Strain identifier

BacDive ID: 17637

Type strain: Yes

Species: Catenulispora rubra

Strain Designation: Aac-30

Strain history: DSM 44948 <-- T. Tamura Aac-30 <-- T. Sakane.

NCBI tax ID(s): 280293 (species)

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General

@ref: 12112

BacDive-ID: 17637

DSM-Number: 44948

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

description: Catenulispora rubra Aac-30 is an aerobe, spore-forming, mesophilic bacterium that builds an aerial mycelium and was isolated from soil.

NCBI tax id

  • NCBI tax id: 280293
  • Matching level: species

strain history

@refhistory
12112<- NBRC <- T. Sakane; Aac-30
67770DSM 44948 <-- T. Tamura Aac-30 <-- T. Sakane.

doi: 10.13145/bacdive17637.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Catenulisporales
  • family: Catenulisporaceae
  • genus: Catenulispora
  • species: Catenulispora rubra
  • full scientific name: Catenulispora rubra Tamura et al. 2007

@ref: 12112

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Catenulisporaceae

genus: Catenulispora

species: Catenulispora rubra

full scientific name: Catenulispora rubra Tamura et al. 2007

strain designation: Aac-30

type strain: yes

Morphology

cell morphology

@refgram staincell widthcell shapemotilityconfidence
32161positive1.1 µmrod-shapedno
69480no93.871
69480positive100

colony morphology

@refcolony colorincubation periodmedium used
19893Yellow orange10-14 daysISP 2
19893Sun yellow10-14 daysISP 3
19893Cream10-14 daysISP 4
19893Yellow orange10-14 daysISP 5
19893Yellow orange10-14 daysISP 6
19893Yellow orange10-14 daysISP 7

multicellular morphology

@refforms multicellular complexmedium namecomplex namecomplex color
19893noISP 2
19893noISP 3
19893noISP 4
19893noISP 5
19893yesISP 6Aerial MyceliumCream
19893noISP 7

pigmentation

  • @ref: 32161
  • production: yes

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
12112YEAST STARCH AGAR (A) (DSMZ Medium 1027)yeshttps://mediadive.dsmz.de/medium/1027Name: YEAST STARCH AGAR (A) (DSMZ Medium 1027) Composition: Agar 15.0 g/l Starch 10.0 g/l Yeast extract 2.0 g/l Distilled water
19893ISP 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
19893ISP 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:
19893ISP 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
19893ISP 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
19893ISP 6yesName: ISP 6 (5318) Composition Peptone 15.0 g/l Proteose peptose 5.0 g/l Ferric ammonium citrate 0.5 g/l Sodium glycerophosphate 1.0 g/l Sodium thiosulfate 0.08 g/l Yeast extract 1.0 g/l Agar 15.0 g/l Sterilisation: 20 minutes at 121°C pH before sterilisation: Usage: Production of melanoid pigments Organisms: All Actinomycetes
19893ISP 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

culture temp

@refgrowthtypetemperaturerange
12112positivegrowth28mesophilic
32161positivegrowth20-30
32161positiveoptimum25mesophilic
67770positivegrowth28mesophilic

culture pH

@refabilitytypepHPH range
32161positivegrowth04-06acidophile
32161positiveoptimum5

Physiology and metabolism

oxygen tolerance

  • @ref: 32161
  • oxygen tolerance: aerobe

spore formation

@refspore formationconfidence
32161yes
69481yes97
69480yes99.999

observation

@refobservation
32161aggregates in chains
67770quinones: MK-9(H6), MK-9(H8)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
1989317234glucose+
1989322599arabinose-
1989317992sucrose+
1989318222xylose-
1989317268myo-inositol-
1989329864mannitol+
1989328757fructose+
1989326546rhamnose-
1989316634raffinose-
1989362968cellulose+
3216122599arabinose+carbon source
3216128757fructose+carbon source
3216117234glucose+carbon source
3216116634raffinose+carbon source
3216117992sucrose+carbon source
3216118222xylose+carbon source
321614853esculin+hydrolysis

enzymes

@refvalueactivityec
32161acid phosphatase+3.1.3.2
32161alkaline phosphatase+3.1.3.1
68382alkaline phosphatase+3.1.3.1
68382esterase (C 4)-
68382esterase lipase (C 8)+
68382lipase (C 14)-
68382leucine arylamidase+3.4.11.1
68382valine arylamidase+
68382cystine arylamidase-3.4.11.3
68382trypsin-3.4.21.4
68382alpha-chymotrypsin-3.4.21.1
68382acid phosphatase+3.1.3.2
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 zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
19893+-+-++---+----++---

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
12112soilOodate, AkitaJapanJPNAsia
67770Forest soilOodate, Akita Pref.JapanJPNAsia

isolation source categories

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

taxonmaps

  • @ref: 69479
  • File name: preview.99_6314.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_94;96_3004;97_3691;98_4676;99_6314&stattab=map
  • Last taxonomy: Catenulispora
  • 16S sequence: AB180773
  • Sequence Identity:
  • Total samples: 21098
  • soil counts: 16042
  • aquatic counts: 870
  • animal counts: 1233
  • plant counts: 2953

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
121121Risk group (German classification)
198931Risk group (German classification)

Sequence information

16S sequences

  • @ref: 12112
  • description: Catenulispora rubra gene for 16S rRNA, partial sequence
  • accession: AB180773
  • length: 1472
  • database: ena
  • NCBI tax ID: 280293

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Catenulispora rubra DSM 44948GCA_015356825contigncbi280293
66792Catenulispora rubra strain DSM 44948280293.3wgspatric280293

GC content

@refGC-contentmethod
1211269.1
6777069.1high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes97no
motileno93.974no
gram-positiveyes88.736no
anaerobicno99.462yes
halophileno94.257no
spore-formingyes93.566yes
glucose-utilyes86.692yes
flagellatedno98.09no
aerobicyes93.884no
thermophileno98.846yes
glucose-fermentno89.661no

External links

@ref: 12112

culture collection no.: DSM 44948, JCM 16000, NBRC 101179

straininfo link

  • @ref: 86629
  • straininfo: 297462

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny17911295Catenulispora rubra sp. nov., an acidophilic actinomycete isolated from forest soil.Tamura T, Ishida Y, Sakane T, Suzuki KIInt J Syst Evol Microbiol10.1099/ijs.0.65056-02007Actinomycetales/chemistry/*classification/genetics/*isolation & purification, Bacterial Typing Techniques, Base Composition, Cell Wall/chemistry, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Diaminopimelic Acid/analysis, Fatty Acids/analysis, Genes, rRNA, Glycine/analysis, Hydrogen-Ion Concentration, Molecular Sequence Data, Peptidoglycan/chemistry, Phylogeny, Quinones/analysis, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sequence Homology, Nucleic Acid, *Soil Microbiology, TreesGenetics
Phylogeny22199217Catenulispora graminis sp. nov., a rhizobacterium from bamboo (Phyllostachys nigro var. henonis) rhizosphere soil.Lee HJ, Han SI, Whang KSInt J Syst Evol Microbiol10.1099/ijs.0.035501-02011Actinomycetales/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Bambusa/*microbiology, DNA, Bacterial/genetics, Fatty Acids/analysis, Molecular Sequence Data, Nucleic Acid Hybridization, *Phylogeny, Quinones/analysis, RNA, Ribosomal, 16S/genetics, Republic of Korea, Rhizosphere, Sequence Analysis, DNA, *Soil MicrobiologyGenetics
Phylogeny26507964Catenulispora fulva sp. nov., isolated from forest soil.Lee HJ, Whang KSInt J Syst Evol Microbiol10.1099/ijsem.0.0007112015Actinomycetales/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, *Forests, Molecular Sequence Data, Nucleic Acid Hybridization, Peptidoglycan/chemistry, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, *Soil Microbiology, Vitamin K 2/analogs & derivatives/chemistryGenetics
Phylogeny33360072Genomic-based classification of Catenulispora pinisilvae sp. nov., novel actinobacteria isolated from a pine forest soil in Poland and emended description of Catenulispora rubra.Swiecimska M, Golinska P, Wypij M, Goodfellow MSyst Appl Microbiol10.1016/j.syapm.2020.1261642020Actinobacteria/*classification/isolation & purification, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, *Forests, Nucleic Acid Hybridization, Peptidoglycan/chemistry, *Phylogeny, Pinus, Poland, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil MicrobiologyTranscriptome

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
12112Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 44948)https://www.dsmz.de/collection/catalogue/details/culture/DSM-44948
19893Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM44948.pdfCompendium of Actinobacteria. HZI-Helmholtz-Centre for Infection Research, Braunschweig
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
32161Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2840428776041
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/
68382Automatically annotated from API zym
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
86629Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID297462.1StrainInfo: A central database for resolving microbial strain identifiers