Strain identifier

BacDive ID: 7443

Type strain: Yes

Species: Microbacterium pygmaeum

Strain Designation: KV-490

Strain history: NRRL B-24469 <-- S. ?mura KV-490.

NCBI tax ID(s): 370764 (species)

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General

@ref: 16727

BacDive-ID: 7443

DSM-Number: 23142

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

description: Microbacterium pygmaeum KV-490 is a mesophilic bacterium that was isolated from soil.

NCBI tax id

  • NCBI tax id: 370764
  • Matching level: species

strain history

@refhistory
16727<- JCM/RIKEN <- NRRL <- S. Omura, Kitasato Inst., Tokyo, Japan; KV-490
67770NRRL B-24469 <-- S. ?mura KV-490.

doi: 10.13145/bacdive7443.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Micrococcales
  • family: Microbacteriaceae
  • genus: Microbacterium
  • species: Microbacterium pygmaeum
  • full scientific name: Microbacterium pygmaeum Kageyama et al. 2008

@ref: 16727

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Microbacteriaceae

genus: Microbacterium

species: Microbacterium pygmaeum

full scientific name: Microbacterium pygmaeum Kageyama et al. 2008

strain designation: KV-490

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram stain
69480no94.095
69480100positive

Culture and growth conditions

culture medium

  • @ref: 16727
  • name: R2A MEDIUM (DSMZ Medium 830)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/830
  • composition: Name: R2A MEDIUM (DSMZ Medium 830) Composition: Agar 15.0 g/l Casamino acids 0.5 g/l Starch 0.5 g/l Glucose 0.5 g/l Proteose peptone 0.5 g/l Yeast extract 0.5 g/l K2HPO4 0.3 g/l Na-pyruvate 0.3 g/l MgSO4 x 7 H2O 0.05 g/l Distilled water

culture temp

@refgrowthtypetemperaturerange
16727positivegrowth28mesophilic
67770positivegrowth28mesophilic

Physiology and metabolism

spore formation

@refspore formationconfidence
69481no100
69480no99.996

observation

  • @ref: 67770
  • observation: quinones: MK-11, MK-12, MK-13

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
16727soilTokyo, Aoyama CemeteryJapanJPNAsia
67770Soil at the Aoyama CemeteryTokyoJapanJPNAsia

isolation source categories

  • Cat1: #Environmental
  • Cat2: #Terrestrial
  • Cat3: #Soil

Safety information

risk assessment

  • @ref: 16727
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 16727
  • description: Microbacterium pygmaeum gene for 16S rRNA, partial sequence
  • accession: AB248875
  • length: 1421
  • database: ena
  • NCBI tax ID: 370764

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Microbacterium pygmaeum DSM 23142GCA_900100885chromosomencbi370764
66792Microbacterium pygmaeum strain DSM 23142370764.3completepatric370764
66792Microbacterium pygmaeum DSM 231422634166516draftimg370764

GC content

@refGC-contentmethod
1672768.0high performance liquid chromatography (HPLC)
6777068high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
gram-positiveyes92.519no
anaerobicno99.571no
halophileno91.863no
spore-formingno93.143no
glucose-utilyes85.029no
aerobicyes94.819no
flagellatedno97.758no
thermophileno99.458yes
motileno92.426no
glucose-fermentno90.802no

External links

@ref: 16727

culture collection no.: DSM 23142, JCM 15925, NBRC 101800, NRRL B-24469

straininfo link

  • @ref: 76891
  • straininfo: 408257

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
16727Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 23142)https://www.dsmz.de/collection/catalogue/details/culture/DSM-23142
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
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)
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/
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
76891Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID408257.1StrainInfo: A central database for resolving microbial strain identifiers