Bacteroides finegoldii (DSM 17565, JCM 13345, CCUG 53890)

Name: Bacteroides finegoldii (DSM 17565, JCM 13345, CCUG 53890)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 1610

Type strain

Strain Designation 199

Culture col. no. DSM 17565 JCM 13345 CCUG 53890 199

NCBI tax ID(s) 483215 338188

Special Collections DSMZ CCUG JCM Literature strains

History DSMZ <- M. Sakamoto <- M. Matsumoto; 199 JCM <-- M. Kitahara 199 <-- M. Matsumoto.

Links

Bacteroides finegoldii 199 is an anaerobe, Gram-negative, rod-shaped bacterium that was isolated from human feces.

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

Name and taxonomic classification

SI-ID 291124

DSM 17565,JCM 13345,CCUG 53890,VTT E-093115

@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 finegoldii

Full scientific name Bacteroides finegoldii Bakir et al. 2006

BacDive ID	Other strains from **Bacteroides finegoldii** (3)	Type strain
154496	B. finegoldii CCUG 53891, JCM 13346
157012	B. finegoldii CCUG 68636
158061	B. finegoldii H1-5, H1_5, DSM 108067

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape	Confidence
31702	negative	1.5-4.5 µm	0.8 µm	rod-shaped
125438	negative				95.269
125439	negative				92.094

Colony morphology

@ref	Incubation period
6977	1-2 days
60059	2 days

Pigmentation

31702

Productionyes

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
6977	CHOPPED MEAT MEDIUM (DSMZ Medium 78)		Medium recipe at MediaDive	Name: CHOPPED MEAT MEDIUM (DSMZ Medium 78) Composition: Ground beef 500.0 g/l Casitone 30.0 g/l Agar 15.0 g/l Ethanol 9.5 g/l (optional) K2HPO4 5.0 g/l Yeast extract 5.0 g/l L-Cysteine HCl 0.5 g/l Haemin 0.005 g/l (optional) Resazurin 0.001 g/l Vitamin K3 0.0005 g/l (optional) Vitamin K1 (optional) NaOH (optional) Distilled water
6977	PYG MEDIUM (MODIFIED) (DSMZ Medium 104)		Medium recipe at MediaDive	Name: PYG MEDIUM (modified) (DSMZ Medium 104) Composition: Yeast extract 10.0 g/l Peptone 5.0 g/l Trypticase peptone 5.0 g/l Beef extract 5.0 g/l Glucose 5.0 g/l L-Cysteine HCl x H2O 0.5 g/l NaHCO3 0.4 g/l NaCl 0.08 g/l K2HPO4 0.04 g/l KH2PO4 0.04 g/l MgSO4 x 7 H2O 0.02 g/l CaCl2 x 2 H2O 0.01 g/l Hemin 0.005 g/l Ethanol 0.0038 g/l Resazurin 0.001 g/l Tween 80 Vitamin K1 NaOH Distilled water

Culture temp

@ref	Growth	Type	Temperature (°C)
6977	positive	growth	37
31702	positive	growth	20-40
31702	positive	optimum	37
60059	positive	growth	37
67770	positive	growth	37

Culture pH

@ref	Ability	Type	PH
31702	positive	optimum	7
31702	positive	growth	7

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
6977	anaerobe
31702	anaerobe
60059	anaerobe
125439	obligate anaerobe	99.515

Spore formation

@ref	Spore formation	Confidence
31702
125439		99.833
125438		90.478

Observation

31702

Observationaggregates in chains

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
31702	22599 ChEBI	arabinose	+	carbon source
68380	29016 ChEBI	arginine	-	hydrolysis	from API rID32A
31702	17057 ChEBI	cellobiose	+	carbon source
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
31702	4853 ChEBI	esculin	+	hydrolysis
68367	4853 ChEBI	esculin	+	hydrolysis	from API 20A
68367	5291 ChEBI	gelatin	-	hydrolysis	from API 20A
31702	17234 ChEBI	glucose	+	carbon source
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
31702	17716 ChEBI	lactose	+	carbon source
68367	17716 ChEBI	lactose	+	builds acid from	from API 20A
31702	17306 ChEBI	maltose	+	carbon source
68367	17306 ChEBI	maltose	+	builds acid from	from API 20A
31702	37684 ChEBI	mannose	+	carbon source
68367	6731 ChEBI	melezitose	-	builds acid from	from API 20A
68380	17632 ChEBI	nitrate	-	reduction	from API rID32A
31702	16634 ChEBI	raffinose	+	carbon source
68367	16634 ChEBI	raffinose	+	builds acid from	from API 20A
31702	26546 ChEBI	rhamnose	+	carbon source
31702	17814 ChEBI	salicin	+	carbon source
68367	30911 ChEBI	sorbitol	-	builds acid from	from API 20A
31702	17992 ChEBI	sucrose	+	carbon source
68367	17992 ChEBI	sucrose	+	builds acid from	from API 20A
68367	27082 ChEBI	trehalose	-	builds acid from	from API 20A
68380	27897 ChEBI	tryptophan	-	energy source	from API rID32A
68367	27897 ChEBI	tryptophan	-	energy source	from API 20A
68380	16199 ChEBI	urea	-	hydrolysis	from API rID32A
68367	16199 ChEBI	urea	-	hydrolysis	from API 20A

Metabolite production

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

Metabolite tests

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

Enzymes

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

Pathway annotation

Computationally determined by

@ref	pathway	enzyme coverage	annotated reactions
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	teichoic acid biosynthesis	100	1 of 1
66794	coenzyme A metabolism	100	4 of 4
66794	d-mannose degradation	100	9 of 9
66794	formaldehyde oxidation	100	3 of 3
66794	glycogen metabolism	100	5 of 5
66794	cis-vaccenate biosynthesis	100	2 of 2
66794	cardiolipin biosynthesis	100	7 of 7
66794	biotin biosynthesis	100	4 of 4
66794	CDP-diacylglycerol biosynthesis	100	2 of 2
66794	folate polyglutamylation	100	1 of 1
66794	UDP-GlcNAc biosynthesis	100	3 of 3
66794	suberin monomers biosynthesis	100	2 of 2
66794	anapleurotic synthesis of oxalacetate	100	1 of 1
66794	ceramide biosynthesis	100	1 of 1
66794	acetate fermentation	100	4 of 4
66794	palmitate biosynthesis	100	22 of 22
66794	NAD metabolism	94.44	17 of 18
66794	starch degradation	90	9 of 10
66794	lipid A biosynthesis	88.89	8 of 9
66794	aspartate and asparagine metabolism	88.89	8 of 9
66794	chorismate metabolism	88.89	8 of 9
66794	propanol degradation	85.71	6 of 7
66794	vitamin B1 metabolism	84.62	11 of 13
66794	pentose phosphate pathway	81.82	9 of 11
66794	vitamin B6 metabolism	81.82	9 of 11
66794	threonine metabolism	80	8 of 10
66794	pyrimidine metabolism	80	36 of 45
66794	vitamin K metabolism	80	4 of 5
66794	peptidoglycan biosynthesis	80	12 of 15
66794	photosynthesis	78.57	11 of 14
66794	valine metabolism	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	glycogen biosynthesis	75	3 of 4
66794	isoleucine metabolism	75	6 of 8
66794	ppGpp biosynthesis	75	3 of 4
66794	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	75	6 of 8
66794	glutamate and glutamine metabolism	75	21 of 28
66794	sulfopterin metabolism	75	3 of 4
66794	CMP-KDO biosynthesis	75	3 of 4
66794	flavin biosynthesis	73.33	11 of 15
66794	purine metabolism	72.34	68 of 94
66794	tetrahydrofolate metabolism	71.43	10 of 14
66794	citric acid cycle	71.43	10 of 14
66794	glycolysis	70.59	12 of 17
66794	propionate fermentation	70	7 of 10
66794	myo-inositol biosynthesis	70	7 of 10
66794	Entner Doudoroff pathway	70	7 of 10
66794	CO2 fixation in Crenarchaeota	66.67	6 of 9
66794	octane oxidation	66.67	2 of 3
66794	acetoin degradation	66.67	2 of 3
66794	d-xylose degradation	63.64	7 of 11
66794	ketogluconate metabolism	62.5	5 of 8
66794	degradation of sugar alcohols	62.5	10 of 16
66794	degradation of hexoses	61.11	11 of 18
66794	non-pathway related	60.53	23 of 38
66794	methylglyoxal degradation	60	3 of 5
66794	cellulose degradation	60	3 of 5
66794	metabolism of amino sugars and derivatives	60	3 of 5
66794	hydrogen production	60	3 of 5
66794	isoprenoid biosynthesis	57.69	15 of 26
66794	methionine metabolism	57.69	15 of 26
66794	degradation of pentoses	57.14	16 of 28
66794	ubiquinone biosynthesis	57.14	4 of 7
66794	lipid metabolism	54.84	17 of 31
66794	metabolism of disaccharids	54.55	6 of 11
66794	proline metabolism	54.55	6 of 11
66794	leucine metabolism	53.85	7 of 13
66794	lysine metabolism	52.38	22 of 42
66794	histidine metabolism	51.72	15 of 29
66794	ethanol fermentation	50	1 of 2
66794	arginine metabolism	50	12 of 24
66794	glycine metabolism	50	5 of 10
66794	phenylmercury acetate degradation	50	1 of 2
66794	adipate degradation	50	1 of 2
66794	pantothenate biosynthesis	50	3 of 6
66794	butanoate fermentation	50	2 of 4
66794	dTDPLrhamnose biosynthesis	50	4 of 8
66794	degradation of sugar acids	48	12 of 25
66794	tryptophan metabolism	47.37	18 of 38
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	tyrosine metabolism	42.86	6 of 14
66794	degradation of aromatic, nitrogen containing compounds	41.67	5 of 12
66794	arachidonate biosynthesis	40	2 of 5
66794	lipoate biosynthesis	40	2 of 5
66794	coenzyme M biosynthesis	40	4 of 10
66794	bacilysin biosynthesis	40	2 of 5
66794	oxidative phosphorylation	39.56	36 of 91
66794	phenylpropanoid biosynthesis	38.46	5 of 13
66794	sulfate reduction	38.46	5 of 13
66794	ascorbate metabolism	36.36	8 of 22
66794	acetyl CoA biosynthesis	33.33	1 of 3
66794	cyanate degradation	33.33	1 of 3
66794	glycolate and glyoxylate degradation	33.33	2 of 6
66794	nitrate assimilation	33.33	3 of 9
66794	IAA biosynthesis	33.33	1 of 3
66794	selenocysteine biosynthesis	33.33	2 of 6
66794	molybdenum cofactor biosynthesis	33.33	3 of 9
66794	enterobactin biosynthesis	33.33	1 of 3
66794	urea cycle	30.77	4 of 13
66794	phosphatidylethanolamine bioynthesis	30.77	4 of 13
66794	glutathione metabolism	28.57	4 of 14
66794	3-phenylpropionate degradation	26.67	4 of 15
66794	lactate fermentation	25	1 of 4
66794	cyclohexanol degradation	25	1 of 4
66794	toluene degradation	25	1 of 4
66794	alginate biosynthesis	25	1 of 4
66794	4-hydroxymandelate degradation	22.22	2 of 9
66794	arachidonic acid metabolism	22.22	4 of 18

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
6977	-	-	+	-	+	+	+	-	+	+	-	+	-	+	+	-	+	-	+	-	not determinedn.d.	not determinedn.d.	not determinedn.d.	not determinedn.d.
6977	-	-	+	-	+	+	+	+/-	+	+	-	+	-	+	+	-	+	-	+	-	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
6977	-	-	+	+	-	+	+	+	-	+	+	+	+	-	-	-	+	-	-	+	-	-	-	+	+	+	-	+	-
6977	-	-	+	+	-	+	+	+	-	+	+	+	+	-	-	-	+	-	-	+	-	-	-	-	+	-	-	-	-
6977	-	-	+	+	-	+	+	+	-	+	+	+/-	+	-	-	-	+	-	-	+	-	-	-	-	+	-	-	-	-

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	Country	Country ISO 3 Code	Continent
6977	human feces	Homo sapiens	Japan	JPN	Asia
60059	Human feces	Homo sapiens
67770	Human feces	Homo sapiens

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
6977	1	Risk group (German classification) According to TRBA 466

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
67770	ASM15619v1 assembly for Bacteroides finegoldii DSM 17565	scaffold	GCA_000156195	483215.6	2562617142	483215	51.32
124043	ASM3029556v1 assembly for Bacteroides finegoldii DSM 17565 JCM 13345	complete	GCA_030295565	483215.86		483215	37.53

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
6977	Bacteroides finegoldii gene for 16S rRNA, partial sequence, strain:JCM 13345	AB222699	1485		483215

GC content

@ref	GC-content (mol%)	Method
6977	42.4-43
31702	42.4-43.0
67770	42	high performance liquid chromatography (HPLC)

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: ASM15619v1 assembly for Bacteroides finegoldii DSM 17565
BV-BRC: 483215.6

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	oxygen_tolerance	BacteriaNetⓘ	obligate anaerobe	99.52	no
125439	gram_stain	BacteriaNetⓘ	negative	92.09	no
125439	motility	BacteriaNetⓘ	no	84.95	no
125439	spore_formation	BacteriaNetⓘ	no	99.83	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Bacteroides finegoldii DSM 17565
PATRIC: 483215.6

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	95.27	yes
125438	anaerobic	anaerobicⓘ	yes	84.26	no
125438	spore-forming	spore-formingⓘ	no	90.48	yes
125438	aerobic	aerobicⓘ	no	90.29	yes
125438	thermophilic	thermophileⓘ	no	95.93	no
125438	flagellated	motile2+ⓘ	no	89.50	yes

Literature

Topic	Title	Authors	Journal	DOI	Year
	Insights into the mechanism of substrate specificity in a novel PL15_3 subfamily oligo-alginate lyase VBAly15A.	Tang Y, Song Z, Xu X, Li Y, Wang L.	Appl Environ Microbiol	10.1128/aem.02351-24	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
	Exploring the Catalytic Mechanisms of a Newly Identified Salt-Activated Alginate Lyase from Pseudoalteromonas carrageenovora ASY5.	Zhuang X, Jiao C, Guo Z, Xiao Q, Chen J, Chen F, Yang Q, Ru Y, Weng H, Wang S, Xiao A, Zhang Y.	Mar Drugs	10.3390/md23060254	2025
	Genomic Background and Phylogeny of cfiA-Positive Bacteroides fragilis Strains Resistant to Meropenem-EDTA.	Valdezate S, Cobo F, Monzon S, Medina-Pascual MJ, Zaballos A, Cuesta I, Pino-Rosa S, Villalon P.	Antibiotics (Basel)	10.3390/antibiotics10030304	2021
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	Discovery of exolytic heparinases and their catalytic mechanism and potential application.	Zhang Q, Cao HY, Wei L, Lu D, Du M, Yuan M, Shi D, Chen X, Wang P, Chen XL, Chi L, Zhang YZ, Li F.	Nat Commun	10.1038/s41467-021-21441-8	2021
	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
Pathogenicity	A multi-omics spatial framework for host-microbiome dissection within the intestinal tissue microenvironment.	Zhu B, Bai Y, Yeo YY, Lu X, Rovira-Clave X, Chen H, Yeung J, Nkosi D, Glickman J, Delgado-Gonzalez A, Gerber GK, Angelo M, Shalek AK, Nolan GP, Jiang S.	Nat Commun	10.1038/s41467-025-56237-7	2025
	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
	Preliminary safety evaluation of a new Bacteroides xylanisolvens isolate.	Ulsemer P, Toutounian K, Schmidt J, Karsten U, Goletz S.	Appl Environ Microbiol	10.1128/aem.06641-11	2012
Metabolism	Structural and functional analysis of gum arabic l-rhamnose-alpha-1,4-d-glucuronate lyase establishes a novel polysaccharide lyase family.	Kondo T, Kichijo M, Maruta A, Nakaya M, Takenaka S, Arakawa T, Fushinobu S, Sakamoto T.	J Biol Chem	10.1016/j.jbc.2021.101001	2021
Proteome	Three alginate lyases provide a new gut Bacteroides ovatus isolate with the ability to grow on alginate.	Ronne ME, Tandrup T, Madsen M, Hunt CJ, Myers PN, Moll JM, Holck J, Brix S, Strube ML, Aachmann FL, Wilkens C, Svensson B.	Appl Environ Microbiol	10.1128/aem.01185-23	2023
	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	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	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
	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	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	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	Strain/species identification in metagenomes using genome-specific markers.	Tu Q, He Z, Zhou J.	Nucleic Acids Res	10.1093/nar/gku138	2014
	In silico characterization of pectate lyase protein sequences from different source organisms.	Dubey AK, Yadav S, Kumar M, Singh VK, Sarangi BK, Yadav D.	Enzyme Res	10.4061/2010/950230	2010
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 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
	Autometa: automated extraction of microbial genomes from individual shotgun metagenomes.	Miller IJ, Rees ER, Ross J, Miller I, Baxa J, Lopera J, Kerby RL, Rey FE, Kwan JC.	Nucleic Acids Res	10.1093/nar/gkz148	2019
Metabolism	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
Metabolism	Methotrexate impacts conserved pathways in diverse human gut bacteria leading to decreased host immune activation.	Nayak RR, Alexander M, Deshpande I, Stapleton-Gray K, Rimal B, Patterson AD, Ubeda C, Scher JU, Turnbaugh PJ.	Cell Host Microbe	10.1016/j.chom.2020.12.008	2021
	Design, construction, and in vivo augmentation of a complex gut microbiome.	Cheng AG, Ho PY, Aranda-Diaz A, Jain S, Yu FB, Meng X, Wang M, Iakiviak M, Nagashima K, Zhao A, Murugkar P, Patil A, Atabakhsh K, Weakley A, Yan J, Brumbaugh AR, Higginbottom S, Dimas A, Shiver AL, Deutschbauer A, Neff N, Sonnenburg JL, Huang KC, Fischbach MA.	Cell	10.1016/j.cell.2022.08.003	2022
Enzymology	Separation of 1-23-kb complementary DNA strands by urea-agarose gel electrophoresis.	Hegedus E, Kokai E, Kotlyar A, Dombradi V, Szabo G.	Nucleic Acids Res	10.1093/nar/gkp539	2009
	Type VI secretion systems of human gut Bacteroidales segregate into three genetic architectures, two of which are contained on mobile genetic elements.	Coyne MJ, Roelofs KG, Comstock LE.	BMC Genomics	10.1186/s12864-016-2377-z	2016
Genetics	Genomic characterization of JG068, a novel virulent podovirus active against Burkholderia cenocepacia.	Lynch KH, Abdu AH, Schobert M, Dennis JJ, Dennis JJ.	BMC Genomics	10.1186/1471-2164-14-574	2013
Phylogeny	Comparative fecal metagenomics unveils unique functional capacity of the swine gut.	Lamendella R, Domingo JW, Ghosh S, Martinson J, Oerther DB.	BMC Microbiol	10.1186/1471-2180-11-103	2011
	The Production of 2,3-Butylene Glycol by Aerobacter aerogenes 199.	Olson BH, Johnson MJ.	J Bacteriol	10.1128/jb.55.2.209-222.1948	1948
	Isolation and identification of hyaluronan-degrading bacteria from Japanese fecal microbiota.	Akazawa H, Fukuda I, Kaneda H, Yoda S, Kimura M, Nomoto R, Ueda S, Shirai Y, Osawa R.	PLoS One	10.1371/journal.pone.0284517	2023
	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
Genetics	Kelpie: generating full-length 'amplicons' from whole-metagenome datasets.	Greenfield P, Tran-Dinh N, Midgley D.	PeerJ	10.7717/peerj.6174	2019
	Characterizing the interactions between a naturally primed immunoglobulin A and its conserved Bacteroides thetaiotaomicron species-specific epitope in gnotobiotic mice.	Peterson DA, Planer JD, Guruge JL, Xue L, Downey-Virgin W, Goodman AL, Seedorf H, Gordon JI.	J Biol Chem	10.1074/jbc.m114.633800	2015
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 luhongzhouii sp. nov. and Bacteroides zhangwenhongii sp. nov., isolated from human faeces.	Ge Y, Zhang G, Yang J, Lai XH, Jin D, Lu S, Pu J, Huang Y, Luo X, Zheng H, Zhang X, Xu J	Int J Syst Evol Microbiol	10.1099/ijsem.0.004772	2021
Phylogeny	Bacteroides faecis sp. nov., isolated from human faeces.	Kim MS, Roh SW, Bae JW	Int J Syst Evol Microbiol	10.1099/ijs.0.020024-0	2009
Phylogeny	Bacteroides finegoldii sp. nov., isolated from human faeces.	Bakir MA, Kitahara M, Sakamoto M, Matsumoto M, Benno Y	Int J Syst Evol Microbiol	10.1099/ijs.0.64084-0	2006

References

#6977	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 17565
#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 )
#27979	IJSEM 931 2006 ( DOI 10.1099/ijs.0.64084-0 , PubMed 16627634 )
#31702	Barberan A, Caceres Velazquez H, Jones S, Fierer N.: Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information. mSphere 2: 2017 ( DOI 10.1128/mSphere.00237-17 , PubMed 28776041 ) - originally annotated from #27979
#60059	Culture Collection University of Gothenburg (CCUG) ; Curators of the CCUG; CCUG 53890
#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 .
#124043	Isabel Schober, Julia Koblitz: Data extracted from sequence databases, automatically matched based on designation and taxonomy .
#125438	Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg Overmann: Predicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets. 2024 ( DOI 10.1101/2024.08.12.607695 )
#125439	Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardy: deepG: Deep Learning for Genome Sequence Data. R package version 0.3.1 .
#126262	A. Lissin, I. Schober, J. F. Witte, H. Lüken, A. Podstawka, J. Koblitz, B. Bunk, P. Dawyndt, P. Vandamme, P. de Vos, J. Overmann, L. C. Reimer: StrainInfo—the central database for linked microbial strain identifiers. ( DOI 10.1093/database/baaf059 )

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Bacteroides finegoldii (DSM 17565, JCM 13345, CCUG 53890)

Name and taxonomic classification

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Genome browser: GCA_000156195

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