Strain identifier

BacDive ID: 2376

Type strain: Yes

Species: Cellulomonas oligotrophica

Strain Designation: Kc5

Strain history: K. Hatayama Kc5.

NCBI tax ID(s): 931536 (species)

For citation purpose refer to the digital object identifier (doi) of the current version.
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General

@ref: 17686

BacDive-ID: 2376

DSM-Number: 24482

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

description: Cellulomonas oligotrophica Kc5 is an aerobe, mesophilic, Gram-positive bacterium that was isolated from soil at an urban area.

NCBI tax id

  • NCBI tax id: 931536
  • Matching level: species

strain history

@refhistory
17686<- K. Hatayama, Sagami Chemical Research Institute, Kanagawa, Japan; Kc5 <- K. Esaki
67770K. Hatayama Kc5.

doi: 10.13145/bacdive2376.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Micrococcales
  • family: Cellulomonadaceae
  • genus: Cellulomonas
  • species: Cellulomonas oligotrophica
  • full scientific name: Cellulomonas oligotrophica Hatayama et al. 2013

@ref: 17686

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Cellulomonadaceae

genus: Cellulomonas

species: Cellulomonas oligotrophica

full scientific name: Cellulomonas oligotrophica Hatayama et al. 2013

strain designation: Kc5

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
30542positive6 µm2 µmrod-shapedyes
69480positive100

pigmentation

  • @ref: 30542
  • production: yes

Culture and growth conditions

culture medium

  • @ref: 17686
  • name: TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/92
  • composition: Name: TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92) Composition: Trypticase soy broth 30.0 g/l Agar 15.0 g/l Yeast extract 3.0 g/l Distilled water

culture temp

@refgrowthtypetemperaturerange
17686positivegrowth28mesophilic
30542positivegrowth25mesophilic
30542positiveoptimum15-37
67770positivegrowth25mesophilic

culture pH

@refabilitytypepHPH range
30542positivegrowth06-11alkaliphile
30542positiveoptimum9

Physiology and metabolism

oxygen tolerance

  • @ref: 30542
  • oxygen tolerance: aerobe

spore formation

@refspore formationconfidence
30542no
69480no99.882

halophily

@refsaltgrowthtested relationconcentration
30542NaClpositivegrowth0-6 %
30542NaClpositiveoptimum3 %

observation

  • @ref: 67770
  • observation: quinones: MK-9(H4), MK-9(H2)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3054230089acetate+carbon source
3054222599arabinose+carbon source
3054217057cellobiose+carbon source
3054228757fructose+carbon source
3054228260galactose+carbon source
3054217234glucose+carbon source
3054217754glycerol+carbon source
3054228087glycogen+carbon source
3054217306maltose+carbon source
3054229864mannitol+carbon source
3054237684mannose+carbon source
3054228053melibiose+carbon source
3054217814salicin+carbon source
3054230911sorbitol+carbon source
3054217992sucrose+carbon source
3054227082trehalose+carbon source
3054218222xylose+carbon source
3054217632nitrate+reduction

enzymes

@refvalueactivityec
30542catalase+1.11.1.6
30542gelatinase+

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
17686soil at an urban areaKanagawa, KawasakiJapanJPNAsia
67770Moist soil from an urban areaKawasaki, Kanagawa Pref.JapanJPNAsia

isolation source categories

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

taxonmaps

  • @ref: 69479
  • File name: preview.99_28313.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_9;96_432;97_1685;98_2637;99_28313&stattab=map
  • Last taxonomy: Cellulomonas oligotrophica
  • 16S sequence: AB602499
  • Sequence Identity:
  • Total samples: 33
  • soil counts: 15
  • aquatic counts: 14
  • animal counts: 4

Safety information

risk assessment

  • @ref: 17686
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 17686
  • description: Cellulomonas oligotrophica gene for 16S ribosomal RNA, partial sequence
  • accession: AB602499
  • length: 1443
  • database: ena
  • NCBI tax ID: 931536

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Cellulomonas oligotrophica NBRC 109435GCA_016862735contigncbi931536
66792Cellulomonas oligotrophica strain DSM 24482931536.4wgspatric931536
66792Cellulomonas oligotrophica strain JCM 17534931536.3wgspatric931536
66792Cellulomonas oligotrophica strain NBRC 109435931536.5wgspatric931536
66792Cellulomonas oligotrophica DSM 244822844845222draftimg931536
67770Cellulomonas oligotrophica DSM 24482GCA_013409875contigncbi931536
67770Cellulomonas oligotrophica JCM 17534GCA_006386485scaffoldncbi931536

GC content

@refGC-contentmethod
1768675.8high performance liquid chromatography (HPLC)
3054275.8

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes88no
motileyes85.744yes
flagellatedno90.655no
gram-positiveyes93.308yes
anaerobicno98.894no
halophileno91.713no
spore-formingno80.413yes
glucose-utilyes87.936yes
aerobicyes89.242yes
thermophileno99.402no
glucose-fermentno64.654no

External links

@ref: 17686

culture collection no.: DSM 24482, JCM 17534, NBRC 109435

straininfo link

  • @ref: 71931
  • straininfo: 399478

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny22328604Cellulomonas soli sp. nov. and Cellulomonas oligotrophica sp. nov., isolated from soil.Hatayama K, Esaki K, Ide TInt J Syst Evol Microbiol10.1099/ijs.0.038364-02012Bacterial Typing Techniques, Base Composition, Cellulomonas/*classification/genetics/isolation & purification, DNA, Bacterial/genetics, Fatty Acids/analysis, Japan, Molecular Sequence Data, Nucleic Acid Hybridization, Peptidoglycan/analysis, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Vitamin K 2/analogs & derivatives/analysisGenetics
Phylogeny31661043Cellulomonas telluris sp. nov., an endoglucanase-producing actinobacterium isolated from Badain Jaran desert sand.Shi YL, Sun Y, Ruan ZY, Su J, Yu LY, Zhang YQInt J Syst Evol Microbiol10.1099/ijsem.0.0038062020Bacterial Typing Techniques, Base Composition, *Cellulase, Cellulomonas/*classification/enzymology/isolation & purification, China, DNA, Bacterial/genetics, *Desert Climate, Fatty Acids/chemistry, Nucleic Acid Hybridization, Peptidoglycan/chemistry, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sand/*microbiology, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/chemistryEnzymology
Phylogeny32038002Cellulomonas shaoxiangyii sp. nov., isolated from faeces of Tibetan antelope (Pantholops hodgsonii) on the Qinghai-Tibet Plateau.Tian Z, Lu S, Jin D, Yang J, Pu J, Lai XH, Ren ZH, Wu XM, Li J, Wang S, Xu JInt J Syst Evol Microbiol10.1099/ijsem.0.0039392020Animals, Antelopes/*microbiology, Bacterial Typing Techniques, Base Composition, Cell Wall/chemistry, Cellulomonas/*classification/isolation & purification, DNA, Bacterial/genetics, Fatty Acids/chemistry, Feces/*microbiology, Nucleic Acid Hybridization, Ornithine/chemistry, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Tibet, Vitamin K 2/analogs & derivatives/chemistryTranscriptome

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
17686Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 24482)https://www.dsmz.de/collection/catalogue/details/culture/DSM-24482
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
30542Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2687328776041
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)
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
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)
71931Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID399478.1StrainInfo: A central database for resolving microbial strain identifiers