Name: Hallella bergensis 94067913
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 12544

Type strain:

Species: Hallella bergensis

Strain Designation: 94067913, W3326

Culture col. no.: JCM 51224, DSM 17361, CCUG 51224, JCM 13869

Strain history: CCUG 51224 <-- J. Downes <-- T. Hofstad 94067913.

NCBI tax ID(s): 585502 (strain), 242750 (species)

SI-ID 290989

CCUG 51224, DSM 17361, JCM 13869, JCM 51224

Section

Hallella bergensis 94067913 is an anaerobe, mesophilic, Gram-negative bacterium that was isolated from soft tissue abscess, human.

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

Information on the name and the taxonomic classification. Name and taxonomic classification

	Last LPSN update	14-12-2023 (DD-MM-YYYY)
	Domain	"Bacteria"
	Phylum	*Bacteroidota*
	Class	*Bacteroidia*
	Order	*Bacteroidales*
	Family	*Prevotellaceae*
	Genus	*Hallella*
	Species	**Hallella bergensis**
	Full Scientific Name (LPSN)	Hallella bergensis (Downes et al. 2006) Hitch et al. 2023

Synonym

Prevotella bergensis

Information on morphological and physiological properties Morphology

[Ref.: #31608]	Gram stain	negative
[Ref.: #69480]	Gram stain	negative Confidence in %100

[Ref.: #31608]	Cell length	0.8-6 µm

[Ref.: #31608]	Cell width	0.7-0.8 µm

[Ref.: #31608]	Cell shape	rod-shaped

[Ref.: #31608]	Motility	no
[Ref.: #69480]	Motility	no Confidence in %94.821

[Ref.: #59110]

Incubation period

2 days

[Ref.: #31608]

Pigment production

Information on culture and growth conditions Culture and growth conditions

[Ref.: #6831]

Culture medium

PYG MEDIUM (MODIFIED) (DSMZ Medium 104)

[Ref.: #6831]

Culture medium growth

[Ref.: #6831]

Culture medium link

Medium recipe at MediaDive

[Ref.: #6831]

Culture medium composition

expand / minimize

		Temperature
[Ref.: #6831]	growth	37 °C
[Ref.: #59110]	growth	37 °C
[Ref.: #67770]	growth	37 °C

[Ref.: #6831]	Temperature range	mesophilic
[Ref.: #59110]	Temperature range	mesophilic
[Ref.: #67770]	Temperature range	mesophilic

Information on physiology and metabolism Physiology and metabolism

[Ref.: #6831]	Oxygen tolerance	anaerobe
[Ref.: #31608]	Oxygen tolerance	anaerobe
[Ref.: #59110]	Oxygen tolerance	anaerobe
[Ref.: #69480]	Oxygen tolerance	anaerobe Confidence in %99.999

[Ref.: #31608]	Ability of spore formation	no
[Ref.: #69481]	Ability of spore formation	no Confidence in %100
[Ref.: #69480]	Ability of spore formation	no Confidence in %99.999

[Ref.: #31608]

Observation

aggregates in chains

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #31608]	arabinose ChEBI	+	carbon source
[Ref.: #68380]	arginine ChEBI	-	hydrolysis	* from API rID32A
[Ref.: #31608]	cellobiose ChEBI	+	carbon source
[Ref.: #68380]	D-mannose ChEBI	-	fermentation	* from API rID32A
[Ref.: #31608]	esculin ChEBI	+	hydrolysis
[Ref.: #68380]	L-glutamate ChEBI	-	degradation	* from API rID32A
[Ref.: #31608]	lactose ChEBI	+	carbon source
[Ref.: #31608]	mannose ChEBI	+	carbon source
[Ref.: #68380]	nitrate ChEBI	-	reduction	* from API rID32A
[Ref.: #31608]	raffinose ChEBI	+	carbon source
[Ref.: #68380]	raffinose ChEBI	-	fermentation	* from API rID32A
[Ref.: #31608]	salicin ChEBI	+	carbon source
[Ref.: #31608]	sucrose ChEBI	+	carbon source
[Ref.: #68380]	tryptophan ChEBI	-	energy source	* from API rID32A
[Ref.: #68380]	urea ChEBI	-	hydrolysis	* from API rID32A
	Only first 10 entries are displayed. Click here to see all.

	Metabolite production	Metabolite	Production
[Ref.: #68380]		indole ChEBI	no	* from API rID32A

	Physiological tests	Metabolite	Indole test
[Ref.: #68380]		indole ChEBI	-	* from API rID32A

	Enzyme	Enzyme activity	EC number
[Ref.: #68380]	alanine arylamidase	+	3.4.11.2	* from API rID32A
[Ref.: #68380]	alkaline phosphatase	+	3.1.3.1	* from API rID32A
[Ref.: #68380]	alpha-arabinosidase	+	3.2.1.55	* from API rID32A
[Ref.: #68380]	alpha-fucosidase	-	3.2.1.51	* from API rID32A
[Ref.: #68380]	alpha-galactosidase	-	3.2.1.22	* from API rID32A
[Ref.: #68380]	alpha-glucosidase	+	3.2.1.20	* from API rID32A
[Ref.: #68380]	arginine dihydrolase	-	3.5.3.6	* from API rID32A
[Ref.: #68380]	beta-galactosidase	+	3.2.1.23	* from API rID32A
[Ref.: #68380]	beta-Galactosidase 6-phosphate	-		* from API rID32A
[Ref.: #68380]	beta-glucosidase	+	3.2.1.21	* from API rID32A
[Ref.: #68380]	beta-glucuronidase	+	3.2.1.31	* from API rID32A
[Ref.: #68380]	glutamate decarboxylase	-	4.1.1.15	* from API rID32A
[Ref.: #68380]	glutamyl-glutamate arylamidase	+		* from API rID32A
[Ref.: #68380]	glycin arylamidase	-		* from API rID32A
[Ref.: #68380]	histidine arylamidase	-		* from API rID32A
[Ref.: #68380]	L-arginine arylamidase	+		* from API rID32A
[Ref.: #68380]	leucine arylamidase	-	3.4.11.1	* from API rID32A
[Ref.: #68380]	leucyl glycin arylamidase	+	3.4.11.1	* from API rID32A
[Ref.: #68380]	N-acetyl-beta-glucosaminidase	+	3.2.1.52	* from API rID32A
[Ref.: #68380]	phenylalanine arylamidase	-		* from API rID32A
[Ref.: #68380]	proline-arylamidase	-	3.4.11.5	* from API rID32A
[Ref.: #68380]	pyrrolidonyl arylamidase	-	3.4.19.3	* from API rID32A
[Ref.: #68380]	serine arylamidase	-		* from API rID32A
[Ref.: #68380]	tryptophan deaminase	-	4.1.99.1	* from API rID32A
[Ref.: #68380]	tyrosine arylamidase	-		* from API rID32A
[Ref.: #68380]	urease	-	3.5.1.5	* from API rID32A
	Only first 10 entries are displayed. Click here to see all.

API® rID32A:

Note that the displayed test results represent raw data and therefore may deviate!

	API ID	Urease/urea hydrolysisURE	Arginine dihydrolaseADH (Arg)	alpha-Galactosidasealpha GAL	beta-Galactosidasebeta GAL	beta-Galactosidase 6-phosphatebeta GP	alpha-Glucosidasealpha GLU	beta-Glucosidasebeta GLU	alpha-Arabinosidasealpha ARA	beta-Glucuronidasebeta GUR	beta-N-Acetyl-beta-glucosaminidasebeta NAG	Fermentation of D-mannoseMNE	Fermentation of raffinoseRAF	Glutamate decarboxylaseGDC	alpha-Fucosidasealpha FUC	Reduction of nitrateNIT	Indole productionIND	Alkaline phosphatasePAL	L-arginine arylamidaseArgA	Proline arylamidaseProA	Leucyl glycin arylamidaseLGA	Phenylalanine arylamidasePheA	Leucine arylamidaseLeuA	Pyrrolidonyl arylamidasePyrA	Tyrosine arylamidaseTyrA	Alanine arylamidaseAlaA	Glycin arylamidaseGlyA	Histidine arylamidaseHisA	Glutamyl-glutamate arylamidaseGGA	Serine arylamidaseSerA
[Ref.: #6831]	12204	-	-	-	+	-	+	+	+	+	+	-	-	-	-	-	-	+	+	-	+	-	-	-	-	+	-	-	+	-

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

Information on isolation source, the sampling and environmental conditions Isolation, sampling and environmental information

[Ref.: #6831]	Sample type/isolated from	soft tissue abscess, human
[Ref.: #6831]	Country	Norway
[Ref.: #6831]	Country ISO 3 Code	NOR
[Ref.: #6831]	Continent	Europe

[Ref.: #59110]	Sample type/isolated from	Human soft tissue abscess
[Ref.: #59110]	Sampling date	1994
[Ref.: #59110]	Geographic location (country and/or sea, region)	Bergen
[Ref.: #59110]	Country	Norway
[Ref.: #59110]	Country ISO 3 Code	NOR
[Ref.: #59110]	Continent	Europe

[Ref.: #67770]	Sample type/isolated from	Human soft tissue abscess
[Ref.: #67770]	Geographic location (country and/or sea, region)	Bergen
[Ref.: #67770]	Country	Norway
[Ref.: #67770]	Country ISO 3 Code	NOR
[Ref.: #67770]	Continent	Europe
* marker position based on {}

Isolation sources categories

#Host	#Human	-
#Host Body-Site	-	-
#Host Body-Site	#Other	#Abscess

What are isolation sources categories?

[Ref.: #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

Information on possible application of the strain and its possible interaction with e.g. potential hosts Safety information

[Ref.: #6831]

Biosafety level

Risk group (German classification)
According to TRBA 466

Information on genomic background e.g. entries in nucleic sequence databass Sequence information

16S Sequence information:

	Sequence accession description	Seq. accession number	Sequence length (bp)	Sequence database	Associated NCBI tax ID
[Ref.: #67770]	Prevotella bergensis gene for 16S ribosomal RNA, partial sequence, strain: JCM 13869	AB547672	1495	ENA	242750 tax ID
[Ref.: #6831]	Prevotella bergensis strain 94067913 16S ribosomal RNA gene, partial sequence	AY350613	1456	ENA	242750 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #67770]	Hallella bergensis DSM 17361	GCA_000160535	scaffold	GenBank	585502 tax ID
[Ref.: #66792]	Prevotella bergensis DSM 17361	585502.3	wgs	PATRIC	585502 tax ID	*
[Ref.: #66792]	Prevotella bergensis DSM 17361	645951825	draft	JGI IMG/M	585502 tax ID	*

[Ref.: #6831]	GC-content	48 mol%
[Ref.: #67770]	GC-content	48 mol%	high performance liquid chromatography (HPLC)

Data predicted using genome information as a basis Genome-based predictions

	Trait	Prediction	Confidence in %	In training data
	Predictions from GenomeNet Sporulation v. 1 based on: Prevotella bergensis DSM 17361 DSM 17361 NCBI: GCA_000160535.1
[Ref.: #69481]	spore-forming	no	100	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Prevotella bergensis DSM 17361 PATRIC: 585502.3
[Ref.: #69480]	gram-positive	no	96.746	yes
[Ref.: #69480]	anaerobic	yes	98.749	yes
[Ref.: #69480]	halophile	no	83.447	no
[Ref.: #69480]	spore-forming	no	96.005	yes
[Ref.: #69480]	glucose-util	yes	90.792	no
[Ref.: #69480]	thermophile	no	96.396	yes
[Ref.: #69480]	flagellated	no	97.286	yes
[Ref.: #69480]	aerobic	no	97.601	yes
[Ref.: #69480]	motile	no	91.524	no
[Ref.: #69480]	glucose-ferment	yes	55.041	no

Availability in culture collections External links

[Ref.: #6831]

Culture collection no.

JCM 51224, DSM 17361, CCUG 51224, JCM 13869

[Ref.: #81759]

SI-ID 290989

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 )

#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 (see below)

#59110 Culture Collection University of Gothenburg (CCUG) ; Curators of the CCUG; CCUG 51224

#66792

Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann: Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) .

#66794

Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg: BRENDA, the ELIXIR core data resource in 2021: new developments and updates. Nucleic Acids Res. 49: D498 - D508 2020 ( DOI 10.1093/nar/gkaa1025 , PubMed 33211880 )

#67770 Japan Collection of Microorganism (JCM) ; Curators of the JCM;

#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 .

#69480

Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann: Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) .

#69481

Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch: Predictions based on the model GenomeNet Sporulation v. 1 . ( DOI 10.21203/rs.3.rs-2527258/v1 )

#81759

Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.: StrainInfo: A central database for resolving microbial strain identifiers . ( DOI 10.60712/SI-ID290989.1 )

#27896

IJSEM 609 2006 ( DOI 10.1099/ijs.0.63888-0 , PubMed 16514036 )

* These data were automatically processed and therefore are not curated

Change proposal

You found an error in BacDive? Please tell us about it!

Note that changes will be reviewed and judged. If your changes are legitimate, changes will occur within the next BacDive update. Only proposed changes supported by the according reference will be reviewed. The BacDive team reserves the right to reject proposed changes.

Search for species Prevotella bergensis in external resources:
SILVA
BRENDA
PANGAEA
StrainInfo
GBIF

Prevotella bergensis DSM 17361 DSM 17361

Prevotella bergensis DSM 17361

Change proposal

Change proposal