Strain identifier

BacDive ID: 6297

Type strain: Yes

Species: Tetrasphaera japonica

Strain Designation: T1-X7

Strain history: IAM 14891 <-- DSM 13192 <-- P. Schumann <-- A. M. Maszenan <-- Y. Tokiwa T1-X7.

NCBI tax ID(s): 99481 (species)

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General

@ref: 4861

BacDive-ID: 6297

DSM-Number: 13192

keywords: genome sequence, 16S sequence, Bacteria, mesophilic

description: Tetrasphaera japonica T1-X7 is a mesophilic bacterium that was isolated from activated sludge.

NCBI tax id

  • NCBI tax id: 99481
  • Matching level: species

strain history

@refhistory
4861<- P. Schumann <- A.M. Maszenan <- Y. Tokiwa; T1-X7
67770IAM 14891 <-- DSM 13192 <-- P. Schumann <-- A. M. Maszenan <-- Y. Tokiwa T1-X7.

doi: 10.13145/bacdive6297.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Micrococcales
  • family: Intrasporangiaceae
  • genus: Tetrasphaera
  • species: Tetrasphaera japonica
  • full scientific name: Tetrasphaera japonica Maszenan et al. 2000

@ref: 4861

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Intrasporangiaceae

genus: Tetrasphaera

species: Tetrasphaera japonica

full scientific name: Tetrasphaera japonica Maszenan et al. 2000

strain designation: T1-X7

type strain: yes

Morphology

colony morphology

@refcolony colorincubation periodmedium used
18374Beige (1001)10-14 daysISP 2
18374Beige (1001)10-14 daysISP 3
18374Beige (1001)10-14 daysISP 4
18374Beige (1001)10-14 daysISP 5
18374Beige (1001)10-14 daysISP 6
18374Beige (1001)10-14 daysISP 7

multicellular morphology

@refforms multicellular complexmedium name
18374noISP 2
18374noISP 3
18374noISP 4
18374noISP 5
18374noISP 6
18374noISP 7

multimedia

  • @ref: 4861
  • multimedia content: https://www.dsmz.de/microorganisms/photos/DSM_13192.jpg
  • caption: Medium 830 28°C
  • intellectual property rights: Leibniz-Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH

Culture and growth conditions

culture medium

@refnamegrowthcompositionlink
18374ISP 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
18374ISP 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:
18374ISP 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
18374ISP 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
18374ISP 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
18374ISP 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
4861R2A MEDIUM (DSMZ Medium 830)yeshttps://www.dsmz.de/microorganisms/medium/pdf/DSMZ_Medium830.pdf
4861TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535)yeshttps://www.dsmz.de/microorganisms/medium/pdf/DSMZ_Medium535.pdf

culture temp

@refgrowthtypetemperaturerange
18374positiveoptimum28mesophilic
67770positivegrowth28mesophilic
4861positivegrowth28mesophilic

Physiology and metabolism

murein

  • @ref: 4861
  • murein short key: A31
  • type: A1gamma m-Dpm-direct

observation

  • @ref: 67770
  • observation: quinones: MK-8(H4)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
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
6837928087glycogen-fermentation

enzymes

@refvalueactivityec
68382alpha-fucosidase-3.2.1.51
68382alpha-mannosidase-3.2.1.24
68382N-acetyl-beta-glucosaminidase-3.2.1.52
68382beta-glucosidase+3.2.1.21
68382alpha-glucosidase+3.2.1.20
68382beta-glucuronidase-3.2.1.31
68382beta-galactosidase+3.2.1.23
68382alpha-galactosidase-3.2.1.22
68382naphthol-AS-BI-phosphohydrolase+
68382acid phosphatase+3.1.3.2
68382alpha-chymotrypsin-3.4.21.1
68382trypsin+3.4.21.4
68382cystine arylamidase-3.4.11.3
68382valine arylamidase-
68382leucine arylamidase+3.4.11.1
68382lipase (C 14)-
68382esterase lipase (C 8)+
68382esterase (C 4)-
68382alkaline phosphatase+3.1.3.1
68379gelatinase-
68379urease-3.5.1.5
68379beta-glucosidase+3.2.1.21
68379N-acetyl-beta-glucosaminidase-3.2.1.52
68379beta-glucuronidase-3.2.1.31
68379alkaline phosphatase+3.1.3.1
68379pyrrolidonyl arylamidase-3.4.19.3
68379pyrazinamidase-3.5.1.B15

API coryne

@refNITPYZPYRAPALbeta GURbeta GALalpha GLUbeta NAGESCUREGELGLURIBXYLMANMALLACSACGLYG
18374---+-+/-+/--+--------+-

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
18374+-+-+--+-++-+-++---

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinent
4861activated sludgeJapanJPNAsia
67770Activated sludgeJapanJPNAsia

isolation source categories

  • Cat1: #Engineered
  • Cat2: #Waste
  • Cat3: #Activated sludge

taxonmaps

  • @ref: 69479
  • File name: preview.99_6897.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_9;96_1391;97_3482;98_5076;99_6897&stattab=map
  • Last taxonomy: Tetrasphaera japonica subclade
  • 16S sequence: AF125092
  • Sequence Identity:
  • Total samples: 1661
  • soil counts: 932
  • aquatic counts: 293
  • animal counts: 387
  • plant counts: 49

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
183741German classification
48611Risk group (German classification)

Sequence information

16S sequences

  • @ref: 4861
  • description: Tetrasphaera japonica strain T1-X7 16S ribosomal RNA gene, partial sequence
  • accession: AF125092
  • length: 1445
  • database: ena
  • NCBI tax ID: 99481

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Tetrasphaera japonica T1-X71194083.4wgspatric1194083
66792Tetrasphaera japonica T1-X72636416099draftimg1194083
67770Tetrasphaera japonica T1-X7GCA_001046855scaffoldncbi1194083

GC content

@refGC-contentmethod
486171high performance liquid chromatography (HPLC)
6777071.51genome sequence analysis

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
motileno94.331no
gram-positiveyes90.663no
anaerobicno98.266no
aerobicyes91.614no
halophileno92.413no
spore-formingno87.046no
glucose-utilyes89.208no
flagellatedno98.723no
thermophileno98.549no
glucose-fermentno89.692yes

External links

@ref: 4861

culture collection no.: DSM 13192, ACM 5116, IAM 14891, JCM 21381, KCTC 39583, NBRC 103088

straininfo link

  • @ref: 75772
  • straininfo: 49434

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny10758865Three isolates of novel polyphosphate-accumulating gram-positive cocci, obtained from activated sludge, belong to a new genus, Tetrasphaera gen. nov., and description of two new species, Tetrasphaera japonica sp. nov. and Tetrasphaera australiensis sp. nov.Maszenan AM, Seviour RJ, Patel BK, Schumann P, Burghardt J, Tokiwa Y, Stratton HMInt J Syst Evol Microbiol10.1099/00207713-50-2-5932000Actinomycetales/*classification/cytology/*isolation & purification/physiology, Base Composition, Culture Media, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Diaminopimelic Acid/analysis, Fatty Acids/analysis, Genes, rRNA, Molecular Sequence Data, Nucleic Acid Hybridization, Phenotype, Phylogeny, Polyphosphates/*metabolism, RNA, Ribosomal, 16S/genetics, Sewage/*microbiologyCultivation
Phylogeny18048719Tetrasphaera remsis sp. nov., isolated from the Regenerative Enclosed Life Support Module Simulator (REMS) air system.Osman S, Moissl C, Hosoya N, Briegel A, Mayilraj S, Satomi M, Venkateswaran KInt J Syst Evol Microbiol10.1099/ijs.0.65137-02007Actinomycetales/chemistry/*classification/genetics/*isolation & purification, *Air Microbiology, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Equipment and Supplies/*microbiology, Fatty Acids/analysis, Genes, rRNA, Microscopy, Electron, Transmission, Molecular Sequence Data, Nucleic Acid Hybridization, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sequence Homology, Nucleic AcidGenetics

Reference

@idauthorscataloguedoi/urltitle
4861Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 13192)https://www.dsmz.de/collection/catalogue/details/culture/DSM-13192
18374Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM13192.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
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/
68379Automatically annotated from API Coryne
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
75772Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID49434.1StrainInfo: A central database for resolving microbial strain identifiers