Prevotella bergensis (JCM 51224, DSM 17361, CCUG 51224)

Name: Prevotella bergensis (JCM 51224, DSM 17361, CCUG 51224)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 12544

Type strain

Strain Designation 94067913, W3326

Culture col. no. JCM 51224 DSM 17361 CCUG 51224 94067913 W3326 1 more

NCBI tax ID(s) 585502 242750

Special Collections DSMZ CCUG JCM Literature strains

History DSMZ <- J. Downes <- T. Hofstad; 94067913 JCM <-- CCUG 51224 <-- J. Downes <-- T. Hofstad 94067913.

Links

Prevotella bergensis 94067913 is an anaerobe, Gram-negative, rod-shaped bacterium that was isolated from soft tissue abscess, human.

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

Name and taxonomic classification

SI-ID 290989

CCUG 51224,DSM 17361,JCM 13869,JCM 51224

@ref 20215

Last LPSN update 2026-05-29 08:27:49

Domain Bacteria

Phylum Bacteroidota

Class Bacteroidia

Order Bacteroidales

Family Prevotellaceae

Genus Prevotella

Species Prevotella bergensis

Full scientific name Prevotella bergensis Downes et al. 2006

Synonyms (1)

Hallella bergensis

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape	Confidence
31608	negative	0.8-6 µm	0.7-0.8 µm	rod-shaped
125438	negative				95.289
125439	negative				96.252

Colony morphology

59110

Incubation period2 days

Pigmentation

31608

Productionno

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
6831	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)
6831	positive	growth	37
59110	positive	growth	37
67770	positive	growth	37

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance
6831	anaerobe
31608	anaerobe
59110	anaerobe

Spore formation

@ref	Spore formation	Confidence
31608
125438		92.388
125439		99.938

Observation

31608

Observationaggregates in chains

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
31608	22599 ChEBI	arabinose	+	carbon source
68380	29016 ChEBI	arginine	-	hydrolysis	from API rID32A
31608	17057 ChEBI	cellobiose	+	carbon source
68380	16024 ChEBI	D-mannose	-	fermentation	from API rID32A
31608	4853 ChEBI	esculin	+	hydrolysis
68380	29985 ChEBI	L-glutamate	-	degradation	from API rID32A
31608	17716 ChEBI	lactose	+	carbon source
31608	37684 ChEBI	mannose	+	carbon source
68380	17632 ChEBI	nitrate	-	reduction	from API rID32A
31608	16634 ChEBI	raffinose	+	carbon source
68380	16634 ChEBI	raffinose	-	fermentation	from API rID32A
31608	17814 ChEBI	salicin	+	carbon source
31608	17992 ChEBI	sucrose	+	carbon source
68380	27897 ChEBI	tryptophan	-	energy source	from API rID32A
68380	16199 ChEBI	urea	-	hydrolysis	from API rID32A

Metabolite production

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

Metabolite tests

@ref	Chebi-ID	Metabolite	Indole test
68380	35581 ChEBI	indole	-	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-glucosidase	+	3.2.1.21	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	L-arginine arylamidase	+		from API rID32A
68380	leucine arylamidase	-	3.4.11.1	from API rID32A
68380	leucyl glycin arylamidase	+	3.4.11.1	from API rID32A
68380	N-acetyl-beta-glucosaminidase	+	3.2.1.52	from API rID32A
68380	phenylalanine arylamidase	-		from API rID32A
68380	proline-arylamidase	-	3.4.11.5	from API rID32A
68380	pyrrolidonyl arylamidase	-	3.4.19.3	from API rID32A
68380	serine arylamidase	-		from API rID32A
68380	tryptophan deaminase	-	4.1.99.1	from API rID32A
68380	tyrosine arylamidase	-		from API rID32A
68380	urease	-	3.5.1.5	from API rID32A

Pathway annotation

Computationally determined by

@ref	pathway	enzyme coverage	annotated reactions
66794	starch degradation	100	10 of 10
66794	CMP-KDO biosynthesis	100	4 of 4
66794	cis-vaccenate biosynthesis	100	2 of 2
66794	vitamin K metabolism	100	5 of 5
66794	gluconeogenesis	100	8 of 8
66794	glycogen metabolism	100	5 of 5
66794	ppGpp biosynthesis	100	4 of 4
66794	coenzyme A metabolism	100	4 of 4
66794	CDP-diacylglycerol biosynthesis	100	2 of 2
66794	palmitate biosynthesis	100	22 of 22
66794	anapleurotic synthesis of oxalacetate	100	1 of 1
66794	chorismate metabolism	88.89	8 of 9
66794	d-mannose degradation	88.89	8 of 9
66794	C4 and CAM-carbon fixation	87.5	7 of 8
66794	NAD metabolism	83.33	15 of 18
66794	peptidoglycan biosynthesis	80	12 of 15
66794	threonine metabolism	80	8 of 10
66794	flavin biosynthesis	80	12 of 15
66794	cellulose degradation	80	4 of 5
66794	photosynthesis	78.57	11 of 14
66794	lipid A biosynthesis	77.78	7 of 9
66794	valine metabolism	77.78	7 of 9
66794	sulfopterin metabolism	75	3 of 4
66794	acetate fermentation	75	3 of 4
66794	glycogen biosynthesis	75	3 of 4
66794	isoleucine metabolism	75	6 of 8
66794	vitamin B6 metabolism	72.73	8 of 11
66794	purine metabolism	70.21	66 of 94
66794	Entner Doudoroff pathway	70	7 of 10
66794	vitamin B1 metabolism	69.23	9 of 13
66794	serine metabolism	66.67	6 of 9
66794	acetoin degradation	66.67	2 of 3
66794	aspartate and asparagine metabolism	66.67	6 of 9
66794	UDP-GlcNAc biosynthesis	66.67	2 of 3
66794	formaldehyde oxidation	66.67	2 of 3
66794	pyrimidine metabolism	66.67	30 of 45
66794	glycolysis	64.71	11 of 17
66794	pentose phosphate pathway	63.64	7 of 11
66794	d-xylose degradation	63.64	7 of 11
66794	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	62.5	5 of 8
66794	dTDPLrhamnose biosynthesis	62.5	5 of 8
66794	degradation of hexoses	61.11	11 of 18
66794	phenylacetate degradation (aerobic)	60	3 of 5
66794	hydrogen production	60	3 of 5
66794	ubiquinone biosynthesis	57.14	4 of 7
66794	CO2 fixation in Crenarchaeota	55.56	5 of 9
66794	leucine metabolism	53.85	7 of 13
66794	isoprenoid biosynthesis	53.85	14 of 26
66794	alanine metabolism	51.72	15 of 29
66794	histidine metabolism	51.72	15 of 29
66794	suberin monomers biosynthesis	50	1 of 2
66794	propionate fermentation	50	5 of 10
66794	adipate degradation	50	1 of 2
66794	citric acid cycle	50	7 of 14
66794	kanosamine biosynthesis II	50	1 of 2
66794	tetrahydrofolate metabolism	50	7 of 14
66794	ethanol fermentation	50	1 of 2
66794	butanoate fermentation	50	2 of 4
66794	non-pathway related	50	19 of 38
66794	degradation of sugar acids	48	12 of 25
66794	degradation of pentoses	46.43	13 of 28
66794	glutamate and glutamine metabolism	46.43	13 of 28
66794	phenylalanine metabolism	46.15	6 of 13
66794	metabolism of disaccharids	45.45	5 of 11
66794	propanol degradation	42.86	3 of 7
66794	cardiolipin biosynthesis	42.86	3 of 7
66794	arginine metabolism	41.67	10 of 24
66794	degradation of aromatic, nitrogen containing compounds	41.67	5 of 12
66794	ascorbate metabolism	40.91	9 of 22
66794	lysine metabolism	40.48	17 of 42
66794	coenzyme M biosynthesis	40	4 of 10
66794	arachidonate biosynthesis	40	2 of 5
66794	lipoate biosynthesis	40	2 of 5
66794	myo-inositol biosynthesis	40	4 of 10
66794	methylglyoxal degradation	40	2 of 5
66794	glycine betaine biosynthesis	40	2 of 5
66794	factor 420 biosynthesis	40	2 of 5
66794	metabolism of amino sugars and derivatives	40	2 of 5
66794	polyamine pathway	39.13	9 of 23
66794	cysteine metabolism	38.89	7 of 18
66794	degradation of sugar alcohols	37.5	6 of 16
66794	ketogluconate metabolism	37.5	3 of 8
66794	oxidative phosphorylation	37.36	34 of 91
66794	tryptophan metabolism	36.84	14 of 38
66794	proline metabolism	36.36	4 of 11
66794	tyrosine metabolism	35.71	5 of 14
66794	lipid metabolism	35.48	11 of 31
66794	IAA biosynthesis	33.33	1 of 3
66794	cyanate degradation	33.33	1 of 3
66794	acetyl CoA biosynthesis	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	pantothenate biosynthesis	33.33	2 of 6
66794	octane oxidation	33.33	1 of 3
66794	selenocysteine biosynthesis	33.33	2 of 6
66794	L-lactaldehyde degradation	33.33	1 of 3
66794	sulfate reduction	30.77	4 of 13
66794	phenylpropanoid biosynthesis	30.77	4 of 13
66794	methionine metabolism	30.77	8 of 26
66794	glycine metabolism	30	3 of 10
66794	reductive acetyl coenzyme A pathway	28.57	2 of 7
66794	dolichyl-diphosphooligosaccharide biosynthesis	27.27	3 of 11
66794	cyclohexanol degradation	25	1 of 4
66794	lactate fermentation	25	1 of 4
66794	urea cycle	23.08	3 of 13
66794	arachidonic acid metabolism	22.22	4 of 18
66794	heme metabolism	21.43	3 of 14
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
6831	-	-	-	+	-	+	+	+	+	+	-	-	-	-	-	-	+	+	-	+	-	-	-	-	+	-	-	+	-

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Host	#Human	-
#Host Body-Site	-	-
#Host Body-Site	#Other	#Abscess

Isolation

@ref	Sample type	Host species	Sampling date	Geographic location	Country	Country ISO 3 Code	Continent
6831	soft tissue abscess, human	Homo sapiens			Norway	NOR	Europe
59110	Human soft tissue abscess	Homo sapiens	1994	Bergen	Norway	NOR	Europe
67770	Human soft tissue abscess	Homo sapiens		Bergen	Norway	NOR	Europe

Taxonmaps

69479

Global distribution of 16S sequence AY350613 (>99% sequence identity) for Prevotella bergensis subclade from Microbeatlas

Aquatic Samples	305
Soil Samples	243
Animal Samples	39891
Plant Samples	111
Total Samples	40550

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
6831	2	Risk group (German classification) According to TRBA 466

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
67770	ASM16053v1 assembly for Hallella bergensis DSM 17361	scaffold	GCA_000160535	585502.3	645951825	585502	56.86

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
6831	Prevotella bergensis strain 94067913 16S ribosomal RNA gene, partial sequence	AY350613	1456		242750
67770	Prevotella bergensis gene for 16S ribosomal RNA, partial sequence, strain: JCM 13869	AB547672	1495		242750

GC content

@ref	GC-content (mol%)	Method
6831	48
67770	48	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: ASM16053v1 assembly for Hallella bergensis DSM 17361
BV-BRC: 585502.3

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	oxygen_tolerance	BacteriaNetⓘ	obligate anaerobe	77.85	no
125439	motility	BacteriaNetⓘ	no	82.23	no
125439	gram_stain	BacteriaNetⓘ	negative	96.25	no
125439	spore_formation	BacteriaNetⓘ	no	99.94	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Prevotella bergensis DSM 17361
PATRIC: 585502.3

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	95.29	yes
125438	anaerobic	anaerobicⓘ	yes	89.12	yes
125438	spore-forming	spore-formingⓘ	no	92.39	yes
125438	aerobic	aerobicⓘ	no	94.64	no
125438	thermophilic	thermophileⓘ	no	95.17	yes
125438	flagellated	motile2+ⓘ	no	89.50	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Prevotella bergensis sp. nov., isolated from human infections.	Downes J, Sutcliffe IC, Hofstad T, Wade WG	Int J Syst Evol Microbiol	10.1099/ijs.0.63888-0	2006

References

#6831	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 17361
#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 )
#27896	IJSEM 609 2006 ( DOI 10.1099/ijs.0.63888-0 , PubMed 16514036 )
#31608	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 #27896
#59110	Culture Collection University of Gothenburg (CCUG) ; Curators of the CCUG; CCUG 51224
#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;
#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 )
#125439	Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardy: deepG: Deep Learning for Genome Sequence Data. R package version 0.3.1 .
#126262	A. Lissin, I. Schober, J. F. Witte, H. Lüken, A. Podstawka, J. Koblitz, B. Bunk, P. Dawyndt, P. Vandamme, P. de Vos, J. Overmann, L. C. Reimer: StrainInfo—the central database for linked microbial strain identifiers. ( DOI 10.1093/database/baaf059 )

Content

About us

Prevotella bergensis (JCM 51224, DSM 17361, CCUG 51224)

Name and taxonomic classification

Morphology

Cell morphology

Colony morphology

Pigmentation

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Oxygen tolerance

Spore formation

Observation

Metabolite utilization

Metabolite production

Metabolite tests

Enzymes

Pathway annotation

API rID32A

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_000160535

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

Help

Social Media