Strain identifier

BacDive ID: 12544

Type strain: Yes

Species: Hallella bergensis

Strain Designation: 94067913, W3326

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

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

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General

@ref: 6831

BacDive-ID: 12544

DSM-Number: 17361

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

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

NCBI tax id

NCBI tax idMatching level
242750species
585502strain

strain history

@refhistory
6831<- J. Downes <- T. Hofstad; 94067913
67770CCUG 51224 <-- J. Downes <-- T. Hofstad 94067913.

doi: 10.13145/bacdive12544.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacteroidota
  • domain: Bacteria
  • phylum: Bacteroidota
  • class: Bacteroidia
  • order: Bacteroidales
  • family: Prevotellaceae
  • genus: Hallella
  • species: Hallella bergensis
  • full scientific name: Hallella bergensis (Downes et al. 2006) Hitch et al. 2023

  • synonyms

    • @ref: 20215
    • synonym: Prevotella bergensis

@ref: 6831

domain: Bacteria

phylum: Bacteroidetes

class: Bacteroidia

order: Bacteroidales

family: Prevotellaceae

genus: Prevotella

species: Prevotella bergensis

full scientific name: Prevotella bergensis Downes et al. 2006

strain designation: 94067913, W3326

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
31608negative0.8-6 µm0.7-0.8 µmrod-shapedno
69480no94.821
69480negative100

colony morphology

  • @ref: 59110
  • incubation period: 2 days

pigmentation

  • @ref: 31608
  • production: no

Culture and growth conditions

culture medium

  • @ref: 6831
  • name: PYG MEDIUM (MODIFIED) (DSMZ Medium 104)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/104
  • composition: 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

@refgrowthtypetemperaturerange
6831positivegrowth37mesophilic
59110positivegrowth37mesophilic
67770positivegrowth37mesophilic

Physiology and metabolism

oxygen tolerance

@refoxygen toleranceconfidence
6831anaerobe
31608anaerobe
59110anaerobe
69480anaerobe99.999

spore formation

@refspore formationconfidence
31608no
69481no100
69480no99.999

observation

  • @ref: 31608
  • observation: aggregates in chains

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3160822599arabinose+carbon source
3160817057cellobiose+carbon source
3160817716lactose+carbon source
3160837684mannose+carbon source
3160816634raffinose+carbon source
3160817814salicin+carbon source
3160817992sucrose+carbon source
316084853esculin+hydrolysis
6838016199urea-hydrolysis
6838029016arginine-hydrolysis
6838016024D-mannose-fermentation
6838016634raffinose-fermentation
6838029985L-glutamate-degradation
6838017632nitrate-reduction
6838027897tryptophan-energy source

metabolite production

  • @ref: 68380
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

  • @ref: 68380
  • Chebi-ID: 35581
  • metabolite: indole
  • indole test: -

enzymes

@refvalueactivityec
68380serine arylamidase-
68380glutamyl-glutamate arylamidase+
68380histidine arylamidase-
68380glycin arylamidase-
68380alanine arylamidase+3.4.11.2
68380tyrosine arylamidase-
68380pyrrolidonyl arylamidase-3.4.19.3
68380leucine arylamidase-3.4.11.1
68380phenylalanine arylamidase-
68380leucyl glycin arylamidase+3.4.11.1
68380proline-arylamidase-3.4.11.5
68380L-arginine arylamidase+
68380alkaline phosphatase+3.1.3.1
68380tryptophan deaminase-4.1.99.1
68380alpha-fucosidase-3.2.1.51
68380glutamate decarboxylase-4.1.1.15
68380N-acetyl-beta-glucosaminidase+3.2.1.52
68380beta-glucuronidase+3.2.1.31
68380alpha-arabinosidase+3.2.1.55
68380beta-glucosidase+3.2.1.21
68380alpha-glucosidase+3.2.1.20
68380beta-Galactosidase 6-phosphate-
68380beta-galactosidase+3.2.1.23
68380alpha-galactosidase-3.2.1.22
68380arginine dihydrolase-3.5.3.6
68380urease-3.5.1.5

API rID32A

@refUREADH Argalpha GALbeta GALbeta GPalpha GLUbeta GLUalpha ARAbeta GURbeta NAGMNERAFGDCalpha FUCNITINDPALArgAProALGAPheALeuAPyrATyrAAlaAGlyAHisAGGASerA
6831---+-+++++------++-+----+--+-

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinentsampling dategeographic location
6831soft tissue abscess, humanNorwayNOREurope
59110Human soft tissue abscessNorwayNOREurope1994Bergen
67770Human soft tissue abscessNorwayNOREuropeBergen

isolation source categories

Cat1Cat2Cat3
#Host#Human
#Host Body-Site
#Host Body-Site#Other#Abscess

taxonmaps

  • @ref: 69479
  • File name: preview.99_1829.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_16035;96_1032;97_1206;98_1445;99_1829&stattab=map
  • Last taxonomy: Prevotella bergensis subclade
  • 16S sequence: AY350613
  • Sequence Identity:
  • Total samples: 40550
  • soil counts: 243
  • aquatic counts: 305
  • animal counts: 39891
  • plant counts: 111

Safety information

risk assessment

  • @ref: 6831
  • biosafety level: 2
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
6831Prevotella bergensis strain 94067913 16S ribosomal RNA gene, partial sequenceAY3506131456ena242750
67770Prevotella bergensis gene for 16S ribosomal RNA, partial sequence, strain: JCM 13869AB5476721495ena242750

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Prevotella bergensis DSM 17361585502.3wgspatric585502
66792Prevotella bergensis DSM 17361645951825draftimg585502
67770Hallella bergensis DSM 17361GCA_000160535scaffoldncbi585502

GC content

@refGC-contentmethod
683148
6777048high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
gram-positiveno96.746yes
anaerobicyes98.749yes
halophileno83.447no
spore-formingno96.005yes
glucose-utilyes90.792no
thermophileno96.396yes
flagellatedno97.286yes
aerobicno97.601yes
motileno91.524no
glucose-fermentyes55.041no

External links

@ref: 6831

culture collection no.: JCM 51224, DSM 17361, CCUG 51224, JCM 13869

straininfo link

  • @ref: 81759
  • straininfo: 290989

literature

  • topic: Phylogeny
  • Pubmed-ID: 16514036
  • title: Prevotella bergensis sp. nov., isolated from human infections.
  • authors: Downes J, Sutcliffe IC, Hofstad T, Wade WG
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.63888-0
  • year: 2006
  • mesh: DNA, Ribosomal/chemistry, Fatty Acids/analysis, Humans, Nucleic Acid Hybridization, Phenotype, Phylogeny, Prevotella/chemistry/*classification/genetics/*isolation & purification, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Skin Diseases, Bacterial/*microbiology, Soft Tissue Infections/*microbiology
  • topic2: Pathogenicity

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmedjournal
6831Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 17361)https://www.dsmz.de/collection/catalogue/details/culture/DSM-17361
20215Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.10.1099/ijsem.0.004332List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ
31608Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2789628776041
59110Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 51224)https://www.ccug.se/strain?id=51224
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
66794Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg10.1093/nar/gkaa1025BRENDA, the ELIXIR core data resource in 2021: new developments and updates33211880Nucleic Acids Res. 49: D498-D508 2020
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
68380Automatically annotated from API rID32A
69479João 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.https://microbeatlas.org/MicrobeAtlas 1.0 beta
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch10.21203/rs.3.rs-2527258/v1Predictions based on the model GenomeNet Sporulation v. 1
81759Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID290989.1StrainInfo: A central database for resolving microbial strain identifiers