Strain identifier

BacDive ID: 2371

Type strain: Yes

Species: Cellulomonas composti

Strain Designation: TR7-06

Strain history: <- ST Lee, KAIST

NCBI tax ID(s): 1305857 (strain), 266130 (species)

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General

@ref: 17943

BacDive-ID: 2371

DSM-Number: 25222

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

description: Cellulomonas composti TR7-06 is an aerobe, mesophilic, Gram-positive bacterium that was isolated from compost from a cattle farm.

NCBI tax id

NCBI tax idMatching level
266130species
1305857strain

strain history

@refhistory
17943<- KCTC <- S.-T. Lee, KAIST; TR7-06
67770NBRC 100758 <-- S.-T. Lee TR7-06.
67771<- ST Lee, KAIST

doi: 10.13145/bacdive2371.20230509.8.1

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 composti
  • full scientific name: Cellulomonas composti Kang et al. 2007

@ref: 17943

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Cellulomonadaceae

genus: Cellulomonas

species: Cellulomonas composti

full scientific name: Cellulomonas composti Kang et al. 2007

strain designation: TR7-06

type strain: yes

Morphology

cell morphology

@refgram staincell shapemotilityconfidence
31943positiverod-shapedno
67771positive
69480positive99.155

pigmentation

  • @ref: 31943
  • production: yes

Culture and growth conditions

culture medium

  • @ref: 17943
  • 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
17943positivegrowth28mesophilic
31943positiveoptimum30mesophilic
67770positivegrowth28mesophilic
67771positivegrowth30mesophilic

culture pH

  • @ref: 31943
  • ability: positive
  • type: optimum
  • pH: 6.8-7.5

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
31943aerobe
67771aerobe

spore formation

@refspore formationconfidence
69481no98
69480no99.993

halophily

@refsaltgrowthtested relationconcentration
31943NaClpositivegrowth01-10 %
31943NaClpositiveoptimum5.5 %

observation

@refobservation
67770quinones: MK-9(H4)
67771quinones: MK-9(H4)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
319435291gelatin+carbon source
3194317234glucose+carbon source
3194317306maltose+carbon source
3194317992sucrose+carbon source
3194318222xylose+carbon source
319434853esculin+hydrolysis
3194317632nitrate+reduction

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
17943compost from a cattle farmnear DaejeonRepublic of KoreaKORAsia
67770Compost from a cattle farm near DaejeonRepublic of KoreaKORAsia
67771Compost from a cattle farm near DaejeonRepublic of KoreaKORAsia

isolation source categories

Cat1Cat2Cat3
#Engineered#Agriculture#Livestock (Husbandry)
#Engineered#Biodegradation#Composting
#Host#Mammals#Bovinae (Cow, Cattle)

taxonmaps

  • @ref: 69479
  • File name: preview.99_58553.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_9;96_432;97_4150;98_5311;99_58553&stattab=map
  • Last taxonomy: Cellulomonas composti
  • 16S sequence: AB166887
  • Sequence Identity:
  • Total samples: 7
  • soil counts: 6
  • animal counts: 1

Safety information

risk assessment

  • @ref: 17943
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 17943
  • description: Cellulomonas composti gene for 16S rRNA, partial sequence
  • accession: AB166887
  • length: 1453
  • database: ena
  • NCBI tax ID: 266130

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Cellulomonas composti JCM 14898GCA_001314045contigncbi1305857
66792Cellulomonas composti JCM 148981305857.3wgspatric1305857
66792Cellulomonas composti strain NBRC 100758266130.4wgspatric266130
66792Cellulomonas composti JCM 148982734481969draftimg1305857
67770Cellulomonas composti NBRC 100758GCA_007990245contigncbi266130

GC content

@refGC-contentmethod
1794373.7high performance liquid chromatography (HPLC)
3194373.7

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno98no
motileno85.382no
gram-positiveyes84.773no
anaerobicno88.275no
halophileno87.44yes
spore-formingno93.08no
thermophileno97.205no
glucose-utilyes89.115yes
aerobicyes64.797yes
flagellatedno95.765yes
glucose-fermentyes55.533no

External links

@ref: 17943

culture collection no.: DSM 25222, JCM 14898, KCTC 19030, NBRC 100758

straininfo link

  • @ref: 71926
  • straininfo: 232296

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny17551039Cellulomonas composti sp. nov., a cellulolytic bacterium isolated from cattle farm compost.Kang MS, Im WT, Jung HM, Kim MK, Goodfellow M, Kim KK, Yang HC, An DS, Lee STInt J Syst Evol Microbiol10.1099/ijs.0.63974-02007Aerobiosis, Anaerobiosis, Animals, Bacterial Typing Techniques, Carbohydrates/analysis, Cattle, Cell Wall/chemistry, Cellulase/analysis, Cellulomonas/chemistry/*classification/*isolation & purification/physiology, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Genes, rRNA, Korea, Lipids/analysis, Locomotion, Molecular Sequence Data, Nucleic Acid Hybridization, Peptidoglycan/analysis, Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sequence Homology, Nucleic Acid, *Soil Microbiology, Vitamin K 2/analysis, beta-Glucosidase/analysisGenetics
Phylogeny20729313Cellulomonas phragmiteti sp. nov., a cellulolytic bacterium isolated from reed (Phragmites australis) periphyton in a shallow soda pond.Rusznyak A, Toth EM, Schumann P, Sproer C, Makk J, Szabo G, Vladar P, Marialigeti K, Borsodi AKInt J Syst Evol Microbiol10.1099/ijs.0.022608-02010Bacterial Typing Techniques, Base Composition, Cellulomonas/*classification/genetics/isolation & purification, DNA, Bacterial/genetics, Fatty Acids/chemistry, Hungary, Molecular Sequence Data, Nucleic Acid Hybridization, Peptidoglycan/chemistry, *Phylogeny, Poaceae/*microbiology, Ponds, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/chemistryGenetics
Phylogeny31218500Cellulomonas aurantiaca sp. nov., isolated from a soil sample from a tangerine field.Kim SK, Kook M, Yan ZF, Trinh H, Zheng SD, Yang JE, Park SY, Yi THAntonie Van Leeuwenhoek10.1007/s10482-019-01288-22019Cellulomonas/*classification/genetics/*isolation & purification, *Citrus, Genome, Bacterial, Genomics/methods, Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Soil, *Soil MicrobiologyGenetics
Phylogeny32877326Cellulomonas citrea sp. nov., isolated from paddy soil.Lee HJ, Kim SY, Whang KSInt J Syst Evol Microbiol10.1099/ijsem.0.0044092020Bacterial Typing Techniques, Base Composition, Cellulomonas/*classification/isolation & purification, DNA, Bacterial/genetics, Fatty Acids/chemistry, Nucleic Acid Hybridization, *Oryza, *Phylogeny, Pigmentation, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, *Soil Microbiology, Vitamin K 2/analogs & derivatives/chemistryTranscriptome

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmedjournal
17943Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 25222)https://www.dsmz.de/collection/catalogue/details/culture/DSM-25222
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
31943Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2819928776041
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/
67771Curators of the KCTChttps://kctc.kribb.re.kr/En/Kctc
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)
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
71926Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID232296.1StrainInfo: A central database for resolving microbial strain identifiers