Strain identifier

BacDive ID: 11163

Type strain: Yes

Species: Thermasporomyces composti

Strain Designation: I3

Strain history: S. Yabe I3.

NCBI tax ID(s): 696763 (species)

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General

@ref: 16606

BacDive-ID: 11163

DSM-Number: 22891

keywords: genome sequence, 16S sequence, Bacteria, aerobe, thermophilic, Gram-positive

description: Thermasporomyces composti I3 is an aerobe, thermophilic, Gram-positive bacterium that was isolated from mature compost.

NCBI tax id

  • NCBI tax id: 696763
  • Matching level: species

strain history

@refhistory
16606<- S. Yabe; Hazaka Plant Research Center, Miyagi, Japan; I3
67770S. Yabe I3.

doi: 10.13145/bacdive11163.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Propionibacteriales
  • family: Actinopolymorphaceae
  • genus: Thermasporomyces
  • species: Thermasporomyces composti
  • full scientific name: Thermasporomyces composti Yabe et al. 2011

@ref: 16606

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Actinopolymorphaceae

genus: Thermasporomyces

species: Thermasporomyces composti

full scientific name: Thermasporomyces composti Yabe et al. 2011

strain designation: I3

type strain: yes

Morphology

cell morphology

@refgram stainmotilityconfidence
29817positive
69480no93.866
69480positive100

colony morphology

@refcolony colorincubation periodmedium used
21369Light ivory (1015)10-14 daysISP 2
21369Traffic yellow (1023)10-14 daysISP 3
21369Oyster white (1013)10-14 daysISP 4
21369Oyster white (1013)10-14 daysISP 5
2136910-14 daysISP 7
21369Light ivory (1015)10-14 dayssuter with tyrosine
21369Light ivory (1015)10-14 dayssuter without tyrosine

multicellular morphology

@refforms multicellular complexmedium name
21369noISP 2
21369noISP 3
21369noISP 4
21369noISP 5
21369noISP 7
21369noSuter with tyrosine
21369noSuter without tyrosine

multimedia

  • @ref: 16606
  • multimedia content: https://www.dsmz.de/microorganisms/photos/DSM_22891.jpg
  • caption: Medium 65 50°C
  • intellectual property rights: © Leibniz-Institut DSMZ

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
16606GYM STREPTOMYCES MEDIUM (DSMZ Medium 65)yeshttps://mediadive.dsmz.de/medium/65Name: GYM STREPTOMYCES MEDIUM (DSMZ Medium 65) Composition: Agar 18.0 g/l Malt extract 10.0 g/l Yeast extract 4.0 g/l Glucose 4.0 g/l CaCO3 2.0 g/l Distilled water
21369ISP 2yesName: ISP 2 / Yeast Malt Agar (5265); 5265 Composition Malt extract 10.0 g/l Yeast extract 4.0 g/l Glucose 4.0 g/l Agar 15.0 g/l Preparation: Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.0 Usage: Maintenance and Taxonomy Organisms: All Actinomycetes
21369ISP 3yesName: ISP 3; 5315 Composition Dog oat flakes 20.0 g/l Trace element solution (5314) 2.5 ml/l Agar 18.0 g/l Preparation: Oat flakes are cooked for 20 minutes, trace element solution and agar are added (in the case of non rolled oat flakes the suspension has to bee filtrated). Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.8 Usage: Maintenance and taxonomy (e.g. SEM As liquid medium for metabolite production) Organisms: All Actinomycetes Trace element solution 5314 Name: Trace element solution 5314; 5314 Composition CaCl2 x H2O 3.0 g/l Fe-III-citrate 1.0 g/l MnSO4 0.2 g/l ZnCl2 0.1 g/l CuSO4 x 5 H2O 0.025 g/l Sodium tetra borate 0.2 g/l CoCl2 x 6 H2O 0.004 g/l Sodium molybdate 0.01 g/l Preparation: Use double destillated water. Sterilisation: 20 minutes at 121°C pH before sterilisation: Usage: Trace element solution for different media Organisms:
21369ISP 4yesName: ISP 4; DSM 547 Solution I: Difco soluble starch, 10.0 g. Make a paste of the starch with a small amount of cold distilled water and bring to a volume of 500 ml. Solution II: CaCO3 2.0 g K2HPO4 (anhydrous) 1.0 g MgSO4 x 7 H2O 1.0 g NaCl 1.0 g (NH4)2SO4 2.0 g Distilled water 500.0 ml Trace salt solution (see below) 1.0 ml The pH should be between 7.0 and 7.4. Do not adjust if it is within this range. Mix solutions I and II together. Add 20.0 g agar. Liquify agar by steaming at 100°C for 10 to 20 min. Trace element solution: FeSO4 x 7 H2O 0.1 g MnCl2 x 4 H2O 0.1 g ZnSO4 x 7 H2O 0.1 g Distilled water 100.0 ml
21369ISP 5yesName: ISP 5 (5323) Composition L-Asparagine 1.0 g/l Glycerol 10.0 g/l K2HPO4 1.0 g/l Salt solution (see preparation) 1.0 ml/l Agar 20.0 g/l Preparation: Salt solution 1.0 g FeSO4 x 7 H2O 1.0 g MnCl2 x 4 H2O 1.0 g ZNSO4 x 7 H2O in 100 ml water Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.2 Usage: Maintenance and taxonomy Organisms: All Actinomycetes
21369ISP 7yesName: ISP 7 (5322) Composition Glycerol 15.0 g/l L-Tyrosine 0.5 g/l L-Asparagine 1.0 g/l K2HPO4 0.5 g/l NaCl 0.5 g/l FeSO4 x 7 H2O 0.01 g/l Trace element solution 5343 1.0 ml/l Agar 20.0 Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.3 Usage: Production of melanoid pigments Organisms: All Actinomycetes
21369suter with tyrosineyesName: Synthetically suter medium (5337) with and without tyrosine - see Kutzner,H.J., R. M. Kroppensted and F. Korn-Wendisch. (1986) Composition: Glycerol 15.0 g/l Tyrosine 1.0 (optional, see preparation comment) L-arginine 5.0 g/l L-glutamic acid 5.0 g/l L-methionine 0.3 g/l L-isoleucine 0.3 g/l K2HPO4 0.5 g/l MgSO4 x 7 H2O 0.2 g/l Agar 20.0 g/l Trace element solution (5341) 1.0 ml Composition of Trace element solution (5341): CuSO4 x 5 H2O 10.0 g/l CaCl2 x 2 H2O 10.0 g/l FeSO4 x 7 H2O 10.0 g/l ZnSO4 x 7 H2O 10.0 g/l MnSO4 x 7 H2O 40.0 g/l Preparation: Control medium is prepared without tyrosine Sterilisation: 20 minutes at 121°C pH before sterilisation: Usage: Production of melanoid pigment Organisms: All Actinomycetes
21369suter without tyrosineyesName: Synthetically suter medium (5337) with and without tyrosine - see Kutzner,H.J., R. M. Kroppensted and F. Korn-Wendisch. (1986) Composition: Glycerol 15.0 g/l Tyrosine 1.0 (optional, see preparation comment) L-arginine 5.0 g/l L-glutamic acid 5.0 g/l L-methionine 0.3 g/l L-isoleucine 0.3 g/l K2HPO4 0.5 g/l MgSO4 x 7 H2O 0.2 g/l Agar 20.0 g/l Trace element solution (5341) 1.0 ml Composition of Trace element solution (5341): CuSO4 x 5 H2O 10.0 g/l CaCl2 x 2 H2O 10.0 g/l FeSO4 x 7 H2O 10.0 g/l ZnSO4 x 7 H2O 10.0 g/l MnSO4 x 7 H2O 40.0 g/l Preparation: Control medium is prepared without tyrosine Sterilisation: 20 minutes at 121°C pH before sterilisation: Usage: Production of melanoid pigment Organisms: All Actinomycetes

culture temp

@refgrowthtypetemperaturerange
16606positivegrowth50thermophilic
29817positivegrowth35-62
29817positiveoptimum52.5thermophilic
67770positivegrowth50thermophilic

culture pH

@refabilitytypepHPH range
29817positivegrowth5.7-10.0alkaliphile
29817positiveoptimum7

Physiology and metabolism

oxygen tolerance

  • @ref: 29817
  • oxygen tolerance: aerobe

spore formation

  • @ref: 29817
  • spore formation: no

halophily

@refsaltgrowthtested relationconcentration
21369NaClpositivegrowth0 %
29817NaClpositivegrowth0-5 %

observation

  • @ref: 67770
  • observation: quinones: MK-9(H4), MK-10(H4), MK-11(H4)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2136917234glucose+
2136922599arabinose+
2136917992sucrose+
2136918222xylose+
2136917268myo-inositol+
2136937684mannose+
2136928757fructose+
2136926546rhamnose+
2136916634raffinose+
2136962968cellulose+
2981722599arabinose+carbon source
2981717057cellobiose+carbon source
2981717716lactose+carbon source
2981716634raffinose+carbon source
2981730911sorbitol+carbon source
2981717632nitrate+reduction
6837917632nitrate-reduction
683794853esculin-hydrolysis
6837916199urea-hydrolysis
683795291gelatin+hydrolysis
6837917634D-glucose-fermentation
6837916988D-ribose-fermentation
6837965327D-xylose-fermentation
6837916899D-mannitol-fermentation
6837917306maltose-fermentation
6837917716lactose-fermentation
6837917992sucrose-fermentation

enzymes

@refvalueactivityec
29817alkaline phosphatase+3.1.3.1
29817alpha-galactosidase+3.2.1.22
29817catalase+1.11.1.6
29817gelatinase+
29817cytochrome oxidase+1.9.3.1
68379gelatinase+
68379urease-3.5.1.5
68379beta-glucosidase-3.2.1.21
68379N-acetyl-beta-glucosaminidase+3.2.1.52
68379alpha-glucosidase+3.2.1.20
68379beta-glucuronidase-3.2.1.31
68379alkaline phosphatase+3.1.3.1
68379pyrrolidonyl arylamidase-3.4.19.3
68379pyrazinamidase-3.5.1.B15
68382alkaline phosphatase+3.1.3.1
68382lipase (C 14)-
68382leucine arylamidase+3.4.11.1
68382valine arylamidase+
68382cystine arylamidase+3.4.11.3
68382alpha-chymotrypsin-3.4.21.1
68382naphthol-AS-BI-phosphohydrolase+
68382alpha-galactosidase+3.2.1.22
68382beta-galactosidase+3.2.1.23
68382beta-glucuronidase-3.2.1.31
68382alpha-glucosidase+3.2.1.20
68382beta-glucosidase-3.2.1.21
68382N-acetyl-beta-glucosaminidase+3.2.1.52
68382alpha-mannosidase+3.2.1.24
68382alpha-fucosidase-3.2.1.51

API coryne

@refNITPYZPYRAPALbeta GURbeta GALalpha GLUbeta NAGESCUREGELGLURIBXYLMANMALLACSACGLYG
21369---+-+/-++--+-------+/-

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
21369++/-+/--++++/--+/-+++-+-++-

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinent
16606mature compostJapanJPNAsia
67770Mature compost produced by a field-scale composterJapanJPNAsia

isolation source categories

  • Cat1: #Engineered
  • Cat2: #Biodegradation
  • Cat3: #Composting

Safety information

risk assessment

  • @ref: 16606
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 16606
  • description: Thermasporomyces composti gene for 16S rRNA gene, partial sequence
  • accession: AB535715
  • length: 1447
  • database: ena
  • NCBI tax ID: 696763

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Thermasporomyces composti strain DSM 22891696763.3wgspatric696763
66792Thermasporomyces composti DSM 228912778260933draftimg696763
67770Thermasporomyces composti DSM 22891GCA_003386795contigncbi696763

GC content

@refGC-contentmethod
1660669.2high performance liquid chromatography (HPLC)
2981769.2

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno82no
gram-positiveyes88.048no
anaerobicno97.982yes
halophileno88.571yes
spore-formingno68.352yes
glucose-utilyes85.635yes
thermophileyes67.757yes
flagellatedno98.694no
aerobicyes87.293no
glucose-fermentno89.738yes
motileno89.437no

External links

@ref: 16606

culture collection no.: DSM 22891, JCM 16421

straininfo link

  • @ref: 80412
  • straininfo: 405916

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny20154327Thermasporomyces composti gen. nov., sp. nov., a thermophilic actinomycete isolated from compost.Yabe S, Aiba Y, Sakai Y, Hazaka M, Yokota AInt J Syst Evol Microbiol10.1099/ijs.0.021741-02010Actinomycetales/*classification/genetics/*isolation & purification/physiology, Base Composition, Cell Wall/chemistry, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Diaminopimelic Acid/analysis, Fatty Acids/analysis, Hydrogen-Ion Concentration, Molecular Sequence Data, Phospholipids/analysis, Phylogeny, Quinones/analysis, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil, *Soil Microbiology, TemperatureGenetics
Enzymology33038404Biochemical characterization of a thermophilic hyaluronate lyase TcHly8C from Thermasporomyces composti DSM22891.Li Y, Zhang S, Wu H, Wang X, Yu W, Han FInt J Biol Macromol10.1016/j.ijbiomac.2020.10.0112020Actinobacteria/*enzymology/genetics, Enzyme Stability/genetics, Escherichia coli/genetics, Hot Temperature/adverse effects, Hyaluronic Acid/chemistry, Oligosaccharides/biosynthesis/*chemistry/genetics, Polysaccharide-Lyases/chemistry/*genetics/isolation & purification, Substrate SpecificityStress
Enzymology33561520Expression and characterization of a thermotolerant and pH-stable hyaluronate lyase from Thermasporomyces composti DSM22891.Wang X, Zhang S, Wu H, Li Y, Yu W, Han FProtein Expr Purif10.1016/j.pep.2021.1058402021*Actinobacteria/enzymology/genetics, *Bacterial Proteins/biosynthesis/chemistry/genetics/isolation & purification, Enzyme Stability, Escherichia coli/genetics/metabolism, Hot Temperature, Hydrogen-Ion Concentration, *Polysaccharide-Lyases/biosynthesis/chemistry/genetics/isolation & purification, Recombinant Proteins/biosynthesis/chemistry/genetics/isolation & purificationPhylogeny

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmedjournal
16606Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 22891)https://www.dsmz.de/collection/catalogue/details/culture/DSM-22891
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
21369Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM22891.pdfCompendium of Actinobacteria. HZI-Helmholtz-Centre for Infection Research, Braunschweig
29817Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2619428776041
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/
68379Automatically annotated from API Coryne
68382Automatically annotated from API zym
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)
80412Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID405916.1StrainInfo: A central database for resolving microbial strain identifiers