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Strain identifier

BacDive ID: 12568

Type strain: Yes

Species: Prevotella scopos

Strain Designation: W2052

Strain history: CCUG 57945 <-- J. Downes <-- W. Wade W2052.

NCBI tax ID(s): 1236518 (strain), 589437 (species)

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General

@ref: 16432

BacDive-ID: 12568

DSM-Number: 22613

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

description: Prevotella scopos W2052 is an anaerobe, mesophilic human pathogen that was isolated from exudate associated with a failing dental implant.

NCBI tax id

NCBI tax idMatching level
1236518strain
589437species

strain history

doi: 10.13145/bacdive12568.20221219.7.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacteroidota
  • domain: Bacteria
  • phylum: Bacteroidota
  • class: Bacteroidia
  • order: Bacteroidales
  • family: Prevotellaceae
  • genus: Prevotella
  • species: Prevotella scopos
  • full scientific name: Prevotella scopos Downes and Wade 2011

@ref: 16432

domain: Bacteria

phylum: Bacteroidetes

class: Bacteroidia

order: Bacteroidales

family: Prevotellaceae

genus: Prevotella

species: Prevotella scopos

full scientific name: Prevotella scopos Downes and Wade 2011

strain designation: W2052

type strain: yes

Morphology

cell morphology

  • @ref: 69480
  • gram stain: negative
  • confidence: 99.569

colony morphology

@refincubation period
164323-7 days
615322 days

Culture and growth conditions

culture medium

  • @ref: 16432
  • name: CHOPPED MEAT MEDIUM WITH CARBOHYDRATES (DSMZ Medium 110)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/110
  • composition: Name: CHOPPED MEAT MEDIUM WITH CARBOHYDRATES (DSMZ Medium 110) Composition: Ground beef 500.0 g/l Casitone 30.0 g/l Agar 15.0 g/l K2HPO4 5.0 g/l Yeast extract 5.0 g/l D-Glucose 4.0 g/l Starch 1.0 g/l Maltose 1.0 g/l Cellobiose 1.0 g/l L-Cysteine HCl 0.5 g/l Ethanol 0.19 g/l Vitamin K3 0.05 g/l Hemin 0.005 g/l Sodium resazurin 0.0005 g/l Vitamin K1 NaOH Distilled water

culture temp

@refgrowthtypetemperaturerange
16432positivegrowth37mesophilic
61532positivegrowth37mesophilic
67770positivegrowth37mesophilic

Physiology and metabolism

oxygen tolerance

@refoxygen toleranceconfidence
16432anaerobe
61532anaerobe
69480anaerobe98.261

spore formation

  • @ref: 69480
  • spore formation: no
  • confidence: 98.755

halophily

  • @ref: 69480
  • halophily level: non-halophilic
  • confidence: 99.586

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
6838027897tryptophan-energy source
6838017632nitrate-reduction
6838029985L-glutamate-degradation
6838016634raffinose-fermentation
6838016024D-mannose-fermentation
6838029016arginine+hydrolysis
6838016199urea-hydrolysis
6836727082trehalose-builds acid from
6836762345L-rhamnose-builds acid from
6836730911sorbitol-builds acid from
6836716634raffinose+builds acid from
683676731melezitose-builds acid from
6836716024D-mannose+builds acid from
6836717057cellobiose-builds acid from
6836717754glycerol-builds acid from
683674853esculin-hydrolysis
683675291gelatin+hydrolysis
6836730849L-arabinose-builds acid from
6836765327D-xylose-builds acid from
6836717814salicin-builds acid from
6836717306maltose+builds acid from
6836717992sucrose+builds acid from
6836717716lactose+builds acid from
6836716899D-mannitol-builds acid from
6836717634D-glucose+builds acid from
6836716199urea-hydrolysis

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
68367beta-glucosidase-3.2.1.21
68367gelatinase+
68367urease-3.5.1.5

API 20A

@refUREGLUMANLACSACMALSALXYLARAGELESCGLYCELMNEMLZRAFSORRHATRE
16432-+-+++---+---+-+---

API rID32A

@refUREADH Argalpha GALbeta GALbeta GPalpha GLUbeta GLUalpha ARAbeta GURbeta NAGMNERAFGDCalpha FUCNITINDPALArgAProALGAPheALeuAPyrATyrAAlaAGlyAHisAGGASerA
16432-+-----------+--++-+----+----

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinentsampling date
16432exudate associated with a failing dental implantUnited KingdomGBREurope
61532Human oral cavity,dental implantUnited KingdomGBREurope2000
67770Human oral cavity

isolation source categories

Cat1Cat2Cat3
#Host Body-Site#Oral cavity and airways#Tooth
#Host Body Product#Fluids

taxonmaps

  • @ref: 69479
  • File name: preview.99_227.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_44;96_87;97_173;98_194;99_227&stattab=map
  • Last taxonomy: Prevotella scopos subclade
  • 16S sequence: FJ545434
  • Sequence Identity:
  • Total samples: 33756
  • soil counts: 331
  • aquatic counts: 484
  • animal counts: 32853
  • plant counts: 88

Safety information

risk assessment

  • @ref: 16432
  • pathogenicity human: yes, in single cases
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
16432Prevotella scopos JCM 17725 strain W2052 16S ribosomal RNA gene, partial sequenceFJ5454341453ena1236518
67770Prevotella scopos gene for 16S ribosomal RNA, partial sequence, strain: JCM 17725AB6832531492ena1236518

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Prevotella scopos JCM 17725 W2052GCA_001683355chromosomencbi1236518
66792Prevotella scopos JCM 17725 W2052GCA_018127785completencbi1236518
66792Prevotella scopos JCM 17725 DSM 22613GCA_900129535scaffoldncbi1236518
66792Prevotella scopos JCM 17725 JCM 17725GCA_000614285contigncbi1236518
66792Prevotella scopos JCM 177251236518.6completepatric1236518
66792Prevotella scopos JCM 177251236518.4wgspatric1236518
66792Prevotella scopos JCM 17725 strain DSM 226131236518.7wgspatric1236518
66792Prevotella scopos JCM 17725 strain W20521236518.13plasmidpatric1236518
66792Prevotella scopos JCM 17725 strain W20521236518.39completepatric1236518
66792Prevotella scopos DSM 226132695420955draftimg1236518
66792Prevotella scopos JCM 177252585427908draftimg1236518
66792Prevotella scopos W20522721755485completeimg1236518
66792Klebsiella pneumoniae AUH_IMP372GCA_002776435contigpatric573
66792Klebsiella pneumoniae 0113070356GCA_021137335contigpatric573
66792Streptococcus pneumoniae 2842STDY5643731GCA_900022535scaffoldpatric1313
66792uncultured Clostridia bacterium SRR7188232_bin.33_metaWRAP_v1.3_MAGGCA_945501375contigpatric244328
66792uncultured Clostridia bacterium SRR11784293_bin.43_metaWRAP_v1.3_MAGGCA_946184365contigpatric244328

External links

@ref: 16432

culture collection no.: DSM 22613, CCUG 57945, JCM 17725

straininfo link

@refpassport
20218http://www.straininfo.net/strains/865282
20218http://www.straininfo.net/strains/865281

literature

  • topic: Phylogeny
  • Pubmed-ID: 20495041
  • title: Prevotella fusca sp. nov. and Prevotella scopos sp. nov., isolated from the human oral cavity.
  • authors: Downes J, Wade WG
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.023861-0
  • year: 2010
  • mesh: Anaerobiosis, Anti-Bacterial Agents/metabolism, Base Composition, Bile/metabolism, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Hemiterpenes, Humans, Lactic Acid/metabolism, Molecular Sequence Data, Mouth/*microbiology, Pentanoic Acids/metabolism, Phylogeny, Prevotella/*classification/genetics/*isolation & purification/physiology, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Succinic Acid/metabolism, Sucrose/metabolism
  • topic2: Metabolism

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
16432Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 22613)https://www.dsmz.de/collection/catalogue/details/culture/DSM-22613
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
20218Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.10.1016/j.syapm.2013.11.002StrainInfo introduces electronic passports for microorganisms.Syst Appl Microbiol. 37: 42-50 201424321274
61532Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 57945)https://www.ccug.se/strain?id=57945
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/
68367Automatically annotated from API 20A
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)