Strain identifier

BacDive ID: 2377

Type strain: Yes

Species: Cellulomonas soli

Strain Designation: Kc1

Strain history: K. Hatayama Kc1.

NCBI tax ID(s): 931535 (species)

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General

@ref: 17687

BacDive-ID: 2377

DSM-Number: 24484

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

description: Cellulomonas soli Kc1 is an aerobe, spore-forming, mesophilic bacterium that was isolated from Soil.

NCBI tax id

  • NCBI tax id: 931535
  • Matching level: species

strain history

@refhistory
17687<- K. Hatayama, Sagami Chemical Research Institute, Kanagawa, Japan; Kc1 <- K. Esaki
67770K. Hatayama Kc1.

doi: 10.13145/bacdive2377.20250331.9.3

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 soli
  • full scientific name: Cellulomonas soli Hatayama et al. 2013

@ref: 17687

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Cellulomonadaceae

genus: Cellulomonas

species: Cellulomonas soli

full scientific name: Cellulomonas soli Hatayama et al. 2013

strain designation: Kc1

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
30542positive6 µm1.5 µmrod-shapedyes
125439positive99.9

pigmentation

  • @ref: 30542
  • production: yes

Culture and growth conditions

culture medium

  • @ref: 17687
  • 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

@refgrowthtypetemperature
17687positivegrowth25
30542positivegrowth15-37
30542positiveoptimum25
67770positivegrowth25

culture pH

@refabilitytypepHPH range
30542positivegrowth06-11alkaliphile
30542positiveoptimum8.5

Physiology and metabolism

oxygen tolerance

@refoxygen toleranceconfidence
30542aerobe
125439obligate aerobe99.7

halophily

@refsaltgrowthtested relationconcentration
30542NaClpositivegrowth0-3 %
30542NaClpositiveoptimum1.5 %

observation

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

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3054222599arabinose+carbon source
3054217057cellobiose+carbon source
3054228757fructose+carbon source
3054228260galactose+carbon source
305425291gelatin+carbon source
3054217234glucose+carbon source
3054217754glycerol+carbon source
3054228087glycogen+carbon source
3054217306maltose+carbon source
3054237684mannose+carbon source
3054216634raffinose+carbon source
3054217814salicin+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
17687SoilKanegawa, Kawasaki, botanical gardenJapanJPNAsia
67770Wet soil from a botanical gardenKawasaki, Kanagawa Pref.JapanJPNAsia

isolation source categories

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

taxonmaps

  • @ref: 69479
  • File name: preview.99_28581.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_9;96_432;97_1685;98_4020;99_28581&stattab=map
  • Last taxonomy: Cellulomonas
  • 16S sequence: AB602498
  • Sequence Identity:
  • Total samples: 229
  • soil counts: 147
  • aquatic counts: 24
  • animal counts: 39
  • plant counts: 19

Safety information

risk assessment

  • @ref: 17687
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 17687
  • description: Cellulomonas soli gene for 16S ribosomal RNA, partial sequence
  • accession: AB602498
  • length: 1446
  • database: nuccore
  • NCBI tax ID: 931535

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Cellulomonas soli NBRC 109434GCA_007992535contigncbi931535
66792Cellulomonas soli strain DSM 24484931535.4wgspatric931535
66792Cellulomonas soli strain NBRC 109434931535.3wgspatric931535
66792Cellulomonas soli DSM 244842831319000draftimg931535
67770Cellulomonas soli DSM 24484GCA_013409305contigncbi931535

GC content

@refGC-contentmethod
1768773.6high performance liquid chromatography (HPLC)
3054273.6

Genome-based predictions

predictions

@refmodeltraitdescriptionpredictionconfidencetraining_data
125438gram-positivegram-positivePositive reaction to Gram-stainingyes84.589yes
125438anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)no94.079yes
125438aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)yes64.836no
125438spore-formingspore-formingAbility to form endo- or exosporesno62.417no
125438thermophilethermophilicAbility to grow at temperatures above or equal to 45°Cno96yes
125438motile2+flagellatedAbility to perform flagellated movementno60.996no
125439BacteriaNetspore_formationAbility to form endo- or exosporesyes65.9
125439BacteriaNetmotilityAbility to perform movementno79.8
125439BacteriaNetgram_stainReaction to gram-stainingpositive99.9
125439BacteriaNetoxygen_toleranceOxygenic conditions needed for growthobligate aerobe99.7

External links

@ref: 17687

culture collection no.: DSM 24484, JCM 17535, NBRC 109434

straininfo link

  • @ref: 71932
  • straininfo: 405946

literature

  • topic: Phylogeny
  • Pubmed-ID: 22328604
  • title: Cellulomonas soli sp. nov. and Cellulomonas oligotrophica sp. nov., isolated from soil.
  • authors: Hatayama K, Esaki K, Ide T
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.038364-0
  • year: 2012
  • mesh: Bacterial 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/analysis
  • topic2: Genetics

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmedjournal
17687Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 24484)https://www.dsmz.de/collection/catalogue/details/culture/DSM-24484
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)
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
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
71932Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID405946.1StrainInfo: A central database for resolving microbial strain identifiers
125438Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg Overmann10.1101/2024.08.12.607695Predicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets
125439Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardyhttps://github.com/GenomeNet/deepGdeepG: Deep Learning for Genome Sequence Data. R package version 0.3.1