Strain identifier

BacDive ID: 15307

Type strain: Yes

Species: Streptomyces humidus

Strain Designation: 23572

Strain history: KCC S-0386 <-- IFO 12877 <-- SAJ <-- ISP 5263 <-- ATCC 12760 <-- K. Nakazawa 23572 (IFO 3520).

NCBI tax ID(s): 52259 (species)

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General

@ref: 9417

BacDive-ID: 15307

DSM-Number: 40263

keywords: genome sequence, 16S sequence, Bacteria, spore-forming, mesophilic, Gram-positive, antibiotic compound production

description: Streptomyces humidus 23572 is a spore-forming, mesophilic, Gram-positive bacterium that produces antibiotic compounds and was isolated from soil.

NCBI tax id

  • NCBI tax id: 52259
  • Matching level: species

strain history

@refhistory
9417<- E.B. Shirling, ISP <- ATCC <- Takeda Pharm. Ind., Ltd., 23572
67770KCC S-0386 <-- IFO 12877 <-- SAJ <-- ISP 5263 <-- ATCC 12760 <-- K. Nakazawa 23572 (IFO 3520).

doi: 10.13145/bacdive15307.20230509.8.1

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 humidus
  • full scientific name: Streptomyces humidus Nakazawa and Shibata 1956 (Approved Lists 1980)

@ref: 9417

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Streptomycetaceae

genus: Streptomyces

species: Streptomyces humidus

full scientific name: Streptomyces humidus Nakazawa and Shibata 1956

strain designation: 23572

type strain: yes

Morphology

cell morphology

  • @ref: 69480
  • gram stain: positive
  • confidence: 100

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
9417GYM 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
9417ROLLED OATS MINERAL MEDIUM (DSMZ Medium 84)yeshttps://www.dsmz.de/microorganisms/medium/pdf/DSMZ_Medium84.pdf

culture temp

@refgrowthtypetemperaturerange
18575positiveoptimum28mesophilic
9417positivegrowth28mesophilic
67770positivegrowth28mesophilic

Physiology and metabolism

tolerance

  • @ref: 18575
  • compound: Lysozyme
  • percentage: 0.1

spore formation

@refspore formationconfidence
69481yes100
69480yes100

compound production

@refcompound
9417cobalamine
9417dihydrostreptomycin
9417humidin

halophily

  • @ref: 18575
  • salt: NaCl
  • growth: positive
  • tested relation: maximum
  • concentration: 5 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
1857517234glucose+
1857522599arabinose+
1857517992sucrose-
1857518222xylose-
1857517268myo-inositol+/-
1857529864mannitol+/-
1857528757fructose+
1857526546rhamnose+
1857516634raffinose+/-
683685291gelatin-hydrolysis
6836827897tryptophan-energy source
6836816199urea+hydrolysis
6836816947citrate-assimilation
6836818257ornithine+degradation
6836825094lysine+degradation
6836829016arginine+hydrolysis

metabolite production

@refChebi-IDmetaboliteproduction
6777038291dihydrostreptomycinyes
6836815688acetoinyes
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

API 20E

@refONPGADH ArgLDC LysODCCITH2SURETDA TrpINDVPGEL
18575++++--+--+-

Isolation, sampling and environmental information

isolation

  • @ref: 9417
  • sample type: soil
  • country: Japan
  • origin.country: JPN
  • continent: Asia

isolation source categories

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

taxonmaps

  • @ref: 69479
  • File name: preview.99_18452.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_15;96_102;97_135;98_152;99_18452&stattab=map
  • Last taxonomy: Streptomyces
  • 16S sequence: DQ442508
  • Sequence Identity:
  • Total samples: 4390
  • soil counts: 2400
  • aquatic counts: 88
  • animal counts: 99
  • plant counts: 1803

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
185751German classification
94171Risk group (German classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Streptomyces humidus 16S ribosomal RNA gene, partial sequenceU72169269ena52259
20218Streptomyces humidus gene for 16S ribosomal RNA, partial sequence, strain: JCM 4386D44101120ena52259
20218Streptomyces humidus humidus strain JCM 4386 16S ribosomal RNA gene, partial sequenceGU383149779ena52259
20218Streptomyces humidus gene for 16S rRNA, partial sequence, strain: NBRC 12877AB1842131469ena52259
20218Streptomyces humidus strain NRRL B-3172T 16S ribosomal RNA gene, partial sequenceDQ4425081495ena52259

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Streptomyces humidus JCM 4386GCA_014649655scaffoldncbi52259
66792Streptomyces humidus strain JCM 438652259.3wgspatric52259

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes100no
flagellatedno98.244no
gram-positiveyes87.656no
anaerobicno98.301no
aerobicyes87.378no
halophileno95.23no
spore-formingyes95.143no
thermophileno98.266yes
glucose-utilyes89.678yes
motileno94.501no
glucose-fermentno86.579no

External links

@ref: 9417

culture collection no.: DSM 40263, ATCC 12760, ATCC 23923, CBS 907.68, IFO 12877, ISP 5263, NBRC 12877, RIA 1186, JCM 4386, BCRC 13707, CGMCC 4.1910, NRRL B-3172, VKM Ac-1703

straininfo link

  • @ref: 84401
  • straininfo: 35650

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
9417Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 40263)https://www.dsmz.de/collection/catalogue/details/culture/DSM-40263
18575Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM40263.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
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
84401Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID35650.1StrainInfo: A central database for resolving microbial strain identifiers