Phocaeicola vulgatus (DSM 1447, ATCC 8482, CCUG 4940)

Name: Phocaeicola vulgatus (DSM 1447, ATCC 8482, CCUG 4940)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 1601

Type strain

Strain Designation LRA 049 07 85

Culture col. no. DSM 1447 ATCC 8482 CCUG 4940 JCM 5826 BCRC 12903 7 more

NCBI tax ID(s) 435590 821

Special Collections DSMZ CCUG JCM CIP

History <- ATCC <- A.H. Eggerth ATCC 8482 <-- A. H. Eggerth. CIP <- 1993, R. Mercier, bioMérieux, La Balme les Grottes, France: strain LRA 049 07 85 <- 1985, Analytab, Plainview, USA <- ATCC <- A.H. Eggerth

Links

Phocaeicola vulgatus LRA 049 07 85 is an anaerobe, Gram-negative, rod-shaped bacterium that was isolated from human faeces.

Gram-negative rod-shaped anaerobe genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 9749

LMG 17767,ATCC 8482,CCUG 4940,DSM 1447,LMG 7956,NCTC 11154,CIP 103714,JCM 5826,CCRC 12903,IFO 14291,NBIMCC 3541,NBRC 14291,BCRC 12903,CCT 2955,IAM 14520,CDBB 1092,ACM 3158,VTT E-001734

@ref 20215

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

Domain Bacteria

Phylum Bacteroidota

Class Bacteroidia

Order Bacteroidales

Family Bacteroidaceae

Genus Phocaeicola

Species Phocaeicola vulgatus

Full scientific name Phocaeicola vulgatus (Eggerth and Gagnon 1933) García-López et al. 2020

Synonyms (1)

Bacteroides vulgatus

BacDive ID	Other strains from **Phocaeicola vulgatus** (8)	Type strain
1588	P. vulgatus mprl 1840, MPRL 1840/MH4, DSM 9670
1602	P. vulgatus CCUG 12546, KCTC 2639, DSM 3289, ATCC 29327, ...
130883	P. vulgatus 39a-cc-B-5824-ARE, DSM 28735
157626	P. vulgatus H4_2, DSM 108222
157627	P. vulgatus H5_1, DSM 108228
157628	P. vulgatus H6_5, DSM 108234
158887	P. vulgatus WCA-389-WT-3C, DSM 107446
174363	P. vulgatus HUN383, NLAE-zl-G202, DSM 116443

Morphology

Cell morphology

@ref	Gram stain	Cell shape	Confidence
123893	negative	rod-shaped
125438			90.595
125438	negative		94.174
125439	negative		94.7

Colony morphology

@ref	Type of hemolysis	Incubation period
769	gamma	1-2 days
123893

Culture and growth conditions

Culture medium

@ref	Name	Medium link	Composition
769	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
769	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
769	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
34918	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)
123893	CIP Medium 20	Medium recipe at CIP

Culture temp

@ref	Growth	Type	Temperature (°C)
769	positive	growth	37
34918	positive	growth	37
44810	positive	growth	37
67770	positive	growth	37
123893	positive	growth	37

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
769	anaerobe
44810	anaerobe
123893	anaerobe
125438	anaerobe	93.809
125439	obligate anaerobe	97.1

Spore formation

@ref	Spore formation	Confidence
125439		96.7

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
68380	16024 ChEBI	D-mannose	+	fermentation	from API rID32A
123893	4853 ChEBI	esculin	-	hydrolysis
68380	29985 ChEBI	L-glutamate	-	degradation	from API rID32A
68380	17632 ChEBI	nitrate	-	reduction	from API rID32A
123893	17632 ChEBI	nitrate	-	reduction
123893	17632 ChEBI	nitrate	+	respiration
123893	16301 ChEBI	nitrite	-	reduction
68380	16634 ChEBI	raffinose	+	fermentation	from API rID32A
68380	27897 ChEBI	tryptophan	-	energy source	from API rID32A
68380	16199 ChEBI	urea	-	hydrolysis	from API rID32A

Antibiotic resistance

@ref	ChEBI	Metabolite	Is sensitive	Is resistant
123893	6909	metronidazole

Metabolite production

@ref	Chebi-ID	Metabolite	Production
68380	35581 ChEBI	indole		from API rID32A
123893	35581 ChEBI	indole

Metabolite tests

@ref	Chebi-ID	Metabolite	Indole test
68380	35581 ChEBI	indole	-	from API rID32A

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	alpha-arabinosidase	+	3.2.1.55	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
68380	alpha-glucosidase	+	3.2.1.20	from API rID32A
68382	alpha-mannosidase	-	3.2.1.24	from API zym
123893	amylase	-
68382	beta-galactosidase	+	3.2.1.23	from API zym
123893	beta-galactosidase	+	3.2.1.23
68380	beta-galactosidase	+	3.2.1.23	from API rID32A
68382	beta-glucosidase	-	3.2.1.21	from API zym
68380	beta-glucosidase	-	3.2.1.21	from API rID32A
68382	beta-glucuronidase	+	3.2.1.31	from API zym
123893	caseinase	+	3.4.21.50
769	catalase	-	1.11.1.6
123893	catalase	-	1.11.1.6
68382	cystine arylamidase	-	3.4.11.3	from API zym
769	cytochrome-c oxidase	-	1.9.3.1
123893	DNase	-
68382	esterase (C 4)	-		from API zym
68382	esterase lipase (C 8)	-		from API zym
123893	gelatinase	-
68380	glutamate decarboxylase	-	4.1.1.15	from API rID32A
68380	glutamyl-glutamate arylamidase	+		from API rID32A
68380	glycin arylamidase	+		from API rID32A
68380	histidine arylamidase	-		from API rID32A
68380	L-arginine arylamidase	-		from API rID32A
123893	lecithinase	-
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
123893	lipase	-
68382	lipase (C 14)	-		from API zym
68382	N-acetyl-beta-glucosaminidase	+	3.2.1.52	from API zym
68380	N-acetyl-beta-glucosaminidase	+	3.2.1.52	from API rID32A
68382	naphthol-AS-BI-phosphohydrolase	+		from API zym
123893	oxidase	-
68380	phenylalanine arylamidase	-		from API rID32A
68380	proline-arylamidase	-	3.4.11.5	from API rID32A
123893	protease	-
68380	pyrrolidonyl arylamidase	-	3.4.19.3	from API rID32A
68380	serine arylamidase	-		from API rID32A
68382	trypsin	-	3.4.21.4	from API zym
68380	tryptophan deaminase	-	4.1.99.1	from API rID32A
123893	tween esterase	-
68380	tyrosine arylamidase	-		from API rID32A
123893	urease	-	3.5.1.5
68380	urease	-	3.5.1.5	from API rID32A
68382	valine arylamidase	-		from API zym

Pathway annotation

Computationally determined by

@ref	pathway	enzyme coverage	annotated reactions
66794	palmitate biosynthesis	100	22 of 22
66794	sulfopterin metabolism	100	4 of 4
66794	coenzyme A metabolism	100	4 of 4
66794	formaldehyde oxidation	100	3 of 3
66794	vitamin K metabolism	100	5 of 5
66794	glycogen metabolism	100	5 of 5
66794	cis-vaccenate biosynthesis	100	2 of 2
66794	ppGpp biosynthesis	100	4 of 4
66794	L-lactaldehyde degradation	100	3 of 3
66794	gluconeogenesis	100	8 of 8
66794	CDP-diacylglycerol biosynthesis	100	2 of 2
66794	suberin monomers biosynthesis	100	2 of 2
66794	folate polyglutamylation	100	1 of 1
66794	UDP-GlcNAc biosynthesis	100	3 of 3
66794	C4 and CAM-carbon fixation	100	8 of 8
66794	anapleurotic synthesis of oxalacetate	100	1 of 1
66794	tetrahydrofolate metabolism	92.86	13 of 14
66794	starch degradation	90	9 of 10
66794	valine metabolism	88.89	8 of 9
66794	lipid A biosynthesis	88.89	8 of 9
66794	chorismate metabolism	88.89	8 of 9
66794	aspartate and asparagine metabolism	88.89	8 of 9
66794	isoleucine metabolism	87.5	7 of 8
66794	propanol degradation	85.71	6 of 7
66794	vitamin B1 metabolism	84.62	11 of 13
66794	vitamin B12 metabolism	82.35	28 of 34
66794	vitamin B6 metabolism	81.82	9 of 11
66794	pentose phosphate pathway	81.82	9 of 11
66794	propionate fermentation	80	8 of 10
66794	threonine metabolism	80	8 of 10
66794	flavin biosynthesis	80	12 of 15
66794	cellulose degradation	80	4 of 5
66794	Entner Doudoroff pathway	80	8 of 10
66794	peptidoglycan biosynthesis	80	12 of 15
66794	metabolism of amino sugars and derivatives	80	4 of 5
66794	pyrimidine metabolism	80	36 of 45
66794	photosynthesis	78.57	11 of 14
66794	serine metabolism	77.78	7 of 9
66794	d-mannose degradation	77.78	7 of 9
66794	NAD metabolism	77.78	14 of 18
66794	phenylalanine metabolism	76.92	10 of 13
66794	purine metabolism	76.6	72 of 94
66794	glycolysis	76.47	13 of 17
66794	glycogen biosynthesis	75	3 of 4
66794	CMP-KDO biosynthesis	75	3 of 4
66794	biotin biosynthesis	75	3 of 4
66794	acetate fermentation	75	3 of 4
66794	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	75	6 of 8
66794	proline metabolism	72.73	8 of 11
66794	alanine metabolism	72.41	21 of 29
66794	histidine metabolism	72.41	21 of 29
66794	citric acid cycle	71.43	10 of 14
66794	glutamate and glutamine metabolism	71.43	20 of 28
66794	cardiolipin biosynthesis	71.43	5 of 7
66794	isoprenoid biosynthesis	69.23	18 of 26
66794	acetoin degradation	66.67	2 of 3
66794	octane oxidation	66.67	2 of 3
66794	degradation of pentoses	64.29	18 of 28
66794	d-xylose degradation	63.64	7 of 11
66794	dTDPLrhamnose biosynthesis	62.5	5 of 8
66794	degradation of sugar alcohols	62.5	10 of 16
66794	lysine metabolism	61.9	26 of 42
66794	leucine metabolism	61.54	8 of 13
66794	phosphatidylethanolamine bioynthesis	61.54	8 of 13
66794	non-pathway related	60.53	23 of 38
66794	methylglyoxal degradation	60	3 of 5
66794	hydrogen production	60	3 of 5
66794	arginine metabolism	58.33	14 of 24
66794	methionine metabolism	57.69	15 of 26
66794	ubiquinone biosynthesis	57.14	4 of 7
66794	degradation of sugar acids	56	14 of 25
66794	degradation of hexoses	55.56	10 of 18
66794	metabolism of disaccharids	54.55	6 of 11
66794	sulfate reduction	53.85	7 of 13
66794	oxidative phosphorylation	51.65	47 of 91
66794	ethanol fermentation	50	1 of 2
66794	toluene degradation	50	2 of 4
66794	alginate biosynthesis	50	2 of 4
66794	adipate degradation	50	1 of 2
66794	heme metabolism	50	7 of 14
66794	pantothenate biosynthesis	50	3 of 6
66794	aminopropanol phosphate biosynthesis	50	1 of 2
66794	degradation of aromatic, nitrogen containing compounds	50	6 of 12
66794	tryptophan metabolism	50	19 of 38
66794	cysteine metabolism	50	9 of 18
66794	butanoate fermentation	50	2 of 4
66794	glycolate and glyoxylate degradation	50	3 of 6
66794	lipid metabolism	45.16	14 of 31
66794	CO2 fixation in Crenarchaeota	44.44	4 of 9
66794	daunorubicin biosynthesis	44.44	4 of 9
66794	polyamine pathway	43.48	10 of 23
66794	reductive acetyl coenzyme A pathway	42.86	3 of 7
66794	glutathione metabolism	42.86	6 of 14
66794	arachidonate biosynthesis	40	2 of 5
66794	O-antigen biosynthesis	40	2 of 5
66794	lipoate biosynthesis	40	2 of 5
66794	glycine metabolism	40	4 of 10
66794	coenzyme M biosynthesis	40	4 of 10
66794	phenylpropanoid biosynthesis	38.46	5 of 13
66794	urea cycle	38.46	5 of 13
66794	ketogluconate metabolism	37.5	3 of 8
66794	ascorbate metabolism	36.36	8 of 22
66794	tyrosine metabolism	35.71	5 of 14
66794	acetyl CoA biosynthesis	33.33	1 of 3
66794	enterobactin biosynthesis	33.33	1 of 3
66794	molybdenum cofactor biosynthesis	33.33	3 of 9
66794	IAA biosynthesis	33.33	1 of 3
66794	cyanate degradation	33.33	1 of 3
66794	nitrate assimilation	33.33	3 of 9
66794	selenocysteine biosynthesis	33.33	2 of 6
66794	1,4-dihydroxy-6-naphthoate biosynthesis	33.33	2 of 6
66794	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
66794	3-phenylpropionate degradation	33.33	5 of 15
66794	4-hydroxyphenylacetate degradation	30	3 of 10
66794	myo-inositol biosynthesis	30	3 of 10
66794	arachidonic acid metabolism	27.78	5 of 18
66794	dolichyl-diphosphooligosaccharide biosynthesis	27.27	3 of 11
66794	catecholamine biosynthesis	25	1 of 4
66794	cyclohexanol degradation	25	1 of 4
66794	lactate fermentation	25	1 of 4

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
123893	-	+	-	-	-	-	-	-	-	-	+	+	+	+	+	+	-	+	-	+

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
769	-	-	+	+	-	+	-	+	-	+	+	+	-	+	-	-	+	-	-	+	-	-	-	-	+	+	-	+	-
769	-	-	+	+	+/-	+	-	+	+/-	+	+	+	-	+	-	-	+	-	-	+	-	-	-	-	+	+	-	+	-
769	-	+	+	+	-	+	-	+	-	+	+	+	-	+	-	-	+	-	-	+	-	-	-	-	+	+	-	+	-
769	-	-	+	+	-	+	-	+	+/-	+	+	+	-	+	-	-	+	-	-	+	-	-	-	-	+	+	-	+	-
769	-	-	+	+	-	+	-	+	+	+	+	+	-	+	-	-	-	-	-	+	-	-	-	-	+	+	-	+	-

Isolation, sampling and environmental information

Isolation source categories

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

Isolation

@ref	Sample type
769	human faeces
67770	Human feces

Taxonmaps

69479

Global distribution of 16S sequence AB510712 (>99% sequence identity) for Phocaeicola vulgatus subclade from Microbeatlas

Aquatic Samples	2761
Soil Samples	881
Animal Samples	148487
Plant Samples	380
Total Samples	152509

Interaction and safety

Risk assessment

@ref	Pathogenicity human	Biosafety level	Biosafety level comment
769	yes, in single cases	1	Risk group (German classification) According to TRBA 466
123893		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	ASM1282v1 assembly for Phocaeicola vulgatus ATCC 8482	complete	GCA_000012825	435590.9	640753008	435590	99.29
124043	ASM1676691v1 assembly for Phocaeicola vulgatus FDAARGOS_1098	chromosome	GCA_016766915	821.4031		821	88.93
66792	81B11 assembly for Phocaeicola dorei	contig	GCA_900624655	435590.45	2886510283	435590	78.92
66792	Phocaeicola vulgatus ATCC 8482	complete			2510065017	435590	52.98
66792	ASM2853891v1 assembly for Phocaeicola vulgatus ATCC 8482	contig	GCA_028538915	435590.182	8119217367	435590	52.83

16S sequences

@ref	Description	Accession	Length	NCBI tax ID
20218	Bacteroides vulgatus 16S-23S rDNA intergenic spacer region	AF176693	426	435590
20218	Bacteroides vulgatus 16S rRNA gene, strain ATCC 8482	AJ867050	1476	435590
20218	Bacteroides vulgatus strain DSM 1447 16S ribosomal RNA gene, partial sequence	HQ012024	931	821
20218	Bacteroides vulgatus 16S ribosomal RNA gene, partial sequence	M58762	1533	821
769	Bacteroides vulgatus gene for 16S ribosomal RNA, partial sequence, strain: JCM 5826	AB510712	1489	821
67770	Bacteroides vulgatus gene for 16S rRNA, partial sequence	AB050111	1397	821
124043	Bacteroides vulgatus strain BCRC12903 16S ribosomal RNA gene, partial sequence.	EU136687	1985	821

GC content

@ref	GC-content (mol%)	Method
769	41.0	thermal denaturation, midpoint method (Tm)
769	42.2	sequence analysis
67770	41	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: Phocaeicola vulgatus ATCC 8482
NCBI: GCA_000012825

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	96.70	no
125439	motility	BacteriaNetⓘ	no	71.70	no
125439	gram_stain	BacteriaNetⓘ	negative	94.70	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate anaerobe	97.10	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Phocaeicola vulgatus ATCC 8482 ATCC 8482
NCBI: GCA_000012825.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	94.17	no
125438	anaerobic	anaerobicⓘ	yes	93.81	no
125438	aerobic	aerobicⓘ	no	93.79	yes
125438	spore-forming	spore-formingⓘ	no	89.90	no
125438	thermophilic	thermophileⓘ	no	95.67	no
125438	flagellated	motile2+ⓘ	no	90.60	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Metabolism	Roles of human colonic bacteria in pectin utilization and associated cross-feeding networks revealed using synthetic co-cultures.	Solvang M, Farquharson FM, Horgan G, Pisano S, Holck J, Zeuner B, Russell WR, Louis P.	Microbiology (Reading)	10.1099/mic.0.001559	2025
	Genetic optimization of the human gut bacterium Phocaeicola vulgatus for enhanced succinate production.	Gindt ME, Luck R, Deppenmeier U.	Appl Microbiol Biotechnol	10.1007/s00253-024-13303-2	2024
	Online monitored characterization of Phocaeicola vulgatus for organic acid production using anaerobic microtiter plate cultivations.	Keitel L, Schick B, Pohen G, Yordanov S, Buchs J.	Biotechnol Prog	10.1002/btpr.3526	2025
	Deciphering oxidative stress responses in human gut microbes and fecal microbiota: a cultivation-based approach.	Zund JN, Caflisch M, Mujezinovic D, Pluss S, Lacroix C, Pugin B.	FEMS Microbiol Ecol	10.1093/femsec/fiaf054	2025
	Carbon dioxide and trace oxygen concentrations impact growth and product formation of the gut bacterium Phocaeicola vulgatus.	Keitel L, Braun K, Finger M, Kosfeld U, Yordanov S, Buchs J.	BMC Microbiol	10.1186/s12866-023-03127-x	2023
	Investigation of the human-gut-kidney axis by fecal proteomics, highlights molecular mechanisms affected in CKD.	Lohia S, Valkenburg S, Stroggilos R, Lygirou V, Makridakis M, Zoidakis J, Verbeke F, Glorieux G, Vlahou A.	Heliyon	10.1016/j.heliyon.2024.e32828	2024
	Genetic tools for the redirection of the central carbon flow towards the production of lactate in the human gut bacterium Phocaeicola (Bacteroides) vulgatus.	Luck R, Deppenmeier U.	Appl Microbiol Biotechnol	10.1007/s00253-022-11777-6	2022
Pathogenicity	Quantifying the varying harvest of fermentation products from the human gut microbiota.	Arnoldini M, Sharma R, Moresi C, Chure G, Chabbey J, Slack E, Cremer J.	Cell	10.1016/j.cell.2025.07.005	2025
Pathogenicity	Modelling Human Gut-Microbiome Interactions in a 3D Bioelectronic Platform.	Moysidou CM, van Niekerk DC, Stoeger V, Pitsalidis C, Draper LA, Withers AM, Hughes K, McCoy R, Acharya R, Hill C, Owens RM.	Small Sci	10.1002/smsc.202300349	2024
	Heterologous expression and antimicrobial potential of class II bacteriocins.	Elisa Heesemann Rosenkilde C, Olsen Lutzhoft D, Vazquez-Uribe R, Otto Alexander Sommer M.	Gut Microbes	10.1080/19490976.2024.2369338	2024
	Modulation of Designed Gut Bacterial Communities by Prebiotics and the Impact of Their Metabolites on Intestinal Cells.	Roupar D, Gonzalez A, Martins JT, Goncalves DA, Teixeira JA, Botelho C, Nobre C.	Foods	10.3390/foods12234216	2023
	Novel Fermented Plant-Based Functional Beverage: Biological Potential and Impact on the Human Gut Microbiota.	Vila-Real C, Costa C, Pimenta-Martins A, Mbugua S, Hagretou SL, Katina K, Maina NH, Pinto E, Gomes AMP.	Foods	10.3390/foods14030433	2025
Pathogenicity	Effect of the standard herbal preparation, STW5, treatment on dysbiosis induced by dextran sodium sulfate in experimental colitis.	Mohamed SS, Abdeltawab NF, Wadie W, Ahmed LA, Ammar RM, Rabini S, Abdel-Aziz H, Khayyal MT.	BMC Complement Med Ther	10.1186/s12906-021-03337-8	2021
	Limited Neonatal Carbohydrate-Specific Antibody Repertoire Consecutive to Partial Prenatal Transfer of Maternal Antibodies.	Kappler K, Restin T, Lasanajak Y, Smith DF, Bassler D, Hennet T.	Front Immunol	10.3389/fimmu.2020.573629	2020
	Increased Antibody Response to Fucosylated Oligosaccharides and Fucose-Carrying Bacteroides Species in Crohn's Disease.	Kappler K, Lasanajak Y, Smith DF, Opitz L, Hennet T.	Front Microbiol	10.3389/fmicb.2020.01553	2020
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	Microbial short-chain fatty acids modulate CD8⁺ T cell responses and improve adoptive immunotherapy for cancer.	Luu M, Riester Z, Baldrich A, Reichardt N, Yuille S, Busetti A, Klein M, Wempe A, Leister H, Raifer H, Picard F, Muhammad K, Ohl K, Romero R, Fischer F, Bauer CA, Huber M, Gress TM, Lauth M, Danhof S, Bopp T, Nerreter T, Mulder IE, Steinhoff U, Hudecek M, Visekruna A.	Nat Commun	10.1038/s41467-021-24331-1	2021
Genetics	Species classifier choice is a key consideration when analysing low-complexity food microbiome data.	Walsh AM, Crispie F, O'Sullivan O, Finnegan L, Claesson MJ, Cotter PD.	Microbiome	10.1186/s40168-018-0437-0	2018
Metabolism	Diastereomer-specific quantification of bioactive hexosylceramides from bacteria and mammals.	von Gerichten J, Schlosser K, Lamprecht D, Morace I, Eckhardt M, Wachten D, Jennemann R, Grone HJ, Mack M, Sandhoff R.	J Lipid Res	10.1194/jlr.d076190	2017
Metabolism	Methotrexate impacts conserved pathways in diverse human gut bacteria leading to decreased host immune activation.	Nayak RR, Alexander M, Deshpande I, Stapleton-Gray K, Rimal B, Patterson AD, Ubeda C, Scher JU, Turnbaugh PJ.	Cell Host Microbe	10.1016/j.chom.2020.12.008	2021
Pathogenicity	Inhibitory activity spectrum of reuterin produced by Lactobacillus reuteri against intestinal bacteria.	Cleusix V, Lacroix C, Vollenweider S, Duboux M, Le Blay G.	BMC Microbiol	10.1186/1471-2180-7-101	2007
Metabolism	Bacteria regulate intestinal epithelial cell differentiation factors both in vitro and in vivo.	Becker S, Oelschlaeger TA, Wullaert A, Vlantis K, Pasparakis M, Wehkamp J, Stange EF, Gersemann M.	PLoS One	10.1371/journal.pone.0055620	2013
Enzymology	Enterohepatic helicobacter in ulcerative colitis: potential pathogenic entities?	Thomson JM, Hansen R, Berry SH, Hope ME, Murray GI, Mukhopadhya I, McLean MH, Shen Z, Fox JG, El-Omar E, Hold GL.	PLoS One	10.1371/journal.pone.0017184	2011
Genetics	Analysis of 1,000 Type-Strain Genomes Improves Taxonomic Classification of Bacteroidetes.	Garcia-Lopez M, Meier-Kolthoff JP, Tindall BJ, Gronow S, Woyke T, Kyrpides NC, Hahnke RL, Goker M.	Front Microbiol	10.3389/fmicb.2019.02083	2019
Genetics	The prototypic crAssphage is a linear phage-plasmid.	Schmidtke DT, Hickey AS, Wirbel J, Lin JD, Liachko I, Sherlock G, Bhatt AS.	Cell Host Microbe	10.1016/j.chom.2025.07.004	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
	Genomes of Bacteroides ovatus, B. cellulosilyticus, B. uniformis, Phocaeicola vulgatus, and P. dorei isolated from gut cavernous fistulous tract micropathologies in Crohn's disease.	Singh V, West G, Fiocchi C, Cominelli F, Good CE, Jacobs MR, Rodriguez-Palacios A.	Microbiol Resour Announc	10.1128/mra.01152-23	2024
	Phocaeicola vulgatus induces immunotherapy resistance in hepatocellular carcinoma via reducing indoleacetic acid production.	Zhao CN, Li SS, Yau T, Chen WQ, Ji R, Guan XY, Kong FS.	Cell Rep Med	10.1016/j.xcrm.2025.102370	2025
Genetics	Structure-dependent degradation of milk oligosaccharides by newly isolated intestinal commensal bacterial strains from suckling piglets and rabbits.	Rumeau M, Chadi S, Pepke F, Beaumont M, Vicente CM, Juppeau A, Vandecasteele C, Cauquil L, Pascal G, Langella P, Knudsen C, Combes S, Martin R.	BMC Microbiol	10.1186/s12866-025-04205-y	2025
	Constituents of stable commensal microbiota imply diverse colonic epithelial cell reactivity in patients with ulcerative colitis.	Inciuraite R, Gedgaudas R, Lukosevicius R, Tilinde D, Ramonaite R, Link A, Kasetiene N, Malakauskas M, Kiudelis G, Jonaitis LV, Kupcinskas J, Juzenas S, Skieceviciene J.	Gut Pathog	10.1186/s13099-024-00612-0	2024
	Tracking and characterization of a novel conjugative transposon identified by shotgun transposon mutagenesis.	Ortanez J, Degnan PH.	Front Microbiol	10.3389/fmicb.2024.1241582	2024
	Susceptibility to inflammatory bowel diseases promotes invasive carcinomas in a murine model of ATF6-driven colon cancer.	Kovilein J, Sorbie A, Khaloian S, Kuntzel V, von Stern M, Ahmed M, Jarosch S, Remke M, Metwaly A, Reuss EM, Busch DH, Allez M, Steiger K, Schraml B, Coleman OI, Haller D.	J Crohns Colitis	10.1093/ecco-jcc/jjaf102	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
	Lessons from the model gut Bacteroidales Bacteroides fragilis and Bacteroides thetaiotaomicron and future opportunities.	Comstock LE.	J Bacteriol	10.1128/jb.00346-25	2025
	A critical role for Phocaeicola vulgatus in negatively impacting metformin response in diabetes	Chen M, Peng Y, Hu Y, Kang Z, Chen T, Zhang Y, Chen X, Li Q, Yuan Z, Wu Y, Xu H, Zhou G, Liu T, Zhou H, Yuan C, Huang W, Zhang W.	Acta pharmaceutica Sinica. B		2025
Genetics	Positive nutritional selection of adults with healthy lifestyle and high daily fiber consumption for the isolation of beneficial intestinal bacteria: The iTARGET cohort study protocol.	Caille A, Connan C, Lyon Belgy N, Borezee E, Cherbuy C, Meunier N, Meslier V.	MethodsX	10.1016/j.mex.2025.103268	2025
	Structural disruption of Ntox15 nuclease effector domains by immunity proteins protects against type VI secretion system intoxication in Bacteroidales.	Bosch DE, Abbasian R, Parajuli B, Peterson SB, Mougous JD.	mBio	10.1128/mbio.01039-23	2023
	Polysaccharide utilization loci from Bacteroidota encode CE15 enzymes with possible roles in cleaving pectin-lignin bonds.	Seveso A, Mazurkewich S, Banerjee S, Poulsen J-CN, Lo Leggio L, Larsbrink J.	Appl Environ Microbiol	10.1128/aem.01768-23	2024
	Phocaeicola vulgatus shapes the long-term growth dynamics and evolutionary adaptations of Clostridioides difficile.	Sulaiman JE, Thompson J, Cheung PLK, Qian Y, Mill J, James I, Im H, Vivas EI, Simcox J, Venturelli OS.	Cell Host Microbe	10.1016/j.chom.2024.12.001	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
	Intestinal microbiota composition and bile salt hydrolase activity in fast and slow growing broiler chickens: implications for growth performance and production efficiency.	Kim HW, Kim NK, Wolf PG, Brandvold K, Rehberger JM, Rehberger TG, Dilger RN, Smith AH, Mackie RI.	J Anim Sci Biotechnol	10.1186/s40104-025-01243-4	2025
Genetics	Development and Clinical Application of a Multilocus Sequence Typing Scheme for Bacteroides fragilis Based on Whole-Genome Sequencing Data.	Nielsen FD, Skov MN, Sydenham TV, Justesen US.	Microbiol Spectr	10.1128/spectrum.05111-22	2023
Pathogenicity	A bacterial sialidase mediates early-life colonization by a pioneering gut commensal.	Buzun E, Hsu CY, Sejane K, Oles RE, Vasquez Ayala A, Loomis LR, Zhao J, Rossitto LA, McGrosso DM, Gonzalez DJ, Bode L, Chu H.	Cell Host Microbe	10.1016/j.chom.2023.12.014	2024
Pathogenicity	The potential effect of gut microbiota on the secretion of selected cytokines by human cells in vitro.	Kopa-Stojak PN, Kleniewska P, Hoffmann A, Pawliczak R.	Sci Rep	10.1038/s41598-025-01581-3	2025
Pathogenicity	Bacteroidetocins Target the Essential Outer Membrane Protein BamA of Bacteroidales Symbionts and Pathogens.	Matano LM, Coyne MJ, Garcia-Bayona L, Comstock LE.	mBio	10.1128/mbio.02285-21	2021
	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
	Predicting metabolomic profiles from microbial composition through neural ordinary differential equations.	Wang T, Wang XW, Lee-Sarwar KA, Litonjua AA, Weiss ST, Sun Y, Maslov S, Liu YY.	Nat Mach Intell	10.1038/s42256-023-00627-3	2023
Genetics	Enrichment of gut microbiome strains for cultivation-free genome sequencing using droplet microfluidics.	Pryszlak A, Wenzel T, Seitz KW, Hildebrand F, Kartal E, Cosenza MR, Benes V, Bork P, Merten CA.	Cell Rep Methods	10.1016/j.crmeth.2021.100137	2022
Genetics	Discovery of antimicrobial peptides in the global microbiome with machine learning.	Santos-Junior CD, Torres MDT, Duan Y, Rodriguez Del Rio A, Schmidt TSB, Chong H, Fullam A, Kuhn M, Zhu C, Houseman A, Somborski J, Vines A, Zhao XM, Bork P, Huerta-Cepas J, de la Fuente-Nunez C, Coelho LP.	Cell	10.1016/j.cell.2024.05.013	2024
	Characterizing the Effect of Amylase Inhibitors on Maltodextrin Metabolism by Gut Bacteria Using Fluorescent Glycan Labeling.	Lui O, Dridi L, Gonzalez E, Yasmine S, Kubinski R, Billings H, Bohlmann J, Withers SG, Maurice C, Castagner B.	ACS Chem Biol	10.1021/acschembio.2c00791	2023
	Bacteroides vulgatus attenuates experimental mice colitis through modulating gut microbiota and immune responses.	Liu L, Xu M, Lan R, Hu D, Li X, Qiao L, Zhang S, Lin X, Yang J, Ren Z, Xu J.	Front Immunol	10.3389/fimmu.2022.1036196	2022
	Gut commensal bacterium Bacteroides vulgatus exacerbates helminth-induced cardiac fibrosis through succinate accumulation.	Wang J, Yin J, Liu X, Liu Y, Jin X.	PLoS Pathog	10.1371/journal.ppat.1013069	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
	The potential immunomodulatory role of the gut microbiota in the pathogenesis of asthma: an in vitro study.	Kleniewska P, Kopa-Stojak PN, Hoffmann A, Pawliczak R.	Sci Rep	10.1038/s41598-023-47003-0	2023
	Novel Bacteroides Vulgatus strain protects against gluten-induced break of human celiac gut epithelial homeostasis: a pre-clinical proof-of-concept study.	Tran T, Senger S, Baldassarre M, Brosnan RA, Cristofori F, Crocco M, De Santis S, Elli L, Faherty CS, Francavilla R, Goodchild-Michelman I, Kenyon VA, Leonard MM, Lima RS, Malerba F, Montuori M, Morelli A, Norsa L, Passaro T, Piemontese P, Reed JC, Sansotta N, Valitutti F, Zomorrodi AR, Fasano A, CDGEMM Team.	Pediatr Res	10.1038/s41390-023-02960-0	2024
	Structural and Biochemical Characterization of a Nonbinding SusD-Like Protein Involved in Xylooligosaccharide Utilization by an Uncultured Human Gut Bacteroides Strain.	Tauzin AS, Wang Z, Cioci G, Li X, Labourel A, Machado B, Lippens G, Potocki-Veronese G.	mSphere	10.1128/msphere.00244-22	2022
Metabolism	A versatile genetic toolbox for Prevotella copri enables studying polysaccharide utilization systems.	Li J, Galvez EJC, Amend L, Almasi E, Iljazovic A, Lesker TR, Bielecka AA, Schorr EM, Strowig T.	EMBO J	10.15252/embj.2021108287	2021
	A proteolytically activated antimicrobial toxin encoded on a mobile plasmid of Bacteroidales induces a protective response.	Evans JC, McEneany VL, Coyne MJ, Caldwell EP, Sheahan ML, Von SS, Coyne EM, Tweten RK, Comstock LE.	Nat Commun	10.1038/s41467-022-31925-w	2022
	A systematic review and meta-analysis of the effects of probiotics on bone outcomes in rodent models.	Yumol JL, Gittings W, de Souza RJ, Ward WE.	J Bone Miner Res	10.1093/jbmr/zjae187	2024
	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
	Deep-learning-enabled antibiotic discovery through molecular de-extinction.	Wan F, Torres MDT, Peng J, de la Fuente-Nunez C.	Nat Biomed Eng	10.1038/s41551-024-01201-x	2024
	The Bacteroidetes Q-rule and glutaminyl cyclase activity increase the stability of extracytoplasmic proteins.	Szczesniak K, Veillard F, Scavenius C, Chudzik K, Ferenc K, Bochtler M, Potempa J, Mizgalska D.	mBio	10.1128/mbio.00980-23	2023
	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
	Experimental evaluation of ecological principles to understand and modulate the outcome of bacterial strain competition in gut microbiomes.	Segura Munoz RR, Mantz S, Martinez I, Li F, Schmaltz RJ, Pudlo NA, Urs K, Martens EC, Walter J, Ramer-Tait AE.	ISME J	10.1038/s41396-022-01208-9	2022
	From gut to bone: deciphering the impact of gut microbiota on osteoporosis pathogenesis and management.	Hao L, Yan Y, Huang G, Li H.	Front Cell Infect Microbiol	10.3389/fcimb.2024.1416739	2024
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
Metabolism	Structure-dependent stimulation of gut bacteria by arabinoxylo-oligosaccharides (AXOS): a review.	Leschonski KP, Mortensen MS, Hansen LBS, Krogh KBRM, Kabel MA, Laursen MF.	Gut Microbes	10.1080/19490976.2024.2430419	2024
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
Genetics	Investigating Host Microbiota Relationships Through Functional Metagenomics.	Laville E, Perrier J, Bejar N, Maresca M, Esque J, Tauzin AS, Bouhajja E, Leclerc M, Drula E, Henrissat B, Berdah S, Di Pasquale E, Robe P, Potocki-Veronese G.	Front Microbiol	10.3389/fmicb.2019.01286	2019
	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
	The gut-brain-axis: A positive relationship between gut microbial dysbiosis and glioblastoma brain tumour.	Ishaq HM, Yasin R, Mohammad IS, Fan Y, Li H, Shahzad M, Xu J.	Heliyon	10.1016/j.heliyon.2024.e30494	2024
	Dietary fiber content in clinical ketogenic diets modifies the gut microbiome and seizure resistance in mice.	Ozcan E, Yu KB, Dinh L, Lum GR, Lau K, Hsu J, Arino M, Paramo J, Lopez-Romero A, Hsiao EY.	Nat Commun	10.1038/s41467-025-56091-7	2025
	Protective role of colitis in inflammatory arthritis via propionate-producing Bacteroides in the gut.	Shon HJ, Kim YM, Kim KS, Choi JO, Cho SH, An S, Park SH, Cho YJ, Park JH, Seo SU, Cho JY, Kim WU, Kim D.	Front Immunol	10.3389/fimmu.2023.1064900	2023
	Interactions between Blastocystis subtype ST4 and gut microbiota in vitro.	Deng L, Tan KSW.	Parasit Vectors	10.1186/s13071-022-05194-x	2022
	Competition and cooperation: The plasticity of bacterial interactions across environments.	Solowiej-Wedderburn J, Pentz JT, Lizana L, Schroeder BO, Lind PA, Libby E.	PLoS Comput Biol	10.1371/journal.pcbi.1013213	2025
	Core microbiome-associated proteins associated with ulcerative colitis interact with cytokines for synergistic or antagonistic effects on gut bacteria.	Zhang T, Zhong H, Lin L, Zhang Z, Xue K, He F, Luo Y, Wang P, Zhao Z, Cong L, Pang P, Li X, Shan H, Yan Z.	ISME J	10.1093/ismejo/wrae146	2024
Metabolism	Porphyromonas gingivalis HmuY and Bacteroides vulgatus Bvu-A Novel Competitive Heme Acquisition Strategy.	Sieminska K, Cierpisz P, Smiga M, Olczak T.	Int J Mol Sci	10.3390/ijms22052237	2021
	Screening for effective cell-penetrating peptides with minimal impact on epithelial cells and gut commensals in vitro.	Gelli HP, Vazquez-Uribe R, Sommer MOA.	Front Pharmacol	10.3389/fphar.2022.1049324	2022
	Gut-Thyroid axis: How gut microbial dysbiosis associated with euthyroid thyroid cancer.	Ishaq HM, Mohammad IS, Hussain R, Parveen R, Shirazi JH, Fan Y, Shahzad M, Hayat K, Li H, Ihsan A, Muhammad KS, Usman M, Zhang S, Yuan L, Ullah S, Paiva-Santos AC, Xu J.	J Cancer	10.7150/jca.66816	2022
	Quantitative real-time PCR analysis of bacterial biomarkers enable fast and accurate monitoring in inflammatory bowel disease.	Sezgin E, Terlemez G, Bozkurt B, Bengi G, Akpinar H, Buyuktorun I.	PeerJ	10.7717/peerj.14217	2022
	Bacteroides vulgatus alleviates dextran sodium sulfate-induced colitis and depression-like behaviour by facilitating gut-brain axis balance.	Wu X, Xu J, Li J, Deng M, Shen Z, Nie K, Luo W, Zhang C, Ma K, Chen X, Wang X.	Front Microbiol	10.3389/fmicb.2023.1287271	2023
	Hemophore-like proteins of the HmuY family in the oral and gut microbiome: unraveling the mystery of their evolution.	Olczak T, Smiga M, Antonyuk SV, Smalley JW.	Microbiol Mol Biol Rev	10.1128/mmbr.00131-23	2024
	Modulation of the Gut Microbiota by Tomato Flours Obtained after Conventional and Ohmic Heating Extraction and Its Prebiotic Properties.	Coelho MC, Costa C, Roupar D, Silva S, Rodrigues AS, Teixeira JA, Pintado ME.	Foods	10.3390/foods12091920	2023
Phylogeny	Evaluation of 16S rRNA gene sequencing for species and strain-level microbiome analysis.	Johnson JS, Spakowicz DJ, Hong BY, Petersen LM, Demkowicz P, Chen L, Leopold SR, Hanson BM, Agresta HO, Gerstein M, Sodergren E, Weinstock GM.	Nat Commun	10.1038/s41467-019-13036-1	2019
	Study on the Biochemical Characterization and Selectivity of Three beta-Glucosidases From Bifidobacterium adolescentis ATCC15703.	Hu Y, Zhai L, Hong H, Shi Z, Zhao J, Liu D.	Front Microbiol	10.3389/fmicb.2022.860014	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
	In vivo manipulation of human gut Bacteroides fitness by abiotic oligosaccharides.	Wesener DA, Beller ZW, Hill MF, Yuan H, Belanger DB, Frankfater C, Terrapon N, Henrissat B, Rodionov DA, Leyn SA, Osterman A, van Hylckama Vlieg JET, Gordon JI.	Nat Chem Biol	10.1038/s41589-024-01763-6	2025
	Azathioprine, Mercaptopurine, and 5-Aminosalicylic Acid Affect the Growth of IBD-Associated Campylobacter Species and Other Enteric Microbes.	Liu F, Ma R, Riordan SM, Grimm MC, Liu L, Wang Y, Zhang L.	Front Microbiol	10.3389/fmicb.2017.00527	2017
	Scalable and cost-effective ribonuclease-based rRNA depletion for transcriptomics.	Huang Y, Sheth RU, Kaufman A, Wang HH.	Nucleic Acids Res	10.1093/nar/gkz1169	2020
Phylogeny	Offline Next Generation Metagenomics Sequence Analysis Using MinION Detection Software (MINDS).	Deshpande SV, Reed TM, Sullivan RF, Kerkhof LJ, Beigel KM, Wade MM.	Genes (Basel)	10.3390/genes10080578	2019
Genetics	A deep siamese neural network improves metagenome-assembled genomes in microbiome datasets across different environments.	Pan S, Zhu C, Zhao XM, Coelho LP.	Nat Commun	10.1038/s41467-022-29843-y	2022
Phylogeny	Berberine alters gut microbial function through modulation of bile acids.	Wolf PG, Devendran S, Doden HL, Ly LK, Moore T, Takei H, Nittono H, Murai T, Kurosawa T, Chlipala GE, Green SJ, Kakiyama G, Kashyap P, McCracken VJ, Gaskins HR, Gillevet PM, Ridlon JM.	BMC Microbiol	10.1186/s12866-020-02020-1	2021
	A molecular toolkit for heterologous protein secretion across Bacteroides species.	Yeh YH, Kelly VW, Rahman Pour R, Sirk SJ.	Nat Commun	10.1038/s41467-024-53845-7	2024
Metabolism	Biochemical and structural basis of sialic acid utilization by gut microbes.	Bell A, Severi E, Owen CD, Latousakis D, Juge N.	J Biol Chem	10.1016/j.jbc.2023.102989	2023
	Evaluation of the Effects of Different Bacteroides vulgatus Strains against DSS-Induced Colitis.	Li S, Wang C, Zhang C, Luo Y, Cheng Q, Yu L, Sun Z.	J Immunol Res	10.1155/2021/9117805	2021
	Genetic Manipulation of Wild Human Gut Bacteroides.	Bencivenga-Barry NA, Lim B, Herrera CM, Trent MS, Goodman AL.	J Bacteriol	10.1128/jb.00544-19	2020
Enzymology	H₂ generated by fermentation in the human gut microbiome influences metabolism and competitive fitness of gut butyrate producers.	Campbell A, Gdanetz K, Schmidt AW, Schmidt TM.	Microbiome	10.1186/s40168-023-01565-3	2023
	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
Genetics	To assemble or not to resemble-A validated Comparative Metatranscriptomics Workflow (CoMW).	Anwar MZ, Lanzen A, Bang-Andreasen T, Jacobsen CS.	Gigascience	10.1093/gigascience/giz096	2019
	Versatility of bacterial outer membrane vesicles in regulating intestinal homeostasis.	Wang X, Lin S, Wang L, Cao Z, Zhang M, Zhang Y, Liu R, Liu J.	Sci Adv	10.1126/sciadv.ade5079	2023
	Axiom Microbiome Array, the next generation microarray for high-throughput pathogen and microbiome analysis.	Thissen JB, Be NA, McLoughlin K, Gardner S, Rack PG, Shapero MH, Rowland RRR, Slezak T, Jaing CJ.	PLoS One	10.1371/journal.pone.0212045	2019
	Potential of Musa sapientum Linn. for digestive function promotion by supporting Lactobacillus sp.	Jaiturong P, Laosirisathian N, Sirithunyalug B, Eitssayeam S, Sirilun S, Chaiyana W, Sirithunyalug J.	Heliyon	10.1016/j.heliyon.2020.e05247	2020
Metabolism	Mapping Interactions of Microbial Metabolites with Human G-Protein-Coupled Receptors.	Colosimo DA, Kohn JA, Luo PM, Piscotta FJ, Han SM, Pickard AJ, Rao A, Cross JR, Cohen LJ, Brady SF.	Cell Host Microbe	10.1016/j.chom.2019.07.002	2019
Metabolism	Depletion of microbiome-derived molecules in the host using Clostridium genetics.	Guo CJ, Allen BM, Hiam KJ, Dodd D, Van Treuren W, Higginbottom S, Nagashima K, Fischer CR, Sonnenburg JL, Spitzer MH, Fischbach MA.	Science	10.1126/science.aav1282	2019
Enzymology	Time-to-detection of bacteria and yeast with the BACTEC FX versus BacT/Alert Virtuo blood culture systems.	Somily AM, Habib HA, Torchyan AA, Sayyed SB, Absar M, Al-Aqeel R, Binkhamis AK.	Ann Saudi Med	10.5144/0256-4947.2018.194	2018
Genetics	Comparative genome characterization of the periodontal pathogen Tannerella forsythia.	Zwickl NF, Stralis-Pavese N, Schaffer C, Dohm JC, Himmelbauer H.	BMC Genomics	10.1186/s12864-020-6535-y	2020
	Altered Immunity of Laboratory Mice in the Natural Environment Is Associated with Fungal Colonization.	Yeung F, Chen YH, Lin JD, Leung JM, McCauley C, Devlin JC, Hansen C, Cronkite A, Stephens Z, Drake-Dunn C, Fulmer Y, Shopsin B, Ruggles KV, Round JL, Loke P, Graham AL, Cadwell K.	Cell Host Microbe	10.1016/j.chom.2020.02.015	2020
Metabolism	Bile Acid 7alpha-Dehydroxylating Gut Bacteria Secrete Antibiotics that Inhibit Clostridium difficile: Role of Secondary Bile Acids.	Kang JD, Myers CJ, Harris SC, Kakiyama G, Lee IK, Yun BS, Matsuzaki K, Furukawa M, Min HK, Bajaj JS, Zhou H, Hylemon PB.	Cell Chem Biol	10.1016/j.chembiol.2018.10.003	2019
Metabolism	Structure and sequence analyses of Bacteroides proteins BVU_4064 and BF1687 reveal presence of two novel predominantly-beta domains, predicted to be involved in lipid and cell surface interactions.	Natarajan P, Punta M, Kumar A, Yeh AP, Godzik A, Aravind L.	BMC Bioinformatics	10.1186/s12859-014-0434-7	2015
	Broccoli consumption affects the human gastrointestinal microbiota.	Kaczmarek JL, Liu X, Charron CS, Novotny JA, Jeffery EH, Seifried HE, Ross SA, Miller MJ, Swanson KS, Holscher HD.	J Nutr Biochem	10.1016/j.jnutbio.2018.09.015	2019
	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
	Influence of the densities and nutritional components of bacterial colonies on the culture-enriched gut bacterial community structure.	Gu Y, Yan D, Wu M, Li M, Li P, Wang J, Chang Y, Yang F, Di S, Ni S, Yang M, Liu J.	AMB Express	10.1186/s13568-021-01240-6	2021
Metabolism	Enterococcus faecalis Gluconate Phosphotransferase System Accelerates Experimental Colitis and Bacterial Killing by Macrophages.	Fan TJ, Goeser L, Naziripour A, Redinbo MR, Hansen JJ.	Infect Immun	10.1128/iai.00080-19	2019
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
	A new Illumina MiSeq high-throughput sequencing-based method for evaluating the composition of the Bacteroides community in the intestine using the rpsD gene sequence.	Wang C, Feng S, Xiao Y, Pan M, Zhao J, Zhang H, Zhai Q, Chen W.	Microb Biotechnol	10.1111/1751-7915.13651	2021
Proteome	Structures of single-layer beta-sheet proteins evolved from beta-hairpin repeats.	Xu Q, Biancalana M, Grant JC, Chiu HJ, Jaroszewski L, Knuth MW, Lesley SA, Godzik A, Elsliger MA, Deacon AM, Wilson IA.	Protein Sci	10.1002/pro.3683	2019
Metabolism	The effects of micronutrient deficiencies on bacterial species from the human gut microbiota.	Hibberd MC, Wu M, Rodionov DA, Li X, Cheng J, Griffin NW, Barratt MJ, Giannone RJ, Hettich RL, Osterman AL, Gordon JI.	Sci Transl Med	10.1126/scitranslmed.aal4069	2017
	Lipidome of the Bacteroides Genus Containing New Peptidolipid and Sphingolipid Families Revealed by Multiple-Stage Mass Spectrometry.	Frankfater CF, Sartorio MG, Valguarnera E, Feldman MF, Hsu FF.	Biochemistry	10.1021/acs.biochem.2c00664	2023
Genetics	Developing a Bacteroides System for Function-Based Screening of DNA from the Human Gut Microbiome.	Lam KN, Martens EC, Charles TC.	mSystems	10.1128/msystems.00195-17	2018
	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
	Physicochemical and prebiotic properties of resistant starch from Musa sapientum Linn., ABB group, cv. Kluai Namwa Luang.	Jaiturong P, Laosirisathian N, Sirithunyalug B, Eitssayeam S, Sirilun S, Chaiyana W, Sirithunyalug J.	Heliyon	10.1016/j.heliyon.2020.e05789	2020
	ANCHOR: a 16S rRNA gene amplicon pipeline for microbial analysis of multiple environmental samples.	Gonzalez E, Pitre FE, Brereton NJB.	Environ Microbiol	10.1111/1462-2920.14632	2019
	DUDE-Seq: Fast, flexible, and robust denoising for targeted amplicon sequencing.	Lee B, Moon T, Yoon S, Weissman T.	PLoS One	10.1371/journal.pone.0181463	2017
	Genetic and environmental interactions contribute to immune variation in rewilded mice.	Oyesola O, Downie AE, Howard N, Barre RS, Kiwanuka K, Zaldana K, Chen YH, Menezes A, Lee SC, Devlin J, Mondragon-Palomino O, Souza COS, Herrmann C, Koralov SB, Cadwell K, Graham AL, Loke P.	Nat Immunol	10.1038/s41590-024-01862-5	2024
Pathogenicity	Inhibition of CD82 improves colitis by increasing NLRP3 deubiquitination by BRCC3.	Kim JS, Kim HK, Lee J, Jang S, Cho E, Mun SJ, Yoon S, Yang CS.	Cell Mol Immunol	10.1038/s41423-022-00971-1	2023
	Evaluation of Microbial-Fructo-Oligosaccharides Metabolism by Human Gut Microbiota Fermentation as Compared to Commercial Inulin-Derived Oligosaccharides.	Roupar D, Coelho MC, Goncalves DA, Silva SP, Coelho E, Silva S, Coimbra MA, Pintado M, Teixeira JA, Nobre C.	Foods	10.3390/foods11070954	2022
	Multi-omics analyses of the ulcerative colitis gut microbiome link Bacteroides vulgatus proteases with disease severity.	Mills RH, Dulai PS, Vazquez-Baeza Y, Sauceda C, Daniel N, Gerner RR, Batachari LE, Malfavon M, Zhu Q, Weldon K, Humphrey G, Carrillo-Terrazas M, Goldasich LD, Bryant M, Raffatellu M, Quinn RA, Gewirtz AT, Chassaing B, Chu H, Sandborn WJ, Dorrestein PC, Knight R, Gonzalez DJ.	Nat Microbiol	10.1038/s41564-021-01050-3	2022
	Commensal bacteria promote type I interferon signaling to maintain immune tolerance in mice.	Vasquez Ayala A, Hsu CY, Oles RE, Matsuo K, Loomis LR, Buzun E, Carrillo Terrazas M, Gerner RR, Lu HH, Kim S, Zhang Z, Park JH, Rivaud P, Thomson M, Lu LF, Min B, Chu H.	J Exp Med	10.1084/jem.20230063	2024
Pathogenicity	Glucose but Not Fructose Alters the Intestinal Paracellular Permeability in Association With Gut Inflammation and Dysbiosis in Mice.	Zhang X, Monnoye M, Mariadassou M, Beguet-Crespel F, Lapaque N, Heberden C, Douard V.	Front Immunol	10.3389/fimmu.2021.742584	2021
Metabolism	The Bacteroidales produce an N-acylated derivative of glycine with both cholesterol-solubilising and hemolytic activity.	Lynch A, Crowley E, Casey E, Cano R, Shanahan R, McGlacken G, Marchesi JR, Clarke DJ.	Sci Rep	10.1038/s41598-017-13774-6	2017
Genetics	Abundance profiling of specific gene groups using precomputed gut metagenomes yields novel biological hypotheses.	Yarygin K, Tyakht A, Larin A, Kostryukova E, Kolchenko S, Bitner V, Alexeev D.	PLoS One	10.1371/journal.pone.0176154	2017
Enzymology	High occurrence of Fusobacterium nucleatum and Clostridium difficile in the intestinal microbiota of colorectal carcinoma patients.	Fukugaiti MH, Ignacio A, Fernandes MR, Ribeiro Junior U, Nakano V, Avila-Campos MJ.	Braz J Microbiol	10.1590/s1517-838246420140665	2015
	Sewage reflects the microbiomes of human populations.	Newton RJ, McLellan SL, Dila DK, Vineis JH, Morrison HG, Eren AM, Sogin ML.	mBio	10.1128/mbio.02574-14	2015
Pathogenicity	Quinones are growth factors for the human gut microbiota.	Fenn K, Strandwitz P, Stewart EJ, Dimise E, Rubin S, Gurubacharya S, Clardy J, Lewis K.	Microbiome	10.1186/s40168-017-0380-5	2017
	Anti-HmuY antibodies specifically recognize Porphyromonas gingivalis HmuY protein but not homologous proteins in other periodontopathogens.	Smiga M, Bielecki M, Olczak M, Smalley JW, Olczak T.	PLoS One	10.1371/journal.pone.0117508	2015
	A dysbiotic gut microbiome suppresses antibody mediated-protection against Vibrio cholerae.	Macbeth JC, Liu R, Alavi S, Hsiao A.	iScience	10.1016/j.isci.2021.103443	2021
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
Genetics	Evaluative profiling of arsenic sensing and regulatory systems in the human microbiome project genomes.	Isokpehi RD, Udensi UK, Simmons SS, Hollman AL, Cain AE, Olofinsae SA, Hassan OA, Kashim ZA, Enejoh OA, Fasesan DE, Nashiru O.	Microbiol Insights	10.4137/mbi.s18076	2014
	Amino acid based de Bruijn graph algorithm for identifying complete coding genes from metagenomic and metatranscriptomic short reads.	Liu J, Lian Q, Chen Y, Qi J.	Nucleic Acids Res	10.1093/nar/gkz017	2019
	Rewilding Nod2 and Atg16l1 Mutant Mice Uncovers Genetic and Environmental Contributions to Microbial Responses and Immune Cell Composition.	Lin JD, Devlin JC, Yeung F, McCauley C, Leung JM, Chen YH, Cronkite A, Hansen C, Drake-Dunn C, Ruggles KV, Cadwell K, Graham AL, Loke P.	Cell Host Microbe	10.1016/j.chom.2020.03.001	2020
Metabolism	Ferritin-like family proteins in the anaerobe Bacteroides fragilis: when an oxygen storm is coming, take your iron to the shelter.	Rocha ER, Smith CJ.	Biometals	10.1007/s10534-013-9650-2	2013
	Stable calcium-free myocilin olfactomedin domain variants reveal challenges in differentiating between benign and glaucoma-causing mutations.	Hill SE, Kwon MS, Martin MD, Suntharalingam A, Hazel A, Dickey CA, Gumbart JC, Lieberman RL.	J Biol Chem	10.1074/jbc.ra119.009419	2019
	Development of a micromanipulation method for single cell isolation of prokaryotes and its application in food safety.	Hohnadel M, Maumy M, Chollet R.	PLoS One	10.1371/journal.pone.0198208	2018
	Clostridium sporogenes uses reductive Stickland metabolism in the gut to generate ATP and produce circulating metabolites.	Liu Y, Chen H, Van Treuren W, Hou BH, Higginbottom SK, Dodd D.	Nat Microbiol	10.1038/s41564-022-01109-9	2022
Metabolism	Enterococcus faecalis Glucosamine Metabolism Exacerbates Experimental Colitis.	Fan TJ, Goeser L, Lu K, Faith JJ, Hansen JJ.	Cell Mol Gastroenterol Hepatol	10.1016/j.jcmgh.2021.06.017	2021
	Tannerella forsythia Tfo belongs to Porphyromonas gingivalis HmuY-like family of proteins but differs in heme-binding properties.	Bielecki M, Antonyuk S, Strange RW, Smalley JW, Mackiewicz P, Smiga M, Stepien P, Olczak M, Olczak T.	Biosci Rep	10.1042/bsr20181325	2018
Enzymology	Gut microbial diversity in rat model induced by rhubarb.	Peng Y, Wu C, Yang J, Li X.	Exp Anim	10.1538/expanim.63.415	2014
	Molecular Alteration Analysis of Human Gut Microbial Composition in Graves' disease Patients.	Ishaq HM, Mohammad IS, Shahzad M, Ma C, Raza MA, Wu X, Guo H, Shi P, Xu J.	Int J Biol Sci	10.7150/ijbs.24151	2018
Genetics	Functional metagenomic discovery of bacterial effectors in the human microbiome and isolation of commendamide, a GPCR G2A/132 agonist.	Cohen LJ, Kang HS, Chu J, Huang YH, Gordon EA, Reddy BV, Ternei MA, Craig JW, Brady SF.	Proc Natl Acad Sci U S A	10.1073/pnas.1508737112	2015
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
Genetics	Investigating host-microbiome interactions by droplet based microfluidics.	Tauzin AS, Pereira MR, Van Vliet LD, Colin PY, Laville E, Esque J, Laguerre S, Henrissat B, Terrapon N, Lombard V, Leclerc M, Dore J, Hollfelder F, Potocki-Veronese G.	Microbiome	10.1186/s40168-020-00911-z	2020
	Species Deletions from Microbiome Consortia Reveal Key Metabolic Interactions between Gut Microbes.	Gutierrez N, Garrido D.	mSystems	10.1128/msystems.00185-19	2019
	Carbohydrate complexity limits microbial growth and reduces the sensitivity of human gut communities to perturbations.	Ostrem Loss E, Thompson J, Cheung PLK, Qian Y, Venturelli OS.	Nat Ecol Evol	10.1038/s41559-022-01930-9	2023
Metabolism	A 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	Novel glycoside hydrolases identified by screening a Chinese Holstein dairy cow rumen-derived metagenome library.	Zhao S, Wang J, Bu D, Liu K, Zhu Y, Dong Z, Yu Z.	Appl Environ Microbiol	10.1128/aem.00361-10	2010
Metabolism	Prebiotics Mediate Microbial Interactions in a Consortium of the Infant Gut Microbiome.	Medina DA, Pinto F, Ovalle A, Thomson P, Garrido D.	Int J Mol Sci	10.3390/ijms18102095	2017
	Complex Bacterial Consortia Reprogram the Colitogenic Activity of Enterococcus faecalis in a Gnotobiotic Mouse Model of Chronic, Immune-Mediated Colitis.	Lengfelder I, Sava IG, Hansen JJ, Kleigrewe K, Herzog J, Neuhaus K, Hofmann T, Sartor RB, Haller D.	Front Immunol	10.3389/fimmu.2019.01420	2019
	Human Tumor-Infiltrating MAIT Cells Display Hallmarks of Bacterial Antigen Recognition in Colorectal Cancer.	Li S, Simoni Y, Becht E, Loh CY, Li N, Lachance D, Koo SL, Lim TP, Tan EKW, Mathew R, Nguyen A, Golovato J, Berkson JD, Prlic M, Lee B, Minot SS, Nagarajan N, Dey N, Tan DSW, Tan IB, Newell EW.	Cell Rep Med	10.1016/j.xcrm.2020.100039	2020
Metabolism	Mapping Molecular Recognition of beta1,3-1,4-Glucans by a Surface Glycan-Binding Protein from the Human Gut Symbiont Bacteroides ovatus.	Correia VG, Trovao F, Pinheiro BA, Bras JLA, Silva LM, Nunes C, Coimbra MA, Liu Y, Feizi T, Fontes CMGA, Mulloy B, Chai W, Carvalho AL, Palma AS.	Microbiol Spectr	10.1128/spectrum.01826-21	2021
Enzymology	Mammalian-like type II glutaminyl cyclases in Porphyromonas gingivalis and other oral pathogenic bacteria as targets for treatment of periodontitis.	Taudte N, Linnert M, Rahfeld JU, Piechotta A, Ramsbeck D, Buchholz M, Kolenko P, Parthier C, Houston JA, Veillard F, Eick S, Potempa J, Schilling S, Demuth HU, Stubbs MT.	J Biol Chem	10.1016/j.jbc.2021.100263	2021
	Bacteroides ovatus ATCC 8483 monotherapy is superior to traditional fecal transplant and multi-strain bacteriotherapy in a murine colitis model.	Ihekweazu FD, Fofanova TY, Queliza K, Nagy-Szakal D, Stewart CJ, Engevik MA, Hulten KG, Tatevian N, Graham DY, Versalovic J, Petrosino JF, Kellermayer R.	Gut Microbes	10.1080/19490976.2018.1560753	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
	Evolution of symbiotic bacteria in the distal human intestine.	Xu J, Mahowald MA, Ley RE, Lozupone CA, Hamady M, Martens EC, Henrissat B, Coutinho PM, Minx P, Latreille P, Cordum H, Van Brunt A, Kim K, Fulton RS, Fulton LA, Clifton SW, Wilson RK, Knight RD, Gordon JI.	PLoS Biol	10.1371/journal.pbio.0050156	2007
	Modeling Metabolic Interactions in a Consortium of the Infant Gut Microbiome.	Pinto F, Medina DA, Perez-Correa JR, Garrido D.	Front Microbiol	10.3389/fmicb.2017.02507	2017
Genetics	Optimizing read mapping to reference genomes to determine composition and species prevalence in microbial communities.	Martin J, Sykes S, Young S, Kota K, Sanka R, Sheth N, Orvis J, Sodergren E, Wang Z, Weinstock GM, Mitreva M.	PLoS One	10.1371/journal.pone.0036427	2012
Metabolism	Probiotics in human gut microbiota can degrade host glycosaminoglycans.	Kawai K, Kamochi R, Oiki S, Murata K, Hashimoto W.	Sci Rep	10.1038/s41598-018-28886-w	2018
	The evolution of cooperation within the gut microbiota.	Rakoff-Nahoum S, Foster KR, Comstock LE.	Nature	10.1038/nature17626	2016
	The structure of BVU2987 from Bacteroides vulgatus reveals a superfamily of bacterial periplasmic proteins with possible inhibitory function.	Das D, Finn RD, Carlton D, Miller MD, Abdubek P, Astakhova T, Axelrod HL, Bakolitsa C, Chen C, Chiu HJ, Chiu M, Clayton T, Deller MC, Duan L, Ellrott K, Ernst D, Farr CL, Feuerhelm J, Grant JC, Grzechnik A, Han GW, Jaroszewski L, Jin KK, Klock HE, Knuth MW, Kozbial P, Krishna SS, Kumar A, Marciano D, McMullan D, Morse AT, Nigoghossian E, Nopakun A, Okach L, Puckett C, Reyes R, Rife CL, Sefcovic N, Tien HJ, Trame CB, van den Bedem H, Weekes D, Wooten T, Xu Q, Hodgson KO, Wooley J, Elsliger MA, Deacon AM, Godzik A, Lesley SA, Wilson IA.	Acta Crystallogr Sect F Struct Biol Cryst Commun	10.1107/s1744309109046788	2010
	Bacteroides spp. promotes branched-chain amino acid catabolism in brown fat and inhibits obesity.	Yoshida N, Yamashita T, Osone T, Hosooka T, Shinohara M, Kitahama S, Sasaki K, Sasaki D, Yoneshiro T, Suzuki T, Emoto T, Saito Y, Ozawa G, Hirota Y, Kitaura Y, Shimomura Y, Okamatsu-Ogura Y, Saito M, Kondo A, Kajimura S, Inagaki T, Ogawa W, Yamada T, Hirata KI.	iScience	10.1016/j.isci.2021.103342	2021
Metabolism	Defining the bacteroides ribosomal binding site.	Wegmann U, Horn N, Carding SR.	Appl Environ Microbiol	10.1128/aem.03086-12	2013
Phylogeny	Sequencing 16S rRNA gene fragments using the PacBio SMRT DNA sequencing system.	Schloss PD, Jenior ML, Koumpouras CC, Westcott SL, Highlander SK.	PeerJ	10.7717/peerj.1869	2016
Metabolism	The gastrointestinal pathogen Campylobacter jejuni metabolizes sugars with potential help from commensal Bacteroides vulgatus.	Garber JM, Nothaft H, Pluvinage B, Stahl M, Bian X, Porfirio S, Enriquez A, Butcher J, Huang H, Glushka J, Line E, Gerlt JA, Azadi P, Stintzi A, Boraston AB, Szymanski CM.	Commun Biol	10.1038/s42003-019-0727-5	2020
Metabolism	Development of a covalent inhibitor of gut bacterial bile salt hydrolases.	Adhikari AA, Seegar TCM, Ficarro SB, McCurry MD, Ramachandran D, Yao L, Chaudhari SN, Ndousse-Fetter S, Banks AS, Marto JA, Blacklow SC, Devlin AS.	Nat Chem Biol	10.1038/s41589-020-0467-3	2020
Metabolism	Functional assignment of multiple catabolic pathways for D-apiose.	Carter MS, Zhang X, Huang H, Bouvier JT, Francisco BS, Vetting MW, Al-Obaidi N, Bonanno JB, Ghosh A, Zallot RG, Andersen HM, Almo SC, Gerlt JA.	Nat Chem Biol	10.1038/s41589-018-0067-7	2018
Metabolism	l-Galactose metabolism in Bacteroides vulgatus from the human gut microbiota.	Hobbs ME, Williams HJ, Hillerich B, Almo SC, Raushel FM.	Biochemistry	10.1021/bi500656m	2014
Phylogeny	Evaluation of the Vitek 2 ANC card for identification of clinical isolates of anaerobic bacteria.	Lee EH, Degener JE, Welling GW, Veloo AC.	J Clin Microbiol	10.1128/jcm.02166-10	2011
	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
	The Growth and Protein Expression of Inflammatory Bowel Disease-Associated Campylobacter concisus Is Affected by the Derivatives of the Food Additive Fumaric Acid.	Ma R, Liu F, Yap SF, Lee H, Leong RW, Riordan SM, Grimm MC, Zhang L.	Front Microbiol	10.3389/fmicb.2018.00896	2018
Metabolism	Resveratrol increases glucose induced GLP-1 secretion in mice: a mechanism which contributes to the glycemic control.	Dao TM, Waget A, Klopp P, Serino M, Vachoux C, Pechere L, Drucker DJ, Champion S, Barthelemy S, Barra Y, Burcelin R, Seree E.	PLoS One	10.1371/journal.pone.0020700	2011
Transcriptome	Evolution and diversity of the Microviridae viral family through a collection of 81 new complete genomes assembled from virome reads.	Roux S, Krupovic M, Poulet A, Debroas D, Enault F.	PLoS One	10.1371/journal.pone.0040418	2012
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
Genetics	Gut bacterial profile in patients newly diagnosed with treatment-naïve Crohn's disease.	Ricanek P, Lothe SM, Frye SA, Rydning A, Vatn MH, Tonjum T.	Clin Exp Gastroenterol	10.2147/ceg.s33858	2012
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
	Insight into biases and sequencing errors for amplicon sequencing with the Illumina MiSeq platform.	Schirmer M, Ijaz UZ, D'Amore R, Hall N, Sloan WT, Quince C.	Nucleic Acids Res	10.1093/nar/gku1341	2015
	gyrA mutations associated with quinolone resistance in Bacteroides fragilis group strains.	Oh H, El Amin N, Davies T, Appelbaum PC, Edlund C.	Antimicrob Agents Chemother	10.1128/aac.45.7.1977-1981.2001	2001
	CRISPR targeting reveals a reservoir of common phages associated with the human gut microbiome.	Stern A, Mick E, Tirosh I, Sagy O, Sorek R.	Genome Res	10.1101/gr.138297.112	2012
Transcriptome	Alignment-free Transcriptomic and Metatranscriptomic Comparison Using Sequencing Signatures with Variable Length Markov Chains.	Liao W, Ren J, Wang K, Wang S, Zeng F, Wang Y, Sun F.	Sci Rep	10.1038/srep37243	2016
Metabolism	Inflammation-induced acid tolerance genes gadAB in luminal commensal Escherichia coli attenuate experimental colitis.	Tchaptchet S, Fan TJ, Goeser L, Schoenborn A, Gulati AS, Sartor RB, Hansen JJ.	Infect Immun	10.1128/iai.00355-13	2013
	Induction of bacterial antigen-specific colitis by a simplified human microbiota consortium in gnotobiotic interleukin-10-/- mice.	Eun CS, Mishima Y, Wohlgemuth S, Liu B, Bower M, Carroll IM, Sartor RB.	Infect Immun	10.1128/iai.01513-13	2014
	Functional screening of a metagenomic library reveals operons responsible for enhanced intestinal colonization by gut commensal microbes.	Yoon MY, Lee KM, Yoon Y, Go J, Park Y, Cho YJ, Tannock GW, Yoon SS.	Appl Environ Microbiol	10.1128/aem.00581-13	2013
Pathogenicity	Tetracycline resistome of the organic pig gut.	Kazimierczak KA, Scott KP, Kelly D, Aminov RI.	Appl Environ Microbiol	10.1128/aem.02206-08	2009
	MetaTrans: an open-source pipeline for metatranscriptomics.	Martinez X, Pozuelo M, Pascal V, Campos D, Gut I, Gut M, Azpiroz F, Guarner F, Manichanh C.	Sci Rep	10.1038/srep26447	2016
Genetics	Codon Usage Optimization in the Prokaryotic Tree of Life: How Synonymous Codons Are Differentially Selected in Sequence Domains with Different Expression Levels and Degrees of Conservation.	Lopez JL, Lozano MJ, Fabre ML, Lagares A.	mBio	10.1128/mbio.00766-20	2020
	Dynamic Modulation of the Gut Microbiota and Metabolome by Bacteriophages in a Mouse Model.	Hsu BB, Gibson TE, Yeliseyev V, Liu Q, Lyon L, Bry L, Silver PA, Gerber GK.	Cell Host Microbe	10.1016/j.chom.2019.05.001	2019
	Immunochemical investigations of antigens isolated from Bacteroides ovatus strain ATCC 8483.	Beckmann I, Paelinck J, Zuijderduijn J, Sawicka-Grzelak A, Meisel-Mikolajczyk F.	Antonie Van Leeuwenhoek	10.1007/bf02439936	1985
	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	Alpha-ketoglutarate metabolism by cytochrome-containing anaerobes.	Caldwell DR, Rasmussen CK.	Can J Microbiol	10.1139/m83-128	1983
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	Systematic assessment of secondary bile acid metabolism in gut microbes reveals distinct metabolic capabilities in inflammatory bowel disease.	Heinken A, Ravcheev DA, Baldini F, Heirendt L, Fleming RMT, Thiele I.	Microbiome	10.1186/s40168-019-0689-3	2019
	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
Genetics	Synthetic spike-in standards for high-throughput 16S rRNA gene amplicon sequencing.	Tourlousse DM, Yoshiike S, Ohashi A, Matsukura S, Noda N, Sekiguchi Y.	Nucleic Acids Res	10.1093/nar/gkw984	2017
Metabolism	Weak Agonistic LPS Restores Intestinal Immune Homeostasis.	Steimle A, Michaelis L, Di Lorenzo F, Kliem T, Munzner T, Maerz JK, Schafer A, Lange A, Parusel R, Gronbach K, Fuchs K, Silipo A, Oz HH, Pichler BJ, Autenrieth IB, Molinaro A, Frick JS.	Mol Ther	10.1016/j.ymthe.2019.07.007	2019
Metabolism	Bacteroides sp. strain D8, the first cholesterol-reducing bacterium isolated from human feces.	Gerard P, Lepercq P, Leclerc M, Gavini F, Raibaud P, Juste C.	Appl Environ Microbiol	10.1128/aem.02806-06	2007
Metabolism	Functional metagenomics reveals novel pathways of prebiotic breakdown by human gut bacteria.	Cecchini DA, Laville E, Laguerre S, Robe P, Leclerc M, Dore J, Henrissat B, Remaud-Simeon M, Monsan P, Potocki-Veronese G.	PLoS One	10.1371/journal.pone.0072766	2013
	Metagenomic analysis of the medicinal leech gut microbiota.	Maltz MA, Bomar L, Lapierre P, Morrison HG, McClure EA, Sogin ML, Graf J.	Front Microbiol	10.3389/fmicb.2014.00151	2014
Genetics	Development of a dual-index sequencing strategy and curation pipeline for analyzing amplicon sequence data on the MiSeq Illumina sequencing platform.	Kozich JJ, Westcott SL, Baxter NT, Highlander SK, Schloss PD.	Appl Environ Microbiol	10.1128/aem.01043-13	2013
	Colonic MUC2 mucin regulates the expression and antimicrobial activity of beta-defensin 2.	Cobo ER, Kissoon-Singh V, Moreau F, Chadee K.	Mucosal Immunol	10.1038/mi.2015.27	2015
Metabolism	A gut bacterial pathway metabolizes aromatic amino acids into nine circulating metabolites.	Dodd D, Spitzer MH, Van Treuren W, Merrill BD, Hryckowian AJ, Higginbottom SK, Le A, Cowan TM, Nolan GP, Fischbach MA, Sonnenburg JL.	Nature	10.1038/nature24661	2017
Phylogeny	Mining the Human Gut Microbiota for Immunomodulatory Organisms.	Geva-Zatorsky N, Sefik E, Kua L, Pasman L, Tan TG, Ortiz-Lopez A, Yanortsang TB, Yang L, Jupp R, Mathis D, Benoist C, Kasper DL.	Cell	10.1016/j.cell.2017.01.022	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
	Abundance and genetic diversity of microbial polygalacturonase and pectate lyase in the sheep rumen ecosystem.	Yuan P, Meng K, Wang Y, Luo H, Huang H, Shi P, Bai Y, Yang P, Yao B.	PLoS One	10.1371/journal.pone.0040940	2012
	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
Enzymology	A distinctive 'microbial signature' in celiac pediatric patients.	Schippa S, Iebba V, Barbato M, Di Nardo G, Totino V, Checchi MP, Longhi C, Maiella G, Cucchiara S, Conte MP.	BMC Microbiol	10.1186/1471-2180-10-175	2010
Proteome	Ab Initio structure prediction for Escherichia coli: towards genome-wide protein structure modeling and fold assignment.	Xu D, Zhang Y.	Sci Rep	10.1038/srep01895	2013
Enzymology	Real-time PCR detection of pathogenic microorganisms in roof-harvested rainwater in Southeast Queensland, Australia.	Ahmed W, Huygens F, Goonetilleke A, Gardner T.	Appl Environ Microbiol	10.1128/aem.00331-08	2008
Phylogeny	Molecular detection of bacterial contamination in gnotobiotic rodent units.	Packey CD, Shanahan MT, Manick S, Bower MA, Ellermann M, Tonkonogy SL, Carroll IM, Sartor RB.	Gut Microbes	10.4161/gmic.25824	2013
Metabolism	Fidaxomicin preserves the intestinal microbiome during and after treatment of Clostridium difficile infection (CDI) and reduces both toxin reexpression and recurrence of CDI.	Louie TJ, Cannon K, Byrne B, Emery J, Ward L, Eyben M, Krulicki W.	Clin Infect Dis	10.1093/cid/cis338	2012
	Deciphering microbial interactions in synthetic human gut microbiome communities.	Venturelli OS, Carr AC, Fisher G, Hsu RH, Lau R, Bowen BP, Hromada S, Northen T, Arkin AP.	Mol Syst Biol	10.15252/msb.20178157	2018
Genetics	Do you cov me? Effect of coverage reduction on metagenome shotgun sequencing studies.	Cattonaro F, Spadotto A, Radovic S, Marroni F.	F1000Res	10.12688/f1000research.16804.4	2018
Genetics	High-throughput clone library analysis of the mucosa-associated microbiota reveals dysbiosis and differences between inflamed and non-inflamed regions of the intestine in inflammatory bowel disease.	Walker AW, Sanderson JD, Churcher C, Parkes GC, Hudspith BN, Rayment N, Brostoff J, Parkhill J, Dougan G, Petrovska L.	BMC Microbiol	10.1186/1471-2180-11-7	2011
Enzymology	Bacteroides vulgatus outer membrane antigens associated with carrageenan-induced colitis in guinea pigs.	Breeling JL, Onderdonk AB, Cisneros RL, Kasper DL.	Infect Immun	10.1128/iai.56.7.1754-1759.1988	1988
Enzymology	Alterations of the dominant faecal bacterial groups in patients with Crohn's disease of the colon.	Seksik P, Rigottier-Gois L, Gramet G, Sutren M, Pochart P, Marteau P, Jian R, Dore J.	Gut	10.1136/gut.52.2.237	2003
	Gut-associated bacterial microbiota in paediatric patients with inflammatory bowel disease.	Conte MP, Schippa S, Zamboni I, Penta M, Chiarini F, Seganti L, Osborn J, Falconieri P, Borrelli O, Cucchiara S.	Gut	10.1136/gut.2005.078824	2006
Metabolism	PG1058 Is a Novel Multidomain Protein Component of the Bacterial Type IX Secretion System.	Heath JE, Seers CA, Veith PD, Butler CA, Nor Muhammad NA, Chen YY, Slakeski N, Peng B, Zhang L, Dashper SG, Cross KJ, Cleal SM, Moore C, Reynolds EC.	PLoS One	10.1371/journal.pone.0164313	2016
Metabolism	Characterizing a model human gut microbiota composed of members of its two dominant bacterial phyla.	Mahowald MA, Rey FE, Seedorf H, Turnbaugh PJ, Fulton RS, Wollam A, Shah N, Wang C, Magrini V, Wilson RK, Cantarel BL, Coutinho PM, Henrissat B, Crock LW, Russell A, Verberkmoes NC, Hettich RL, Gordon JI.	Proc Natl Acad Sci U S A	10.1073/pnas.0901529106	2009
	The human gut virome: inter-individual variation and dynamic response to diet.	Minot S, Sinha R, Chen J, Li H, Keilbaugh SA, Wu GD, Lewis JD, Bushman FD.	Genome Res	10.1101/gr.122705.111	2011
Metabolism	Human Secretory IgM Emerges from Plasma Cells Clonally Related to Gut Memory B Cells and Targets Highly Diverse Commensals.	Magri G, Comerma L, Pybus M, Sintes J, Llige D, Segura-Garzon D, Bascones S, Yeste A, Grasset EK, Gutzeit C, Uzzan M, Ramanujam M, van Zelm MC, Albero-Gonzalez R, Vazquez I, Iglesias M, Serrano S, Marquez L, Mercade E, Mehandru S, Cerutti A.	Immunity	10.1016/j.immuni.2017.06.013	2017
Metabolism	Glycan complexity dictates microbial resource allocation in the large intestine.	Rogowski A, Briggs JA, Mortimer JC, Tryfona T, Terrapon N, Lowe EC, Basle A, Morland C, Day AM, Zheng H, Rogers TE, Thompson P, Hawkins AR, Yadav MP, Henrissat B, Martens EC, Dupree P, Gilbert HJ, Bolam DN.	Nat Commun	10.1038/ncomms8481	2015
Genetics	Evaluation of 16S rDNA-based community profiling for human microbiome research.	Jumpstart Consortium Human Microbiome Project Data Generation Working Group.	PLoS One	10.1371/journal.pone.0039315	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
Genetics	Characterizing the native codon usages of a genome: an axis projection approach.	Davis JJ, Olsen GJ.	Mol Biol Evol	10.1093/molbev/msq185	2011
Enzymology	PCR detection and quantitation of predominant anaerobic bacteria in human and animal fecal samples.	Wang RF, Cao WW, Cerniglia CE.	Appl Environ Microbiol	10.1128/aem.62.4.1242-1247.1996	1996
	Luminex detection of fecal indicators in river samples, marine recreational water, and beach sand.	Baums IB, Goodwin KD, Kiesling T, Wanless D, Diaz MR, Fell JW.	Mar Pollut Bull	10.1016/j.marpolbul.2006.12.018	2007
Enzymology	Superoxide dismutase in Bacteroides fragilis and related Bacteroides species.	Carlsson J, Wrethen J, Beckman G.	J Clin Microbiol	10.1128/jcm.6.3.280-284.1977	1977
Phylogeny	Serogrouping of Bacteroides vulgatus by the agglutination test.	Okamura N, Miyazaki K, Chida T, Niwayama K, Nakaya R, Benno Y, Mitsuoka T.	J Clin Microbiol	10.1128/jcm.22.1.56-61.1985	1985
Phylogeny	Characterization of Treponema phagedenis-like spirochetes isolated from papillomatous digital dermatitis lesions in dairy cattle.	Trott DJ, Moeller MR, Zuerner RL, Goff JP, Waters WR, Alt DP, Walker RL, Wannemuehler MJ.	J Clin Microbiol	10.1128/jcm.41.6.2522-2529.2003	2003
Metabolism	Identification and functional analysis of the gene cluster for L-arabinose utilization in Corynebacterium glutamicum.	Kawaguchi H, Sasaki M, Vertes AA, Inui M, Yukawa H.	Appl Environ Microbiol	10.1128/aem.02912-08	2009
	High-density microarray of small-subunit ribosomal DNA probes.	Wilson KH, Wilson WJ, Radosevich JL, DeSantis TZ, Viswanathan VS, Kuczmarski TA, Andersen GL.	Appl Environ Microbiol	10.1128/aem.68.5.2535-2541.2002	2002
Enzymology	Quantitative analysis of mycobacterial and propionibacterial DNA in lymph nodes of Japanese and European patients with sarcoidosis.	Eishi Y, Suga M, Ishige I, Kobayashi D, Yamada T, Takemura T, Takizawa T, Koike M, Kudoh S, Costabel U, Guzman J, Rizzato G, Gambacorta M, du Bois R, Nicholson AG, Sharma OP, Ando M.	J Clin Microbiol	10.1128/jcm.40.1.198-204.2002	2002
Metabolism	A selective gut bacterial bile salt hydrolase alters host metabolism.	Yao L, Seaton SC, Ndousse-Fetter S, Adhikari AA, DiBenedetto N, Mina AI, Banks AS, Bry L, Devlin AS.	Elife	10.7554/elife.37182	2018
Genetics	Biotechnological applications of functional metagenomics in the food and pharmaceutical industries.	Coughlan LM, Cotter PD, Hill C, Alvarez-Ordonez A.	Front Microbiol	10.3389/fmicb.2015.00672	2015
Enzymology	Use of randomly cloned DNA fragments for identification of Bacteroides thetaiotaomicron.	Salyers AA, Lynn SP, Gardner JF.	J Bacteriol	10.1128/jb.154.1.287-293.1983	1983
Metabolism	Role of starch as a substrate for Bacteroides vulgatus growing in the human colon.	McCarthy RE, Pajeau M, Salyers AA.	Appl Environ Microbiol	10.1128/aem.54.8.1911-1916.1988	1988
Metabolism	Synthesis of alpha-ketoglutarate by reductive carboxylation of succinate in Veillonella, Selenomonas, and Bacteriodes species.	Allison MJ, Robinson IM, Baetz AL.	J Bacteriol	10.1128/jb.140.3.980-986.1979	1979
Enzymology	Use of a species-specific DNA hybridization probe for enumerating Bacteroides vulgatus in human feces.	Kuritza AP, Salyers AA.	Appl Environ Microbiol	10.1128/aem.50.4.958-964.1985	1985
Metabolism	Evidence that polygalacturonic acid may not be a major source of carbon and energy for some colonic Bacteroides species.	McCarthy RE, Salyers AA.	Appl Environ Microbiol	10.1128/aem.52.1.9-16.1986	1986
	Phocaeicola dorei and Phocaeicola vulgatus Protect against Atherosclerosis by Regulating Gut Immunity.	Nakashima H, Shinohara R, Emoto T, Saito Y, Yoshida N, Hirata KI, Murakami T, Mori H, Toyoda A, Sugiyama T, Yamada T, Yamashita T.	J Atheroscler Thromb	10.5551/jat.65460	2025
	Metabolite-mediated interactions and direct contact between Fusobacterium varium and Faecalibacterium prausnitzii.	Hosomi K, Maruyama S, Matsuoka T, Furuta M, Tojima Y, Uchiyama K, Morita M, Kawashima H, Kobayashi T, Kunisawa J.	Microbiome	10.1186/s40168-025-02168-w	2025
	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
	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
Genetics	A simple method that enhances minority species detection in the microbiota: 16S metagenome-DRIP (Deeper Resolution using an Inhibitory Primer).	Nakajima A, Yoshida K, Gotoh A, Katoh T, Ojima MN, Sakanaka M, Xiao JZ, Odamaki T, Katayama T.	Microbiome Res Rep	10.20517/mrr.2022.08	2022
	Estrogen-related receptor alpha mitigates radiation-induced bowel injury through gut enrichment of Bacteroides vulgatus.	Shin SG, Lee JY, Choi JW, Yoo JH, Jeong IC, Kim DY, Kim HS, Paik S, Song GY, Kim KH, Kim JM, Bae JW, Jo EK, Kim S.	Gut Microbes	10.1080/19490976.2025.2541020	2025
	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
Metabolism	Oral administration of Blautia wexlerae ameliorates obesity and type 2 diabetes via metabolic remodeling of the gut microbiota.	Hosomi K, Saito M, Park J, Murakami H, Shibata N, Ando M, Nagatake T, Konishi K, Ohno H, Tanisawa K, Mohsen A, Chen YA, Kawashima H, Natsume-Kitatani Y, Oka Y, Shimizu H, Furuta M, Tojima Y, Sawane K, Saika A, Kondo S, Yonejima Y, Takeyama H, Matsutani A, Mizuguchi K, Miyachi M, Kunisawa J.	Nat Commun	10.1038/s41467-022-32015-7	2022
Phylogeny	Identification and characterization of potential performance-related gut microbiotas in broiler chickens across various feeding trials.	Torok VA, Hughes RJ, Mikkelsen LL, Perez-Maldonado R, Balding K, MacAlpine R, Percy NJ, Ophel-Keller K.	Appl Environ Microbiol	10.1128/aem.00165-11	2011
	Succinate-producing microbiota drives tuft cell hyperplasia to protect against Clostridioides difficile.	Kellogg TD, Ceglia S, Mortzfeld BM, Tanna TM, Zeamer AL, Mancini MR, Foley SE, Ward DV, Bhattarai SK, McCormick BA, Reboldi A, Bucci V.	J Exp Med	10.1084/jem.20232055	2025
Genetics	An accurate and efficient experimental approach for characterization of the complex oral microbiota.	Zheng W, Tsompana M, Ruscitto A, Sharma A, Genco R, Sun Y, Buck MJ.	Microbiome	10.1186/s40168-015-0110-9	2015
Pathogenicity	Gut microbiota dysbiosis in Chinese children with type 1 diabetes mellitus: An observational study.	Liu X, Cheng YW, Shao L, Sun SH, Wu J, Song QH, Zou HS, Ling ZX	World J Gastroenterol	10.3748/wjg.v27.i19.2394	2021
Pathogenicity	Bacteroides vulgatus diminishes colonic microbiota dysbiosis ameliorating lumbar bone loss in ovariectomized mice.	Yuan S, Shen J	Bone	10.1016/j.bone.2020.115710	2020
Pathogenicity	Binary interactions between the yeast Candida albicans and two gut-associated Bacteroides species.	Valentine M, Benade E, Mouton M, Khan W, Botha A	Microb Pathog	10.1016/j.micpath.2019.103619	2019
Metabolism	The 'in vivo lifestyle' of bile acid 7alpha-dehydroxylating bacteria: comparative genomics, metatranscriptomic, and bile acid metabolomics analysis of a defined microbial community in gnotobiotic mice.	Ridlon JM, Devendran S, Alves JM, Doden H, Wolf PG, Pereira GV, Ly L, Volland A, Takei H, Nittono H, Murai T, Kurosawa T, Chlipala GE, Green SJ, Hernandez AG, Fields CJ, Wright CL, Kakiyama G, Cann I, Kashyap P, McCracken V, Gaskins HR	Gut Microbes	10.1080/19490976.2019.1618173	2019
Metabolism	The Biosynthesis of Lipooligosaccharide from Bacteroides thetaiotaomicron.	Jacobson AN, Choudhury BP, Fischbach MA	mBio	10.1128/mBio.02289-17	2018
Pathogenicity	The gut bacterium and pathobiont Bacteroides vulgatus activates NF-kappaB in a human gut epithelial cell line in a strain and growth phase dependent manner.	O Cuiv P, de Wouters T, Giri R, Mondot S, Smith WJ, Blottiere HM, Begun J, Morrison M	Anaerobe	10.1016/j.anaerobe.2017.06.002	2017
Metabolism	Anaerobic utilization of Fe(III)-xenosiderophores among Bacteroides species and the distinct assimilation of Fe(III)-ferrichrome by Bacteroides fragilis within the genus.	Rocha ER, Krykunivsky AS	Microbiologyopen	10.1002/mbo3.479	2017
Genetics	Extensive Mobilome-Driven Genome Diversification in Mouse Gut-Associated Bacteroides vulgatus mpk.	Lange A, Beier S, Steimle A, Autenrieth IB, Huson DH, Frick JS	Genome Biol Evol	10.1093/gbe/evw070	2016
Pathogenicity	Expression of arsenic resistance genes in the obligate anaerobe Bacteroides vulgatus ATCC 8482, a gut microbiome bacterium.	Li J, Mandal G, Rosen BP	Anaerobe	10.1016/j.anaerobe.2016.03.012	2016
Metabolism	Production of AI-2 is mediated by the S-ribosylhomocystein lyase gene luxS in Bacteroides fragilis and Bacteroides vulgatus.	Peixoto RJ, Miranda KR, Ferreira EO, de Paula GR, Rocha ER, Lobo LA, Domingues RM	J Basic Microbiol	10.1002/jobm.201300311	2013
Metabolism	Utilization of major fucosylated and sialylated human milk oligosaccharides by isolated human gut microbes.	Yu ZT, Chen C, Newburg DS	Glycobiology	10.1093/glycob/cwt065	2013
Pathogenicity	Structural characterization of BVU_3255, a methyltransferase from human intestine antibiotic resistant pathogen Bacteroides vulgatus.	Kumar V, Sivaraman J	J Struct Biol	10.1016/j.jsb.2011.08.007	2011
Pathogenicity	Growth stimulator for bifidobacteria produced by Propionibacterium freudenreichii and several intestinal bacteria.	Kaneko T, Mori H, Iwata M, Meguro S	J Dairy Sci	10.3168/jds.S0022-0302(94)76965-4	1994
	Demonstration of bacteroides capsules by light microscopy and ultrastructural cytochemistry.	Strohm H, Payne CM, Ryan KJ	Am J Clin Pathol	10.1093/ajcp/79.5.591	1983
Genetics	Noncontiguous finished genome sequence and description of Mediterranea massiliensis gen. nov., sp. nov., a new member of the Bacteroidaceae family isolated from human colon.	Ngom II, Mailhe M, Ricaboni D, Vitton V, Benezech A, Khelaifia S, Michelle C, Cadoret F, Armstrong N, Levasseur A, Raoult D, Million M.	New Microbes New Infect	10.1016/j.nmni.2017.11.009	2018
Phylogeny	Bacteroides chinchillae sp. nov. and Bacteroides rodentium sp. nov., isolated from chinchilla (Chinchilla lanigera) faeces.	Kitahara M, Tsuchida S, Kawasumi K, Amao H, Sakamoto M, Benno Y, Ohkuma M	Int J Syst Evol Microbiol	10.1099/ijs.0.024026-0	2010
Phylogeny	Bacteroides dorei sp. nov., isolated from human faeces.	Bakir MA, Sakamoto M, Kitahara M, Matsumoto M, Benno Y	Int J Syst Evol Microbiol	10.1099/ijs.0.64257-0	2006

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@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
769	-	-	+	+	-	+	-	+	-	+	+	+	-	+	-	-	+	-	-	+	-	-	-	-	+	+	-	+	-
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769	-	+	+	+	-	+	-	+	-	+	+	+	-	+	-	-	+	-	-	+	-	-	-	-	+	+	-	+	-
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@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
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Content

About us

Phocaeicola vulgatus (DSM 1447, ATCC 8482, CCUG 4940)

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

Antibiotic resistance

Metabolite production

Metabolite tests

Enzymes

Pathway annotation

API zym

API rID32A

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_000012825

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

Help

Social Media

@ref	URE	ADH (Arg)	alpha GAL	beta GAL	beta-Galactosidase 6-phosphatebeta GP	alpha GLU	beta GLU	alpha ARA	beta GUR	beta-N-Acetyl-beta-glucosaminidasebeta NAG	MNE	RAF	GDC	alpha FUC	Reduction of nitrateNIT	IND	PAL	L-arginine arylamidaseArgA	ProA	LGA	Phenylalanine arylamidasePheA	Leucine arylamidaseLeuA	PyrA	Tyrosine arylamidaseTyrA	Alanine arylamidaseAlaA	Glycin arylamidaseGlyA	Histidine arylamidaseHisA	Glutamyl-glutamate arylamidaseGGA	Serine arylamidaseSerA
769	-	-	+	+	-	+	-	+	-	+	+	+	-	+	-	-	+	-	-	+	-	-	-	-	+	+	-	+	-
769	-	-	+	+	+/-	+	-	+	+/-	+	+	+	-	+	-	-	+	-	-	+	-	-	-	-	+	+	-	+	-
769	-	+	+	+	-	+	-	+	-	+	+	+	-	+	-	-	+	-	-	+	-	-	-	-	+	+	-	+	-
769	-	-	+	+	-	+	-	+	+/-	+	+	+	-	+	-	-	+	-	-	+	-	-	-	-	+	+	-	+	-
769	-	-	+	+	-	+	-	+	+	+	+	+	-	+	-	-	-	-	-	+	-	-	-	-	+	+	-	+	-