkina AA, Smirnova SV, Chaplin AV, Efimov BA.	Front Microbiol	10.3389/fmicb.2025.1495971	2025
Phylogeny	Unveiling the negative association of Faecalibacterium prausnitzii with ischemic stroke severity, impaired prognosis and pro-inflammatory markers.	Luo Y, Chang G, Yu G, Lin Y, Zhang Q, Wang Z, Han J.	Heliyon	10.1016/j.heliyon.2024.e26651	2024
	Randomized trial assessing impact of probiotic supplementation on gut microbiome and clinical outcome from targeted therapy in metastatic renal cell carcinoma.	Dizman N, Hsu J, Bergerot PG, Gillece JD, Folkerts M, Reining L, Trent J, Highlander SK, Pal SK.	Cancer Med	10.1002/cam4.3569	2021
	A framework for predictive modeling of microbiome multi-omics data: latent interacting variable-effects (LIVE) modeling.	Munoz Briones J, Brubaker DK.	BMC Bioinformatics	10.1186/s12859-025-06134-z	2025
	Using whole-genome sequencing (WGS) to plot colorectal cancer-related gut microbiota in a population with varied geography.	Shuwen H, Yinhang W, Xingming Z, Jing Z, Jinxin L, Wei W, Kefeng D.	Gut Pathog	10.1186/s13099-022-00524-x	2022
Pathogenicity	Altered Gut Microbial Profile Accompanied by Abnormal Fatty Acid Metabolism Activity Exacerbates Endometrial Cancer Progression.	Zhao SS, Chen L, Yang J, Wu ZH, Wang XY, Zhang Q, Liu WJ, Liu HX.	Microbiol Spectr	10.1128/spectrum.02612-22	2022
	Does gut microbiota dysbiosis impact the metabolic alterations of hydrogen sulfide and lanthionine in patients with chronic kidney disease?	Garcia-Martinez Y, Alexandrova E, Iebba V, Ferravante C, Spinelli M, Franci G, Amoresano A, Weisz A, Trepiccione F, Borriello M, Ingrosso D, Perna AF.	BMC Microbiol	10.1186/s12866-024-03590-0	2024
Metabolism	Taxonomic variations in the gut microbiome of gout patients with and without tophi might have a functional impact on urate metabolism.	Mendez-Salazar EO, Vazquez-Mellado J, Casimiro-Soriguer CS, Dopazo J, Cubuk C, Zamudio-Cuevas Y, Francisco-Balderas A, Martinez-Flores K, Fernandez-Torres J, Lozada-Perez C, Pineda C, Sanchez-Gonzalez A, Silveira LH, Burguete-Garcia AI, Orbe-Orihuela C, Lagunas-Martinez A, Vazquez-Gomez A, Lopez-Reyes A, Palacios-Gonzalez B, Martinez-Nava GA.	Mol Med	10.1186/s10020-021-00311-5	2021
	Effects of exercise and physical activity on gut microbiota composition and function in older adults: a systematic review.	Aya V, Jimenez P, Munoz E, Ramirez JD.	BMC Geriatr	10.1186/s12877-023-04066-y	2023
	Development of an infant colon simulating in vitro model, I-TIM-2, to study the effects of modulation strategies on the infant gut microbiome composition and function.	Colberg O, Hermes GDA, Licht TR, Wichmann A, Baker A, Laursen MF, Wellejus A.	Microbiol Spectr	10.1128/spectrum.00724-24	2024
	Association Between Adult Antibiotic Use, Microbial Dysbiosis and Atopic Conditions - A Systematic Review.	Ng WZJ, van Hasselt J, Aggarwal B, Manoharan A.	J Asthma Allergy	10.2147/jaa.s401755	2023
	Astragalus Polysaccharide Modulates the Gut Microbiota and Metabolites of Patients with Type 2 Diabetes in an In Vitro Fermentation Model.	Zhang X, Jia L, Ma Q, Zhang X, Chen M, Liu F, Zhang T, Jia W, Zhu L, Qi W, Wang N.	Nutrients	10.3390/nu16111698	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
Metabolism	Targeting the Gut Microbiome to Improve Immunotherapy Outcomes: A Review.	David A, Lev-Ari S.	Integr Cancer Ther	10.1177/15347354241269870	2024
	Seasonal Variations in Production Performance, Health Status, and Gut Microbiota of Meat Rabbit Reared in Semi-Confined Conditions.	Ye D, Ding X, Pang S, Gan Y, Li Z, Gan Q, Fang S.	Animals (Basel)	10.3390/ani14010113	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
	Clinical effectiveness of fecal microbial transplantation for metabolic syndrome: Advances in clinical efficacy and multi-omics research.	Wang H, Tian J, Mi J.	Curr Res Microb Sci	10.1016/j.crmicr.2025.100415	2025
	Perforation of sigmoid neovagina in a patient with Mayer-Rokitansky-Küster-Hauser syndrome.	Kamath A, Butt S.	IDCases	10.1016/j.idcr.2021.e01110	2021
	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
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
	Characterization of Gut Microbiome Composition in Patients with Triple-Negative Breast Cancer Treated with Neoadjuvant Chemotherapy.	Vernaci G, Savarino EV, Patuzzi I, Facchin S, Zingone F, Massa D, Faggioni G, Giarratano T, Miglietta F, Griguolo G, Fassan M, Lo Mele M, Gasparini E, Bisagni G, Guarneri V, Dieci MV.	Oncologist	10.1093/oncolo/oyad060	2023
	Harnessing gut-derived bioactives and AI diagnostics for the next generation of type 2 diabetes solutions.	Tseyslyer Y, Malyi V, Saifullina M, Tsyryuk O, Shvets Y, Penchuk Y, Kovalchuk I, Kovalchuk O, Korotkyi O, Bulda V, Lazarieva O.	Front Endocrinol (Lausanne)	10.3389/fendo.2025.1699954	2025
	Fangyukangsuan granules ameliorate hyperuricemia and modulate gut microbiota in rats.	Zhang QZ, Zhang JR, Li X, Yin JL, Jin LM, Xun ZR, Xue H, Yang WQ, Zhang H, Qu J, Xing ZK, Wang XM.	Front Immunol	10.3389/fimmu.2024.1362642	2024
	Effects of Konjaku Flour on the Gut Microbiota of Obese Patients.	Li Y, Kang Y, Du Y, Chen M, Guo L, Huang X, Li T, Chen S, Yang F, Yu F, Hong J, Kong X.	Front Cell Infect Microbiol	10.3389/fcimb.2022.771748	2022
	The gut microbiome, chronic kidney disease, and sarcopenia.	Zheng G, Cao J, Wang XH, He W, Wang B.	Cell Commun Signal	10.1186/s12964-024-01922-1	2024
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
	Sarecycline Demonstrated Reduced Activity Compared to Minocycline against Microbial Species Representing Human Gastrointestinal Microbiota.	Ghannoum MA, Long L, Bunick CG, Del Rosso JQ, Gamal A, Tyring SK, McCormick TS, Grada A.	Antibiotics (Basel)	10.3390/antibiotics11030324	2022
	The gut microbiota modifies antibody durability and booster responses after SARS-CoV-2 vaccination.	Seong H, Yoon JG, Nham E, Choi YJ, Noh JY, Cheong HJ, Kim WJ, Kim EH, Kim C, Han YH, Lim S, Song JY.	J Transl Med	10.1186/s12967-024-05637-2	2024
	Colorectal cancer-specific microbiome in peripheral circulation and cancer tissues.	Yan S, Liu T, Zhao H, Zhao C, Zhu Y, Dai W, Sun W, Wang H, Sun J, Zhao L, Xu D.	Front Microbiol	10.3389/fmicb.2024.1422536	2024
	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
Enzymology	A widespread hydrogenase supports fermentative growth of gut bacteria in healthy people.	Welsh C, Cabotaje PR, Marcelino VR, Watts TD, Kountz DJ, Jespersen M, Gould JA, Doan NQ, Lingford JP, Koralegedara T, Solari J, D'Adamo GL, Huang P, Bong N, Gulliver EL, Young RB, Land H, Walter K, Cann I, Pereira GV, Martens EC, Wolf PG, Ridlon JM, Gaskins HR, Giles EM, Lyras D, Lappan R, Berggren G, Forster SC, Greening C.	Nat Microbiol	10.1038/s41564-025-02154-w	2025
	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
	Gut microbiome features associated with liver fibrosis in Hispanics, a population at high risk for fatty liver disease.	Kwan SY, Jiao J, Joon A, Wei P, Petty LE, Below JE, Daniel CR, Wu X, Zhang J, Jenq RR, Futreal PA, Hawk ET, McCormick JB, Fisher-Hoch SP, Beretta L.	Hepatology	10.1002/hep.32197	2022
	Prebiotics improve frailty status in community-dwelling older individuals in a double-blind, randomized, controlled trial.	Yang J, Hou L, Wang A, Shang L, Jia X, Xu R, Wang X.	J Clin Invest	10.1172/jci176507	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
Genetics	Gut resistome of NSCLC patients treated with immunotherapy.	Iwan E, Grenda A, Bomba A, Bielinska K, Wasyl D, Kieszko R, Rolska-Kopinska A, Chmielewska I, Krawczyk P, Rybczynska-Tkaczyk K, Olejnik M, Milanowski J.	Front Genet	10.3389/fgene.2024.1378900	2024
Phylogeny	Uncovering specific taxonomic and functional alteration of gut microbiota in chronic kidney disease through 16S rRNA data.	Zhang Y, Zhong W, Liu W, Wang X, Lin G, Lin J, Fang J, Mou X, Jiang S, Huang J, Zhao W, Zheng Z.	Front Cell Infect Microbiol	10.3389/fcimb.2024.1363276	2024
Genetics	Gut microbiota dysbiosis induced by alcohol exposure in pubertal and adult mice.	Yang J, Wang H, Lin X, Liu J, Feng Y, Bai Y, Liang H, Hu T, Wu Z, Lai J, Liu J, Zou Y, Wei S, Yan P.	mSystems	10.1128/msystems.01366-24	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
	Influence of Microbiome and Antibiotics on the Efficacy of Immune Checkpoint Inhibitors.	Patel P, Poudel A, Kafle S, Thapa Magar M, Cancarevic I.	Cureus	10.7759/cureus.16829	2021
	Impact of cigarette smoking on gut microbial dysbiosis: a structured literature review.	Imade EE, Obayagbona NO.	Gut Microbiome (Camb)	10.1017/gmb.2024.3	2024
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
Genetics	Physical activity, sedentary behavior and microbiome: A systematic review and meta-analysis.	Perez-Prieto I, Plaza-Florido A, Ubago-Guisado E, Ortega FB, Altmae S.	J Sci Med Sport	10.1016/j.jsams.2024.07.003	2024
Phylogeny	Improved DNA Extraction and Amplification Strategy for 16S rRNA Gene Amplicon-Based Microbiome Studies.	Hong BY, Driscoll M, Gratalo D, Jarvie T, Weinstock GM.	Int J Mol Sci	10.3390/ijms25052966	2024
	Myricetin alleviates diabetic cardiomyopathy by regulating gut microbiota and their metabolites.	Zhu J, Bao Z, Hu Z, Wu S, Tian C, Zhou Y, Ding Z, Tan X.	Nutr Diabetes	10.1038/s41387-024-00268-4	2024
	Gut microbiota composition and type 2 diabetes: Are these subjects linked Together?	Razavi S, Amirmozafari N, Zahedi Bialvaei A, Navab-Moghadam F, Khamseh ME, Alaei-Shahmiri F, Sedighi M.	Heliyon	10.1016/j.heliyon.2024.e39464	2024
	Pharmacomicrobiomics: a new field contributing to optimizing drug therapy in Parkinson's disease.	Zhang Y, Mo C, Ai P, He X, Xiao Q, Yang X.	Gut Microbes	10.1080/19490976.2025.2454937	2025
	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
	Carrot RG-I Reduces Interindividual Differences between 24 Adults through Consistent Effects on Gut Microbiota Composition and Function Ex Vivo.	Van den Abbeele P, Deyaert S, Albers R, Baudot A, Mercenier A.	Nutrients	10.3390/nu15092090	2023
	The Gut Microbiome and Cancer Immunotherapy: Can We Use the Gut Microbiome as a Predictive Biomarker for Clinical Response in Cancer Immunotherapy?	Oh B, Boyle F, Pavlakis N, Clarke S, Eade T, Hruby G, Lamoury G, Carroll S, Morgia M, Kneebone A, Stevens M, Liu W, Corless B, Molloy M, Kong B, Libermann T, Rosenthal D, Back M.	Cancers (Basel)	10.3390/cancers13194824	2021
	How resistant is anammox biofilm against antibiotics: A special insight into anammox response towards fluoroquinolones.	Mamun FA, Kumar R, Anwuta KU, Das S, Jaagura M, Herodes K, Kyrpel T, Borzyszkowska AF, Zielinska-Jurek A, Vincevica-Gaile Z, Burlakovs J, Krauklis AE, Azra MN, Salauddin M, Zhong J, Tenno T, Bester K, Zekker I.	Heliyon	10.1016/j.heliyon.2024.e41339	2025
	The gut microbiota in persistent post-operative pain following breast cancer surgery.	Masaud K, Collins JM, Rubio RC, Corrigan M, Cotter PD, O'Brien N, Bluett R, Jimenez CK, O'Mahony SM, Shorten GD.	Sci Rep	10.1038/s41598-024-62397-1	2024
	Gut-on-a-Chip for the Analysis of Bacteria-Bacteria Interactions in Gut Microbial Community: What Would Be Needed for Bacterial Co-Culture Study to Explore the Diet-Microbiota Relationship?	Lee KW, Shin JS, Lee CM, Han HY, O Y, Kim HW, Cho TJ.	Nutrients	10.3390/nu15051131	2023
	Identification of novel fructo-oligosaccharide bacterial consumers by pulse metatranscriptomics in a human stool sample.	Prattico C, Gonzalez E, Dridi L, Jazestani S, Low KE, Abbott DW, Maurice CF, Castagner B.	mSphere	10.1128/msphere.00668-24	2025
	Non-stochastic reassembly of a metabolically cohesive gut consortium shaped by N-acetyl-lactosamine-enriched fibers.	Moore M, Whittington HD, Knickmeyer R, Azcarate-Peril MA, Bruno-Barcena JM.	Gut Microbes	10.1080/19490976.2024.2440120	2025
	Effects of Ecologically Relevant Concentrations of Cadmium on the Microbiota, Short-Chain Fatty Acids, and FFAR₂ Expression in Zebrafish.	Yang J, Li J, Zhang X, Zhou Q, Wang J, Chen Q, Meng X, Xia Y.	Metabolites	10.3390/metabo13050657	2023
	Identifying Gut Microbiota associated with Gastrointestinal Symptoms upon Roux-en-Y Gastric Bypass.	Wijdeveld M, van Olst N, van der Vossen EWJ, de Brauw M, Acherman YIZ, de Goffau MC, Gerdes VEA, Nieuwdorp M.	Obes Surg	10.1007/s11695-023-06610-6	2023
	Altered Nasal Microbiome in Atrophic Rhinitis: A Novel Theory of Etiopathogenesis and Therapy.	Sarkar S, Magne F, Venugopal G, Purkait S, Mutha NVR, Maiti R, Sharma P, Ramadass B.	Microorganisms	10.3390/microorganisms10112092	2022
	Sulfated and non-sulfated chondroitin affect the composition and metabolism of human colonic microbiota simulated in an in vitro fermentation system.	Inokuma K, Sasaki D, Kurata K, Ichikawa M, Otsuka Y, Kondo A.	Sci Rep	10.1038/s41598-023-38849-5	2023
	The Impact of Integrating a Low-Lectin Diet with Traditional ADHD Treatments on Gut Microbiota Composition and Symptom Improvement in Children - A Cohort Study.	Long L, Peng H, Chen X, Wang F, Long W, Cheng M, Ma J.	Neuropsychiatr Dis Treat	10.2147/ndt.s449186	2024
	Identifying Microbiome Dynamics in Pediatric IBD: More than a Family Matter.	Dovrolis N, Moschoviti A, Fessatou S, Karamanolis G, Kolios G, Gazouli M.	Biomedicines	10.3390/biomedicines11071979	2023
	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
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
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
	Multi-omics analysis reveals the interaction of gut microbiome and host microRNAs in ulcerative colitis.	Ma L, Hou C, Yang H, Chen Q, Lyu W, Wang Z, Wang J, Xiao Y.	Ann Med	10.1080/07853890.2023.2261477	2023
Pathogenicity	Effects of Smoking on Inflammatory Markers in a Healthy Population as Analyzed via the Gut Microbiota.	Yan S, Ma Z, Jiao M, Wang Y, Li A, Ding S.	Front Cell Infect Microbiol	10.3389/fcimb.2021.633242	2021
Pathogenicity	Alteration of the gut microbiota in patients with lung cancer accompanied by chronic obstructive pulmonary diseases.	Wang T, Su W, Li L, Wu H, Huang H, Li Z.	Heliyon	10.1016/j.heliyon.2024.e30380	2024
	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
	Temporal relationship among adiposity, gut microbiota, and insulin resistance in a longitudinal human cohort.	Deng K, Shuai M, Zhang Z, Jiang Z, Fu Y, Shen L, Zheng JS, Chen YM.	BMC Med	10.1186/s12916-022-02376-3	2022
Metabolism	Sulfoquinovose is exclusively metabolized by the gut microbiota and degraded differently in mice and humans.	Krasenbrink J, Hanson BT, Weiss AS, Borusak S, Tanabe TS, Lang M, Aichinger G, Hausmann B, Berry D, Richter A, Marko D, Mussmann M, Schleheck D, Stecher B, Loy A.	Microbiome	10.1186/s40168-025-02175-x	2025
Genetics	Type 1 diabetes in pregnancy is associated with distinct changes in the composition and function of the gut microbiome.	Roth-Schulze AJ, Penno MAS, Ngui KM, Oakey H, Bandala-Sanchez E, Smith AD, Allnutt TR, Thomson RL, Vuillermin PJ, Craig ME, Rawlinson WD, Davis EA, Harris M, Soldatos G, Colman PG, Wentworth JM, Haynes A, Barry SC, Sinnott RO, Morahan G, Bediaga NG, Smyth GK, Papenfuss AT, Couper JJ, Harrison LC, ENDIA Study Group.	Microbiome	10.1186/s40168-021-01104-y	2021
	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
Phylogeny	Absolute quantification of viable bacteria abundances in food by next-generation sequencing: Quantitative NGS of viable microbes.	Kallastu A, Malv E, Aro V, Meikas A, Vendelin M, Kattel A, Nahku R, Kazantseva J.	Curr Res Food Sci	10.1016/j.crfs.2023.100443	2023
Transcriptome	Characterization of liver, adipose, and fecal microbiome in obese patients with MASLD: links with disease severity and metabolic dysfunction parameters.	Schwenger KJP, Copeland JK, Ghorbani Y, Chen L, Comelli EM, Guttman DS, Fischer SE, Jackson TD, Okrainec A, Allard JP.	Microbiome	10.1186/s40168-024-02004-7	2025
Pathogenicity	Function-based selection of synthetic communities enables mechanistic microbiome studies.	Hitch TCA, Bosch J, Bolsega S, Deschamps C, Etienne-Mesmin L, Treichel N, Blanquet-Diot S, Ocvirk S, Basic M, Clavel T.	ISME J	10.1093/ismejo/wraf209	2025
Genetics	Alterations in the gut virome are associated with type 2 diabetes and diabetic nephropathy.	Fan G, Cao F, Kuang T, Yi H, Zhao C, Wang L, Peng J, Zhuang Z, Xu T, Luo Y, Xie Y, Li H, Zhang K, Zeng Y, Zhang X, Peng S, Qiu X, Zhou D, Liang H, Yang B, Kang J, Liu Y, Zhang Y.	Gut Microbes	10.1080/19490976.2023.2226925	2023
	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
	First Study on profiling of gut microbiome in wild and captive Sumatran orangutans (Pongo abelii).	Safika S, Indrawati A, Afiff U, Hastuti YT, Zureni Z, Jati AP.	Vet World	10.14202/vetworld.2023.717-727	2023
	Traditional Chinese Medicine: An Exogenous Regulator of Crosstalk between the Gut Microbial Ecosystem and CKD.	Sun X, Sun W, Huang Y, Chen J.	Evid Based Complement Alternat Med	10.1155/2022/7940684	2022
	Snapshot into the Type-2-Diabetes-Associated Microbiome of a Romanian Cohort.	Gradisteanu Pircalabioru G, Chifiriuc MC, Picu A, Petcu LM, Trandafir M, Savu O.	Int J Mol Sci	10.3390/ijms232315023	2022
Genetics	Case-Control Study of the Effects of Gut Microbiota Composition on Neurotransmitter Metabolic Pathways in Children With Attention Deficit Hyperactivity Disorder.	Wan L, Ge WR, Zhang S, Sun YL, Wang B, Yang G.	Front Neurosci	10.3389/fnins.2020.00127	2020
Pathogenicity	Sexual behavior is linked to changes in gut microbiome and systemic inflammation that lead to HIV-1 infection in men who have sex with men.	Lin H, Chen Y, Abror-Lacks G, Price M, Morris A, Sun J, Palella F, Chew KW, Brown TT, Rinaldo CR, Peddada SD.	Commun Biol	10.1038/s42003-024-06816-z	2024
	Immunological design of commensal communities to treat intestinal infection and inflammation.	Brown RL, Larkinson MLY, Clarke TB.	PLoS Pathog	10.1371/journal.ppat.1009191	2021
	Infection leaves a genetic and functional mark on the gut population of a commensal bacterium.	Tawk C, Lim B, Bencivenga-Barry NA, Lees HJ, Ramos RJF, Cross J, Goodman AL.	Cell Host Microbe	10.1016/j.chom.2023.04.005	2023
	Microbial Dysbiosis Linked to Metabolic Dysfunction-Associated Fatty Liver Disease in Asians: Prevotella copri Promotes Lipopolysaccharide Biosynthesis and Network Instability in the Prevotella Enterotype.	Yuan H, Wu X, Wang X, Zhou JY, Park S.	Int J Mol Sci	10.3390/ijms25042183	2024
	New insights into the links between anti-diabetes drugs and gut microbiota.	Hu R, Yuan Y, Liu C, Zhou J, Ji L, Jiang G.	Endocr Connect	10.1530/ec-20-0431	2021
	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
	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
Pathogenicity	The Role of Host Genetics and Intestinal Microbiota and Metabolome as a New Insight into IBD Pathogenesis.	Zakerska-Banaszak O, Zuraszek-Szymanska J, Eder P, Ladziak K, Slomski R, Skrzypczak-Zielinska M.	Int J Mol Sci	10.3390/ijms25179589	2024
	[Necrotizing fasciitis after a cat bite: a case report].	Hosoda T, Yanagisawa N, Morioka H, Suganuma A, Imamura A, Ajisawa A.	Kansenshogaku Zasshi	10.11150/kansenshogakuzasshi.87.211	2013
	The effect of intestinal flora on immune checkpoint inhibitors in tumor treatment: a narrative review.	Wang D, Hao H, Li X, Wang Z.	Ann Transl Med	10.21037/atm-20-4535	2020
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
	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
Genetics	The gut microbiome as a potential source of non-invasive biomarkers of chronic obstructive pulmonary disease.	Li N, Yi X, Chen C, Dai Z, Deng Z, Pu J, Zhou Y, Li B, Wang Z, Ran P.	Front Microbiol	10.3389/fmicb.2023.1173614	2023
	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
	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
Genetics	Strain-resolved microbiome sequencing reveals mobile elements that drive bacterial competition on a clinical timescale.	Zlitni S, Bishara A, Moss EL, Tkachenko E, Kang JB, Culver RN, Andermann TM, Weng Z, Wood C, Handy C, Ji HP, Batzoglou S, Bhatt AS.	Genome Med	10.1186/s13073-020-00747-0	2020
	Gut Microbiota and Host Cometabolism Are Altered by Patiromer-Induced Changes in Serum and Stool Potassium.	Gao B, Friedman ES, Regunathan R, Shrivastava A, Barrows IR, Amdur RL, Andrews SC, Barrows ED, Raj DS.	Kidney Int Rep	10.1016/j.ekir.2020.12.026	2021
	Postbiotics Enhance NK Cell Activation in Stress-Induced Mice through Gut Microbiome Regulation.	Jung YJ, Kim HS, Jaygal G, Cho HR, Lee KB, Song IB, Kim JH, Kwak MS, Han KH, Bae MJ, Sung MH.	J Microbiol Biotechnol	10.4014/jmb.2111.11027	2022
	Identifying microbial signatures for patients with postmenopausal osteoporosis using gut microbiota analyses and feature selection approaches.	Huang D, Wang J, Zeng Y, Li Q, Wang Y.	Front Microbiol	10.3389/fmicb.2023.1113174	2023
Metabolism	Metabolites with SARS-CoV-2 Inhibitory Activity Identified from Human Microbiome Commensals.	Piscotta FJ, Hoffmann HH, Choi YJ, Small GI, Ashbrook AW, Koirala B, Campbell EA, Darst SA, Rice CM, Brady SF.	mSphere	10.1128/msphere.00711-21	2021
	Characteristics of gut microbiota in patients with metabolic associated fatty liver disease.	Yang C, Xu J, Xu X, Xu W, Tong B, Wang S, Ji R, Tan Y, Zhu Y.	Sci Rep	10.1038/s41598-023-37163-4	2023
	Big data analytics frameworks for the influence of gut microbiota on the development of tic disorder.	Fan F, Bian Z, Zhang X, Wu H, Wang S, Zhang S, Wang Q, Han F.	Front Comput Neurosci	10.3389/fncom.2022.986591	2022
	Effects of prebiotic oligofructose-enriched inulin on gut-derived uremic toxins and disease progression in rats with adenine-induced chronic kidney disease.	Melekoglu E, Cetinkaya MA, Kepekci-Tekkeli SE, Kul O, Samur G.	PLoS One	10.1371/journal.pone.0258145	2021
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
	The functional landscape of the appendix microbiome under conditions of health and disease	Sagor M, Islam T, Tamanna N, Bappy M, Danishuddin, Haque M, Lackner M.	Gut Pathog		2025
Phylogeny	Distinct gut microbiomes in Thai patients with colorectal polyps.	Intarajak T, Udomchaiprasertkul W, Khoiri AN, Sutheeworapong S, Kusonmano K, Kittichotirat W, Thammarongtham C, Cheevadhanarak S.	World J Gastroenterol	10.3748/wjg.v30.i27.3336	2024
	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
	Diet-gut microbiome interaction and its impact on host blood glucose homeostasis: a series of nutritional n-of-1 trials.	Fu Y, Gou W, Zhong H, Tian Y, Zhao H, Liang X, Shuai M, Zhuo LB, Jiang Z, Tang J, Ordovas JM, Chen YM, Zheng JS.	EBioMedicine	10.1016/j.ebiom.2024.105483	2025
Metabolism	Interrelationship of Stress, Environment, and Herpes Simplex Virus Type-1 on Behçet's Disease: Using a Mouse Model.	Islam SMS, Ryu HM, Sayeed HM, Sohn S.	Front Immunol	10.3389/fimmu.2021.607768	2021
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
Enzymology	Structure and function of microbial alpha-l-fucosidases: a mini review.	Wu H, Owen CD, Juge N.	Essays Biochem	10.1042/ebc20220158	2023
	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
	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
	Hermetia illucens Fermented with Lactobacillus plantarum KCCM12757P Alleviates Dextran Sodium Sulfate-Induced Colitis in Mice.	Son SJ, Han AR, Sung MJ, Hong SM, Lee SH.	Antioxidants (Basel)	10.3390/antiox12101822	2023
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
	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
	Attributes of intestinal microbiota composition and their correlation with clinical primary non-response to anti-TNF-alpha agents in inflammatory bowel disease patients.	Alatawi H, Mosli M, Saadah OI, Annese V, Al-Hindi R, Alatawy M, Al-Amrah H, Alshehri D, Bahieldin A, Edris S.	Bosn J Basic Med Sci	10.17305/bjbms.2021.6436	2022
Genetics	Nasal Microbiome and Its Interaction with the Host in Childhood Asthma.	Zeng Y, Liang JQ.	Cells	10.3390/cells11193155	2022
	Carbohydrate-active enzymes from Akkermansia muciniphila break down mucin O-glycans to completion.	Bakshani CR, Ojuri TO, Pilgaard B, Holck J, McInnes R, Kozak RP, Zakhour M, Cakaj S, Kerouedan M, Newton E, Bolam DN, Crouch LI.	Nat Microbiol	10.1038/s41564-024-01911-7	2025
Metabolism	A Soluble Fiber Diet Increases Bacteroides fragilis Group Abundance and Immunoglobulin A Production in the Gut.	Nakajima A, Sasaki T, Itoh K, Kitahara T, Takema Y, Hiramatsu K, Ishikawa D, Shibuya T, Kobayashi O, Osada T, Watanabe S, Nagahara A.	Appl Environ Microbiol	10.1128/aem.00405-20	2020
	Association between Dietary Habits and Fecal Microbiota Composition in Irritable Bowel Syndrome Patients: A Pilot Study.	Altomare A, Del Chierico F, Rocchi G, Emerenziani S, Nuglio C, Putignani L, Angeletti S, Lo Presti A, Ciccozzi M, Russo A, Cocca S, Ribolsi M, Muscaritoli M, Cicala M, Guarino MPL.	Nutrients	10.3390/nu13051479	2021
	Group A Streptococci-Associated Necrotizing Fasciitis following Cat Bite in an Immunocompromised Patient.	Nambiar S, Karippot A, Devasahayam J, Oliver T.	Case Rep Crit Care	10.1155/2017/3718360	2017
	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
	Akkermansia muciniphila Improves Depressive-Like Symptoms by Modulating the Level of 5-HT Neurotransmitters in the Gut and Brain of Mice.	Guo H, Liu X, Chen T, Wang X, Zhang X.	Mol Neurobiol	10.1007/s12035-023-03602-6	2024
Genetics	When old metagenomic data meet newly sequenced genomes, a case study.	Li X, Naser SA, Khaled A, Hu H, Li X.	PLoS One	10.1371/journal.pone.0198773	2018
	Gut commensals-derived succinate impels colonic inflammation in ulcerative colitis.	Dalal R, Sadhu S, Batra A, Goswami S, Dandotiya J, K V V, Yadav R, Singh V, Chaturvedi K, Kannan R, Kumar S, Kumar Y, Rathore DK, Salunke DB, Ahuja V, Awasthi A.	NPJ Biofilms Microbiomes	10.1038/s41522-025-00672-3	2025
	Simulated digestions of free oligosaccharides and mucin-type O-glycans reveal a potential role for Clostridium perfringens.	McDonald AG, Lisacek F.	Sci Rep	10.1038/s41598-023-51012-4	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
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
Pathogenicity	Intestinal microbiome and metabolome signatures in patients with chronic granulomatous disease.	Chandrasekaran P, Han Y, Zerbe CS, Heller T, DeRavin SS, Kreuzberg SA, Marciano BE, Siu Y, Jones DR, Abraham RS, Stephens MC, Tsou AM, Snapper S, Conlan S, Subramanian P, Quinones M, Grou C, Calderon V, Deming C, Leiding JW, Arnold DE, Logan BR, Griffith LM, Petrovic A, Mousallem TI, Kapoor N, Heimall JR, Barnum JL, Kapadia M, Wright N, Rayes A, Chandra S, Broglie LA, Chellapandian D, Deal CL, Grunebaum E, Lim SS, Mallhi K, Marsh RA, Murguia-Favela L, Parikh S, Touzot F, Cowan MJ, Dvorak CC, Haddad E, Kohn DB, Notarangelo LD, Pai SY, Puck JM, Pulsipher MA, Torgerson TR, Kang EM, Malech HL, Segre JA, Bryant CE, Holland SM, Falcone EL.	J Allergy Clin Immunol	10.1016/j.jaci.2023.07.022	2023
	Fecal microbiota transplantation and its repercussions in patients with melanoma refractory to anti-PD-1 therapy: scope review.	Barbosa EC, Bucar EEC, Jube GR, Silveira LB, Silva NCD, Faria PCC, Ramos PLC, Moraes VRY, Barros JOB.	Rev Col Bras Cir	10.1590/0100-6991e-20233490-en	2023
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
	Multi-level analysis of gut microbiome extracellular vesicles-host interaction reveals a connection to gut-brain axis signaling.	Mottawea W, Yousuf B, Sultan S, Ahmed T, Yeo J, Huttmann N, Li Y, Bouhlel NE, Hassan H, Zhang X, Minic Z, Hammami R.	Microbiol Spectr	10.1128/spectrum.01368-24	2025
	Systematic review of the impact of intestinal microbiota on vaccine responses.	Ardura-Garcia C, Curtis N, Zimmermann P.	NPJ Vaccines	10.1038/s41541-024-01000-0	2024
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
Genetics	A metagenomics pipeline reveals insertion sequence-driven evolution of the microbiota.	Kirsch JM, Hryckowian AJ, Duerkop BA.	Cell Host Microbe	10.1016/j.chom.2024.03.005	2024
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
	Immunotherapy and Microbiota for Targeting of Liver Tumor-Initiating Stem-like Cells.	Machida K, Tahara SM.	Cancers (Basel)	10.3390/cancers14102381	2022
	Structures of the Skin Microbiome and Mycobiome Depending on Skin Sensitivity.	Keum HL, Kim H, Kim HJ, Park T, Kim S, An S, Sul WJ.	Microorganisms	10.3390/microorganisms8071032	2020
Metabolism	Analysis of correlations between gut microbiota, stool short chain fatty acids, calprotectin and cardiometabolic risk factors in postmenopausal women with obesity: a cross-sectional study.	Loniewski I, Szulinska M, Kaczmarczyk M, Podsiadlo K, Styburski D, Skonieczna-Zydecka K, Bogdanski P.	J Transl Med	10.1186/s12967-022-03801-0	2022
	Effect and Potential Mechanism of Lactobacillus plantarum Q7 on Hyperuricemia in vitro and in vivo.	Cao J, Bu Y, Hao H, Liu Q, Wang T, Liu Y, Yi H.	Front Nutr	10.3389/fnut.2022.954545	2022
	Examining the immunoepigenetic-gut microbiome axis in the context of self-esteem among Native Hawaiians and other Pacific Islanders.	Becerra CY, Wells RK, Kunihiro BP, Lee RH, Umeda L, Allan NP, Rubas NC, McCracken TA, Nunokawa CKL, Lee MH, Pidlaoan FGS, Phankitnirondorn K, Dye CK, Yamamoto BY, Peres R, Juarez R, Maunakea AK.	Front Genet	10.3389/fgene.2023.1125217	2023
	The Local Microbiome in Esophageal Cancer and Treatment Response: A Review of Emerging Data and Future Directions.	Pandey A, Lieu CH, Kim SS.	Cancers (Basel)	10.3390/cancers15143562	2023
	Perturbed Microbiota/Immune Homeostasis in Multiple Sclerosis.	Sterlin D, Larsen M, Fadlallah J, Parizot C, Vignes M, Autaa G, Dorgham K, Juste C, Lepage P, Aboab J, Vicart S, Maillart E, Gout O, Lubetzki C, Deschamps R, Papeix C, Gorochov G.	Neurol Neuroimmunol Neuroinflamm	10.1212/nxi.0000000000000997	2021
Pathogenicity	COVID-19 Infection Alters the Microbiome: Elite Athletes and Sedentary Patients Have Similar Bacterial Flora.	Babszky G, Torma F, Aczel D, Bakonyi P, Gombos Z, Feher J, Szabo D, Ligeti B, Pongor S, Balogh L, Posa A, Radak Z.	Genes (Basel)	10.3390/genes12101577	2021
	Dynamics of the gut microbiota in rats after hypobaric hypoxia exposure.	Han Y, Xu J, Yan Y, Zhao X.	PeerJ	10.7717/peerj.14090	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
	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
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
	Gut bacterial metabolism contributes to host global purine homeostasis.	Kasahara K, Kerby RL, Zhang Q, Pradhan M, Mehrabian M, Lusis AJ, Bergstrom G, Backhed F, Rey FE.	Cell Host Microbe	10.1016/j.chom.2023.05.011	2023
	Dysbiosis signatures of gut microbiota and the progression of type 2 diabetes: a machine learning approach in a Mexican cohort.	Neri-Rosario D, Martinez-Lopez YE, Esquivel-Hernandez DA, Sanchez-Castaneda JP, Padron-Manrique C, Vazquez-Jimenez A, Giron-Villalobos D, Resendis-Antonio O.	Front Endocrinol (Lausanne)	10.3389/fendo.2023.1170459	2023
Phylogeny	Maternal microbiota and gestational diabetes: impact on infant health.	Singh P, Elhaj DAI, Ibrahim I, Abdullahi H, Al Khodor S.	J Transl Med	10.1186/s12967-023-04230-3	2023
	Lactobacillus gasseri LG08 and Leuconostoc mesenteroides LM58 exert preventive effect on the development of hyperuricemia by repairing antioxidant system and intestinal flora balance.	Liang L, Meng Z, Zhang F, Jianguo Z, Fang S, Hu Q, Tang X, Li Y.	Front Microbiol	10.3389/fmicb.2023.1211831	2023
	The global RNA-binding protein RbpB is a regulator of polysaccharide utilization in Bacteroides thetaiotaomicron.	Ruttiger AS, Ryan D, Spiga L, Lamm-Schmidt V, Prezza G, Reichardt S, Langford M, Barquist L, Faber F, Zhu W, Westermann AJ.	Nat Commun	10.1038/s41467-024-55383-8	2025
	Influence of Bifidobacterium breve on the Glycaemic Control, Lipid Profile and Microbiome of Type 2 Diabetic Subjects: A Preliminary Randomized Clinical Trial.	Chaiyasut C, Sivamaruthi BS, Lailerd N, Sirilun S, Thangaleela S, Khongtan S, Bharathi M, Kesika P, Saelee M, Choeisoongnern T, Fukngoen P, Peerajan S, Sittiprapaporn P.	Pharmaceuticals (Basel)	10.3390/ph16050695	2023
	Early microbial markers of celiac disease.	Viitasalo L, Niemi L, Ashorn M, Ashorn S, Braun J, Huhtala H, Collin P, Maki M, Kaukinen K, Kurppa K, Iltanen S.	J Clin Gastroenterol	10.1097/mcg.0000000000000089	2014
	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
	In vitro digestive characteristics and microbial degradation of polysaccharides from lotus leaves and related effects on the modulation of intestinal microbiota.	Wu DT, Feng KL, Li F, Hu YC, Wang SP, Gan RY, Zou L.	Curr Res Food Sci	10.1016/j.crfs.2022.04.004	2022
	Association of antimicrobial resistance and gut microbiota composition in human and non-human primates at an urban ecotourism site.	Chong CW, Alkatheeri AHS, Ali N, Tay ZH, Lee YL, Paramasivam SJ, Jeevaratnam K, Low WY, Lim SHE.	Gut Pathog	10.1186/s13099-020-00352-x	2020
	GH136-encoding gene (perB) is involved in gut colonization and persistence by Bifidobacterium bifidum PRL2010.	Rizzo SM, Vergna LM, Alessandri G, Lee C, Fontana F, Lugli GA, Carnevali L, Bianchi MG, Barbetti M, Taurino G, Sgoifo A, Bussolati O, Turroni F, van Sinderen D, Ventura M.	Microb Biotechnol	10.1111/1751-7915.14406	2024
	Multi-omics of the gut microbial ecosystem in patients with microsatellite-instability-high gastrointestinal cancer resistant to immunotherapy.	Cheng S, Han Z, Dai D, Li F, Zhang X, Lu M, Lu Z, Wang X, Zhou J, Li J, Guo X, Song P, Qiu C, Shen W, Zhang Q, Zhu N, Wang X, Tan Y, Kou Y, Yin X, Shen L, Peng Z.	Cell Rep Med	10.1016/j.xcrm.2023.101355	2024
	Exploring the Involvement of Gut Microbiota in Cancer Therapy-Induced Cardiotoxicity.	Kunika, Frey N, Rangrez AY.	Int J Mol Sci	10.3390/ijms24087261	2023
	Higher pathogen load in children from Mozambique vs. USA revealed by comparative fecal microbiome profiling.	Kim M, Rodriguez-R LM, Hatt JK, Kayali O, Nala R, Dunlop AL, Brennan PA, Corwin E, Smith AK, Brown J, Konstantinidis KT.	ISME Commun	10.1038/s43705-022-00154-z	2022
	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
Enzymology	Design of species-specific oligonucleotide probes for the detection of Bacteroides and Parabacteroides by fluorescence in situ hybridization and their application to the analysis of mouse caecal Bacteroides-Parabacteroides microbiota.	Momose Y, Park SH, Miyamoto Y, Itoh K.	J Appl Microbiol	10.1111/j.1365-2672.2011.05039.x	2011
Metabolism	Sex differences in the phylum-level human gut microbiota composition.	Koliada A, Moseiko V, Romanenko M, Lushchak O, Kryzhanovska N, Guryanov V, Vaiserman A.	BMC Microbiol	10.1186/s12866-021-02198-y	2021
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
	Host-Population Microbial Diversity Scaling of Chinese Gut Microbiomes in Gout Patients.	Zhou J, Yuan Y, Xu P, Yi B, Chen H, Su W.	Evol Bioinform Online	10.1177/11769343221095858	2022
Metabolism	Analysis of the gut microbiome in obese native Tibetan children living at different altitudes: A case-control study.	Du W, Liu L, Ma Y, Zhu Q, Jia R, Han Y, Wu Z, Yan X, Ailizire A, Zhang W.	Front Public Health	10.3389/fpubh.2022.963202	2022
	Changes in Gut Microbiome upon Orchiectomy and Testosterone Administration in AOM/DSS-Induced Colon Cancer Mouse Model.	Song CH, Kim N, Nam RH, Choi SI, Jang JY, Lee HN.	Cancer Res Treat	10.4143/crt.2022.080	2023
	Human Fecal Microbiota Transplantation Reduces the Susceptibility to Dextran Sulfate Sodium-Induced Germ-Free Mouse Colitis.	Yang Y, Zheng X, Wang Y, Tan X, Zou H, Feng S, Zhang H, Zhang Z, He J, Cui B, Zhang X, Wu Z, Dong M, Cheng W, Tao S, Wei H.	Front Immunol	10.3389/fimmu.2022.836542	2022
Enzymology	Prosthetic joint infections present diverse and unique microbial communities using combined whole-genome shotgun sequencing and culturing methods.	Weaver AA, Hasan NA, Klaassen M, Karathia H, Colwell RR, Shrout JD.	J Med Microbiol	10.1099/jmm.0.001068	2019
Genetics	SARS-CoV-2 triggered oxidative stress and abnormal energy metabolism in gut microbiota.	Zhou T, Wu J, Zeng Y, Li J, Yan J, Meng W, Han H, Feng F, He J, Zhao S, Zhou P, Wu Y, Yang Y, Han R, Jin W, Li X, Yang Y, Li X.	MedComm (2020)	10.1002/mco2.112	2022
	Metaproteomics reveals parallel utilization of colonic mucin glycans and dietary fibers by the human gut microbiota.	Raba G, Luis AS, Schneider H, Morell I, Jin C, Adamberg S, Hansson GC, Adamberg K, Arike L.	iScience	10.1016/j.isci.2024.110093	2024
	Potential Gut Microbiota Features for Non-Invasive Detection of Schistosomiasis.	Lin D, Song Q, Liu J, Chen F, Zhang Y, Wu Z, Sun X, Wu X.	Front Immunol	10.3389/fimmu.2022.941530	2022
	Lactobacillus paracasei X11 Ameliorates Hyperuricemia and Modulates Gut Microbiota in Mice.	Cao J, Liu Q, Hao H, Bu Y, Tian X, Wang T, Yi H.	Front Immunol	10.3389/fimmu.2022.940228	2022
	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
	Dynamics of bacterial recombination in the human gut microbiome.	Liu Z, Good BH.	PLoS Biol	10.1371/journal.pbio.3002472	2024
	Do proton pump inhibitors alter the response to immune checkpoint inhibitors in cancer patients? A meta-analysis.	Lopes S, Pabst L, Dory A, Klotz M, Gourieux B, Michel B, Mascaux C.	Front Immunol	10.3389/fimmu.2023.1070076	2023
	Vaccination with an HIV T-cell immunogen induces alterations in the mouse gut microbiota.	Borgognone A, Elizalde-Torrent A, Casadella M, Romero L, Escriba T, Parera M, Catala-Moll F, Noguera-Julian M, Brander C, Olvera A, Paredes R.	NPJ Biofilms Microbiomes	10.1038/s41522-022-00368-y	2022
Metabolism	Gut microbes impact stroke severity via the trimethylamine N-oxide pathway.	Zhu W, Romano KA, Li L, Buffa JA, Sangwan N, Prakash P, Tittle AN, Li XS, Fu X, Androjna C, DiDonato AJ, Brinson K, Trapp BD, Fischbach MA, Rey FE, Hajjar AM, DiDonato JA, Hazen SL.	Cell Host Microbe	10.1016/j.chom.2021.05.002	2021
	Gut microbiota is involved in male reproductive function: a review.	Lv S, Huang J, Luo Y, Wen Y, Chen B, Qiu H, Chen H, Yue T, He L, Feng B, Yu Z, Zhao M, Yang Q, He M, Xiao W, Zou X, Gu C, Lu R.	Front Microbiol	10.3389/fmicb.2024.1371667	2024
	Microbiota composition effect on immunotherapy outcomes in colorectal cancer patients: A systematic review.	Ajab SM, Zoughbor SH, Labania LA, Ostlundh LM, Orsud HS, Olanda MA, Alkaabi O, Alkuwaiti SH, Alnuaimi SM, Al Rasbi Z.	PLoS One	10.1371/journal.pone.0307639	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
Metabolism	Combining functional metagenomics and glycoanalytics to identify enzymes that facilitate structural characterization of sulfated N-glycans.	Chuzel L, Fossa SL, Boisvert ML, Cajic S, Hennig R, Ganatra MB, Reichl U, Rapp E, Taron CH.	Microb Cell Fact	10.1186/s12934-021-01652-w	2021
	Baseline gut microbiota and metabolome predict durable immunogenicity to SARS-CoV-2 vaccines.	Peng Y, Zhang L, Mok CKP, Ching JYL, Zhao S, Wong MKL, Zhu J, Chen C, Wang S, Yan S, Qin B, Liu Y, Zhang X, Cheung CP, Cheong PK, Ip KL, Fung ACH, Wong KKY, Hui DSC, Chan FKL, Ng SC, Tun HM.	Signal Transduct Target Ther	10.1038/s41392-023-01629-8	2023
	Adhesive intestinal obstruction increases the risk of intestinal perforation in peritoneal dialysis patients: a case report.	Fujii K, Washida N, Arai E, Tsuruta M, Wakino S, Itoh H.	BMC Nephrol	10.1186/s12882-018-0954-x	2018
	Determinants of raffinose family oligosaccharide use in Bacteroides species.	Basu A, Adams AND, Degnan PH, Vanderpool CK.	J Bacteriol	10.1128/jb.00235-24	2024
Enzymology	Human-specific fecal bacteria in wastewater treatment plant effluents.	Wery N, Monteil C, Pourcher AM, Godon JJ.	Water Res	10.1016/j.watres.2009.11.027	2010
	Ruminococcus torques is a keystone degrader of intestinal mucin glycoprotein, releasing oligosaccharides used by Bacteroides thetaiotaomicron.	Schaus SR, Vasconcelos Pereira G, Luis AS, Madlambayan E, Terrapon N, Ostrowski MP, Jin C, Henrissat B, Hansson GC, Martens EC.	mBio	10.1128/mbio.00039-24	2024
Phylogeny	Microbiome Profiling from Fecal Immunochemical Test Reveals Microbial Signatures with Potential for Colorectal Cancer Screening.	Khannous-Lleiffe O, Willis JR, Saus E, Moreno V, Castellvi-Bel S, Gabaldon T, On Behalf Of The Criprev Consortium.	Cancers (Basel)	10.3390/cancers15010120	2022
	Use of Changestat for Growth Rate Studies of Gut Microbiota.	Adamberg K, Raba G, Adamberg S.	Front Bioeng Biotechnol	10.3389/fbioe.2020.00024	2020
	Immunotherapy in Colorectal Cancer: Potential of Fecal Transplant and Microbiota-augmented Clinical Trials.	Park R, Umar S, Kasi A.	Curr Colorectal Cancer Rep	10.1007/s11888-020-00456-1	2020
	High Antioxidant Capacity of Lacticaseibacillus paracasei TDM-2 and Pediococcus pentosaceus TCM-3 from Qinghai Tibetan Plateau and Their Function towards Gut Modulation.	Yang T, Fan X, Li D, Zhao T, Wu D, Liu Z, Long D, Li B, Huang X.	Foods	10.3390/foods12091814	2023
	Effects of Ramadan intermittent fasting on gut microbiome: is the diet key?	Saglam D, Colak GA, Sahin E, Ekren BY, Sezerman U, Bas M.	Front Microbiol	10.3389/fmicb.2023.1203205	2023
	Gut Microbiota Markers in Obese Adolescent and Adult Patients: Age-Dependent Differential Patterns.	Del Chierico F, Abbatini F, Russo A, Quagliariello A, Reddel S, Capoccia D, Caccamo R, Ginanni Corradini S, Nobili V, De Peppo F, Dallapiccola B, Leonetti F, Silecchia G, Putignani L.	Front Microbiol	10.3389/fmicb.2018.01210	2018
Pathogenicity	A Six-Day, Lifestyle-Based Immersion Program Mitigates Cardiovascular Risk Factors and Induces Shifts in Gut Microbiota, Specifically Lachnospiraceae, Ruminococcaceae, Faecalibacterium prausnitzii: A Pilot Study.	Ahrens AP, Culpepper T, Saldivar B, Anton S, Stoll S, Handberg EM, Xu K, Pepine C, Triplett EW, Aggarwal M.	Nutrients	10.3390/nu13103459	2021
	The Intricate Connection between Bacterial alpha-Diversity and Fungal Engraftment in the Human Gut of Healthy and Impaired Individuals as Studied Using the In Vitro SHIME^® Model.	Marsaux B, Moens F, Marzorati M, Van de Wiele T.	J Fungi (Basel)	10.3390/jof9090877	2023
	The genomic landscape of reference genomes of cultivated human gut bacteria.	Lin X, Hu T, Chen J, Liang H, Zhou J, Wu Z, Ye C, Jin X, Xu X, Zhang W, Jing X, Yang T, Wang J, Yang H, Kristiansen K, Xiao L, Zou Y.	Nat Commun	10.1038/s41467-023-37396-x	2023
	Multimodal metagenomic analysis reveals microbial single nucleotide variants as superior biomarkers for early detection of colorectal cancer.	Gao W, Gao X, Zhu L, Gao S, Sun R, Feng Z, Wu D, Liu Z, Zhu R, Jiao N.	Gut Microbes	10.1080/19490976.2023.2245562	2023
	Detection and characterization of bacterial nucleic acids in culture-negative synovial tissue and fluid samples from rheumatoid arthritis or osteoarthritis patients.	Zhao Y, Chen B, Li S, Yang L, Zhu D, Wang Y, Wang H, Wang T, Shi B, Gai Z, Yang J, Heng X, Yang J, Zhang L.	Sci Rep	10.1038/s41598-018-32675-w	2018
Metabolism	Silicon-Enriched Meat Ameliorates Diabetic Dyslipidemia by Improving Cholesterol, Bile Acid Metabolism and Ileal Barrier Integrity in Rats with Late-Stage Type 2 Diabetes.	Hernandez-Martin M, Garcimartin A, Bocanegra A, Macho-Gonzalez A, Garcia-Fernandez RA, de Pascual-Teresa S, Redondo-Castillejo R, Bastida S, Sanchez-Muniz FJ, Benedi J, Lopez-Oliva ME.	Int J Mol Sci	10.3390/ijms252111405	2024
	Reduced gut microbiota diversity in patients with congenital generalized lipodystrophy.	Montenegro Junior RM, Ponte CMM, Castelo MHCG, de Oliveira Silveira AC, Fernandes VO, D'Alva CB, Oliveira LFV, Hristov AD, Bandeira SP, da Cruz Paiva GE, Levi JE.	Diabetol Metab Syndr	10.1186/s13098-022-00908-8	2022
	Alterations in co-abundant bacteriome in colorectal cancer and its persistence after surgery: a pilot study.	Png CW, Chua YK, Law JH, Zhang Y, Tan KK.	Sci Rep	10.1038/s41598-022-14203-z	2022
Pathogenicity	Gut microbiota composition reflects disease severity and dysfunctional immune responses in patients with COVID-19.	Yeoh YK, Zuo T, Lui GC, Zhang F, Liu Q, Li AY, Chung AC, Cheung CP, Tso EY, Fung KS, Chan V, Ling L, Joynt G, Hui DS, Chow KM, Ng SSS, Li TC, Ng RW, Yip TC, Wong GL, Chan FK, Wong CK, Chan PK, Ng SC.	Gut	10.1136/gutjnl-2020-323020	2021
	Mechanisms of Hormonal, Genetic, and Temperature Regulation of Germ Cell Proliferation, Differentiation, and Death During Spermatogenesis.	Maroto M, Torvisco SN, Garcia-Merino C, Fernandez-Gonzalez R, Pericuesta E.	Biomolecules	10.3390/biom15040500	2025
	Distinct Gut Microbiota in Patients with Asymptomatic Hyperuricemia: A Potential Protector against Gout Development.	Kim HW, Yoon EJ, Jeong SH, Park MC.	Yonsei Med J	10.3349/ymj.2022.63.3.241	2022
	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
	Airway Fusobacterium is Associated with Poor Response to Immunotherapy in Lung Cancer.	Chu S, Cheng Z, Yin Z, Xu J, Wu F, Jin Y, Yang G.	Onco Targets Ther	10.2147/ott.s348382	2022
	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
	A randomized pilot trial assessing the reduction of gout episodes in hyperuricemic patients by oral administration of Ligilactobacillus salivarius CECT 30632, a strain with the ability to degrade purines.	Rodriguez JM, Garranzo M, Segura J, Orgaz B, Arroyo R, Alba C, Beltran D, Fernandez L.	Front Microbiol	10.3389/fmicb.2023.1111652	2023
Genetics	Alterations of the Composition and Neurometabolic Profile of Human Gut Microbiota in Major Depressive Disorder.	Kovtun AS, Averina OV, Angelova IY, Yunes RA, Zorkina YA, Morozova AY, Pavlichenko AV, Syunyakov TS, Karpenko OA, Kostyuk GP, Danilenko VN.	Biomedicines	10.3390/biomedicines10092162	2022
	The Roles of Gut Microbiome and Plasma Metabolites in the Associations between ABO Blood Groups and Insulin Homeostasis: The Microbiome and Insulin Longitudinal Evaluation Study (MILES).	Li-Gao R, Grubbs K, Bertoni AG, Hoffman KL, Petrosino JF, Ramesh G, Wu M, Rotter JI, Chen YI, Evans AM, Robinson RJ, Sommerville L, Mook-Kanamori D, Goodarzi MO, Michelotti GA, Sheridan PA.	Metabolites	10.3390/metabo12090787	2022
	Infant gut microbiota and environment associate with juvenile idiopathic arthritis many years prior to disease onset, especially in genetically vulnerable children.	Kindgren E, Ahrens AP, Triplett EW, Ludvigsson J.	EBioMedicine	10.1016/j.ebiom.2023.104654	2023
	Dietary fibers boost gut microbiota-produced B vitamin pool and alter host immune landscape.	Grant ET, Parrish A, Boudaud M, Hunewald O, Hirayama A, Ollert M, Fukuda S, Desai MS.	Microbiome	10.1186/s40168-024-01898-7	2024
	Global status and trends in gout research from 2012 to 2021: a bibliometric and visual analysis.	Wang Y, Li W, Wu H, Han Y, Wu H, Lin Z, Zhang B.	Clin Rheumatol	10.1007/s10067-023-06508-9	2023
Genetics	Meta-Analysis and Validation of a Colorectal Cancer Risk Prediction Model Using Deep Sequenced Fecal Metagenomes.	Obon-Santacana M, Mas-Lloret J, Bars-Cortina D, Criado-Mesas L, Carreras-Torres R, Diez-Villanueva A, Moratalla-Navarro F, Guino E, Ibanez-Sanz G, Rodriguez-Alonso L, Mulet-Margalef N, Mata A, Garcia-Rodriguez A, Duell EJ, Pimenoff VN, Moreno V.	Cancers (Basel)	10.3390/cancers14174214	2022
Pathogenicity	Food as Treatment of Inflammatory Bowel Diseases.	Maldonado-Contreras A.	Infect Immun	10.1128/iai.00583-21	2022
Pathogenicity	Uremic Toxin-Producing Bacteroides Species Prevail in the Gut Microbiota of Taiwanese CKD Patients: An Analysis Using the New Taiwan Microbiome Baseline.	Shivani S, Kao CY, Chattopadhyay A, Chen JW, Lai LC, Lin WH, Lu TP, Huang IH, Tsai MH, Teng CH, Wu JJ, Hsieh YH, Wang MC, Chuang EY.	Front Cell Infect Microbiol	10.3389/fcimb.2022.726256	2022
	Melatonin in the colon modulates intestinal microbiota in response to stress and sleep deprivation.	Park YS, Kim SH, Park JW, Kho Y, Seok PR, Shin JH, Choi YJ, Jun JH, Jung HC, Kim EK.	Intest Res	10.5217/ir.2019.00093	2020
	Phage Targeting Neonatal Meningitis E. coli K1 In Vitro in the Intestinal Microbiota of Pregnant Donors and Impact on Bacterial Populations.	Antoine C, Laforet F, Goya-Jorge E, Gonza I, Lebrun S, Douny C, Duprez JN, Fall A, Taminiau B, Scippo ML, Daube G, Thiry D, Delcenserie V.	Int J Mol Sci	10.3390/ijms241310580	2023
	Microbiome and cancer: from mechanistic implications in disease progression and treatment to development of novel antitumoral strategies.	Constantin M, Chifiriuc MC, Mihaescu G, Corcionivoschi N, Burlibasa L, Bleotu C, Tudorache S, Mitache MM, Filip R, Munteanu SG, Gradisteanu Pircalabioru G.	Front Immunol	10.3389/fimmu.2024.1373504	2024
	Modulation of gut microbiota with Ayurveda diet and lifestyle: A review on its possible way to treat type 2 diabetes.	Chauhan A, Semwal DK, Semwal RB, Joshi SK, Adhana RK, Goswami MS.	Ayu	10.4103/ayu.ayu_7_20	2022
Genetics	Gut metagenome profile of the Nunavik Inuit youth is distinct from industrial and non-industrial counterparts.	Abed JY, Godon T, Mehdaoui F, Plante PL, Boissinot M, Bergeron MG, Belanger RE, Muckle G, Poliakova N, Ayotte P, Corbeil J, Rousseau E.	Commun Biol	10.1038/s42003-022-04372-y	2022
	Microbiota-Focused Dietary Approaches to Support Health: A Systematic Review.	Hindle VK, Veasley NM, Holscher HD.	J Nutr	10.1016/j.tjnut.2024.10.043	2025
	Using fluorescent promoter-reporters to study sugar utilization control in Bifidobacterium longum NCC 2705.	Duboux S, Muller JA, De Franceschi F, Mercenier A, Kleerebezem M.	Sci Rep	10.1038/s41598-022-14638-4	2022
	Analysis of Effector and Immunity Proteins of the GA2 Type VI Secretion Systems of Gut Bacteroidales.	Bao H, Coyne MJ, Garcia-Bayona L, Comstock LE.	J Bacteriol	10.1128/jb.00122-22	2022
	Impact of the Synbiotics and Urate-Lowering Therapy on Gut Microbiota and Cytokine Profile in Patients with Chronic Gouty Arthritis.	Kondratiuk VE, Tarasenko OM, Karmazina OM, Taranchuk VV.	J Med Life	10.25122/jml-2020-0065	2020
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
	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
	Is stool frequency associated with the richness and community composition of gut microbiota?	Kwon HJ, Lim JH, Kang D, Lim S, Park SJ, Kim JH.	Intest Res	10.5217/ir.2018.00149	2019
	Reconstruction of intestinal microecology of type 2 diabetes by fecal microbiota transplantation: Why and how.	Hou K, Zhang S, Wu Z, Zhu D, Chen F, Lei ZN, Liu W, Xiao C, Chen ZS.	Bosn J Basic Med Sci	10.17305/bjbms.2021.6323	2022
Pathogenicity	Lessons learned from the anaerobe survey: historical perspective and review of the most recent data (2005-2007).	Snydman DR, Jacobus NV, McDermott LA, Golan Y, Hecht DW, Goldstein EJ, Harrell L, Jenkins S, Newton D, Pierson C, Rihs JD, Yu VL, Venezia R, Finegold SM, Rosenblatt JE, Gorbach SL.	Clin Infect Dis	10.1086/647940	2010
	Characterizing the mucin-degrading capacity of the human gut microbiota.	Glover JS, Ticer TD, Engevik MA.	Sci Rep	10.1038/s41598-022-11819-z	2022
	Advanced Organotypic In Vitro Model Systems for Host-Microbial Coculture.	Kim R.	Biochip J	10.1007/s13206-023-00103-5	2023
Enzymology	Intestinal Microbiota Distinguish Gout Patients from Healthy Humans.	Guo Z, Zhang J, Wang Z, Ang KY, Huang S, Hou Q, Su X, Qiao J, Zheng Y, Wang L, Koh E, Danliang H, Xu J, Lee YK, Zhang H.	Sci Rep	10.1038/srep20602	2016
	Sodium acetate/sodium butyrate alleviates lipopolysaccharide-induced diarrhea in mice via regulating the gut microbiota, inflammatory cytokines, antioxidant levels, and NLRP3/Caspase-1 signaling.	Chen X, Kong Q, Zhao X, Zhao C, Hao P, Irshad I, Lei H, Kulyar MF, Bhutta ZA, Ashfaq H, Sha Q, Li K, Wu Y.	Front Microbiol	10.3389/fmicb.2022.1036042	2022
	Faecal microbiota transplantation halts progression of human new-onset type 1 diabetes in a randomised controlled trial.	de Groot P, Nikolic T, Pellegrini S, Sordi V, Imangaliyev S, Rampanelli E, Hanssen N, Attaye I, Bakker G, Duinkerken G, Joosten A, Prodan A, Levin E, Levels H, Potter van Loon B, van Bon A, Brouwer C, van Dam S, Simsek S, van Raalte D, Stam F, Gerdes V, Hoogma R, Diekman M, Gerding M, Rustemeijer C, de Bakker B, Hoekstra J, Zwinderman A, Bergman J, Holleman F, Piemonti L, De Vos W, Roep B, Nieuwdorp M.	Gut	10.1136/gutjnl-2020-322630	2021
Genetics	Variations in the Relative Abundance of Gut Bacteria Correlate with Lipid Profiles in Healthy Adults.	Kalnina I, Gudra D, Silamikelis I, Viksne K, Roga A, Skinderskis E, Fridmanis D, Klovins J.	Microorganisms	10.3390/microorganisms11112656	2023
	Inflammatory pseudotumor of the liver: A case report and literature review.	Zhang Y, Lu H, Ji H, Li Y.	Intractable Rare Dis Res	10.5582/irdr.2015.01021	2015
Genetics	Probiotics maintain the intestinal microbiome homeostasis of the sailors during a long sea voyage.	Zhang J, Zhao J, Jin H, Lv R, Shi H, De G, Yang B, Sun Z, Zhang H.	Gut Microbes	10.1080/19490976.2020.1722054	2020
	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
	Uncovering the role of the gut microbiota in immune checkpoint blockade therapy: A mini-review.	Halsey T, Ologun G, Wargo J, Jenq RR.	Semin Hematol	10.1053/j.seminhematol.2020.05.002	2020
	Effects of Shenling Baizhu powder on intestinal microflora metabolites and liver mitochondrial energy metabolism in nonalcoholic fatty liver mice.	Yao Z, Guo J, Du B, Hong L, Zhu Y, Feng X, Hou Y, Shi A.	Front Microbiol	10.3389/fmicb.2023.1147067	2023
	Sex Differences in Fecal Microbiota Correlation With Physiological and Biochemical Indices Associated With End-Stage Renal Disease Caused by Immunoglobulin a Nephropathy or Diabetes.	Zhang P, Fang J, Li G, Zhang L, Lai X, Xu L, Liu L, Xiong Y, Li L, Zhang T, Wan J, Xu H, Chen R, Zhang W, Ma J, Chen Z.	Front Microbiol	10.3389/fmicb.2021.752393	2021
	Gut Microbial Succession Patterns and Metabolic Profiling during Pregnancy and Lactation in a Goat Model.	Zhang K, Liu G, Wu Y, Zhang T, Guo M, Lei Y, Cao X, Suo L, Brugger D, Wang X, Yang Y, Chen Y.	Microbiol Spectr	10.1128/spectrum.02955-22	2023
	Network Analysis of Gut Microbiome and Metabolome to Discover Microbiota-Linked Biomarkers in Patients Affected by Non-Small Cell Lung Cancer.	Vernocchi P, Gili T, Conte F, Del Chierico F, Conta G, Miccheli A, Botticelli A, Paci P, Caldarelli G, Nuti M, Marchetti P, Putignani L.	Int J Mol Sci	10.3390/ijms21228730	2020
	Elevated serum anti-I2 and anti-OmpW antibody levels in children with IBD.	Iltanen S, Tervo L, Halttunen T, Wei B, Braun J, Rantala I, Honkanen T, Kronenberg M, Cheroutre H, Turovskaya O, Autio V, Ashorn M.	Inflamm Bowel Dis	10.1097/01.mib.0000218765.84087.42	2006
Genetics	Dysbiosis and relapse-related microbiome in inflammatory bowel disease: A shotgun metagenomic approach.	Serrano-Gomez G, Mayorga L, Oyarzun I, Roca J, Borruel N, Casellas F, Varela E, Pozuelo M, Machiels K, Guarner F, Vermeire S, Manichanh C.	Comput Struct Biotechnol J	10.1016/j.csbj.2021.11.037	2021
	Microbiota Changes in Fathers Consuming a High Prebiotic Fiber Diet Have Minimal Effects on Male and Female Offspring in Rats.	Chleilat F, Schick A, Reimer RA.	Nutrients	10.3390/nu13030820	2021
	Association of the characteristics of the blood metabolome and gut microbiome with the outcome of methotrexate therapy in psoriasis.	Qiu Q, Deng J, Deng H, Yao D, Yan Y, Ye S, Shang X, Deng Y, Han L, Zheng G, Roy B, Chen Y, Han L, Huang R, Fang X, Lu C.	Front Immunol	10.3389/fimmu.2022.937539	2022
	A comparative study of the gut microbiome in Egyptian patients with Type I and Type II diabetes.	Radwan S, Gilfillan D, Eklund B, Radwan HM, El Menofy NG, Lee J, Kapuscinski M, Abdo Z.	PLoS One	10.1371/journal.pone.0238764	2020
	The immunomodulatory effects of Qushi Jianpi Hewei Decoction (QJHD) for patients with COVID-19 by metagenomics and transcriptomic sequencing	Li J, Yang Y, Xiong B, Lu J, Zhou Y, Li C, Hu X.	Pharmacological Research - Modern Chinese Medicine		2022
	Phage-encoded carbohydrate-interacting proteins in the human gut.	Rothschild-Rodriguez D, Hedges M, Kaplan M, Karav S, Nobrega FL.	Front Microbiol	10.3389/fmicb.2022.1083208	2022
Metabolism	Fermentation of pectin and glucose, and activity of pectin-degrading enzymes in the rabbit caecal bacterium Bacteroides caccae.	Sirotek K, Slovakova L, Kopecny J, Marounek M.	Lett Appl Microbiol	10.1111/j.1472-765x.2004.01492.x	2004
	Changes to the Gut Microbiome in Young Children Showing Early Behavioral Signs of Autism.	Jones J, Reinke SN, Mousavi-Derazmahalleh M, Palmer DJ, Christophersen CT.	Front Microbiol	10.3389/fmicb.2022.905901	2022
	Source Tracking and Global Distribution of the Tigecycline Non-Susceptible tet(X).	Zhang RM, Sun J, Sun RY, Wang MG, Cui CY, Fang LX, Liao MN, Lu XQ, Liu YX, Liao XP, Liu YH.	Microbiol Spectr	10.1128/spectrum.01164-21	2021
Pathogenicity	The gut microbiome stability is altered by probiotic ingestion and improved by the continuous supplementation of galactooligosaccharide.	Ma C, Wasti S, Huang S, Zhang Z, Mishra R, Jiang S, You Z, Wu Y, Chang H, Wang Y, Huo D, Li C, Sun Z, Sun Z, Zhang J.	Gut Microbes	10.1080/19490976.2020.1785252	2020
	Grazing and Supplementation of Dietary Yeast Probiotics Shape the Gut Microbiota and Improve the Immunity of Black Fattening Goats (Capra hircus).	Emu Q, Guan H, Zhu J, Zhang L, Fan J, Ji Y, Lin Y, Li C, Dan X, Aguo Y, Wei X, Zhang M, Zhang B, Yang C, Li B, Xiong C.	Front Microbiol	10.3389/fmicb.2021.666837	2021
	Paediatric Inflammatory Bowel Disease and its Relationship with the Microbiome.	Fitzgerald RS, Sanderson IR, Claesson MJ.	Microb Ecol	10.1007/s00248-021-01697-9	2021
Pathogenicity	[Bacteria isolated from surgical infections and their susceptibility to antimicrobial agents--special reference to bacteria isolated between April 2007 and March 2008].	Shinagawa N, Hasegawa M, Hirata K, Katsuramaki T, Mizukuchi T, Ushijima Y, Ushida T, Aikawa N, Yo K, Yura J, Takeyama H, Wakasugi T, Taniguchi M, Mizuno I, Mashita K, Ishikawa S, Mizuno A, Tsumura H, Yokoyama T, Moori N, Sumita N, Kubo S, Lee S, Oomura T, Kobayashi Y, Tsuji T, Yamaue H, Kawai M, Takesue Y, Tanaka N, Kimura H, Iwagaki H, Sueda T, Hiyama E, Murakami Y, Ooge H, Uemura K, Takeuchi H, Yasui Y, Yasunami Y, Ryu S.	Jpn J Antibiot		2009
	Predictive Factors in Metastatic Melanoma Treated with Immune Checkpoint Inhibitors: From Clinical Practice to Future Perspective.	Poletto S, Paruzzo L, Nepote A, Caravelli D, Sangiolo D, Carnevale-Schianca F.	Cancers (Basel)	10.3390/cancers16010101	2023
Genetics	Modulation of Gut Microbiota and Metabolites by Berberine in Treating Mice With Disturbances in Glucose and Lipid Metabolism.	Fang X, Wu H, Wang X, Lian F, Li M, Miao R, Wei J, Tian J.	Front Pharmacol	10.3389/fphar.2022.870407	2022
Cultivation	Metabolic modelling as a powerful tool to identify critical components of Pneumocystis growth medium.	Nev OA, Zamaraeva E, De Oliveira R, Ryzhkov I, Duvenage L, Abou-Jaoude W, Ouattara DA, Hoving JC, Gudelj I, Brown AJP.	PLoS Comput Biol	10.1371/journal.pcbi.1012545	2024
	Programming bacteria for multiplexed DNA detection.	Cheng YY, Chen Z, Cao X, Ross TD, Falbel TG, Burton BM, Venturelli OS.	Nat Commun	10.1038/s41467-023-37582-x	2023
Pathogenicity	Effects of ondansetron and [6]-gingerol on pica and gut microbiota in rats treated with cisplatin.	Feng X, Cheng Q, Meng Q, Yang Y, Nie K.	Drug Des Devel Ther	10.2147/dddt.s211845	2019
	Divergent maturational patterns of the infant bacterial and fungal gut microbiome in the first year of life are associated with inter-kingdom community dynamics and infant nutrition.	Mercer EM, Ramay HR, Moossavi S, Laforest-Lapointe I, Reyna ME, Becker AB, Simons E, Mandhane PJ, Turvey SE, Moraes TJ, Sears MR, Subbarao P, Azad MB, Arrieta MC.	Microbiome	10.1186/s40168-023-01735-3	2024
	Personalized Paths: Unlocking Alzheimer's via the Gut-Brain Axis.	Ceccon M, Kantsjo JB, Ronchi F.	Visc Med	10.1159/000535869	2024
Metabolism	Metagenomic Shotgun Sequencing and Unbiased Metabolomic Profiling Identify Specific Human Gut Microbiota and Metabolites Associated with Immune Checkpoint Therapy Efficacy in Melanoma Patients.	Frankel AE, Coughlin LA, Kim J, Froehlich TW, Xie Y, Frenkel EP, Koh AY.	Neoplasia	10.1016/j.neo.2017.08.004	2017
	Probiotic Bifidobacterium lactis V9 Regulates the Secretion of Sex Hormones in Polycystic Ovary Syndrome Patients through the Gut-Brain Axis.	Zhang J, Sun Z, Jiang S, Bai X, Ma C, Peng Q, Chen K, Chang H, Fang T, Zhang H.	mSystems	10.1128/msystems.00017-19	2019
Pathogenicity	Maternal PBDE exposure disrupts gut microbiome and promotes hepatic proinflammatory signaling in humanized PXR-transgenic mouse offspring over time.	Kim S, Li H, Jin Y, Armad J, Gu H, Mani S, Cui JY.	Toxicol Sci	10.1093/toxsci/kfad056	2023
	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
	Gut microbiome composition may be an indicator of preclinical Alzheimer's disease.	Ferreiro AL, Choi J, Ryou J, Newcomer EP, Thompson R, Bollinger RM, Hall-Moore C, Ndao IM, Sax L, Benzinger TLS, Stark SL, Holtzman DM, Fagan AM, Schindler SE, Cruchaga C, Butt OH, Morris JC, Tarr PI, Ances BM, Dantas G.	Sci Transl Med	10.1126/scitranslmed.abo2984	2023
Genetics	Metagenome Sequencing Reveals the Midgut Microbiota Makeup of Culex pipiens quinquefasciatus and Its Possible Relationship With Insecticide Resistance.	Wang YT, Shen RX, Xing D, Zhao CP, Gao HT, Wu JH, Zhang N, Zhang HD, Chen Y, Zhao TY, Li CX.	Front Microbiol	10.3389/fmicb.2021.625539	2021
	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
Enzymology	[Bacteria isolated from surgical infections and its susceptibilities to antimicrobial agents--special references to bacteria isolated between April 2006 and March 2007].	Shinagawa N, Hirata K, Katsuramaki T, Mizukuchi T, Ushijima Y, Ushida T, Aikawa N, Yo K, Mashita K, Ishikawa S, Mizuno A, Kubo S, Lee S, Fujimoto M, Higaki K, Taniguchi K, Tsuji T, Ohnishi H, Yamaue H, Kawai M, Takesue Y, Tanaka N, Iwagaki H, Takayama T, Sato T, Kato K, Yura J, Takeyama H, Wakasugi T, Taniguchi M, Mizuno I, Kimura H, Fuchimoto S, Sueda T, Hiyama E, Murakami Y, Ooge H, Uemura K, Tsumura H, Yokoyama T, Takeuchi H, Yasui Y, Ikeda S, Yasunami Y, Ryu S.	Jpn J Antibiot		2008
	Identifying glycan consumers in human gut microbiota samples using metabolic labeling coupled with fluorescence-activated cell sorting.	Dridi L, Altamura F, Gonzalez E, Lui O, Kubinski R, Pidgeon R, Montagut A, Chong J, Xia J, Maurice CF, Castagner B.	Nat Commun	10.1038/s41467-023-36365-8	2023
Pathogenicity	In vitro interactions of Alternaria mycotoxins, an emerging class of food contaminants, with the gut microbiota: a bidirectional relationship.	Crudo F, Aichinger G, Mihajlovic J, Varga E, Dellafiora L, Warth B, Dall'Asta C, Berry D, Marko D.	Arch Toxicol	10.1007/s00204-021-03043-x	2021
	Muscle strength is increased in mice that are colonized with microbiota from high-functioning older adults.	Fielding RA, Reeves AR, Jasuja R, Liu C, Barrett BB, Lustgarten MS.	Exp Gerontol	10.1016/j.exger.2019.110722	2019
	Relationship between changes in microbiota induced by resveratrol and its anti-diabetic effect on type 2 diabetes.	Fernandez-Quintela A, Macarulla MT, Gomez-Zorita S, Gonzalez M, Milton-Laskibar I, Portillo MP.	Front Nutr	10.3389/fnut.2022.1084702	2022
	Identifying oral microbiome alterations in adult betel quid chewing population of Delhi, India.	Bahuguna M, Hooda S, Mohan L, Gupta RK, Diwan P.	PLoS One	10.1371/journal.pone.0278221	2023
Phylogeny	Reanalysis of the Mars500 experiment reveals common gut microbiome alterations in astronauts induced by long-duration confinement.	Brereton NJB, Pitre FE, Gonzalez E.	Comput Struct Biotechnol J	10.1016/j.csbj.2021.03.040	2021
	Robust cross-cohort gut microbiome associations with COVID-19 severity.	Li J, Li J, Ghosh TS, McCann R, Mallon P, Hill C, Draper L, Schult D, Fanning LJ, Shannon R, Sadlier C, Horgan M, O'Mahony L, O'Toole PW.	Gut Microbes	10.1080/19490976.2023.2242615	2023
	Persistence of birth mode-dependent effects on gut microbiome composition, immune system stimulation and antimicrobial resistance during the first year of life.	Busi SB, de Nies L, Habier J, Wampach L, Fritz JV, Heintz-Buschart A, May P, Halder R, de Beaufort C, Wilmes P.	ISME Commun	10.1038/s43705-021-00003-5	2021
	Drastic Effects on the Microbiome of a Young Rower Engaged in High-Endurance Exercise After a Month Usage of a Dietary Fiber Supplement.	Jaago M, Timmusk US, Timmusk T, Palm K.	Front Nutr	10.3389/fnut.2021.654008	2021
Genetics	Composition and Functions of the Gut Microbiome in Pediatric Obesity: Relationships with Markers of Insulin Resistance.	Orsso CE, Peng Y, Deehan EC, Tan Q, Field CJ, Madsen KL, Walter J, Prado CM, Tun HM, Haqq AM.	Microorganisms	10.3390/microorganisms9071490	2021
	Rapid change of fecal microbiome and disappearance of Clostridium difficile in a colonized infant after transition from breast milk to cow milk.	Davis MY, Zhang H, Brannan LE, Carman RJ, Boone JH.	Microbiome	10.1186/s40168-016-0198-6	2016
Metabolism	Human intestinal models to study interactions between intestine and microbes.	Aguilar-Rojas A, Olivo-Marin JC, Guillen N.	Open Biol	10.1098/rsob.200199	2020
Genetics	Alleviation of Metabolic Disturbance by Substituting Kanjang High in Bacillus for Salt through Modulation of Gut Microbiota in Estrogen-Deficient Rats.	Park S, Zhang T, Yue Y, Jeong SJ, Ryu MS, Wu X, Yang HJ, Jeong DY.	Foods	10.3390/foods11131951	2022
Metabolism	Concentrated Raw Fibers Enhance the Fiber-Degrading Capacity of a Synthetic Human Gut Microbiome.	Steimle A, Neumann M, Grant ET, Turner JD, Desai MS.	Int J Mol Sci	10.3390/ijms22136855	2021
	Gut microbiota composition is associated with SARS-CoV-2 vaccine immunogenicity and adverse events.	Ng SC, Peng Y, Zhang L, Mok CK, Zhao S, Li A, Ching JY, Liu Y, Yan S, Chan DLS, Zhu J, Chen C, Fung AC, Wong KK, Hui DS, Chan FK, Tun HM.	Gut	10.1136/gutjnl-2021-326563	2022
	An untargeted fecal and urine metabolomics analysis of the interplay between the gut microbiome, diet and human metabolism in Indian and Chinese adults.	Jain A, Li XH, Chen WN.	Sci Rep	10.1038/s41598-019-45640-y	2019
Phylogeny	Major Lipids, Apolipoproteins, and Alterations of Gut Microbiota.	Yun KE, Kim J, Kim MH, Park E, Kim HL, Chang Y, Ryu S, Kim HN.	J Clin Med	10.3390/jcm9051589	2020
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
Pathogenicity	Early-Life Microbial Restitution Reduces Colitis Risk Promoted by Antibiotic-Induced Gut Dysbiosis in Interleukin 10^-/- Mice.	Miyoshi J, Miyoshi S, Delmont TO, Cham C, Lee STM, Sakatani A, Yang K, Shan Y, Kennedy M, Kiefl E, Yousef M, Crosson S, Sogin M, Antonopoulos DA, Eren AM, Leone V, Chang EB.	Gastroenterology	10.1053/j.gastro.2021.05.054	2021
Metabolism	1-Kestose supplementation mitigates the progressive deterioration of glucose metabolism in type 2 diabetes OLETF rats.	Watanabe A, Kadota Y, Kamio R, Tochio T, Endo A, Shimomura Y, Kitaura Y.	Sci Rep	10.1038/s41598-020-72773-2	2020
Phylogeny	Fecal metagenomic profiles in subgroups of patients with myalgic encephalomyelitis/chronic fatigue syndrome.	Nagy-Szakal D, Williams BL, Mishra N, Che X, Lee B, Bateman L, Klimas NG, Komaroff AL, Levine S, Montoya JG, Peterson DL, Ramanan D, Jain K, Eddy ML, Hornig M, Lipkin WI.	Microbiome	10.1186/s40168-017-0261-y	2017
Enzymology	Oral and Gut Microbial Carbohydrate-Active Enzymes Landscape in Health and Disease.	Onyango SO, Juma J, De Paepe K, Van de Wiele T.	Front Microbiol	10.3389/fmicb.2021.653448	2021
Pathogenicity	16S rRNA Sequencing and Metagenomics Study of Gut Microbiota: Implications of BDB on Type 2 Diabetes Mellitus.	Zhang L, Luo J, Li X, Guo S, Shi D.	Mar Drugs	10.3390/md18090469	2020
	Modulatory effects of gut microbiome in cancer immunotherapy: A novel paradigm for blockade of immune checkpoint inhibitors.	Rezasoltani S, Yadegar A, Asadzadeh Aghdaei H, Reza Zali M.	Cancer Med	10.1002/cam4.3694	2021
Metabolism	Potential role of ovomucin and its peptides in modulation of intestinal health: A review.	Tu A, Zhao X, Shan Y, Lu X.	Int J Biol Macromol	10.1016/j.ijbiomac.2020.06.148	2020
Pathogenicity	Analysis of Gut Microbiota in Rheumatoid Arthritis Patients: Disease-Related Dysbiosis and Modifications Induced by Etanercept.	Picchianti-Diamanti A, Panebianco C, Salemi S, Sorgi ML, Di Rosa R, Tropea A, Sgrulletti M, Salerno G, Terracciano F, D'Amelio R, Lagana B, Pazienza V.	Int J Mol Sci	10.3390/ijms19102938	2018
Phylogeny	Distribution of different species of the Bacteroides fragilis group in individuals with Japanese cedar pollinosis.	Odamaki T, Xiao JZ, Sakamoto M, Kondo S, Yaeshima T, Iwatsuki K, Togashi H, Enomoto T, Benno Y.	Appl Environ Microbiol	10.1128/aem.01106-08	2008
Metabolism	High-resolution temporal profiling of the human gut microbiome reveals consistent and cascading alterations in response to dietary glycans.	Creswell R, Tan J, Leff JW, Brooks B, Mahowald MA, Thieroff-Ekerdt R, Gerber GK.	Genome Med	10.1186/s13073-020-00758-x	2020
Metabolism	Probiotic Bifidobacterium longum alters gut luminal metabolism through modification of the gut microbial community.	Sugahara H, Odamaki T, Fukuda S, Kato T, Xiao JZ, Abe F, Kikuchi J, Ohno H.	Sci Rep	10.1038/srep13548	2015
	Gut-on-a-Chip Research for Drug Development: Implications of Chip Design on Preclinical Oral Bioavailability or Intestinal Disease Studies.	Donkers JM, van der Vaart JI, van de Steeg E.	Biomimetics (Basel)	10.3390/biomimetics8020226	2023
Pathogenicity	Berberine Slows the Progression of Prediabetes to Diabetes in Zucker Diabetic Fatty Rats by Enhancing Intestinal Secretion of Glucagon-Like Peptide-2 and Improving the Gut Microbiota.	Wang Y, Liu H, Zheng M, Yang Y, Ren H, Kong Y, Wang S, Wang J, Jiang Y, Yang J, Shan C.	Front Endocrinol (Lausanne)	10.3389/fendo.2021.609134	2021
	Targeting gut microbiota: a potential promising therapy for diabetic kidney disease.	Chen Z, Zhu S, Xu G.	Am J Transl Res		2016
Enzymology	Novel 3-O-alpha-d-Galactosyl-alpha-l-Arabinofuranosidase for the Assimilation of Gum Arabic Arabinogalactan Protein in Bifidobacterium longum subsp. longum.	Sasaki Y, Horigome A, Odamaki T, Xiao JZ, Ishiwata A, Ito Y, Kitahara K, Fujita K.	Appl Environ Microbiol	10.1128/aem.02690-20	2021
	Measuring the Antimicrobial Activity of Lauric Acid against Various Bacteria in Human Gut Microbiota Using a New Method.	Matsue M, Mori Y, Nagase S, Sugiyama Y, Hirano R, Ogai K, Ogura K, Kurihara S, Okamoto S.	Cell Transplant	10.1177/0963689719881366	2019
	FiberGrowth Pipeline: A Framework Toward Predicting Fiber-Specific Growth From Human Gut Bacteroidetes Genomes.	Colnet B, Sieber CMK, Perraudeau F, Leclerc M.	Front Microbiol	10.3389/fmicb.2021.632567	2021
Pathogenicity	The Roles of Probiotics in the Gut Microbiota Composition and Metabolic Outcomes in Asymptomatic Post-Gestational Diabetes Women: A Randomized Controlled Trial.	Hasain Z, Raja Ali RA, Ahmad HF, Abdul Rauf UF, Oon SF, Mokhtar NM.	Nutrients	10.3390/nu14183878	2022
Genetics	Longitudinal flux balance analyses of a patient with episodic colonic inflammation reveals microbiome metabolic dynamics.	Basile A, Heinken A, Hertel J, Smarr L, Li W, Treu L, Valle G, Campanaro S, Thiele I.	Gut Microbes	10.1080/19490976.2023.2226921	2023
Pathogenicity	Inulin supplementation ameliorates hyperuricemia and modulates gut microbiota in Uox-knockout mice.	Guo Y, Yu Y, Li H, Ding X, Li X, Jing X, Chen J, Liu G, Lin Y, Jiang C, Liu Z, He Y, Li C, Tian Z.	Eur J Nutr	10.1007/s00394-020-02414-x	2021
Pathogenicity	Probiotic-directed modulation of gut microbiota is basal microbiome dependent.	Hou Q, Zhao F, Liu W, Lv R, Khine WWT, Han J, Sun Z, Lee YK, Zhang H.	Gut Microbes	10.1080/19490976.2020.1736974	2020
Metabolism	Elevated serum anti-Saccharomyces cerevisiae, anti-I2 and anti-OmpW antibody levels in patients with suspicion of celiac disease.	Ashorn S, Raukola H, Valineva T, Ashorn M, Wei B, Braun J, Rantala I, Kaukinen K, Luukkaala T, Collin P, Maki M, Iltanen S.	J Clin Immunol	10.1007/s10875-008-9200-9	2008
	Serological responses to microbial antigens in celiac disease patients during a gluten-free diet.	Ashorn S, Valineva T, Kaukinen K, Ashorn M, Braun J, Raukola H, Rantala I, Collin P, Maki M, Luukkaala T, Iltanen S.	J Clin Immunol	10.1007/s10875-008-9255-7	2009
Enzymology	The Fecal Metagenomics of Malayan Pangolins Identifies an Extensive Adaptation to Myrmecophagy.	Ma JE, Jiang HY, Li LM, Zhang XJ, Li GY, Li HM, Jin XJ, Chen JP.	Front Microbiol	10.3389/fmicb.2018.02793	2018
Pathogenicity	Eubacterium rectale Attenuates HSV-1 Induced Systemic Inflammation in Mice by Inhibiting CD83.	Islam SMS, Ryu HM, Sayeed HM, Byun HO, Jung JY, Kim HA, Suh CH, Sohn S.	Front Immunol	10.3389/fimmu.2021.712312	2021
Phylogeny	Gut Microbiota Composition Associated With Clostridium difficile-Positive Diarrhea and C. difficile Type in ICU Patients.	Duan J, Meng X, Liu S, Zhou P, Zeng C, Fu C, Dou Q, Wu A, Li C.	Front Cell Infect Microbiol	10.3389/fcimb.2020.00190	2020
	Controlled Complexity: Optimized Systems to Study the Role of the Gut Microbiome in Host Physiology.	Glowacki RWP, Engelhart MJ, Ahern PP.	Front Microbiol	10.3389/fmicb.2021.735562	2021
	Advances in clinical laboratory tests for inflammatory bowel disease.	Nakamura RM, Matsutani M, Barry M.	Clin Chim Acta	10.1016/s0009-8981(03)00286-9	2003
	Fecal calprotectin levels and serological responses to microbial antigens among children and adolescents with inflammatory bowel disease.	Ashorn S, Honkanen T, Kolho KL, Ashorn M, Valineva T, Wei B, Braun J, Rantala I, Luukkaala T, Iltanen S.	Inflamm Bowel Dis	10.1002/ibd.20535	2009
Phylogeny	Rapid identification of the species of the Bacteroides fragilis group by multiplex PCR assays using group- and species-specific primers.	Liu C, Song Y, McTeague M, Vu AW, Wexler H, Finegold SM.	FEMS Microbiol Lett	10.1016/s0378-1097(03)00296-9	2003
	Microbiota profile in new-onset pediatric Crohn's disease: data from a non-Western population.	El Mouzan MI, Winter HS, Assiri AA, Korolev KS, Al Sarkhy AA, Dowd SE, Al Mofarreh MA, Menon R.	Gut Pathog	10.1186/s13099-018-0276-3	2018
	Ecological memory of prior nutrient exposure in the human gut microbiome.	Letourneau J, Holmes ZC, Dallow EP, Durand HK, Jiang S, Carrion VM, Gupta SK, Mincey AC, Muehlbauer MJ, Bain JR, David LA.	ISME J	10.1038/s41396-022-01292-x	2022
	Anaerobes in diabetic foot infections: pathophysiology, epidemiology, virulence, and management.	Villa F, Marchandin H, Lavigne J-P, Schuldiner S, Cellier N, Sotto A, Loubet P.	Clin Microbiol Rev	10.1128/cmr.00143-23	2024
	Transplantation of an obesity-associated human gut microbiota to mice induces vascular dysfunction and glucose intolerance.	Trikha SRJ, Lee DM, Ecton KE, Wrigley SD, Vazquez AR, Litwin NS, Thomas KN, Wei Y, Battson ML, Johnson SA, Kuhn KA, Colgan SP, Gentile CL, Weir TL.	Gut Microbes	10.1080/19490976.2021.1940791	2021
	Human gut microbial communities dictate efficacy of anti-PD-1 therapy in a humanized microbiome mouse model of glioma.	Dees KJ, Koo H, Humphreys JF, Hakim JA, Crossman DK, Crowley MR, Nabors LB, Benveniste EN, Morrow CD, McFarland BC.	Neurooncol Adv	10.1093/noajnl/vdab023	2021
	The gut microbiome and response to immune checkpoint inhibitors: preclinical and clinical strategies.	Gong J, Chehrazi-Raffle A, Placencio-Hickok V, Guan M, Hendifar A, Salgia R.	Clin Transl Med	10.1186/s40169-019-0225-x	2019
	Analysis of 1135 gut metagenomes identifies sex-specific resistome profiles.	Sinha T, Vich Vila A, Garmaeva S, Jankipersadsing SA, Imhann F, Collij V, Bonder MJ, Jiang X, Gurry T, Alm EJ, D'Amato M, Weersma RK, Scherjon S, Wijmenga C, Fu J, Kurilshikov A, Zhernakova A.	Gut Microbes	10.1080/19490976.2018.1528822	2019
Phylogeny	Discovering Potential Taxonomic Biomarkers of Type 2 Diabetes From Human Gut Microbiota via Different Feature Selection Methods.	Bakir-Gungor B, Bulut O, Jabeer A, Nalbantoglu OU, Yousef M.	Front Microbiol	10.3389/fmicb.2021.628426	2021
	Gut OncoMicrobiome Signatures (GOMS) as next-generation biomarkers for cancer immunotherapy.	Thomas AM, Fidelle M, Routy B, Kroemer G, Wargo JA, Segata N, Zitvogel L.	Nat Rev Clin Oncol	10.1038/s41571-023-00785-8	2023
	The Digestive Health among Participants of the Woodstock Rock Festival in Poland-A Cross-Sectional Survey.	Skonieczna-Zydecka K, Stachowska E, Maciejewska D, Ryterska K, Palma J, Czerwinska-Rogowska M, Kaczmarczyk M, Gudan A, Mruk H, Swiniarska B, Kaldunska J, Stachowska Z, Mijal P, Mazur T, Kupczynski M, Marlicz W.	Int J Environ Res Public Health	10.3390/ijerph15102256	2018
Metabolism	MMinte: an application for predicting metabolic interactions among the microbial species in a community.	Mendes-Soares H, Mundy M, Soares LM, Chia N.	BMC Bioinformatics	10.1186/s12859-016-1230-3	2016
Genetics	Enabling rational gut microbiome manipulations by understanding gut ecology through experimentally-evidenced in silico models.	Molina Ortiz JP, McClure DD, Shanahan ER, Dehghani F, Holmes AJ, Read MN.	Gut Microbes	10.1080/19490976.2021.1965698	2021
	Antidiabetic Function of Lactobacillus fermentum MF423-Fermented Rice Bran and Its Effect on Gut Microbiota Structure in Type 2 Diabetic Mice.	Ai X, Wu C, Yin T, Zhur O, Liu C, Yan X, Yi C, Liu D, Xiao L, Li W, Xie B, He H.	Front Microbiol	10.3389/fmicb.2021.682290	2021
Phylogeny	Mucosa-associated bacteria in two middle-aged women diagnosed with collagenous colitis.	Gustafsson RJ, Ohlsson B, Benoni C, Jeppsson B, Olsson C.	World J Gastroenterol	10.3748/wjg.v18.i14.1628	2012
Enzymology	Gut-on-chip: Recreating human intestine in vitro.	Xiang Y, Wen H, Yu Y, Li M, Fu X, Huang S.	J Tissue Eng	10.1177/2041731420965318	2020
	Gut microbiota in regulatory T cell generation and function: mechanisms and health implications.	Sharma A, Sharma G, Im SH.	Gut Microbes	10.1080/19490976.2025.2516702	2025
Pathogenicity	Beneficial Actions of Essential Fatty Acids in Streptozotocin-Induced Type 1 Diabetes Mellitus.	Shen J, Zhang L, Wang Y, Chen Z, Ma J, Fang X, Das UN, Yao K.	Front Nutr	10.3389/fnut.2022.890277	2022
	Revealing links between gut microbiome and its fungal community in Type 2 Diabetes Mellitus among Emirati subjects: A pilot study.	Al Bataineh MT, Dash NR, Bel Lassen P, Banimfreg BH, Nada AM, Belda E, Clement K.	Sci Rep	10.1038/s41598-020-66598-2	2020
	A compendium of 32,277 metagenome-assembled genomes and over 80 million genes from the early-life human gut microbiome.	Zeng S, Patangia D, Almeida A, Zhou Z, Mu D, Paul Ross R, Stanton C, Wang S.	Nat Commun	10.1038/s41467-022-32805-z	2022
	Prolonged Impairment of Short-Chain Fatty Acid and L-Isoleucine Biosynthesis in Gut Microbiome in Patients With COVID-19.	Zhang F, Wan Y, Zuo T, Yeoh YK, Liu Q, Zhang L, Zhan H, Lu W, Xu W, Lui GCY, Li AYL, Cheung CP, Wong CK, Chan PKS, Chan FKL, Ng SC.	Gastroenterology	10.1053/j.gastro.2021.10.013	2022
Enzymology	Urinary TMAO Levels Are Associated with the Taxonomic Composition of the Gut Microbiota and with the Choline TMA-Lyase Gene (cutC) Harbored by Enterobacteriaceae.	Dalla Via A, Gargari G, Taverniti V, Rondini G, Velardi I, Gambaro V, Visconti GL, De Vitis V, Gardana C, Ragg E, Pinto A, Riso P, Guglielmetti S.	Nutrients	10.3390/nu12010062	2019
	Competitive exclusion culture for swine	Nisbet DJ, Corrier DE, Stanker LH.	United States Department of Agriculture patents.		1999
Pathogenicity	In vitro activity of telithromycin (HMR 3647) and seven other antimicrobial agents against anaerobic bacteria.	Ackermann G, Schaumann R, Pless B, Claros MC, Rodloff AC.	J Antimicrob Chemother	10.1093/jac/46.1.115	2000
Pathogenicity	The Relationship between Frequently Used Glucose-Lowering Agents and Gut Microbiota in Type 2 Diabetes Mellitus.	Lv Y, Zhao X, Guo W, Gao Y, Yang S, Li Z, Wang G.	J Diabetes Res	10.1155/2018/1890978	2018
Proteome	Distinct factors associated with short-term and long-term weight loss induced by low-fat or low-carbohydrate diet intervention.	Li X, Perelman D, Leong AK, Fragiadakis G, Gardner CD, Snyder MP.	Cell Rep Med	10.1016/j.xcrm.2022.100870	2022
Metabolism	A commensal-encoded genotoxin drives restriction of Vibrio cholerae colonization and host gut microbiome remodeling.	Chen J, Byun H, Liu R, Jung IJ, Pu Q, Zhu CY, Tanchoco E, Alavi S, Degnan PH, Ma AT, Roggiani M, Beld J, Goulian M, Hsiao A, Zhu J.	Proc Natl Acad Sci U S A	10.1073/pnas.2121180119	2022
	Changes of saliva microbiota in the onset and after the treatment of diabetes in patients with periodontitis.	Yang Y, Liu S, Wang Y, Wang Z, Ding W, Sun X, He K, Feng Q, Zhang X.	Aging (Albany NY)	10.18632/aging.103399	2020
	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
	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
	Akkermansia muciniphila exacerbates food allergy in fibre-deprived mice.	Parrish A, Boudaud M, Grant ET, Willieme S, Neumann M, Wolter M, Craig SZ, De Sciscio A, Cosma A, Hunewald O, Ollert M, Desai MS.	Nat Microbiol	10.1038/s41564-023-01464-1	2023
Pathogenicity	Effects of Synbiotic Supplementation on Chronic Inflammation and the Gut Microbiota in Obese Patients with Type 2 Diabetes Mellitus: A Randomized Controlled Study.	Kanazawa A, Aida M, Yoshida Y, Kaga H, Katahira T, Suzuki L, Tamaki S, Sato J, Goto H, Azuma K, Shimizu T, Takahashi T, Yamashiro Y, Watada H.	Nutrients	10.3390/nu13020558	2021
Metabolism	Carbohydrates great and small, from dietary fiber to sialic acids: How glycans influence the gut microbiome and affect human health.	Coker JK, Moyne O, Rodionov DA, Zengler K.	Gut Microbes	10.1080/19490976.2020.1869502	2021
Genetics	A cryptic plasmid is among the most numerous genetic elements in the human gut.	Fogarty EC, Schechter MS, Lolans K, Sheahan ML, Veseli I, Moore RM, Kiefl E, Moody T, Rice PA, Yu MK, Mimee M, Chang EB, Ruscheweyh HJ, Sunagawa S, Mclellan SL, Willis AD, Comstock LE, Eren AM.	Cell	10.1016/j.cell.2024.01.039	2024
	Advances in modelling the human microbiome-gut-brain axis in vitro.	Moysidou CM, Owens RM.	Biochem Soc Trans	10.1042/bst20200338	2021
	Enteric Phageome Alterations in Patients With Type 2 Diabetes.	Chen Q, Ma X, Li C, Shen Y, Zhu W, Zhang Y, Guo X, Zhou J, Liu C.	Front Cell Infect Microbiol	10.3389/fcimb.2020.575084	2020
	Inflammatory pseudotumor of the liver: a case report and review of the literature.	Ntinas A, Kardassis D, Miliaras D, Tsinoglou K, Dimitriades A, Vrochides D.	J Med Case Rep	10.1186/1752-1947-5-196	2011
Metabolism	Host DNA contents in fecal metagenomics as a biomarker for intestinal diseases and effective treatment.	Jiang P, Lai S, Wu S, Zhao XM, Chen WH, Chen WH.	BMC Genomics	10.1186/s12864-020-6749-z	2020
Metabolism	Identification of Allobaculum mucolyticum as a novel human intestinal mucin degrader.	van Muijlwijk GH, van Mierlo G, Jansen PWTC, Vermeulen M, Bleumink-Pluym NMC, Palm NW, van Putten JPM, de Zoete MR.	Gut Microbes	10.1080/19490976.2021.1966278	2021
	Treatment of a chronic recurrent fistulized tibial osteomyelitis: administration of a novel antibiotic-loaded bone substitute combined with a pedicular muscle flap sealing.	Franceschini M, Di Matteo A, Bosebeck H, Buchner H, Vogt S.	Eur J Orthop Surg Traumatol	10.1007/s00590-012-0956-5	2012
Phylogeny	Genotypic diversity of anaerobic isolates from bloodstream infections.	Simmon KE, Mirrett S, Reller LB, Petti CA.	J Clin Microbiol	10.1128/jcm.02469-07	2008
	Gut microbiota varies by opioid use, circulating leptin and oxytocin in African American men with diabetes and high burden of chronic disease.	Barengolts E, Green SJ, Eisenberg Y, Akbar A, Reddivari B, Layden BT, Dugas L, Chlipala G.	PLoS One	10.1371/journal.pone.0194171	2018
	Safety and efficacy of probiotic supplementation in 8 types of inflammatory arthritis: A systematic review and meta-analysis of 34 randomized controlled trials.	Zeng L, Deng Y, He Q, Yang K, Li J, Xiang W, Liu H, Zhu X, Chen H.	Front Immunol	10.3389/fimmu.2022.961325	2022
Metabolism	Identification of phenol- and p-cresol-producing intestinal bacteria by using media supplemented with tyrosine and its metabolites.	Saito Y, Sato T, Nomoto K, Tsuji H.	FEMS Microbiol Ecol	10.1093/femsec/fiy125	2018
Genetics	Variation and transmission of the human gut microbiota across multiple familial generations.	Valles-Colomer M, Bacigalupe R, Vieira-Silva S, Suzuki S, Darzi Y, Tito RY, Yamada T, Segata N, Raes J, Falony G.	Nat Microbiol	10.1038/s41564-021-01021-8	2022
	The gut microbiome, immune check point inhibition and immune-related adverse events in non-small cell lung cancer.	Bredin P, Naidoo J.	Cancer Metastasis Rev	10.1007/s10555-022-10039-1	2022
	Combined Signature of the Fecal Microbiome and Metabolome in Patients with Gout.	Shao T, Shao L, Li H, Xie Z, He Z, Wen C.	Front Microbiol	10.3389/fmicb.2017.00268	2017
	Mapping the early life gut microbiome in neonates with critical congenital heart disease: multiomics insights and implications for host metabolic and immunological health.	Huang Y, Lu W, Zeng M, Hu X, Su Z, Liu Y, Liu Z, Yuan J, Li L, Zhang X, Huang L, Hu W, Wang X, Li S, Zhang H.	Microbiome	10.1186/s40168-022-01437-2	2022
	The effect of body mass index at diagnosis on clinical outcome in children with newly diagnosed acute lymphoblastic leukemia.	Eissa HM, Zhou Y, Panetta JC, Browne EK, Jeha S, Cheng C, Relling MV, Campana D, Pui CH, Inaba H.	Blood Cancer J	10.1038/bcj.2017.11	2017
Pathogenicity	Comparative activity of moxifloxacin in vitro against obligately anaerobic bacteria.	Ackermann G, Schaumann R, Pless B, Claros MC, Goldstein EJ, Rodloff AC.	Eur J Clin Microbiol Infect Dis	10.1007/s100960050465	2000
Phylogeny	Gut Microbiome Profiles Are Associated With Type 2 Diabetes in Urban Africans.	Doumatey AP, Adeyemo A, Zhou J, Lei L, Adebamowo SN, Adebamowo C, Rotimi CN.	Front Cell Infect Microbiol	10.3389/fcimb.2020.00063	2020
	Lactobacillus rhamnosus GG ameliorates hyperuricemia in a novel model.	Fu Y, Chen YS, Xia DY, Luo XD, Luo HT, Pan J, Ma WQ, Li JZ, Mo QY, Tu Q, Li MM, Zhao Y, Li Y, Huang YT, Chen ZX, Li ZJ, Bernard L, Dione M, Zhang YM, Miao K, Chen JY, Zhu SS, Ren J, Zhou LJ, Jiang XZ, Chen J, Lin ZP, Chen JP, Ye H, Cao QY, Zhu YW, Yang L, Wang X, Wang WC.	NPJ Biofilms Microbiomes	10.1038/s41522-024-00486-9	2024
Pathogenicity	Gut Microbiota-Mediated Inflammation and Gut Permeability in Patients with Obesity and Colorectal Cancer.	Sanchez-Alcoholado L, Ordonez R, Otero A, Plaza-Andrade I, Laborda-Illanes A, Medina JA, Ramos-Molina B, Gomez-Millan J, Queipo-Ortuno MI.	Int J Mol Sci	10.3390/ijms21186782	2020
	Bacteroides ovatus colonization influences the abundance of intestinal short chain fatty acids and neurotransmitters.	Horvath TD, Ihekweazu FD, Haidacher SJ, Ruan W, Engevik KA, Fultz R, Hoch KM, Luna RA, Oezguen N, Spinler JK, Haag AM, Versalovic J, Engevik MA.	iScience	10.1016/j.isci.2022.104158	2022
Metabolism	Vancomycin relieves mycophenolate mofetil-induced gastrointestinal toxicity by eliminating gut bacterial beta-glucuronidase activity.	Taylor MR, Flannigan KL, Rahim H, Mohamud A, Lewis IA, Hirota SA, Greenway SC.	Sci Adv	10.1126/sciadv.aax2358	2019
Phenotype	Temporal evolution of the microbiome, immune system and epigenome with disease progression in ALS mice.	Figueroa-Romero C, Guo K, Murdock BJ, Paez-Colasante X, Bassis CM, Mikhail KA, Pawlowski KD, Evans MC, Taubman GF, McDermott AJ, O'Brien PD, Savelieff MG, Hur J, Feldman EL.	Dis Model Mech	10.1242/dmm.041947	2019
Pathogenicity	Epidemiology and antimicrobial susceptibilities of wound isolates of obligate anaerobes from combat casualties.	White BK, Mende K, Weintrob AC, Beckius ML, Zera WC, Lu D, Bradley W, Tribble DR, Schnaubelt ER, Murray CK, Infectious Disease Clinical Research Program Trauma Infectious Disease Outcome Study Group.	Diagn Microbiol Infect Dis	10.1016/j.diagmicrobio.2015.10.010	2016
	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
Pathogenicity	Deconstructing Mechanisms of Diet-Microbiome-Immune Interactions.	Alexander M, Turnbaugh PJ.	Immunity	10.1016/j.immuni.2020.07.015	2020
	Inflammatory pseudotumor of the colon causing intussusception: a case report and literature review.	Huang Y, Li LP, Wang J, Lun ZJ, Li W, Yang Z.	World J Gastroenterol	10.3748/wjg.v21.i2.704	2015
	A comprehensive overview of advanced dynamic in vitro intestinal and hepatic cell culture models.	Leal F, Zeiringer S, Jeitler R, Costa PF, Roblegg E.	Tissue Barriers	10.1080/21688370.2022.2163820	2024
	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
	Clinical features, image findings, and prognosis of inflammatory pseudotumor of the liver: a multicenter experience of 45 cases.	Park JY, Choi MS, Lim YS, Park JW, Kim SU, Min YW, Gwak GY, Paik YH, Lee JH, Koh KC, Paik SW, Yoo BC.	Gut Liver	10.5009/gnl.2014.8.1.58	2014
	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
Phylogeny	Bacteroides thetaiotaomicron-Infecting Bacteriophage Isolates Inform Sequence-Based Host Range Predictions.	Hryckowian AJ, Merrill BD, Porter NT, Van Treuren W, Nelson EJ, Garlena RA, Russell DA, Martens EC, Sonnenburg JL.	Cell Host Microbe	10.1016/j.chom.2020.06.011	2020
Metabolism	Gastrointestinal microbiota contributes to the development of murine transfusion-related acute lung injury.	Kapur R, Kim M, Rebetz J, Hallstrom B, Bjorkman JT, Takabe-French A, Kim N, Liu J, Shanmugabhavananthan S, Milosevic S, McVey MJ, Speck ER, Semple JW.	Blood Adv	10.1182/bloodadvances.2018018903	2018
Genetics	Metagenomic analysis revealed the potential role of gut microbiome in gout.	Chu Y, Sun S, Huang Y, Gao Q, Xie X, Wang P, Li J, Liang L, He X, Jiang Y, Wang M, Yang J, Chen X, Zhou C, Zhao Y, Ding F, Zhang Y, Wu X, Bai X, Wu J, Wei X, Chen X, Yue Z, Fang X, Huang Q, Wang Z, Huang R.	NPJ Biofilms Microbiomes	10.1038/s41522-021-00235-2	2021
	Single Donor FMT Reverses Microbial/Immune Dysbiosis and Induces Clinical Remission in a Rat Model of Acute Colitis.	Adamkova P, Hradicka P, Gancarcikova S, Kassayova M, Ambro L, Bertkova I, Maronek M, Farkasova Iannaccone S, Demeckova V.	Pathogens	10.3390/pathogens10020152	2021
Pathogenicity	A Novel Non-Digestible, Carrot-Derived Polysaccharide (cRG-I) Selectively Modulates the Human Gut Microbiota while Promoting Gut Barrier Integrity: An Integrated in Vitro Approach.	Van den Abbeele P, Verstrepen L, Ghyselinck J, Albers R, Marzorati M, Mercenier A.	Nutrients	10.3390/nu12071917	2020
	Benign inflammatory pseudotumour mimicking extrahepatic bile duct cholangiocarcinoma in an adult man presenting with painless obstructive jaundice.	Abu-Wasel B, Eltawil KM, Molinari M.	BMJ Case Rep	10.1136/bcr-2012-006514	2012
Transcriptome	Relating the gut metagenome and metatranscriptome to immunotherapy responses in melanoma patients.	Peters BA, Wilson M, Moran U, Pavlick A, Izsak A, Wechter T, Weber JS, Osman I, Ahn J.	Genome Med	10.1186/s13073-019-0672-4	2019
	Akkermansia muciniphila upregulates genes involved in maintaining the intestinal barrier function via ADP-heptose-dependent activation of the ALPK1/TIFA pathway.	Martin-Gallausiaux C, Garcia-Weber D, Lashermes A, Larraufie P, Marinelli L, Teixeira V, Rolland A, Beguet-Crespel F, Brochard V, Quatremare T, Jamet A, Dore J, Gray-Owen SD, Blottiere HM, Arrieumerlou C, Lapaque N.	Gut Microbes	10.1080/19490976.2022.2110639	2022
Metabolism	Host-centric proteomics of stool: a novel strategy focused on intestinal responses to the gut microbiota.	Lichtman JS, Marcobal A, Sonnenburg JL, Elias JE.	Mol Cell Proteomics	10.1074/mcp.m113.029967	2013
Phylogeny	Structure and Function of the Fecal Microbiota in Diarrheic Neonatal Piglets.	Yang Q, Huang X, Zhao S, Sun W, Yan Z, Wang P, Li S, Huang W, Zhang S, Liu L, Gun S.	Front Microbiol	10.3389/fmicb.2017.00502	2017
	Loss of Diurnal Oscillatory Rhythms in Gut Microbiota Correlates with Changes in Circulating Metabolites in Type 2 Diabetic db/db Mice.	Beli E, Prabakaran S, Krishnan P, Evans-Molina C, Grant MB.	Nutrients	10.3390/nu11102310	2019
Phylogeny	Fecal Microbiome Characteristics and the Resistome Associated With Acquisition of Multidrug-Resistant Organisms Among Elderly Subjects.	Araos R, Battaglia T, Ugalde JA, Rojas-Herrera M, Blaser MJ, D'Agata EMC.	Front Microbiol	10.3389/fmicb.2019.02260	2019
Metabolism	A Novel Family of RNA-Binding Proteins Regulate Polysaccharide Metabolism in Bacteroides thetaiotaomicron.	Adams AND, Azam MS, Costliow ZA, Ma X, Degnan PH, Vanderpool CK.	J Bacteriol	10.1128/jb.00217-21	2021
Genetics	Massive expansion of human gut bacteriophage diversity.	Camarillo-Guerrero LF, Almeida A, Rangel-Pineros G, Finn RD, Lawley TD.	Cell	10.1016/j.cell.2021.01.029	2021
	Current Perspectives on Gastrointestinal Models to Assess Probiotic-Pathogen Interactions.	Anjum M, Laitila A, Ouwehand AC, Forssten SD.	Front Microbiol	10.3389/fmicb.2022.831455	2022
	Metagenomic analysis of bacterial community structure and diversity of lignocellulolytic bacteria in Vietnamese native goat rumen.	Do TH, Dao TK, Nguyen KHV, Le NG, Nguyen TMP, Le TL, Phung TN, van Straalen NM, Roelofs D, Truong NH.	Asian-Australas J Anim Sci	10.5713/ajas.17.0174	2018
Phylogeny	Metagenomic reconstructions of gut microbial metabolism in weanling pigs.	Wang W, Hu H, Zijlstra RT, Zheng J, Ganzle MG.	Microbiome	10.1186/s40168-019-0662-1	2019
	Microbiome Analytics of the Gut Microbiota in Patients With Juvenile Idiopathic Arthritis: A Longitudinal Observational Cohort Study.	van Dijkhuizen EHP, Del Chierico F, Malattia C, Russo A, Pires Marafon D, Ter Haar NM, Magni-Manzoni S, Vastert SJ, Dallapiccola B, Prakken B, Martini A, De Benedetti F, Putignani L, Model Driven Paediatric European Digital Repository Consortium.	Arthritis Rheumatol	10.1002/art.40827	2019
Pathogenicity	The Gut Microbiome, Aging, and Longevity: A Systematic Review.	Badal VD, Vaccariello ED, Murray ER, Yu KE, Knight R, Jeste DV, Nguyen TT.	Nutrients	10.3390/nu12123759	2020
Pathogenicity	Expansion and persistence of antibiotic-specific resistance genes following antibiotic treatment.	Kang K, Imamovic L, Misiakou MA, Bornakke Sorensen M, Heshiki Y, Ni Y, Zheng T, Li J, Ellabaan MMH, Colomer-Lluch M, Rode AA, Bytzer P, Panagiotou G, Sommer MOA.	Gut Microbes	10.1080/19490976.2021.1900995	2021
	Leukemoid reaction in epidermal squamous cell carcinoma.	Kiyosawa T, Hirano S, Nakamura J, Murata S, Demitsu T, Kato H, Yaoita H.	J Dermatol	10.1111/j.1346-8138.1996.tb02648.x	1996
	Inflammatory pseudotumor of the liver associated with extrahepatic infection.	White JE, Chase CW, Kelley JE, Brock WB, Clark MO.	South Med J	10.1097/00007611-199701000-00005	1997
	The AT1 Receptor Blocker Telmisartan Reduces Intestinal Mucus Thickness in Obese Mice.	Nickel L, Sunderhauf A, Rawish E, Stolting I, Derer S, Thorns C, Matschl U, Othman A, Sina C, Raasch W.	Front Pharmacol	10.3389/fphar.2022.815353	2022
Pathogenicity	First national survey of antibiotic susceptibility of the Bacteroides fragilis group: emerging resistance to carbapenems in Argentina.	Fernandez-Canigia L, Litterio M, Legaria MC, Castello L, Predari SC, Di Martino A, Rossetti A, Rollet R, Carloni G, Bianchini H, Cejas D, Radice M, Gutkind G, Anaerobe Surveillance Team.	Antimicrob Agents Chemother	10.1128/aac.05622-11	2012
Genetics	The development of metabolic endotoxemia is dependent on the type of sweetener and the presence of saturated fat in the diet.	Sanchez-Tapia M, Miller AW, Granados-Portillo O, Tovar AR, Torres N.	Gut Microbes	10.1080/19490976.2020.1801301	2020
	The Emerging Role of Microbiota and Microbiome in Pancreatic Ductal Adenocarcinoma.	Ciernikova S, Novisedlakova M, Cholujova D, Stevurkova V, Mego M.	Biomedicines	10.3390/biomedicines8120565	2020
Genetics	A human gut bacterial genome and culture collection for improved metagenomic analyses.	Forster SC, Kumar N, Anonye BO, Almeida A, Viciani E, Stares MD, Dunn M, Mkandawire TT, Zhu A, Shao Y, Pike LJ, Louie T, Browne HP, Mitchell AL, Neville BA, Finn RD, Lawley TD.	Nat Biotechnol	10.1038/s41587-018-0009-7	2019
	Remodeling of colon plasma cell repertoire within ulcerative colitis patients.	Scheid JF, Eraslan B, Hudak A, Brown EM, Sergio D, Delorey TM, Phillips D, Lefkovith A, Jess AT, Duck LW, Elson CO, Vlamakis H, Plichta DR, Deguine J, Ananthakrishnan AN, Graham DB, Regev A, Xavier RJ.	J Exp Med	10.1084/jem.20220538	2023
Phylogeny	Identification of clinically important anaerobic bacteria by an oligonucleotide array.	Lin YT, Vaneechoutte M, Huang AH, Teng LJ, Chen HM, Su SL, Chang TC.	J Clin Microbiol	10.1128/jcm.01620-09	2010
	A microfluidics-based in vitro model of the gastrointestinal human-microbe interface.	Shah P, Fritz JV, Glaab E, Desai MS, Greenhalgh K, Frachet A, Niegowska M, Estes M, Jager C, Seguin-Devaux C, Zenhausern F, Wilmes P.	Nat Commun	10.1038/ncomms11535	2016
Pathogenicity	Porphyromonas gingivalis RagB is a proinflammatory signal transducer and activator of transcription 4 agonist.	Hutcherson JA, Bagaitkar J, Nagano K, Yoshimura F, Wang H, Scott DA.	Mol Oral Microbiol	10.1111/omi.12089	2015
Metabolism	ICOS ligand and IL-10 synergize to promote host-microbiota mutualism.	Landuyt AE, Klocke BJ, Duck LW, Kemp KM, Muir RQ, Jennings MS, Blum SI, Tse HM, Lee G, Morrow CD, Elson CO, Maynard CL.	Proc Natl Acad Sci U S A	10.1073/pnas.2018278118	2021
Enzymology	Dissecting the human gut microbiome to better decipher drug liability: A once-forgotten organ takes center stage.	Cai J, Auster A, Cho S, Lai Z.	J Adv Res	10.1016/j.jare.2023.07.002	2023
Metabolism	Dietary supplementation with inulin-propionate ester or inulin improves insulin sensitivity in adults with overweight and obesity with distinct effects on the gut microbiota, plasma metabolome and systemic inflammatory responses: a randomised cross-over trial.	Chambers ES, Byrne CS, Morrison DJ, Murphy KG, Preston T, Tedford C, Garcia-Perez I, Fountana S, Serrano-Contreras JI, Holmes E, Reynolds CJ, Roberts JF, Boyton RJ, Altmann DM, McDonald JAK, Marchesi JR, Akbar AN, Riddell NE, Wallis GA, Frost GS.	Gut	10.1136/gutjnl-2019-318424	2019
	Infection-related complications during treatment for childhood acute lymphoblastic leukemia.	Inaba H, Pei D, Wolf J, Howard SC, Hayden RT, Go M, Varechtchouk O, Hahn T, Buaboonnam J, Metzger ML, Rubnitz JE, Ribeiro RC, Sandlund JT, Jeha S, Cheng C, Evans WE, Relling MV, Pui CH.	Ann Oncol	10.1093/annonc/mdw557	2017
Genetics	Phenotypic and Genomic Diversification in Complex Carbohydrate-Degrading Human Gut Bacteria.	Pudlo NA, Urs K, Crawford R, Pirani A, Atherly T, Jimenez R, Terrapon N, Henrissat B, Peterson D, Ziemer C, Snitkin E, Martens EC.	mSystems	10.1128/msystems.00947-21	2022
Pathogenicity	Treatment-Specific Composition of the Gut Microbiota Is Associated With Disease Remission in a Pediatric Crohn's Disease Cohort.	Sprockett D, Fischer N, Boneh RS, Turner D, Kierkus J, Sladek M, Escher JC, Wine E, Yerushalmi B, Dias JA, Shaoul R, Kori M, Snapper SB, Holmes S, Bousvaros A, Levine A, Relman DA.	Inflamm Bowel Dis	10.1093/ibd/izz130	2019
Pathogenicity	Total Lipopolysaccharide from the Human Gut Microbiome Silences Toll-Like Receptor Signaling.	d'Hennezel E, Abubucker S, Murphy LO, Cullen TW.	mSystems	10.1128/msystems.00046-17	2017
	Sex differences in NSAID-induced perturbation of human intestinal barrier function and microbiota.	Edogawa S, Peters SA, Jenkins GD, Gurunathan SV, Sundt WJ, Johnson S, Lennon RJ, Dyer RB, Camilleri M, Kashyap PC, Farrugia G, Chen J, Singh RJ, Grover M.	FASEB J	10.1096/fj.201800560r	2018
	Modulation of cytokine patterns and microbiome during pregnancy in IBD.	van der Giessen J, Binyamin D, Belogolovski A, Frishman S, Tenenbaum-Gavish K, Hadar E, Louzoun Y, Peppelenbosch MP, van der Woude CJ, Koren O, Fuhler GM.	Gut	10.1136/gutjnl-2019-318263	2020
Metabolism	Pregnane X receptor exacerbates nonalcoholic fatty liver disease accompanied by obesity- and inflammation-prone gut microbiome signature.	Kim S, Choi S, Dutta M, Asubonteng JO, Polunas M, Goedken M, Gonzalez FJ, Cui JY, Gyamfi MA.	Biochem Pharmacol	10.1016/j.bcp.2021.114698	2021
Enzymology	Co-evolution of HAD phosphatase and hotdog-fold thioesterase domain function in the menaquinone-pathway fusion proteins BF1314 and PG1653.	Wang M, Song F, Wu R, Allen KN, Mariano PS, Dunaway-Mariano D.	FEBS Lett	10.1016/j.febslet.2013.07.009	2013
Genetics	CD44 deletion leading to attenuation of experimental autoimmune encephalomyelitis results from alterations in gut microbiome in mice.	Chitrala KN, Guan H, Singh NP, Busbee B, Gandy A, Mehrpouya-Bahrami P, Ganewatta MS, Tang C, Chatterjee S, Nagarkatti P, Nagarkatti M.	Eur J Immunol	10.1002/eji.201646792	2017
	Link between gut-microbiome derived metabolite and shared gene-effects with hepatic steatosis and fibrosis in NAFLD.	Caussy C, Hsu C, Lo MT, Liu A, Bettencourt R, Ajmera VH, Bassirian S, Hooker J, Sy E, Richards L, Schork N, Schnabl B, Brenner DA, Sirlin CB, Chen CH, Loomba R, Genetics of NAFLD in Twins Consortium.	Hepatology	10.1002/hep.29892	2018
Biotechnology	Lifestyle and the presence of helminths is associated with gut microbiome composition in Cameroonians.	Rubel MA, Abbas A, Taylor LJ, Connell A, Tanes C, Bittinger K, Ndze VN, Fonsah JY, Ngwang E, Essiane A, Fokunang C, Njamnshi AK, Bushman FD, Tishkoff SA.	Genome Biol	10.1186/s13059-020-02020-4	2020
	Chitooligosaccharides Prevents the Development of Colitis-Associated Colorectal Cancer by Modulating the Intestinal Microbiota and Mycobiota.	Wu M, Li J, An Y, Li P, Xiong W, Li J, Yan D, Wang M, Zhong G.	Front Microbiol	10.3389/fmicb.2019.02101	2019
Pathogenicity	Colon Cancer: From Epidemiology to Prevention.	Katsaounou K, Nicolaou E, Vogazianos P, Brown C, Stavrou M, Teloni S, Hatzis P, Agapiou A, Fragkou E, Tsiaoussis G, Potamitis G, Zaravinos A, Andreou C, Antoniades A, Shiammas C, Apidianakis Y.	Metabolites	10.3390/metabo12060499	2022
Genetics	Distinct gut metagenomics and metaproteomics signatures in prediabetics and treatment-naïve type 2 diabetics.	Zhong H, Ren H, Lu Y, Fang C, Hou G, Yang Z, Chen B, Yang F, Zhao Y, Shi Z, Zhou B, Wu J, Zou H, Zi J, Chen J, Bao X, Hu Y, Gao Y, Zhang J, Xu X, Hou Y, Yang H, Wang J, Liu S, Jia H, Madsen L, Brix S, Kristiansen K, Liu F, Li J.	EBioMedicine	10.1016/j.ebiom.2019.08.048	2019
Transcriptome	The colitis-associated transcriptional profile of commensal Bacteroides thetaiotaomicron enhances adaptive immune responses to a bacterial antigen.	Hansen JJ, Huang Y, Peterson DA, Goeser L, Fan TJ, Chang EB, Sartor RB.	PLoS One	10.1371/journal.pone.0042645	2012
	Fecal microbial transplant effect on clinical outcomes and fecal microbiome in active Crohn's disease.	Suskind DL, Brittnacher MJ, Wahbeh G, Shaffer ML, Hayden HS, Qin X, Singh N, Damman CJ, Hager KR, Nielson H, Miller SI.	Inflamm Bowel Dis	10.1097/mib.0000000000000307	2015
Metabolism	Distinct microbes, metabolites, and ecologies define the microbiome in deficient and proficient mismatch repair colorectal cancers.	Hale VL, Jeraldo P, Chen J, Mundy M, Yao J, Priya S, Keeney G, Lyke K, Ridlon J, White BA, French AJ, Thibodeau SN, Diener C, Resendis-Antonio O, Gransee J, Dutta T, Petterson XM, Sung J, Blekhman R, Boardman L, Larson D, Nelson H, Chia N.	Genome Med	10.1186/s13073-018-0586-6	2018
Phylogeny	Inflammatory bowel disease unclassified.	Zhou N, Chen WX, Chen SH, Xu CF, Li YM.	J Zhejiang Univ Sci B	10.1631/jzus.b1000172	2011
	A Multicenter Clinical Study To Demonstrate the Diagnostic Accuracy of the GenMark Dx ePlex Blood Culture Identification Gram-Negative Panel.	Wolk DM, Young S, Whitfield NN, Reid JL, Thornberg A, Carroll KC, Buchan BW, Davis TE, Salimnia H.	J Clin Microbiol	10.1128/jcm.02484-20	2021
Pathogenicity	Household triclosan and triclocarban effects on the infant and maternal microbiome.	Ribado JV, Ley C, Haggerty TD, Tkachenko E, Bhatt AS, Parsonnet J.	EMBO Mol Med	10.15252/emmm.201707882	2017
	Utility of platforms Viteks MS and Microflex LT for the identification of complex clinical isolates that require molecular methods for their taxonomic classification.	Rocca MF, Barrios R, Zintgraff J, Martinez C, Irazu L, Vay C, Prieto M.	PLoS One	10.1371/journal.pone.0218077	2019
	Early-Life Events, Including Mode of Delivery and Type of Feeding, Siblings and Gender, Shape the Developing Gut Microbiota.	Martin R, Makino H, Cetinyurek Yavuz A, Ben-Amor K, Roelofs M, Ishikawa E, Kubota H, Swinkels S, Sakai T, Oishi K, Kushiro A, Knol J.	PLoS One	10.1371/journal.pone.0158498	2016
	From obesity through gut microbiota to cardiovascular diseases: a dangerous journey.	Marzullo P, Di Renzo L, Pugliese G, De Siena M, Barrea L, Muscogiuri G, Colao A, Savastano S, Obesity Programs of nutrition, Education, Research and Assessment (OPERA) Group.	Int J Obes Suppl	10.1038/s41367-020-0017-1	2020
Phylogeny	The underlying microbial mechanism of epizootic rabbit enteropathy triggered by a low fiber diet.	Jin DX, Zou HW, Liu SQ, Wang LZ, Xue B, Wu, Tian G, Cai J, Yan TH, Wang ZS, Peng QH.	Sci Rep	10.1038/s41598-018-30178-2	2018
Pathogenicity	Interspecies Competition Impacts Targeted Manipulation of Human Gut Bacteria by Fiber-Derived Glycans.	Patnode ML, Beller ZW, Han ND, Cheng J, Peters SL, Terrapon N, Henrissat B, Le Gall S, Saulnier L, Hayashi DK, Meynier A, Vinoy S, Giannone RJ, Hettich RL, Gordon JI.	Cell	10.1016/j.cell.2019.08.011	2019
	Diagnosis of inflammatory bowel disease: Potential role of molecular biometrics.	M'Koma AE.	World J Gastrointest Surg	10.4240/wjgs.v6.i11.208	2014
Pathogenicity	Commensal-derived metabolites govern Vibrio cholerae pathogenesis in host intestine.	You JS, Yong JH, Kim GH, Moon S, Nam KT, Ryu JH, Yoon MY, Yoon SS.	Microbiome	10.1186/s40168-019-0746-y	2019
Genetics	An Integrated Outlook on the Metagenome and Metabolome of Intestinal Diseases.	Aw W, Fukuda S.	Diseases	10.3390/diseases3040341	2015
Pathogenicity	Colon Targeting of Naringin for Enhanced Cytoprotection Against Indomethacin-Induced Colitis in Rabbits.	El Naggar EE, Mohamed EA, Borg TM, El-Sheakh AR, Hamed MF.	Drug Des Devel Ther	10.2147/dddt.s218357	2020
	Changes in Microbial Community Composition Related to Sex and Colon Cancer by Nrf2 Knockout.	Song CH, Kim N, Nam RH, Choi SI, Yu JE, Nho H, Surh YJ.	Front Cell Infect Microbiol	10.3389/fcimb.2021.636808	2021
	Bioengineered Systems and Designer Matrices That Recapitulate the Intestinal Stem Cell Niche.	Wang Y, Kim R, Hinman SS, Zwarycz B, Magness ST, Allbritton NL.	Cell Mol Gastroenterol Hepatol	10.1016/j.jcmgh.2018.01.008	2018
	In Vitro and In Vivo Models for Evaluating the Oral Toxicity of Nanomedicines.	Lama S, Merlin-Zhang O, Yang C.	Nanomaterials (Basel)	10.3390/nano10112177	2020
Metabolism	Structure of RagB, a major immunodominant outer-membrane surface receptor antigen of Porphyromonas gingivalis.	Goulas T, Garcia-Ferrer I, Hutcherson JA, Potempa BA, Potempa J, Scott DA, Gomis-Ruth FX.	Mol Oral Microbiol	10.1111/omi.12140	2016
	Celiac disease.	Rubio-Tapia A, Murray JA.	Curr Opin Gastroenterol	10.1097/mog.0b013e3283365263	2010
Metabolism	Fecal metatranscriptomics of macaques with idiopathic chronic diarrhea reveals altered mucin degradation and fucose utilization.	Westreich ST, Ardeshir A, Alkan Z, Kable ME, Korf I, Lemay DG.	Microbiome	10.1186/s40168-019-0664-z	2019
	The role of bacteria in the pathogenesis of ulcerative colitis.	Sasaki M, Klapproth JM.	J Signal Transduct	10.1155/2012/704953	2012
Transcriptome	Simplified Intestinal Microbiota to Study Microbe-Diet-Host Interactions in a Mouse Model.	Kovatcheva-Datchary P, Shoaie S, Lee S, Wahlstrom A, Nookaew I, Hallen A, Perkins R, Nielsen J, Backhed F.	Cell Rep	10.1016/j.celrep.2019.02.090	2019
Genetics	More than just a gut feeling: constraint-based genome-scale metabolic models for predicting functions of human intestinal microbes.	van der Ark KCH, van Heck RGA, Martins Dos Santos VAP, Belzer C, de Vos WM.	Microbiome	10.1186/s40168-017-0299-x	2017
	Interaction between microbiota and immunity and its implication in colorectal cancer.	Xing C, Du Y, Duan T, Nim K, Chu J, Wang HY, Wang RF.	Front Immunol	10.3389/fimmu.2022.963819	2022
Pathogenicity	Prevalence of antimicrobial resistance among clinical isolates of Bacteroides fragilis group in Canada in 2010-2011: CANWARD surveillance study.	Karlowsky JA, Walkty AJ, Adam HJ, Baxter MR, Hoban DJ, Zhanel GG.	Antimicrob Agents Chemother	10.1128/aac.05823-11	2012
Pathogenicity	Antrodia cinnamomea reduces obesity and modulates the gut microbiota in high-fat diet-fed mice.	Chang CJ, Lu CC, Lin CS, Martel J, Ko YF, Ojcius DM, Wu TR, Tsai YH, Yeh TS, Lu JJ, Lai HC, Young JD.	Int J Obes (Lond)	10.1038/ijo.2017.149	2018
	Identification of Specific Oral and Gut Pathogens in Full Thickness Colon of Colitis Patients: Implications for Colon Motility.	Dinakaran V, Mandape SN, Shuba K, Pratap S, Sakhare SS, Tabatabai MA, Smoot DT, Farmer-Dixon CM, Kesavalu LN, Adunyah SE, Southerland JH, Gangula PR.	Front Microbiol	10.3389/fmicb.2018.03220	2018
Metabolism	A family of anti-Bacteroidales peptide toxins wide-spread in the human gut microbiota.	Coyne MJ, Bechon N, Matano LM, McEneany VL, Chatzidaki-Livanis M, Comstock LE.	Nat Commun	10.1038/s41467-019-11494-1	2019
Metabolism	Structural robustness of the gut mucosal microbiota is associated with Crohn's disease remission after surgery.	Mondot S, Lepage P, Seksik P, Allez M, Treton X, Bouhnik Y, Colombel JF, Leclerc M, Pochart P, Dore J, Marteau P, GETAID.	Gut	10.1136/gutjnl-2015-309184	2016
Metabolism	Interactions between Roseburia intestinalis and diet modulate atherogenesis in a murine model.	Kasahara K, Krautkramer KA, Org E, Romano KA, Kerby RL, Vivas EI, Mehrabian M, Denu JM, Backhed F, Lusis AJ, Rey FE.	Nat Microbiol	10.1038/s41564-018-0272-x	2018
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
	Gut-educated IgA plasma cells defend the meningeal venous sinuses.	Fitzpatrick Z, Frazer G, Ferro A, Clare S, Bouladoux N, Ferdinand J, Tuong ZK, Negro-Demontel ML, Kumar N, Suchanek O, Tajsic T, Harcourt K, Scott K, Bashford-Rogers R, Helmy A, Reich DS, Belkaid Y, Lawley TD, McGavern DB, Clatworthy MR.	Nature	10.1038/s41586-020-2886-4	2020
Pathogenicity	Impact of genistein on the gut microbiome of humanized mice and its role in breast tumor inhibition.	Paul B, Royston KJ, Li Y, Stoll ML, Skibola CF, Wilson LS, Barnes S, Morrow CD, Tollefsbol TO.	PLoS One	10.1371/journal.pone.0189756	2017
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
	Considerations for best practices in studies of fiber or other dietary components and the intestinal microbiome.	Klurfeld DM, Davis CD, Karp RW, Allen-Vercoe E, Chang EB, Chassaing B, Fahey GC, Hamaker BR, Holscher HD, Lampe JW, Marette A, Martens E, O'Keefe SJ, Rose DJ, Saarela M, Schneeman BO, Slavin JL, Sonnenburg JL, Swanson KS, Wu GD, Lynch CJ.	Am J Physiol Endocrinol Metab	10.1152/ajpendo.00058.2018	2018
Phylogeny	Host contributes to longitudinal diversity of fecal microbiota in swine selected for lean growth.	Lu D, Tiezzi F, Schillebeeckx C, McNulty NP, Schwab C, Shull C, Maltecca C.	Microbiome	10.1186/s40168-017-0384-1	2018
Metabolism	Microbiota and body weight control: Weight watchers within?	Boscaini S, Leigh SJ, Lavelle A, Garcia-Cabrerizo R, Lipuma T, Clarke G, Schellekens H, Cryan JF.	Mol Metab	10.1016/j.molmet.2021.101427	2022
Metabolism	Microbial and Genetic Resources for Cobalamin (Vitamin B12) Biosynthesis: From Ecosystems to Industrial Biotechnology.	Balabanova L, Averianova L, Marchenok M, Son O, Tekutyeva L.	Int J Mol Sci	10.3390/ijms22094522	2021
	Shotgun Metagenomics of 250 Adult Twins Reveals Genetic and Environmental Impacts on the Gut Microbiome.	Xie H, Guo R, Zhong H, Feng Q, Lan Z, Qin B, Ward KJ, Jackson MA, Xia Y, Chen X, Chen B, Xia H, Xu C, Li F, Xu X, Al-Aama JY, Yang H, Wang J, Kristiansen K, Wang J, Steves CJ, Bell JT, Li J, Spector TD, Jia H.	Cell Syst	10.1016/j.cels.2016.10.004	2016
	Analytical performance of a PCR assay for the detection of KRAS mutations (codons 12/13 and 61) in formalin-fixed paraffin-embedded tissue samples of colorectal carcinoma.	Lee S, Brophy VH, Cao J, Velez M, Hoeppner C, Soviero S, Lawrence HJ.	Virchows Arch	10.1007/s00428-011-1180-0	2012
Genetics	The impact of sequence database choice on metaproteomic results in gut microbiota studies.	Tanca A, Palomba A, Fraumene C, Pagnozzi D, Manghina V, Deligios M, Muth T, Rapp E, Martens L, Addis MF, Uzzau S.	Microbiome	10.1186/s40168-016-0196-8	2016
Pathogenicity	Comparative activities of eight quinolones against members of the Bacteroides fragilis group.	Borobio MV, Conejo M, Ramirez E, Suarez AI, Perea EJ.	Antimicrob Agents Chemother	10.1128/aac.38.6.1442	1994
	Genometa--a fast and accurate classifier for short metagenomic shotgun reads.	Davenport CF, Neugebauer J, Beckmann N, Friedrich B, Kameri B, Kokott S, Paetow M, Siekmann B, Wieding-Drewes M, Wienhofer M, Wolf S, Tummler B, Ahlers V, Sprengel F.	PLoS One	10.1371/journal.pone.0041224	2012
	Genome-wide detection of conservative site-specific recombination in bacteria.	Sekulovic O, Mathias Garrett E, Bourgeois J, Tamayo R, Shen A, Camilli A.	PLoS Genet	10.1371/journal.pgen.1007332	2018
	Molecular cloning of a Bacteroides caccae TonB-linked outer membrane protein identified by an inflammatory bowel disease marker antibody.	Wei B, Dalwadi H, Gordon LK, Landers C, Bruckner D, Targan SR, Braun J.	Infect Immun	10.1128/iai.69.10.6044-6054.2001	2001
Metabolism	Decreased microbial co-occurrence network stability and SCFA receptor level correlates with obesity in African-origin women.	Dugas LR, Bernabe BP, Priyadarshini M, Fei N, Park SJ, Brown L, Plange-Rhule J, Nelson D, Toh EC, Gao X, Dong Q, Sun J, Kliethermes S, Gottel N, Luke A, Gilbert JA, Layden BT.	Sci Rep	10.1038/s41598-018-35230-9	2018
Pathogenicity	Gut Microbiota and Gestational Diabetes Mellitus: A Review of Host-Gut Microbiota Interactions and Their Therapeutic Potential.	Hasain Z, Mokhtar NM, Kamaruddin NA, Mohamed Ismail NA, Razalli NH, Gnanou JV, Raja Ali RA.	Front Cell Infect Microbiol	10.3389/fcimb.2020.00188	2020
	Intestinal Microbiota Is Influenced by Gender and Body Mass Index.	Haro C, Rangel-Zuniga OA, Alcala-Diaz JF, Gomez-Delgado F, Perez-Martinez P, Delgado-Lista J, Quintana-Navarro GM, Landa BB, Navas-Cortes JA, Tena-Sempere M, Clemente JC, Lopez-Miranda J, Perez-Jimenez F, Camargo A.	PLoS One	10.1371/journal.pone.0154090	2016
	The role of the microbiome in cancer development and therapy.	Bhatt AP, Redinbo MR, Bultman SJ.	CA Cancer J Clin	10.3322/caac.21398	2017
Metabolism	The human gut Firmicute Roseburia intestinalis is a primary degrader of dietary beta-mannans.	La Rosa SL, Leth ML, Michalak L, Hansen ME, Pudlo NA, Glowacki R, Pereira G, Workman CT, Arntzen MO, Pope PB, Martens EC, Hachem MA, Westereng B.	Nat Commun	10.1038/s41467-019-08812-y	2019
Pathogenicity	In vitro activity of gemifloxacin (SB 265805) against anaerobes.	Goldstein EJ, Citron DM, Warren Y, Tyrrell K, Merriam CV.	Antimicrob Agents Chemother	10.1128/aac.43.9.2231	1999
Pathogenicity	Dietary Factors: Major Regulators of the Gut's Microbiota.	Moschen AR, Wieser V, Tilg H.	Gut Liver	10.5009/gnl.2012.6.4.411	2012
	Human intestinal lumen and mucosa-associated microbiota in patients with colorectal cancer.	Chen W, Liu F, Ling Z, Tong X, Xiang C.	PLoS One	10.1371/journal.pone.0039743	2012
Pathogenicity	The Microbiome and the Gut-Liver-Brain Axis for Central Nervous System Clinical Pharmacology: Challenges in Specifying and Integrating In Vitro and In Silico Models.	Hawkins KG, Casolaro C, Brown JA, Edwards DA, Wikswo JP.	Clin Pharmacol Ther	10.1002/cpt.1870	2020
Metabolism	Composition and metabolic activities of bacterial biofilms colonizing food residues in the human gut.	Macfarlane S, Macfarlane GT.	Appl Environ Microbiol	10.1128/aem.00754-06	2006
	Toward an understanding of changes in diversity associated with fecal microbiome transplantation based on 16S rRNA gene deep sequencing.	Shahinas D, Silverman M, Sittler T, Chiu C, Kim P, Allen-Vercoe E, Weese S, Wong A, Low DE, Pillai DR.	mBio	10.1128/mbio.00338-12	2012
Metabolism	Metabolic niche of a prominent sulfate-reducing human gut bacterium.	Rey FE, Gonzalez MD, Cheng J, Wu M, Ahern PP, Gordon JI.	Proc Natl Acad Sci U S A	10.1073/pnas.1312524110	2013
Pathogenicity	Occurrence of enterotoxigenic and nonenterotoxigenic Bacteroides fragilis in calves and evaluation of their antimicrobial susceptibility.	Almeida FS, Nakano V, Avila-Campos MJ.	FEMS Microbiol Lett	10.1111/j.1574-6968.2007.00732.x	2007
Genetics	Microbial strain-level population structure and genetic diversity from metagenomes.	Truong DT, Tett A, Pasolli E, Huttenhower C, Segata N.	Genome Res	10.1101/gr.216242.116	2017
Phylogeny	The treatment-naive microbiome in new-onset Crohn's disease.	Gevers D, Kugathasan S, Denson LA, Vazquez-Baeza Y, Van Treuren W, Ren B, Schwager E, Knights D, Song SJ, Yassour M, Morgan XC, Kostic AD, Luo C, Gonzalez A, McDonald D, Haberman Y, Walters T, Baker S, Rosh J, Stephens M, Heyman M, Markowitz J, Baldassano R, Griffiths A, Sylvester F, Mack D, Kim S, Crandall W, Hyams J, Huttenhower C, Knight R, Xavier RJ.	Cell Host Microbe	10.1016/j.chom.2014.02.005	2014
	Evaluation of pathogen detection from clinical samples by real-time polymerase chain reaction using a sepsis pathogen DNA detection kit.	Yanagihara K, Kitagawa Y, Tomonaga M, Tsukasaki K, Kohno S, Seki M, Sugimoto H, Shimazu T, Tasaki O, Matsushima A, Ikeda Y, Okamoto S, Aikawa N, Hori S, Obara H, Ishizaka A, Hasegawa N, Takeda J, Kamihira S, Sugahara K, Asari S, Murata M, Kobayashi Y, Ginba H, Sumiyama Y, Kitajima M.	Crit Care	10.1186/cc9234	2010
Genetics	Gnotobiotic mouse model of phage-bacterial host dynamics in the human gut.	Reyes A, Wu M, McNulty NP, Rohwer FL, Gordon JI.	Proc Natl Acad Sci U S A	10.1073/pnas.1319470110	2013
	Colonic bacteria express an ulcerative colitis pANCA-related protein epitope.	Cohavy O, Bruckner D, Gordon LK, Misra R, Wei B, Eggena ME, Targan SR, Braun J.	Infect Immun	10.1128/iai.68.3.1542-1548.2000	2000
Metabolism	Responsiveness of cardiometabolic-related microbiota to diet is influenced by host genetics.	O'Connor A, Quizon PM, Albright JE, Lin FT, Bennett BJ.	Mamm Genome	10.1007/s00335-014-9540-0	2014
Pathogenicity	In vitro activity of Biapenem plus RPX7009, a carbapenem combined with a serine beta-lactamase inhibitor, against anaerobic bacteria.	Goldstein EJ, Citron DM, Tyrrell KL, Merriam CV.	Antimicrob Agents Chemother	10.1128/aac.02418-12	2013
	Gut microbiome diversity influenced more by the Westernized dietary regime than the body mass index as assessed using effect size statistic.	Davis SC, Yadav JS, Barrow SD, Robertson BK.	Microbiologyopen	10.1002/mbo3.476	2017
Enzymology	Temperature gradient gel electrophoresis of fecal 16S rRNA reveals active Escherichia coli in the microbiota of patients with ulcerative colitis.	Sokol H, Lepage P, Seksik P, Dore J, Marteau P.	J Clin Microbiol	10.1128/jcm.02600-05	2006
	Phylogeny-corrected identification of microbial gene families relevant to human gut colonization.	Bradley PH, Nayfach S, Pollard KS.	PLoS Comput Biol	10.1371/journal.pcbi.1006242	2018
Pathogenicity	Ganoderma lucidum reduces obesity in mice by modulating the composition of the gut microbiota.	Chang CJ, Lin CS, Lu CC, Martel J, Ko YF, Ojcius DM, Tseng SF, Wu TR, Chen YY, Young JD, Lai HC.	Nat Commun	10.1038/ncomms8489	2015
	Therapeutic Strategies to Modulate Gut Microbial Health: Approaches for Chronic Metabolic Disorder Management.	Rondanelli M, Borromeo S, Cavioni A, Gasparri C, Gattone I, Genovese E, Lazzarotti A, Minonne L, Moroni A, Patelli Z, Razza C, Sivieri C, Valentini EM, Barrile GC.	Metabolites	10.3390/metabo15020127	2025
Enzymology	Crystal structure and putative substrate identification for the Entamoeba histolytica low molecular weight tyrosine phosphatase.	Linford AS, Jiang NM, Edwards TE, Sherman NE, Van Voorhis WC, Stewart LJ, Myler PJ, Staker BL, Petri WA.	Mol Biochem Parasitol	10.1016/j.molbiopara.2014.01.003	2014
	Anti-microbial antibodies in celiac disease: trick or treat?	Papp M, Foldi I, Altorjay I, Palyu E, Udvardy M, Tumpek J, Sipka S, Korponay-Szabo IR, Nemes E, Veres G, Dinya T, Tordai A, Andrikovics H, Norman GL, Lakatos PL.	World J Gastroenterol	10.3748/wjg.15.3891	2009
Enzymology	Biochemical and structural analyses of a bacterial endo-beta-1,2-glucanase reveal a new glycoside hydrolase family.	Abe K, Nakajima M, Yamashita T, Matsunaga H, Kamisuki S, Nihira T, Takahashi Y, Sugimoto N, Miyanaga A, Nakai H, Arakawa T, Fushinobu S, Taguchi H.	J Biol Chem	10.1074/jbc.m116.762724	2017
	In vitro communities derived from oral and gut microbial floras inhibit the growth of bacteria of foreign origins.	He X, Tian Y, Guo L, Ano T, Lux R, Zusman DR, Shi W.	Microb Ecol	10.1007/s00248-010-9711-9	2010
Phylogeny	Stressor exposure disrupts commensal microbial populations in the intestines and leads to increased colonization by Citrobacter rodentium.	Bailey MT, Dowd SE, Parry NM, Galley JD, Schauer DB, Lyte M.	Infect Immun	10.1128/iai.00862-09	2010
Enzymology	Metagenomic analysis of human diarrhea: viral detection and discovery.	Finkbeiner SR, Allred AF, Tarr PI, Klein EJ, Kirkwood CD, Wang D.	PLoS Pathog	10.1371/journal.ppat.1000011	2008
Pathogenicity	Tobacco-induced alterations to Porphyromonas gingivalis-host interactions.	Bagaitkar J, Williams LR, Renaud DE, Bemakanakere MR, Martin M, Scott DA, Demuth DR.	Environ Microbiol	10.1111/j.1462-2920.2008.01852.x	2009
Phylogeny	Direct analysis of genes encoding 16S rRNA from complex communities reveals many novel molecular species within the human gut.	Suau A, Bonnet R, Sutren M, Godon JJ, Gibson GR, Collins MD, Dore J.	Appl Environ Microbiol	10.1128/aem.65.11.4799-4807.1999	1999
Metabolism	Transposons to toxins: the provenance, architecture and diversification of a widespread class of eukaryotic effectors.	Zhang D, Burroughs AM, Vidal ND, Iyer LM, Aravind L.	Nucleic Acids Res	10.1093/nar/gkw221	2016
Phylogeny	PCR-restriction fragment length polymorphism analysis for identification of Bacteroides spp. and characterization of nitroimidazole resistance genes.	Stubbs SL, Brazier JS, Talbot PR, Duerden BI.	J Clin Microbiol	10.1128/jcm.38.9.3209-3213.2000	2000
	Mining the human gut microbiota for effector strains that shape the immune system.	Ahern PP, Faith JJ, Gordon JI.	Immunity	10.1016/j.immuni.2014.05.012	2014
Pathogenicity	Comparative In vitro activities of ertapenem (MK-0826) against 1,001 anaerobes isolated from human intra-abdominal infections.	Goldstein EJ, Citron DM, Vreni Merriam C, Warren Y, Tyrrell KL.	Antimicrob Agents Chemother	10.1128/aac.44.9.2389-2394.2000	2000
Pathogenicity	The Crohn's disease polymorphism, ATG16L1 T300A, alters the gut microbiota and enhances the local Th1/Th17 response.	Lavoie S, Conway KL, Lassen KG, Jijon HB, Pan H, Chun E, Michaud M, Lang JK, Gallini Comeau CA, Dreyfuss JM, Glickman JN, Vlamakis H, Ananthakrishnan A, Kostic A, Garrett WS, Xavier RJ.	Elife	10.7554/elife.39982	2019
Metabolism	Insights into the evolution of sialic acid catabolism among bacteria.	Almagro-Moreno S, Boyd EF.	BMC Evol Biol	10.1186/1471-2148-9-118	2009
Pathogenicity	Multicenter study of in vitro susceptibility of the Bacteroides fragilis group, 1995 to 1996, with comparison of resistance trends from 1990 to 1996.	Snydman DR, Jacobus NV, McDermott LA, Supran S, Cuchural GJ, Finegold S, Harrell L, Hecht DW, Iannini P, Jenkins S, Pierson C, Rihs J, Gorbach SL.	Antimicrob Agents Chemother	10.1128/aac.43.10.2417	1999
Metabolism	Colonization of mucin by human intestinal bacteria and establishment of biofilm communities in a two-stage continuous culture system.	Macfarlane S, Woodmansey EJ, Macfarlane GT.	Appl Environ Microbiol	10.1128/aem.71.11.7483-7492.2005	2005
Pathogenicity	High incidence of cefoxitin and clindamycin resistance among anaerobes in Taiwan.	Teng LJ, Hsueh PR, Tsai JC, Liaw SJ, Ho SW, Luh KT.	Antimicrob Agents Chemother	10.1128/aac.46.9.2908-2913.2002	2002
Pathogenicity	Multicenter survey of the changing in vitro antimicrobial susceptibilities of clinical isolates of Bacteroides fragilis group, Prevotella, Fusobacterium, Porphyromonas, and Peptostreptococcus species.	Aldridge KE, Ashcraft D, Cambre K, Pierson CL, Jenkins SG, Rosenblatt JE.	Antimicrob Agents Chemother	10.1128/aac.45.4.1238-1243.2001	2001
Phylogeny	Genome-Based Taxonomic Classification of Bacteroidetes.	Hahnke RL, Meier-Kolthoff JP, Garcia-Lopez M, Mukherjee S, Huntemann M, Ivanova NN, Woyke T, Kyrpides NC, Klenk HP, Goker M.	Front Microbiol	10.3389/fmicb.2016.02003	2016
	Arabinogalactan Utilization by Bifidobacterium longum subsp. longum NCC 2705 and Bacteroides caccae ATCC 43185 in Monoculture and Coculture.	Wang Y, LaPointe G	Microorganisms	10.3390/microorganisms8111703	2020
Phylogeny	"Bacteroides goldsteinii sp. nov." isolated from clinical specimens of human intestinal origin.	Song Y, Liu C, Lee J, Bolanos M, Vaisanen ML, Finegold SM.	J Clin Microbiol	10.1128/jcm.43.9.4522-4527.2005	2005
Phylogeny	Bacteroides stercorirosoris sp. nov. and Bacteroides faecichinchillae sp. nov., isolated from chinchilla (Chinchilla lanigera) faeces.	Kitahara M, Sakamoto M, Tsuchida S, Kawasumi K, Amao H, Benno Y, Ohkuma M	Int J Syst Evol Microbiol	10.1099/ijs.0.032706-0	2011

References

#7844	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 19024
#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 )
#34561	; Curators of the CIP;
#54426	Culture Collection University of Gothenburg (CCUG) ; Curators of the CCUG; CCUG 38735
#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) .
#66794	Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg: BRENDA, the ELIXIR core data resource in 2021: new developments and updates. Nucleic Acids Res. 49: D498 - D508 2020 ( DOI 10.1093/nar/gkaa1025 , PubMed 33211880 )
#67770	Japan Collection of Microorganism (JCM) ; Curators of the JCM;
#68367	Automatically annotated from API 20A .
#68380	Automatically annotated from API rID32A .
#68382	Automatically annotated from API zym .
#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 .
#117087	Collection of Institut Pasteur ; Curators of the CIP; CIP 104201
#124043	Isabel Schober, Julia Koblitz: Data extracted from sequence databases, automatically matched based on designation and taxonomy .
#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 )

Content

About us

Bacteroides caccae (DSM 19024, ATCC 43185, CCUG 38735)

Name and taxonomic classification

Morphology

Cell morphology

Colony morphology

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Oxygen tolerance

Spore formation

Metabolite utilization

Metabolite production

Metabolite tests

Enzymes

Pathway annotation

API zym

API 20A

API rID32A

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_002222615

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

Help

Social Media