Bacteroides acidifaciens (DSM 100502, JJM0207_2)

Name: Bacteroides acidifaciens (DSM 100502, JJM0207_2)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 131098

Type strain

Strain Designation JJM0207_2

Culture col. no. DSM 100502 JJM0207_2

NCBI tax ID(s) 85831

Special Collections DSMZ Mouse DZIF

Links

Bacteroides acidifaciens JJM0207_2 is an anaerobe, mesophilic prokaryote that was isolated from wild mouse.

anaerobe mesophilic genome sequence 16S sequence

Name and taxonomic classification

SI-ID 406808

DSM 100502

@ref 20215

Last LPSN update 2025-12-16 10:01:09

Domain Pseudomonadati

Phylum Bacteroidota

Class Bacteroidia

Order Bacteroidales

Family Bacteroidaceae

Genus Bacteroides

Species Bacteroides acidifaciens

Full scientific name Bacteroides acidifaciens Miyamoto and Itoh 2000

BacDive ID	Other strains from **Bacteroides acidifaciens** (2)	Type strain
1606	B. acidifaciens A40, DSM 15896, JCM 10556, CCUG 51929, BCRC ... (type strain)
175101	B. acidifaciens CLA-AP-2, DSM 111135

Morphology

Cell morphology

@ref	Gram stain	Confidence
125438	negative	94.49

Colony morphology

22390

Incubation period1-2 days

Culture and growth conditions

Culture medium

@ref	Name	Medium link	Composition
22390	FASTIDIOUS ANAEROBE AGAR (DSMZ Medium 1203)	Medium recipe at MediaDive	Name: FASTIDIOUS ANAEROBE AGAR (DSMZ Medium 1203) Composition: Horse blood 100.0 g/l Fastidious Anaerobe Agar 45.7 g/l Distilled water
22390	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
22390	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

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
22390	positive	growth	37	mesophilic

Physiology and metabolism

Oxygen tolerance

22390

Oxygen toleranceanaerobe

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
68380	29016 ChEBI	arginine	-	hydrolysis	from API rID32A
68380	29985 ChEBI	L-glutamate	-	degradation	from API rID32A
68380	17632 ChEBI	nitrate	-	reduction	from API rID32A
68380	16199 ChEBI	urea	-	hydrolysis	from API rID32A

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-glucuronidase	-	3.2.1.31	from API rID32A
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	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	tyrosine arylamidase	-		from API rID32A
68380	urease	-	3.5.1.5	from API rID32A

Pathway annotation

Computationally determined by

@ref	pathway	enzyme coverage	annotated reactions
66794	L-lactaldehyde degradation	100	3 of 3
66794	suberin monomers biosynthesis	100	2 of 2
66794	UDP-GlcNAc biosynthesis	100	3 of 3
66794	CDP-diacylglycerol biosynthesis	100	2 of 2
66794	sulfopterin metabolism	100	4 of 4
66794	glycogen metabolism	100	5 of 5
66794	coenzyme A metabolism	100	4 of 4
66794	formaldehyde oxidation	100	3 of 3
66794	vitamin K metabolism	100	5 of 5
66794	cis-vaccenate biosynthesis	100	2 of 2
66794	biotin biosynthesis	100	4 of 4
66794	C4 and CAM-carbon fixation	100	8 of 8
66794	gluconeogenesis	100	8 of 8
66794	folate polyglutamylation	100	1 of 1
66794	palmitate biosynthesis	100	22 of 22
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	aspartate and asparagine metabolism	88.89	8 of 9
66794	chorismate metabolism	88.89	8 of 9
66794	lipid A biosynthesis	88.89	8 of 9
66794	NAD metabolism	88.89	16 of 18
66794	vitamin B1 metabolism	84.62	11 of 13
66794	vitamin B6 metabolism	81.82	9 of 11
66794	pentose phosphate pathway	81.82	9 of 11
66794	metabolism of amino sugars and derivatives	80	4 of 5
66794	pyrimidine metabolism	80	36 of 45
66794	peptidoglycan biosynthesis	80	12 of 15
66794	threonine metabolism	80	8 of 10
66794	photosynthesis	78.57	11 of 14
66794	valine metabolism	77.78	7 of 9
66794	d-mannose degradation	77.78	7 of 9
66794	phenylalanine metabolism	76.92	10 of 13
66794	glycogen biosynthesis	75	3 of 4
66794	CMP-KDO biosynthesis	75	3 of 4
66794	ppGpp biosynthesis	75	3 of 4
66794	acetate fermentation	75	3 of 4
66794	isoleucine metabolism	75	6 of 8
66794	purine metabolism	73.4	69 of 94
66794	flavin biosynthesis	73.33	11 of 15
66794	propanol degradation	71.43	5 of 7
66794	degradation of pentoses	71.43	20 of 28
66794	propionate fermentation	70	7 of 10
66794	Entner Doudoroff pathway	70	7 of 10
66794	histidine metabolism	68.97	20 of 29
66794	alanine metabolism	68.97	20 of 29
66794	glutamate and glutamine metabolism	67.86	19 of 28
66794	octane oxidation	66.67	2 of 3
66794	degradation of hexoses	66.67	12 of 18
66794	serine metabolism	66.67	6 of 9
66794	acetoin degradation	66.67	2 of 3
66794	methionine metabolism	65.38	17 of 26
66794	glycolysis	64.71	11 of 17
66794	d-xylose degradation	63.64	7 of 11
66794	non-pathway related	63.16	24 of 38
66794	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	62.5	5 of 8
66794	degradation of sugar alcohols	62.5	10 of 16
66794	isoprenoid biosynthesis	61.54	16 of 26
66794	cellulose degradation	60	3 of 5
66794	methylglyoxal degradation	60	3 of 5
66794	hydrogen production	60	3 of 5
66794	ubiquinone biosynthesis	57.14	4 of 7
66794	proline metabolism	54.55	6 of 11
66794	leucine metabolism	53.85	7 of 13
66794	degradation of sugar acids	52	13 of 25
66794	selenocysteine biosynthesis	50	3 of 6
66794	ethanol fermentation	50	1 of 2
66794	citric acid cycle	50	7 of 14
66794	lysine metabolism	50	21 of 42
66794	phenylmercury acetate degradation	50	1 of 2
66794	pantothenate biosynthesis	50	3 of 6
66794	adipate degradation	50	1 of 2
66794	dTDPLrhamnose biosynthesis	50	4 of 8
66794	butanoate fermentation	50	2 of 4
66794	cysteine metabolism	50	9 of 18
66794	tryptophan metabolism	47.37	18 of 38
66794	sulfate reduction	46.15	6 of 13
66794	lipid metabolism	45.16	14 of 31
66794	CO2 fixation in Crenarchaeota	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	tyrosine metabolism	42.86	6 of 14
66794	cardiolipin biosynthesis	42.86	3 of 7
66794	degradation of aromatic, nitrogen containing compounds	41.67	5 of 12
66794	arginine metabolism	41.67	10 of 24
66794	O-antigen biosynthesis	40	2 of 5
66794	factor 420 biosynthesis	40	2 of 5
66794	myo-inositol biosynthesis	40	4 of 10
66794	lipoate biosynthesis	40	2 of 5
66794	glycine metabolism	40	4 of 10
66794	arachidonate biosynthesis	40	2 of 5
66794	phosphatidylethanolamine bioynthesis	38.46	5 of 13
66794	oxidative phosphorylation	38.46	35 of 91
66794	ketogluconate metabolism	37.5	3 of 8
66794	metabolism of disaccharids	36.36	4 of 11
66794	acetyl CoA biosynthesis	33.33	1 of 3
66794	IAA biosynthesis	33.33	1 of 3
66794	cyanate degradation	33.33	1 of 3
66794	molybdenum cofactor biosynthesis	33.33	3 of 9
66794	glycolate and glyoxylate degradation	33.33	2 of 6
66794	enterobactin biosynthesis	33.33	1 of 3
66794	sphingosine metabolism	33.33	2 of 6
66794	ascorbate metabolism	31.82	7 of 22
66794	urea cycle	30.77	4 of 13
66794	coenzyme M biosynthesis	30	3 of 10
66794	heme metabolism	28.57	4 of 14
66794	mevalonate metabolism	28.57	2 of 7
66794	dolichyl-diphosphooligosaccharide biosynthesis	27.27	3 of 11
66794	alginate biosynthesis	25	1 of 4
66794	lactate fermentation	25	1 of 4
66794	cyclohexanol degradation	25	1 of 4
66794	toluene degradation	25	1 of 4
66794	phenylpropanoid biosynthesis	23.08	3 of 13
66794	nitrate assimilation	22.22	2 of 9
66794	glutathione metabolism	21.43	3 of 14

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
22390	-	-	+	+	-	+	-	+	-	+	-	-	-	+	-	+	+	-	-	+	-	+	-	-	+	-	-	+	-
22390	-	-	+	+	-	+	+/-	+	-	+	+	+	-	+	-	+/-	+	+/-	-	+	-	+/-	-	-	+	-	-	+	-

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Host	#Mammals	#Muridae (Mouse/Rat)

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
22390	wild mouse	Plön	Germany	DEU	Europe

Taxonmaps

69479

Global distribution of 16S sequence KR364740 (>99% sequence identity) for Bacteroides acidifaciens subclade from Microbeatlas

Aquatic Samples	1548
Soil Samples	1207
Animal Samples	168578
Plant Samples	483
Total Samples	171816

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
22390	1	Risk group (German classification)

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
66792	ASM2462311v1 assembly for Bacteroides acidifaciens DSM 100502	contig	GCA_024623115	85831.64	8078935718	85831	56.63

Genome browser: GCA_024623115

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
22390	Bacteroides acidifaciens strain JJM0207-2 16S ribosomal RNA gene, partial sequence	KR364740	1467		85831

Genome-based predictions

Predictions

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Bacteroides acidifaciens DSM 100502
NCBI: GCA_024623115.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	94.49	no
125438	anaerobic	anaerobicⓘ	yes	87.35	yes
125438	aerobic	aerobicⓘ	no	92.98	yes
125438	spore-forming	spore-formingⓘ	no	89.51	no
125438	thermophilic	thermophileⓘ	no	92.97	yes
125438	flagellated	motile2+ⓘ	no	88.50	no

Literature

References

#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 )
#22390	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 100502
#66792	Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann: Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) .
#66794	Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg: BRENDA, the ELIXIR core data resource in 2021: new developments and updates. Nucleic Acids Res. 49: D498 - D508 2020 ( DOI 10.1093/nar/gkaa1025 , PubMed 33211880 )
#68380	Automatically annotated from API rID32A .
#69479	João F Matias Rodrigues, Janko Tackmann,Gregor Rot, Thomas SB Schmidt, Lukas Malfertheiner, Mihai Danaila,Marija Dmitrijeva, Daniela Gaio, Nicolas Näpflin and Christian von Mering. University of Zurich.: MicrobeAtlas 1.0 beta .
#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 )
#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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