Strain identifier

BacDive ID: 14117

Type strain: No

Species: Sphingobacterium versatilis

Strain Designation: KM 2138

Strain history: <- ATCC <- E. Yabuuchi, KM 2138 (GIFU 2138) <- W. Minamide (Flavobacterium sp. No. 6)

NCBI tax ID(s): 525372 (strain), 258 (species)

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General

@ref: 1132

BacDive-ID: 14117

DSM-Number: 2582

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

description: Sphingobacterium versatilis KM 2138 is a mesophilic, Gram-negative bacterium that was isolated from vaginal secretion.

NCBI tax id

NCBI tax idMatching level
525372strain
258species

strain history

  • @ref: 1132
  • history: <- ATCC <- E. Yabuuchi, KM 2138 (GIFU 2138) <- W. Minamide (Flavobacterium sp. No. 6)

doi: 10.13145/bacdive14117.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacteroidota
  • domain: Bacteria
  • phylum: Bacteroidota
  • class: Sphingobacteriia
  • order: Sphingobacteriales
  • family: Sphingobacteriaceae
  • genus: Sphingobacterium
  • species: Sphingobacterium versatilis
  • full scientific name: Sphingobacterium versatilis Yabuuchi et al. 1981

@ref: 1132

domain: Bacteria

phylum: Bacteroidetes

class: Sphingobacteriia

order: Sphingobacteriales

family: Sphingobacteriaceae

genus: Sphingobacterium

species: Sphingobacterium spiritivorum

full scientific name: Sphingobacterium spiritivorum (Holmes et al. 1982) Yabuuchi et al. 1983 emend. Lai et al. 2016

strain designation: KM 2138

type strain: no

Morphology

cell morphology

  • @ref: 69480
  • gram stain: negative
  • confidence: 99.98

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
1132NUTRIENT AGAR (DSMZ Medium 1)yeshttps://mediadive.dsmz.de/medium/1Name: NUTRIENT AGAR (DSMZ Medium 1) Composition: Agar 15.0 g/l Peptone 5.0 g/l Meat extract 3.0 g/l Distilled water
1132CY-AGAR (DSMZ Medium 67)yeshttps://mediadive.dsmz.de/medium/67Name: CY-AGAR (DSMZ Medium 67) Composition: Agar 15.0 g/l Casitone 3.0 g/l CaCl2 x 2 H2O 1.36 g/l Yeast extract 1.0 g/l Distilled water

culture temp

@refgrowthtypetemperaturerange
1132positivegrowth28mesophilic
1132positivegrowth30mesophilic

Physiology and metabolism

spore formation

@refspore formationconfidence
69481no100
69480no99.996

Isolation, sampling and environmental information

isolation

  • @ref: 1132
  • sample type: vaginal secretion

isolation source categories

Cat1Cat2Cat3
#Host Body-Site#Urogenital tract#Vagina
#Host Body Product#Urogenital tract#Vaginal secretion

taxonmaps

  • @ref: 69479
  • File name: preview.99_3331.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_15366;96_1738;97_2079;98_2555;99_3331&stattab=map
  • Last taxonomy: Sphingobacterium spiritivorum subclade
  • 16S sequence: AJ459411
  • Sequence Identity:
  • Total samples: 7762
  • soil counts: 926
  • aquatic counts: 1560
  • animal counts: 4723
  • plant counts: 553

Safety information

risk assessment

  • @ref: 1132
  • biosafety level: 2
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 20218
  • description: Sphingobacterium spiritivorum partial 16S rRNA gene, strain DSM 2582
  • accession: AJ459411
  • length: 1476
  • database: ena
  • NCBI tax ID: 258

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Sphingobacterium spiritivorum ATCC 33300GCA_000159515scaffoldncbi525372
66792Sphingobacterium spiritivorum ATCC 33300525372.3wgspatric525372
66792Sphingobacterium spiritivorum strain FDAARGOS_1146258.9completepatric258
66792Sphingobacterium spiritivorum ATCC 33300643886135draftimg525372

GC content

  • @ref: 1132
  • GC-content: 39.9

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileno93.307no
gram-positiveno98.118no
anaerobicno99.238no
aerobicyes88.954no
halophileno96.311no
spore-formingno94.708no
glucose-utilyes91.781no
flagellatedno95.789no
thermophileno98.916yes
glucose-fermentno90.441no

External links

@ref: 1132

culture collection no.: DSM 2582, ATCC 33300, GIFU 2138

straininfo link

  • @ref: 83284
  • straininfo: 311050

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
1132Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 2582)https://www.dsmz.de/collection/catalogue/details/culture/DSM-2582
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
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)
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
83284Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID311050.1StrainInfo: A central database for resolving microbial strain identifiers