Strain identifier

BacDive ID: 12525

Type strain: Yes

Species: Prevotella bivia

Strain Designation: 653C

Strain history: CIP <- 1997, J.P. Carlier, Inst. Pasteur, Paris, France: strain AIP 10109 <- L.V. Holdeman: strain VPI 6822 <- D. Blazevic: strain 653C

NCBI tax ID(s): 868129 (strain), 28125 (species)

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General

@ref: 8886

BacDive-ID: 12525

DSM-Number: 20514

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

description: Prevotella bivia 653C is an anaerobe, mesophilic, Gram-negative human pathogen that was isolated from endometrium.

NCBI tax id

NCBI tax idMatching level
28125species
868129strain

strain history

@refhistory
8886<- ATCC; ATCC 29303 <- L. V. Holdeman; VPI 6822 (Bacteroides bivius) <- D. Blazevic; 653C
67770T. Mitsuoka <-- L. V. Holdeman VPI 6822 <-- D. Balzeric.
116825CIP <- 1997, J.P. Carlier, Inst. Pasteur, Paris, France: strain AIP 10109 <- L.V. Holdeman: strain VPI 6822 <- D. Blazevic: strain 653C

doi: 10.13145/bacdive12525.20250331.9.3

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacteroidota
  • domain: Bacteria
  • phylum: Bacteroidota
  • class: Bacteroidia
  • order: Bacteroidales
  • family: Prevotellaceae
  • genus: Prevotella
  • species: Prevotella bivia
  • full scientific name: Prevotella bivia (Holdeman and Johnson 1977) Shah and Collins 1990

  • synonyms

    • @ref: 20215
    • synonym: Bacteroides bivius

@ref: 8886

domain: Bacteria

phylum: Bacteroidetes

class: Bacteroidia

order: Bacteroidales

family: Prevotellaceae

genus: Prevotella

species: Prevotella bivia

full scientific name: Prevotella bivia (Holdeman and Johnson 1977) Shah and Collins 1990

strain designation: 653C

type strain: yes

Morphology

cell morphology

@refgram staincell shapemotilityconfidence
116825negativerod-shapedno
125438no90
125438negative95.234
125439negative99.5

colony morphology

@reftype of hemolysisincubation period
8886gamma2-3 days
451931-2 days

multimedia

@refmultimedia contentcaptionintellectual property rights
66793EM_DSM_20514_1.jpgelectron microscopic image© HZI/Manfred Rohde
66793EM_DSM_20514_2.jpgelectron microscopic image© HZI/Manfred Rohde
66793EM_DSM_20514_3.jpgelectron microscopic image© HZI/Manfred Rohde
66793EM_DSM_20514_4.jpgelectron microscopic image© HZI/Manfred Rohde
66793EM_DSM_20514_5.jpgelectron microscopic image© HZI/Manfred Rohde

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
8886COLUMBIA BLOOD MEDIUM (DSMZ Medium 693)yeshttps://mediadive.dsmz.de/medium/693Name: COLUMBIA BLOOD MEDIUM (DSMZ Medium 693) Composition: Defibrinated sheep blood 50.0 g/l Columbia agar base
39197MEDIUM 20 - for Anaerobic bacteriayesAgar (15.000 g);Glucose (5.000 g);Yeast extract (20.000 g);Tryptone (30.000 g);Cysteine hydrochloride (0.500 g);distilled water (1000.000 ml);Hemin solution -M00149 (25.000 ml)
8886CHOPPED MEAT MEDIUM WITH CARBOHYDRATES (DSMZ Medium 110)yeshttps://www.dsmz.de/microorganisms/medium/pdf/DSMZ_Medium110.pdf
116825CIP Medium 20yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=20

culture temp

@refgrowthtypetemperature
8886positivegrowth37
39197positivegrowth37
45193positivegrowth37
67770positivegrowth37

Physiology and metabolism

oxygen tolerance

@refoxygen toleranceconfidence
8886anaerobe
45193anaerobe
125438anaerobe91.546
125439anaerobe93.1

spore formation

@refspore formationconfidence
125438no94.995
125439no99.6

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
6838027897tryptophan-energy source
6838029985L-glutamate-degradation
6838017632nitrate-reduction
6838016199urea-hydrolysis
6838029016arginine-hydrolysis
11682517632nitrate-reduction
11682516301nitrite-reduction
6838016634raffinose-fermentation

metabolite production

@refChebi-IDmetaboliteproduction
6838035581indoleno
11682535581indoleno

metabolite tests

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

enzymes

@refvalueactivityec
68382alpha-fucosidase-3.2.1.51
68382alpha-mannosidase-3.2.1.24
68382N-acetyl-beta-glucosaminidase+3.2.1.52
68382beta-glucosidase-3.2.1.21
68382alpha-glucosidase+3.2.1.20
68382beta-glucuronidase-3.2.1.31
68382beta-galactosidase-3.2.1.23
68382alpha-galactosidase-3.2.1.22
68382naphthol-AS-BI-phosphohydrolase+
68382acid phosphatase+3.1.3.2
68382alpha-chymotrypsin-3.4.21.1
68382cystine arylamidase-3.4.11.3
68382trypsin-3.4.21.4
68382valine arylamidase-
68382leucine arylamidase-3.4.11.1
68382lipase (C 14)-
68382esterase lipase (C 8)-
68382esterase (C 4)-
68382alkaline phosphatase+3.1.3.1
116825oxidase-
116825catalase-1.11.1.6
116825urease-3.5.1.5
68380serine arylamidase-
68380tyrosine arylamidase-
68380pyrrolidonyl arylamidase-3.4.19.3
68380leucine arylamidase-3.4.11.1
68380phenylalanine arylamidase-
68380alpha-fucosidase+3.2.1.51
68380N-acetyl-beta-glucosaminidase+3.2.1.52
68380beta-glucuronidase-3.2.1.31
68380beta-glucosidase-3.2.1.21
68380histidine arylamidase-
68380alanine arylamidase+3.4.11.2
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
68380glutamate decarboxylase-4.1.1.15
68380alpha-arabinosidase-3.2.1.55
68380alpha-glucosidase+3.2.1.20
68380beta-galactosidase+3.2.1.23
68380alpha-galactosidase-3.2.1.22
68380arginine dihydrolase-3.5.3.6
68380urease-3.5.1.5

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
116825-+--------++---+-+--

API rID32A

@refUREADH Argalpha GALbeta GALbeta GPalpha GLUbeta GLUalpha ARAbeta GURbeta NAGMNERAFGDCalpha FUCNITINDPALArgAProALGAPheALeuAPyrATyrAAlaAGlyAHisAGGASerA
8886---+++---++--+--+--+----++-+-
8886---+-+---+---+--+--+----++/----
8886---+++---+---+--+--+----++-+/--
8886---+++---++--+--+--+----++/--+/--
8886---++/-+---++--+--+--+----++-+-

Isolation, sampling and environmental information

isolation

@refsample type
8886endometrium
45193Human endometrium
67770Endometrium
116825Endometrium

isolation source categories

  • Cat1: #Host Body-Site
  • Cat2: #Urogenital tract

taxonmaps

  • @ref: 69479
  • File name: preview.99_379.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_44;96_260;97_284;98_317;99_379&stattab=map
  • Last taxonomy: Prevotella bivia subclade
  • 16S sequence: AB547673
  • Sequence Identity:
  • Total samples: 92490
  • soil counts: 1096
  • aquatic counts: 1913
  • animal counts: 88928
  • plant counts: 553

Safety information

risk assessment

@refpathogenicity humanpathogenicity animalbiosafety levelbiosafety level comment
8886yesyes2Risk group (German classification)
1168252Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
8886Prevotella bivia gene for 16S ribosomal RNA, partial sequence, strain: JCM 6331AB5476731490nuccore28125
67770Prevotella bivia strain ATCC 29303 16S ribosomal RNA gene, partial sequenceL164751471nuccore28125

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Prevotella bivia DSM 20514868129.3wgspatric868129
66792Prevotella bivia JCVIHMP010553171.3wgspatric553171
66792Prevotella bivia 653C, DSM 205142509601036draftimg868129
67770Prevotella bivia DSM 20514GCA_000262545scaffoldncbi868129

GC content

@refGC-contentmethod
888640.0
6777040thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

@refmodeltraitdescriptionpredictionconfidencetraining_data
125438gram-positivegram-positivePositive reaction to Gram-stainingno95.234no
125438anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)yes91.546yes
125438aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)no96.615yes
125438spore-formingspore-formingAbility to form endo- or exosporesno94.995no
125438thermophilethermophilicAbility to grow at temperatures above or equal to 45°Cno94.809yes
125438motile2+flagellatedAbility to perform flagellated movementno90no
125439BacteriaNetspore_formationAbility to form endo- or exosporesno99.6
125439BacteriaNetmotilityAbility to perform movementno77.1
125439BacteriaNetgram_stainReaction to gram-stainingnegative99.5
125439BacteriaNetoxygen_toleranceOxygenic conditions needed for growthanaerobe93.1

External links

@ref: 8886

culture collection no.: DSM 20514, ATCC 29303, NCTC 11156, CCUG 9557, CIP 105105, JCM 6331, LMG 6452, VPI 6822, AIP 10109

straininfo link

  • @ref: 81744
  • straininfo: 3862

literature

  • topic: Enzymology
  • Pubmed-ID: 2324268
  • title: Protein banding patterns of the outer membrane-enriched fraction of Bacteroides bivius.
  • authors: Dinsmoor MJ, Ebersole JE, Gibbs RS
  • journal: J Clin Microbiol
  • DOI: 10.1128/jcm.28.3.405-408.1990
  • year: 1990
  • mesh: Bacterial Outer Membrane Proteins/*analysis/immunology, Bacteroides/*chemistry/immunology, Cross Reactions, Electrophoresis, Polyacrylamide Gel, Enzyme-Linked Immunosorbent Assay, Humans, Immune Sera/immunology, Molecular Weight, Predictive Value of Tests
  • topic2: Pathogenicity

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
8886Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 20514)https://www.dsmz.de/collection/catalogue/details/culture/DSM-20514
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
39197Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/17086
45193Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 9557)https://www.ccug.se/strain?id=9557
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)
66793Mukherjee et al.10.1038/nbt.3886GEBA: 1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life 35: 676-683 201728604660
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 updatesNucleic Acids Res. 49: D498-D508 202033211880
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
68380Automatically annotated from API rID32A
68382Automatically annotated from API zym
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
81744Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID3862.1StrainInfo: A central database for resolving microbial strain identifiers
116825Curators of the CIPCollection of Institut Pasteur (CIP 105105)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20105105
125438Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg Overmann10.1101/2024.08.12.607695Predicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets
125439Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardyhttps://github.com/GenomeNet/deepGdeepG: Deep Learning for Genome Sequence Data. R package version 0.3.1