Strain identifier

BacDive ID: 7430

Type strain: Yes

Species: Microbacterium pumilum

Strain Designation: KV-488

Strain history: CIP <- 2006, NBRC <- S. Omura, Kitasato Univ., Tokyo, Japan: strain KV-488

NCBI tax ID(s): 344165 (species)

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General

@ref: 15480

BacDive-ID: 7430

DSM-Number: 21018

keywords: 16S sequence, Bacteria, mesophilic, Gram-positive, rod-shaped

description: Microbacterium pumilum KV-488 is a mesophilic, Gram-positive, rod-shaped bacterium that was isolated from soil.

NCBI tax id

  • NCBI tax id: 344165
  • Matching level: species

strain history

@refhistory
15480<- CIP; CIP 109364
67770NBRC 101279 <-- S. ?mura KV-488.
122053CIP <- 2006, NBRC <- S. Omura, Kitasato Univ., Tokyo, Japan: strain KV-488

doi: 10.13145/bacdive7430.20230509.8.1

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 pumilum
  • full scientific name: Microbacterium pumilum Kageyama et al. 2006

@ref: 15480

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Microbacteriaceae

genus: Microbacterium

species: Microbacterium pumilum

full scientific name: Microbacterium pumilum Kageyama et al. 2006

strain designation: KV-488

type strain: yes

Morphology

cell morphology

  • @ref: 122053
  • gram stain: positive
  • cell shape: rod-shaped
  • motility: no

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
15480R2A MEDIUM (DSMZ Medium 830)yeshttps://mediadive.dsmz.de/medium/830Name: 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
36803MEDIUM 328- for nutrient agaryesDistilled water make up to (1000.000 ml);Agar (15.000 g);Peptone (5.000g);Beef extract (3.000 g)
122053CIP Medium 328yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=328

culture temp

@refgrowthtypetemperaturerange
15480positivegrowth28mesophilic
36803positivegrowth30mesophilic
67770positivegrowth28mesophilic

Physiology and metabolism

observation

  • @ref: 67770
  • observation: quinones: MK-13, MK-12, MK-14

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
12205317632nitrate+reduction
12205316301nitrite+reduction

metabolite production

  • @ref: 122053
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

enzymes

@refvalueactivityec
68382alpha-fucosidase-3.2.1.51
68382alpha-mannosidase-3.2.1.24
68382N-acetyl-beta-glucosaminidase+3.2.1.52
68382beta-glucosidase+3.2.1.21
68382alpha-glucosidase+3.2.1.20
68382beta-glucuronidase+3.2.1.31
68382beta-galactosidase+3.2.1.23
68382alpha-galactosidase+3.2.1.22
68382naphthol-AS-BI-phosphohydrolase-
68382acid phosphatase-3.1.3.2
68382alpha-chymotrypsin-3.4.21.1
68382trypsin-3.4.21.4
68382cystine arylamidase-3.4.11.3
68382valine arylamidase-
68382leucine arylamidase+3.4.11.1
68382lipase (C 14)-
68382esterase lipase (C 8)-
68382esterase (C 4)+
68382alkaline phosphatase-3.1.3.1
122053oxidase-
122053catalase+1.11.1.6
122053urease-3.5.1.5

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
122053--+--+------++++++--

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentisolation date
15480soilAoyamareien, TokyoJapanJPNAsia
67770Soil form a cemetery in AoyamaTokyoJapanJPNAsia
122053Environment, SoilTokyoJapanJPNAsia2002

isolation source categories

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

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
154801Risk group (German classification)
1220531Risk group (French classification)

Sequence information

16S sequences

  • @ref: 15480
  • description: Microbacterium pumilum gene for 16S rRNA, partial sequence
  • accession: AB234027
  • length: 1403
  • database: ena
  • NCBI tax ID: 344165

GC content

@refGC-contentmethod
1548071
6777071high performance liquid chromatography (HPLC)

External links

@ref: 15480

culture collection no.: DSM 21018, CIP 109364, NBRC 101279, NRRL B-24452, JCM 14902

straininfo link

  • @ref: 76879
  • straininfo: 295943

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny16957107Microbacterium deminutum sp. nov., Microbacterium pumilum sp. nov. and Microbacterium aoyamense sp. nov.Kageyama A, Takahashi Y, Omura SInt J Syst Evol Microbiol10.1099/ijs.0.64236-02006Actinomycetales/*classification/genetics, Bacterial Typing Techniques, DNA, Bacterial/analysis, Molecular Sequence Data, RNA, Ribosomal, 16S/*analysis/geneticsGenetics
Phylogeny23315408Microbacterium saccharophilum sp. nov., isolated from a sucrose-refining factory.Ohta Y, Ito T, Mori K, Nishi S, Shimane Y, Mikuni K, Hatada YInt J Syst Evol Microbiol10.1099/ijs.0.047258-02013Actinomycetales/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/analysis, Japan, Lysine/analysis, Molecular Sequence Data, Nucleic Acid Hybridization, Peptidoglycan/analysis, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Sucrose/*metabolism, Vitamin K 2/analysisGenetics

Reference

@idauthorscataloguedoi/urltitle
15480Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 21018)https://www.dsmz.de/collection/catalogue/details/culture/DSM-21018
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
36803Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/7097
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
68382Automatically annotated from API zym
76879Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID295943.1StrainInfo: A central database for resolving microbial strain identifiers
122053Curators of the CIPCollection of Institut Pasteur (CIP 109364)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20109364