Strain identifier

BacDive ID: 12564

Type strain: Yes

Species: Prevotella micans

Strain Designation: E7.56

Strain history: <- DSM <- J Downes, King`s College London, UK, E7.56 <- M Munson, King`s College, London, UK

NCBI tax ID(s): 1122987 (strain), 189723 (species)

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General

@ref: 15725

BacDive-ID: 12564

DSM-Number: 21469

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

description: Prevotella micans E7.56 is an anaerobe, mesophilic, Gram-negative human pathogen that was isolated from human tooth necrotic pulp.

NCBI tax id

NCBI tax idMatching level
1122987strain
189723species

strain history

@refhistory
15725<- J. Downes, King's College London, UK; E7.56 <- M. Munson, King's College London, UK
67770CCUG 56105 <-- J. Downes strain E7.56.
67771<- DSM <- J Downes, King`s College London, UK, E7.56 <- M Munson, King`s College, London, UK

doi: 10.13145/bacdive12564.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacteroidota
  • domain: Bacteria
  • phylum: Bacteroidota
  • class: Bacteroidia
  • order: Bacteroidales
  • family: Prevotellaceae
  • genus: Prevotella
  • species: Prevotella micans
  • full scientific name: Prevotella micans Downes et al. 2009

@ref: 15725

domain: Bacteria

phylum: Bacteroidetes

class: Bacteroidia

order: Bacteroidales

family: Prevotellaceae

genus: Prevotella

species: Prevotella micans

full scientific name: Prevotella micans Downes et al. 2009

strain designation: E7.56

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthmotilityconfidence
28945negative3.25 µm0.7 µmno
67771no
67771negative
69480negative99.998

colony morphology

  • @ref: 60859
  • incubation period: 2 days

pigmentation

  • @ref: 28945
  • production: yes

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
15725COLUMBIA 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
15725PYG MEDIUM (MODIFIED) (DSMZ Medium 104)yeshttps://mediadive.dsmz.de/medium/104Name: PYG MEDIUM (modified) (DSMZ Medium 104; with strain-specific modifications) Composition: Horse serum 50.0 g/l Yeast extract 10.0 g/l Trypticase peptone 5.0 g/l 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 Vitamin K1 NaOH Tween 80 Distilled water

culture temp

@refgrowthtypetemperaturerange
15725positivegrowth37mesophilic
60859positivegrowth37mesophilic
67770positivegrowth37mesophilic
67771positivegrowth37mesophilic

Physiology and metabolism

oxygen tolerance

@refoxygen toleranceconfidence
15725anaerobe
28945anaerobe
60859anaerobe
67771anaerobe
69480anaerobe99.635

spore formation

@refspore formationconfidence
69481no100
69480no100

observation

  • @ref: 28945
  • observation: aggregates in clumps

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2894530089acetate+carbon source
2894517057cellobiose+carbon source
2894528757fructose+carbon source
289455291gelatin+carbon source
2894517234glucose+carbon source
2894517716lactose+carbon source
2894517306maltose+carbon source
2894537684mannose+carbon source
2894528053melibiose+carbon source
2894516634raffinose+carbon source
2894517814salicin+carbon source
2894530031succinate+carbon source
2894517992sucrose+carbon source
6838016199urea-hydrolysis
6838029016arginine-hydrolysis
6838016024D-mannose-fermentation
6838016634raffinose-fermentation
6838029985L-glutamate-degradation
6838017632nitrate-reduction
6838027897tryptophan+energy source

metabolite production

@refChebi-IDmetaboliteproduction
2894535581indoleyes
6838035581indoleyes

metabolite tests

@refChebi-IDmetaboliteindole test
2894535581indole+
6838035581indole+

enzymes

@refvalueactivityec
28945alkaline phosphatase+3.1.3.1
28945alpha-galactosidase+3.2.1.22
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
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
15725--++-+/----+---+-++--+----+----

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
15725human tooth necrotic pulpLondonUnited KingdomGBREurope
60859Human oral necrotic pulp,2-yr-old childLondonUnited KingdomGBREurope
67770Human oral cavity
67771From human tooth necrotic pulp(oral cavity)LondonUnited KingdomGBREurope

isolation source categories

Cat1Cat2Cat3
#Host#Human
#Host Body-Site#Oral cavity and airways#Tooth

taxonmaps

  • @ref: 69479
  • File name: preview.99_68.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_15785;96_54;97_57;98_62;99_68&stattab=map
  • Last taxonomy: Prevotella micans subclade
  • 16S sequence: AF481228
  • Sequence Identity:
  • Total samples: 32820
  • soil counts: 268
  • aquatic counts: 453
  • animal counts: 31972
  • plant counts: 127

Safety information

risk assessment

  • @ref: 15725
  • pathogenicity human: yes, in single cases
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
15725Prevotella micans strain E7.56 16S ribosomal RNA gene, partial sequenceAF4812281480ena189723
67770Prevotella micans gene for 16S ribosomal RNA, partial sequence, strain: JCM 16134AB5476921490ena189723

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Prevotella micans DSM 214691122987.3wgspatric1122987
66792Prevotella micans JCM 161341236510.3wgspatric1122987
66792Prevotella micans DSM 214692515154159draftimg1122987
66792Prevotella micans JCM 161342585427903draftimg1122987
67770Prevotella micans DSM 21469 = JCM 16134GCA_000373705scaffoldncbi1122987
67771Prevotella micans DSM 21469 = JCM 16134GCA_000614105contigncbi1122987

GC content

@refGC-contentmethod
1572546high performance liquid chromatography (HPLC)
2894546
6777146.0high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileno92.925yes
flagellatedno97.374no
gram-positiveno97.281yes
anaerobicyes99.205no
aerobicno98.497yes
halophileno83.759no
spore-formingno97.706no
glucose-utilyes83.443no
thermophileno92.34no
glucose-fermentyes62.069no

External links

@ref: 15725

culture collection no.: DSM 21469, CCUG 56105, KCTC 15163, JCM 16134

straininfo link

  • @ref: 81778
  • straininfo: 400100

literature

  • topic: Phylogeny
  • Pubmed-ID: 19329604
  • title: Prevotella micans sp. nov., isolated from the human oral cavity.
  • authors: Downes J, Liu M, Kononen E, Wade WG
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.002337-0
  • year: 2009
  • mesh: Bacterial Typing Techniques, Base Composition, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Humans, Molecular Sequence Data, Mouth/*microbiology, Phylogeny, Prevotella/*classification/genetics/*isolation & purification/physiology, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sequence Homology, Nucleic Acid
  • topic2: Pathogenicity

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
15725Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 21469)https://www.dsmz.de/collection/catalogue/details/culture/DSM-21469
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
28945Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2538428776041
60859Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 56105)https://www.ccug.se/strain?id=56105
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/
67771Curators of the KCTChttps://kctc.kribb.re.kr/En/Kctc
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
81778Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID400100.1StrainInfo: A central database for resolving microbial strain identifiers