Strain identifier

BacDive ID: 12550

Type strain: Yes

Species: Segatella oris

Strain history: CIP <- 1996, J.P. Carlier, Inst. Pasteur, Paris, France: strain AIP 10115 <- ATCC <- L.V. Holdeman: strain VPI DIA-1A, Bacteroides oris

NCBI tax ID(s): 1122989 (strain), 28135 (species)

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General

@ref: 7672

BacDive-ID: 12550

DSM-Number: 18711

keywords: genome sequence, 16S sequence, Bacteria, anaerobe, mesophilic

description: Segatella oris JCM 12252 is an anaerobe, mesophilic bacterium that was isolated from gingival crevice.

NCBI tax id

NCBI tax idMatching level
28135species
1122989strain

strain history

@refhistory
7672<- CIP <- J.-P. Carlier <- ATCC <- L. V. Holdeman
67770ATCC 33573 <-- L. V. Holdeman VPI D1A-1A.
121445CIP <- 1996, J.P. Carlier, Inst. Pasteur, Paris, France: strain AIP 10115 <- ATCC <- L.V. Holdeman: strain VPI DIA-1A, Bacteroides oris

doi: 10.13145/bacdive12550.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacteroidota
  • domain: Bacteria
  • phylum: Bacteroidota
  • class: Bacteroidia
  • order: Bacteroidales
  • family: Prevotellaceae
  • genus: Segatella
  • species: Segatella oris
  • full scientific name: Segatella oris (Holdeman et al. 1982) Hitch et al. 2023

  • synonyms

    @refsynonym
    20215Bacteroides oris
    20215Prevotella oris

@ref: 7672

domain: Bacteria

phylum: Bacteroidetes

class: Bacteroidia

order: Bacteroidales

family: Prevotellaceae

genus: Prevotella

species: Prevotella oris

full scientific name: Prevotella oris (Holdeman et al. 1982) Shah and Collins 1990 emend. Hahnke et al. 2016

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram stain
69480no91.931
6948099.999negative

colony morphology

  • @ref: 46245
  • incubation period: 1-2 days

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
7672COLUMBIA 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
7672PYG MEDIUM (MODIFIED) (DSMZ Medium 104)yeshttps://mediadive.dsmz.de/medium/104Name: 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
41190MEDIUM 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)
121445CIP Medium 20yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=20

culture temp

@refgrowthtypetemperaturerange
7672positivegrowth37mesophilic
41190positivegrowth37mesophilic
46245positivegrowth37mesophilic
67770positivegrowth37mesophilic

Physiology and metabolism

oxygen tolerance

@refoxygen toleranceconfidence
7672anaerobe
46245anaerobe
69480anaerobe100

spore formation

@refspore formationconfidence
69481no100
69480no99.998

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
6838016199urea-hydrolysis
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-
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
68380urease-3.5.1.5

API rID32A

@refUREADH Argalpha GALbeta GALbeta GPalpha GLUbeta GLUalpha ARAbeta GURbeta NAGMNERAFGDCalpha FUCNITINDPALArgAProALGAPheALeuAPyrATyrAAlaAGlyAHisAGGASerA
7672--++-+++-+---+--+-------+----
7672-+++-+++-++/-+/--+--+--+----+----

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinent
7672gingival crevice
46245Human gingival crevice with moderate periodontitis
67770Gingival crevice with periodontitis
121445Human, Gingival crevice with moderate suppurationUnited States of AmericaUSANorth America

isolation source categories

  • Cat1: #Host Body-Site
  • Cat2: #Oral cavity and airways
  • Cat3: #Gingiva

taxonmaps

  • @ref: 69479
  • File name: preview.99_7018.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_44;96_1478;97_1764;98_2158;99_7018&stattab=map
  • Last taxonomy: Prevotella oris subclade
  • 16S sequence: NR_044628
  • Sequence Identity:
  • Total samples: 1716
  • soil counts: 14
  • aquatic counts: 7
  • animal counts: 1690
  • plant counts: 5

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
76722Risk group (German classification)
1214452Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
7672Prevotella oris strain ATCC 33573 16S ribosomal RNA, partial sequenceNR_0446281480nuccore28135
67770Prevotella oris gene for 16S ribosomal RNA, partial sequence, strain: JCM 8540AB5477011481ena28135
67770Prevotella oris strain ATCC 33573 16S ribosomal RNA gene, partial sequenceL164741480ena28135

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Prevotella oris NCTC13071GCA_900637655completencbi28135
66792Prevotella oris DSM 187111122989.3wgspatric1122989
66792Prevotella oris JCM 122521235820.4wgspatric1122989
66792Prevotella oris strain NCTC1307128135.5completepatric28135
66792Prevotella oris JCM 122522579778709draftimg1122989
66792Prevotella oris DSM 187112517572237draftimg1122989
67770Prevotella oris DSM 18711 = JCM 12252GCA_000377685scaffoldncbi1122989
67770Prevotella oris DSM 18711 = JCM 12252GCA_000613505contigncbi1122989

GC content

  • @ref: 7672
  • GC-content: 43.8
  • method: sequence analysis

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
flagellatedno97.264no
gram-positiveno97.887no
anaerobicyes99.246yes
aerobicno98.202no
halophileno89.339no
spore-formingno96.55no
thermophileno97.535no
glucose-utilyes84.537no
motileno91.976no
glucose-fermentyes70.213no

External links

@ref: 7672

culture collection no.: JCM 12252, DSM 18711, ATCC 33573, CCUG 15405, CIP 104480, AIP 10115, JCM 8540, NCTC 13071, VPI D1A-1A

straininfo link

  • @ref: 81765
  • straininfo: 40565

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Enzymology1398963Identification of proteases from periodontopathogenic bacteria as activators of latent human neutrophil and fibroblast-type interstitial collagenases.Sorsa T, Ingman T, Suomalainen K, Haapasalo M, Konttinen YT, Lindy O, Saari H, Uitto VJInfect Immun10.1128/iai.60.11.4491-4495.19921992Collagenases/*metabolism, Dental Plaque/enzymology/*microbiology, Endopeptidases/*metabolism, Enzyme Activation, Fibroblasts/enzymology, Glycoproteins/metabolism, Humans, In Vitro Techniques, Matrix Metalloproteinase 1, Matrix Metalloproteinase 8, Neutrophils/enzymology, Periodontitis/enzymology/*microbiology, Tissue Inhibitor of Metalloproteinases, Treponema/enzymologyMetabolism
Phylogeny15143039Prevotella shahii sp. nov. and Prevotella salivae sp. nov., isolated from the human oral cavity.Sakamoto M, Suzuki M, Huang Y, Umeda M, Ishikawa I, Benno YInt J Syst Evol Microbiol10.1099/ijs.0.02876-02004DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Fatty Acids/analysis, Humans, Molecular Sequence Data, Mouth/*microbiology, Phenotype, Phylogeny, Prevotella/*classification/genetics/*isolation & purification, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Species SpecificityPathogenicity

Reference

@idauthorscataloguedoi/urltitle
7672Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 18711)https://www.dsmz.de/collection/catalogue/details/culture/DSM-18711
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
41190Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/16393
46245Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 15405)https://www.ccug.se/strain?id=15405
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)
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
81765Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID40565.1StrainInfo: A central database for resolving microbial strain identifiers
121445Curators of the CIPCollection of Institut Pasteur (CIP 104480)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20104480