Strain identifier
BacDive ID: 7443
Type strain:
Species: Microbacterium pygmaeum
Strain Designation: KV-490
Strain history: NRRL B-24469 <-- S. ?mura KV-490.
NCBI tax ID(s): 370764 (species)
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
@ref | history |
---|---|
16727 | <- JCM/RIKEN <- NRRL <- S. Omura, Kitasato Inst., Tokyo, Japan; KV-490 |
67770 | NRRL 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
@ref | motility | confidence | gram stain |
---|---|---|---|
69480 | no | 94.095 | |
69480 | 100 | positive |
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
@ref | growth | type | temperature | range |
---|---|---|---|---|
16727 | positive | growth | 28 | mesophilic |
67770 | positive | growth | 28 | mesophilic |
Physiology and metabolism
spore formation
@ref | spore formation | confidence |
---|---|---|
69481 | no | 100 |
69480 | no | 99.996 |
observation
- @ref: 67770
- observation: quinones: MK-11, MK-12, MK-13
Isolation, sampling and environmental information
isolation
@ref | sample type | geographic location | country | origin.country | continent |
---|---|---|---|---|---|
16727 | soil | Tokyo, Aoyama Cemetery | Japan | JPN | Asia |
67770 | Soil at the Aoyama Cemetery | Tokyo | Japan | JPN | Asia |
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
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Microbacterium pygmaeum DSM 23142 | GCA_900100885 | chromosome | ncbi | 370764 |
66792 | Microbacterium pygmaeum strain DSM 23142 | 370764.3 | complete | patric | 370764 |
66792 | Microbacterium pygmaeum DSM 23142 | 2634166516 | draft | img | 370764 |
GC content
@ref | GC-content | method |
---|---|---|
16727 | 68.0 | high performance liquid chromatography (HPLC) |
67770 | 68 | high performance liquid chromatography (HPLC) |
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
spore-forming | no | 100 | no |
gram-positive | yes | 92.519 | no |
anaerobic | no | 99.571 | no |
halophile | no | 91.863 | no |
spore-forming | no | 93.143 | no |
glucose-util | yes | 85.029 | no |
aerobic | yes | 94.819 | no |
flagellated | no | 97.758 | no |
thermophile | no | 99.458 | yes |
motile | no | 92.426 | no |
glucose-ferment | no | 90.802 | no |
External links
@ref: 16727
culture collection no.: DSM 23142, JCM 15925, NBRC 101800, NRRL B-24469
straininfo link
- @ref: 76891
- straininfo: 408257
Reference
@id | authors | catalogue | doi/url | title | journal | pubmed |
---|---|---|---|---|---|---|
16727 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 23142) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-23142 | |||
20215 | Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M. | 10.1099/ijsem.0.004332 | List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ | |||
66792 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | https://diaspora-project.de/progress.html#genomes | Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | |||
66794 | Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg | 10.1093/nar/gkaa1025 | BRENDA, the ELIXIR core data resource in 2021: new developments and updates | Nucleic Acids Res. 49: D498-D508 2020 | 33211880 | |
67770 | Curators of the JCM | https://jcm.brc.riken.jp/en/ | ||||
69480 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | https://diaspora-project.de/progress.html#genomes | Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | |||
69481 | Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch | 10.21203/rs.3.rs-2527258/v1 | Predictions based on the model GenomeNet Sporulation v. 1 | |||
76891 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID408257.1 | StrainInfo: A central database for resolving microbial strain identifiers |