Strain identifier

BacDive ID: 16057

Type strain: Yes

Species: Streptomyces toxytricini

Strain history: KCC S-0421 <-- IFO 12823 <-- SAJ <-- ISP 5178 <-- T. P. Preobrazhenskaya INA 13887/54.

NCBI tax ID(s): 67369 (species)

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General

@ref: 9371

BacDive-ID: 16057

DSM-Number: 40178

keywords: genome sequence, 16S sequence, Bacteria, spore-forming, mesophilic

description: Streptomyces toxytricini DSM 40178 is a spore-forming, mesophilic bacterium that builds an aerial mycelium and was isolated from soil.

NCBI tax id

  • NCBI tax id: 67369
  • Matching level: species

strain history

@refhistory
9371<- E.B. Shirling, ISP <- T.P. Preobrazhenskaya, INA
67770KCC S-0421 <-- IFO 12823 <-- SAJ <-- ISP 5178 <-- T. P. Preobrazhenskaya INA 13887/54.

doi: 10.13145/bacdive16057.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Kitasatosporales
  • family: Streptomycetaceae
  • genus: Streptomyces
  • species: Streptomyces toxytricini
  • full scientific name: Streptomyces toxytricini (Preobrazhenskaya and Sveshnikova 1957) Pridham et al. 1958 (Approved Lists 1980)

  • synonyms

    • @ref: 20215
    • synonym: Actinomyces toxytricini

@ref: 9371

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Streptomycetaceae

genus: Streptomyces

species: Streptomyces toxytricini

full scientific name: Streptomyces toxytricini (Preobrazhenskaya and Sveshnikova 1957) Pridham et al. 1958

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram stain
69480no93.958
69480100positive

colony morphology

@refcolony colormedium used
69250Beige (1001), brown beige (1011)ISP 3
69250Beige (1001)suter without tyrosine
69250Grey brown (8019), brown beige (1011)suter with tyrosine
69250Light ivory (1015)ISP 2
69250Light ivory (1015)ISP 4
69250Light ivory (1015)ISP 7
69250Oyster white (1013)ISP 5
69250Pale brown (8025), brown beige (1011)ISP 6

multicellular morphology

@refforms multicellular complexcomplex namecomplex colormedium name
69250yesAerial myceliumSignal white (9001), beige red (3012), signal brown (8002)ISP 2
69250yesAerial myceliumCream (9001), beige red (3012)ISP 3
69250yesAerial myceliumSignal white (9001), beige red (3012), signal brown (8002)ISP 4
69250yesAerial myceliumCream (9001)ISP 5
69250noAerial myceliumISP 6
69250yesAerial myceliumSignal white (9001), beige red (3012)ISP 7
69250noAerial myceliumsuter with tyrosine
69250noAerial myceliumsuter without tyrosine

pigmentation

@refproductionnamecolor
69250yesMelanin
69250yessoluble pigmentOlive brown (8008), mahogany brown (8016)

multimedia

@refmultimedia contentcaptionintellectual property rights
9371https://www.dsmz.de/microorganisms/photos/DSM_40178.jpgMedium 65 28°C© Leibniz-Institut DSMZ
69250DSM_40178_image5.jpeg(ISP6, ISP7)Helmholtz-Zentrum für Infektionsforschung GmbH
69250DSM_40178_image6.jpeg(ISP6, ISP7)Helmholtz-Zentrum für Infektionsforschung GmbH

Culture and growth conditions

culture medium

  • @ref: 9371
  • name: GYM STREPTOMYCES MEDIUM (DSMZ Medium 65)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/65
  • composition: Name: 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

culture temp

@refgrowthtypetemperaturerange
9371positivegrowth28mesophilic
67770positivegrowth28mesophilic

Physiology and metabolism

spore formation

@refspore formationconfidence
69481yes100
69480yes100

halophily

  • @ref: 69250
  • salt: NaCl
  • growth: positive
  • tested relation: growth
  • concentration: 0-7.5 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
6925022599arabinose-growth
6925062968cellulose-growth
6925028757fructose-growth
6925017234glucose+growth
6925017268inositol-growth
6925037684mannose-growth
6925016634raffinose-growth
6925026546rhamnose-growth
6925017992sucrose-growth
6925018222xylose-growth
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
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-galactosidase-3.2.1.23
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
68382esterase (C 4)+
68382esterase lipase (C 8)+
68382leucine arylamidase+3.4.11.1
68382valine arylamidase+
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 coryne

@refNITPYZPYRAPALbeta GURbeta GALalpha GLUbeta NAGESCUREGELGLURIBXYLMANMALLACSAC
69250---+------+-------

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
69250++++/-+++/-++++------+-

Isolation, sampling and environmental information

isolation

@refsample typecountrycontinentgeographic location
9371soilUSSRAsia
67770SoilUSSRKazakh

isolation source categories

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

taxonmaps

  • @ref: 69479
  • File name: preview.99_1810.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_15;96_102;97_109;98_144;99_1810&stattab=map
  • Last taxonomy: Streptomyces
  • 16S sequence: AB184173
  • Sequence Identity:
  • Total samples: 6072
  • soil counts: 4236
  • aquatic counts: 230
  • animal counts: 299
  • plant counts: 1307

Safety information

risk assessment

  • @ref: 9371
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Streptomyces toxytricini gene for 16S rRNA, partial sequenceAB122736564ena67369
20218Streptomyces toxytricini gene for 16S ribosomal RNA, partial sequence, strain: JCM 4421D44133120ena67369
20218Streptomyces toxytricini gene for 16S rRNA, partial sequence, strain: NBRC 12823AB1841731475ena67369
20218Streptomyces toxytricini strain NRRL B-5426T 16S ribosomal RNA gene, partial sequenceDQ4425481484ena67369

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Streptomyces toxytricini JCM 4421GCA_014649915scaffoldncbi67369
66792Streptomyces toxytricini strain JCM 442167369.7wgspatric67369

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes100no
flagellatedno97.655no
gram-positiveyes85.155no
anaerobicno99.105no
aerobicyes90.388no
halophileno96.086no
spore-formingyes94.29no
glucose-utilyes88.793yes
thermophileno98.137no
motileno94.459no
glucose-fermentno89.683yes

External links

@ref: 9371

culture collection no.: DSM 40178, ATCC 19813, CBS 566.68, IFO 12823, INA 13887/54, ISP 5178, KCC S-0421, NBRC 12823, RIA 1093, JCM 4421, BCRC 13472, CGMCC 4.1734, CGMCC 4.1804, NCAIM B.01883, NCAIM B.02267, NCIMB 9847, NRRL B-5426, VKM Ac-1279, CCRC 13472, NCIB 9847, NRRL-ISP 5178, UNIQEM 200

straininfo link

  • @ref: 85130
  • straininfo: 389328

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny24664662Streptomyces amritsarensis sp. nov., exhibiting broad-spectrum antimicrobial activity.Sharma D, Mayilraj S, Manhas RKAntonie Van Leeuwenhoek10.1007/s10482-014-0151-22014Anti-Infective Agents/*metabolism, Bacterial Typing Techniques, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fungi/drug effects, Gram-Negative Bacteria/drug effects, Gram-Positive Bacteria/drug effects, India, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Soil Microbiology, Streptomyces/*classification/genetics/*isolation & purification/metabolismPathogenicity
Phylogeny26703868Streptomyces yangpuensis sp. nov., isolated from soil.Tang B, Yu Y, Zhi X, Yang L, Cen X, Zhao G, Ding XInt J Syst Evol Microbiol10.1099/ijsem.0.0008612015

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
9371Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 40178)https://www.dsmz.de/collection/catalogue/details/culture/DSM-40178
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
20218Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.10.1016/j.syapm.2013.11.002StrainInfo introduces electronic passports for microorganisms.Syst Appl Microbiol. 37: 42-50 201424321274
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
69250Wink, J.https://cdn.dsmz.de/wink/DSM%2040178.pdfCompendium of Actinobacteria. HZI-Helmholtz-Centre for Infection Research, Braunschweig
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
85130Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID389328.1StrainInfo: A central database for resolving microbial strain identifiers