Strain identifier

BacDive ID: 16733

Type strain: Yes

Species: Thermus composti

Strain Designation: K-39

Strain history: DSM 21686 <-- B. Vajna K-39.

NCBI tax ID(s): 532059 (species)

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General

@ref: 15886

BacDive-ID: 16733

DSM-Number: 21686

keywords: genome sequence, 16S sequence, Bacteria, aerobe, thermophilic, Gram-negative, rod-shaped

description: Thermus composti K-39 is an aerobe, thermophilic, Gram-negative bacterium that was isolated from oyster mushroom compost.

NCBI tax id

  • NCBI tax id: 532059
  • Matching level: species

strain history

@refhistory
15886<- B. Vajna, Eötvös Loránd Univ. Budapest, Hungary; K-39
67770DSM 21686 <-- B. Vajna K-39.

doi: 10.13145/bacdive16733.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/deinococcota
  • domain: Bacteria
  • phylum: Deinococcota
  • class: Deinococci
  • order: Thermales
  • family: Thermaceae
  • genus: Thermus
  • species: Thermus composti
  • full scientific name: Thermus composti Vajna et al. 2012

@ref: 15886

domain: Bacteria

phylum: Deinococcus-Thermus

class: Deinococci

order: Thermales

family: Thermaceae

genus: Thermus

species: Thermus composti

full scientific name: Thermus composti Vajna et al. 2012

strain designation: K-39

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
30212negative5 µm0.6 µmrod-shapedno
69480no91.47
69480negative99.739

pigmentation

  • @ref: 30212
  • production: yes

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
15886R2A MEDIUM (DSMZ Medium 830)yeshttps://mediadive.dsmz.de/medium/830Name: 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
15886NUTRIENT AGAR (DSMZ Medium 1)yeshttps://mediadive.dsmz.de/medium/1Name: NUTRIENT AGAR (DSMZ Medium 1) Composition: Agar 15.0 g/l Peptone 5.0 g/l Meat extract 3.0 g/l Distilled water

culture temp

@refgrowthtypetemperaturerangeconfidence
15886positivegrowth45thermophilic
30212positivegrowth40-80hyperthermophilic
30212positiveoptimum67.5thermophilic
67770positivegrowth70thermophilic
69480thermophilic100

culture pH

@refabilitytypepHPH range
30212positivegrowth05-09alkaliphile
30212positiveoptimum7

Physiology and metabolism

oxygen tolerance

  • @ref: 30212
  • oxygen tolerance: aerobe

spore formation

@refspore formationconfidence
69481no99
69480no99.845

halophily

  • @ref: 30212
  • salt: NaCl
  • growth: positive
  • tested relation: growth
  • concentration: 0.5-1.5 %

observation

  • @ref: 67770
  • observation: quinones: MK-8

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3021230089acetate+carbon source
3021228757fructose+carbon source
3021217234glucose+carbon source
3021217306maltose+carbon source
3021215361pyruvate+carbon source
3021227082trehalose+carbon source
302124853esculin+hydrolysis

enzymes

@refvalueactivityec
30212catalase+1.11.1.6
30212gelatinase+
30212cytochrome oxidase+1.9.3.1

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
15886oyster mushroom compostKecskemétHungaryHUNEurope
67770Thermophilic phase of the composting process for oyster mushroom substrate preparation

isolation source categories

Cat1Cat2Cat3
#Engineered#Biodegradation#Composting
#Host#Fungi#Mushroom
#Host#Invertebrates (Other)#Mollusca

taxonmaps

  • @ref: 69479
  • File name: preview.99_174645.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_87;96_2025;97_42262;98_67949;99_174645&stattab=map
  • Last taxonomy: Thermus composti subclade
  • 16S sequence: EU701067
  • Sequence Identity:
  • Total samples: 104
  • soil counts: 25
  • aquatic counts: 41
  • animal counts: 36
  • plant counts: 2

Safety information

risk assessment

  • @ref: 15886
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 15886
  • description: Thermus composti strain K-39 16S ribosomal RNA gene, partial sequence
  • accession: EU701067
  • length: 1445
  • database: ena
  • NCBI tax ID: 532059

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Thermus composti JCM 19902GCA_014647535contigncbi532059
66792Thermus composti strain JCM 19902532059.3wgspatric532059

GC content

@refGC-contentmethod
1588671.3high performance liquid chromatography (HPLC)
3021271.3

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno99no
gram-positiveno95.009yes
anaerobicno94.992yes
halophileno90.219yes
spore-formingno91.891no
glucose-utilyes84.373yes
thermophileyes100yes
motileno87.71yes
aerobicyes81.8yes
flagellatedno97.431yes
glucose-fermentno84.048no

External links

@ref: 15886

culture collection no.: DSM 21686, JCM 19902, NCAIM B 02340

straininfo link

  • @ref: 85751
  • straininfo: 403964

literature

  • topic: Phylogeny
  • Pubmed-ID: 21856987
  • title: Thermus composti sp. nov., isolated from oyster mushroom compost.
  • authors: Vajna B, Kanizsai S, Keki Z, Marialigeti K, Schumann P, Toth EM
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.030866-0
  • year: 2011
  • mesh: Bacterial Typing Techniques, Base Composition, Cluster Analysis, Culture Media/chemistry, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Hydrogen-Ion Concentration, Molecular Sequence Data, Phylogeny, *Pleurotus, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sodium Chloride/metabolism, *Soil Microbiology, Temperature, Thermus/*classification/genetics/*isolation & purification/physiology, Vitamin K 2/analysis
  • topic2: Genetics

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
15886Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 21686)https://www.dsmz.de/collection/catalogue/details/culture/DSM-21686
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
30212Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2655628776041
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)
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
85751Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID403964.1StrainInfo: A central database for resolving microbial strain identifiers