Strain identifier

BacDive ID: 7514

Type strain: Yes

Species: Compostimonas suwonensis

Strain history: <- KACC; KACC 13354

NCBI tax ID(s): 1048394 (species)

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General

@ref: 18069

BacDive-ID: 7514

DSM-Number: 25625

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

description: Compostimonas suwonensis DSM 25625 is an aerobe, mesophilic, Gram-positive bacterium that was isolated from spent mushroom compost.

NCBI tax id

  • NCBI tax id: 1048394
  • Matching level: species

strain history

  • @ref: 18069
  • history: <- KACC; KACC 13354

doi: 10.13145/bacdive7514.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Micrococcales
  • family: Microbacteriaceae
  • genus: Compostimonas
  • species: Compostimonas suwonensis
  • full scientific name: Compostimonas suwonensis Kim et al. 2012

@ref: 18069

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Microbacteriaceae

genus: Compostimonas

species: Compostimonas suwonensis

full scientific name: Compostimonas suwonensis Kim et al. 2012 emend. Nouioui et al. 2018

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
30448positive1.55 µm0.5 µmrod-shapedno
69480no92.127
69480positive100

pigmentation

  • @ref: 30448
  • production: yes

Culture and growth conditions

culture medium

  • @ref: 18069
  • 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
18069positivegrowth28mesophilic
30448positivegrowth10-37
30448positiveoptimum28mesophilic

culture pH

@refabilitytypepH
30448positivegrowth06-08
30448positiveoptimum7

Physiology and metabolism

oxygen tolerance

  • @ref: 30448
  • oxygen tolerance: aerobe

spore formation

@refspore formationconfidence
30448no
69481no96
69480no100

halophily

@refsaltgrowthtested relationconcentration
30448NaClpositivegrowth<3 %
30448NaClpositiveoptimum<1 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3044817234glucose+carbon source
3044837684mannose+carbon source
3044826546rhamnose+carbon source
3044817992sucrose+carbon source

enzymes

@refvalueactivityec
30448acid phosphatase+3.1.3.2
30448alpha-galactosidase+3.2.1.22
30448cytochrome oxidase+1.9.3.1

Isolation, sampling and environmental information

isolation

  • @ref: 18069
  • sample type: spent mushroom compost
  • geographic location: Suwon region
  • country: Republic of Korea
  • origin.country: KOR
  • continent: Asia

isolation source categories

Cat1Cat2Cat3
#Engineered#Biodegradation#Composting
#Host#Fungi#Mushroom

Safety information

risk assessment

  • @ref: 18069
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 18069
  • description: Compostimonas suwonensis strain SMC46 16S ribosomal RNA gene, partial sequence
  • accession: JN000316
  • length: 1422
  • database: ena
  • NCBI tax ID: 1048394

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Compostimonas suwonensis DSM 25625GCA_002797855contigncbi1048394
66792Compostimonas suwonensis strain DSM 256251048394.3wgspatric1048394
66792Compostimonas suwonensis DSM 256252731639183draftimg1048394

GC content

@refGC-contentmethod
1806968high performance liquid chromatography (HPLC)
3044868

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno96no
motileno90.129no
flagellatedno97.735yes
gram-positiveyes92.992yes
anaerobicno99.577no
aerobicyes93.71no
halophileno93.518no
spore-formingno90.856yes
thermophileno99.36yes
glucose-utilyes86.817yes
glucose-fermentno87.235no

External links

@ref: 18069

culture collection no.: DSM 25625, KACC 13354, NBRC 106304, SMC 46

straininfo link

  • @ref: 76959
  • straininfo: 405799

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny22140170Compostimonas suwonensis gen. nov., sp. nov., isolated from spent mushroom compost.Kim SJ, Tamura T, Hamada M, Ahn JH, Weon HY, Park IC, Suzuki KI, Kwon SWInt J Syst Evol Microbiol10.1099/ijs.0.036343-02011Actinomycetales/*classification/genetics/isolation & purification, Agaricales, Bacterial Typing Techniques, Base Composition, Cell Wall/chemistry, DNA, Bacterial/genetics, Fatty Acids/analysis, Molecular Sequence Data, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, *Soil, *Soil Microbiology, Vitamin K 2/analysisGenetics
Phylogeny24158943Glaciihabitans tibetensis gen. nov., sp. nov., a psychrotolerant bacterium of the family Microbacteriaceae, isolated from glacier ice water.Li AH, Liu HC, Xin YH, Kim SG, Zhou YGInt J Syst Evol Microbiol10.1099/ijs.0.052670-02013Actinomycetales/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Ice Cover/microbiology, Molecular Sequence Data, Nucleic Acid Hybridization, Peptidoglycan/chemistry, Phosphatidylglycerols/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Tibet, Ubiquinone/chemistry, *Water MicrobiologyGenetics

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmedjournal
18069Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 25625)https://www.dsmz.de/collection/catalogue/details/culture/DSM-25625
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
30448Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2678328776041
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 updates33211880Nucleic Acids Res. 49: D498-D508 2020
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
76959Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID405799.1StrainInfo: A central database for resolving microbial strain identifiers