Strain identifier

BacDive ID: 15291

Type strain: Yes

Species: Streptomyces helvaticus

Strain history: KCC S-0768 <-- IFO 13382 <-- SAJ <-- ISP 5431 <-- INMI 1013-B.

NCBI tax ID(s): 68186 (species)

For citation purpose refer to the digital object identifier (doi) of the current version.
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General

@ref: 9539

BacDive-ID: 15291

DSM-Number: 40431

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

description: Streptomyces helvaticus DSM 40431 is a spore-forming, mesophilic bacterium that was isolated from Soil.

NCBI tax id

  • NCBI tax id: 68186
  • Matching level: species

strain history

@refhistory
9539<- E.B. Shirling, ISP <- N.A. Krassilnikov, INMI
67770KCC S-0768 <-- IFO 13382 <-- SAJ <-- ISP 5431 <-- INMI 1013-B.

doi: 10.13145/bacdive15291.20230509.8.1

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 helvaticus
  • full scientific name: Streptomyces helvaticus (Krassilnikov et al. 1965) Pridham 1970 (Approved Lists 1980)
  • synonyms

    • @ref: 20215
    • synonym: Actinomyces helvaticus

@ref: 9539

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Streptomycetaceae

genus: Streptomyces

species: Streptomyces helvaticus

full scientific name: Streptomyces helvaticus (Krassilnikov et al. 1965) Pridham 1970

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram stain
69480no92.637
69480100positive

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
9539GYM 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
9539ROLLED OATS MINERAL MEDIUM (DSMZ Medium 84)yeshttps://www.dsmz.de/microorganisms/medium/pdf/DSMZ_Medium84.pdf

culture temp

@refgrowthtypetemperaturerange
18590positiveoptimum28mesophilic
9539positivegrowth28mesophilic
67770positivegrowth28mesophilic

Physiology and metabolism

spore formation

@refspore formationconfidence
69481yes100
69480yes100

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
1859017234glucose+
1859022599arabinose+
1859017992sucrose-
1859018222xylose-
1859017268myo-inositol+
1859029864mannitol-
1859028757fructose-
1859026546rhamnose-
1859016634raffinose-
1859062968cellulose-
683685291gelatin-hydrolysis
6836827897tryptophan-energy source
6836816199urea+hydrolysis
6836816947citrate-assimilation
6836818257ornithine+degradation
6836825094lysine+degradation
6836829016arginine+hydrolysis

metabolite production

@refChebi-IDmetaboliteproduction
6836815688acetoinno
6836835581indoleno
6836816136hydrogen sulfideno

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testindole test
6836815688acetoin-
6836835581indole-

enzymes

@refvalueactivityec
68368gelatinase-
68368tryptophan deaminase-4.1.99.1
68368urease+3.5.1.5
68368ornithine decarboxylase+4.1.1.17
68368lysine decarboxylase+4.1.1.18
68368arginine dihydrolase+3.5.3.6
68368beta-galactosidase-3.2.1.23
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
18590+++-+++++++-+-+++--

API 20E

@refONPGADH ArgLDC LysODCCITH2SURETDA TrpINDVPGEL
18590-+++--+----

Isolation, sampling and environmental information

isolation

  • @ref: 67770
  • sample type: Soil

taxonmaps

  • @ref: 69479
  • File name: preview.99_834.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_15;96_102;97_109;98_662;99_834&stattab=map
  • Last taxonomy: Streptomyces
  • 16S sequence: AB184367
  • Sequence Identity:
  • Total samples: 1611
  • soil counts: 953
  • aquatic counts: 126
  • animal counts: 103
  • plant counts: 429

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
185901German classification
95391Risk group (German classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Streptomyces helvaticus gene for 16S ribosomal RNA, partial sequence, strain: JCM 4768D44346120ena68216
20218Streptomyces helvaticus gene for 16S rRNA, partial sequence, strain: NBRC 13382AB1843671477ena68216
20218Streptomyces helvaticus strain NRRL B-12365T 16S ribosomal RNA gene, partial sequenceDQ4425041453ena68216

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Streptomyces chryseus JCM 4768GCA_014650855scaffoldncbi68186
66792Streptomyces chryseus strain JCM 476868186.6wgspatric68186
66792Streptomyces helvaticus strain DSM 4043168216.4wgspatric68186
67770Streptomyces chryseus DSM 40431GCA_005981965contigncbi68186

GC content

  • @ref: 67770
  • GC-content: 76.9
  • method: thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes100no
flagellatedno98.585no
gram-positiveyes88.261no
anaerobicno98.709no
aerobicyes89.665no
halophileno95.331no
spore-formingyes93.87no
thermophileno96.884yes
glucose-utilyes90.365no
motileno94.847no
glucose-fermentno88.77no

External links

@ref: 9539

culture collection no.: DSM 40431, ATCC 19841, CBS 683.72, IFO 13382, INMI 1013B, ISP 5431, NBRC 13382, RIA 1343, JCM 4768, BCRC 16245, CGMCC 4.1911, INMI 1013-B, NRRL B-12365, VKM Ac-192

straininfo link

  • @ref: 84385
  • straininfo: 389276

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny19567563Streptomyces hypolithicus sp. nov., isolated from an Antarctic hypolith community.Le Roes-Hill M, Rohland J, Meyers PR, Cowan DA, Burton SGInt J Syst Evol Microbiol10.1099/ijs.0.007971-02009Antarctic Regions, Bacterial Typing Techniques, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Microscopy, Electron, Scanning, Molecular Sequence Data, Nucleic Acid Hybridization, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Streptomyces/*classification/genetics/*isolation & purification/physiologyGenetics
Phylogeny31204968Streptomyces altiplanensis sp. nov., an alkalitolerant species isolated from Chilean Altiplano soil, and emended description of Streptomyces chryseus (Krasil'nikov et al. 1965) Pridham 1970.Cortes-Albayay C, Dorador C, Schumann P, Schniete JK, Herron P, Andrews B, Asenjo J, Nouioui IInt J Syst Evol Microbiol10.1099/ijsem.0.0035252019Alkalies, Altitude, Bacterial Typing Techniques, Base Composition, Chile, DNA, Bacterial/genetics, *Desert Climate, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Hydrogen-Ion Concentration, Nucleic Acid Hybridization, Peptidoglycan/chemistry, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Streptomyces/*classification/isolation & purificationTranscriptome

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
9539Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 40431)https://www.dsmz.de/collection/catalogue/details/culture/DSM-40431
18590Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM40431.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
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/
68368Automatically annotated from API 20E
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
84385Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID389276.1StrainInfo: A central database for resolving microbial strain identifiers