Strain identifier

BacDive ID: 15066

Type strain: Yes

Species: Streptomyces candidus

Strain history: KCC S-0629 <-- IFO 12846 <-- SAJ <-- ISP 5141 <-- INA 5855/54.

NCBI tax ID(s): 67283 (species)

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General

@ref: 9343

BacDive-ID: 15066

DSM-Number: 40141

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

description: Streptomyces candidus DSM 40141 is a spore-forming, mesophilic bacterium that was isolated from soil.

NCBI tax id

  • NCBI tax id: 67283
  • Matching level: species

strain history

@refhistory
9343<- E.B. Shirling, ISP (Streptomyces candidus) <- T.P. Preobrazhenskaya, INA
67770KCC S-0629 <-- IFO 12846 <-- SAJ <-- ISP 5141 <-- INA 5855/54.

doi: 10.13145/bacdive15066.20230509.8.1

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 candidus
  • full scientific name: Streptomyces candidus (ex Krassilnikov 1941) Sveshnikova 1986

@ref: 9343

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Streptomycetaceae

genus: Streptomyces

species: Streptomyces candidus

full scientific name: Streptomyces candidus (ex Krassilnikov 1941) Sveshnikova 1986

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram stain
69480no90.711
69480100positive

Culture and growth conditions

culture medium

  • @ref: 9343
  • 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
18543positiveoptimum28mesophilic
9343positivegrowth28mesophilic
67770positivegrowth28mesophilic

Physiology and metabolism

spore formation

@refspore formationconfidence
69481yes100
69480yes100

halophily

  • @ref: 18543
  • salt: NaCl
  • growth: positive
  • tested relation: maximum
  • concentration: 5 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
683685291gelatin-hydrolysis
6836827897tryptophan-energy source
6836816199urea+hydrolysis
6836816947citrate+assimilation
6836818257ornithine+degradation
6836825094lysine+degradation
6836829016arginine+hydrolysis

metabolite production

@refChebi-IDmetaboliteproduction
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
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
18543+++-++---++-+-+++--

API 20E

@refONPGADH ArgLDC LysODCCITH2SURETDA TrpINDVPGEL
18543+++++-+--+-

Isolation, sampling and environmental information

isolation

@refsample typecountrycontinent
9343soilUSSRAsia
67770Soil

isolation source categories

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

taxonmaps

  • @ref: 69479
  • File name: preview.99_210.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_15;96_102;97_109;98_120;99_210&stattab=map
  • Last taxonomy: Streptomyces
  • 16S sequence: DQ026663
  • Sequence Identity:
  • Total samples: 112
  • soil counts: 103
  • aquatic counts: 1
  • animal counts: 6
  • plant counts: 2

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
93431Risk group (German classification)
185431German classification

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Streptomyces candidus strain NRRL ISP-5141 16S ribosomal RNA gene, partial sequenceDQ0266631483ena67283
20218Streptomyces candidus gene for 16S ribosomal RNA, partial sequence, strain: JCM 4629D44276120ena67283
20218Streptomyces candidus gene for 16S rRNA, partial sequence, strain: NBRC 12846AB1841901478ena67283

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Streptomyces candidus JCM 4629GCA_014655855scaffoldncbi67283
66792Streptomyces candidus DSM 40141GCA_014207445scaffoldncbi67283
66792Streptomyces candidus strain DSM 4014167283.5wgspatric67283
66792Streptomyces candidus strain JCM 462967283.6wgspatric67283
66792Streptomyces candidus DSM 401412861171287draftimg67283

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes100no
motileno93.977no
flagellatedno98.199no
gram-positiveyes91.16no
anaerobicno99.213no
aerobicyes93.449no
halophileno92.416no
spore-formingyes95.513no
glucose-utilyes88.32no
thermophileno99.02yes
glucose-fermentno87.711no

External links

@ref: 9343

culture collection no.: DSM 40141, ATCC 19735, ATCC 19891, ATCC 23891, CBS 677.68, ETH 28543, IFO 12846, INA 5855/54, ISP 5141, JCM 4629, KCC S-0629, NBRC 12846, PSA 183, RIA 1131, BCRC 13760, CGMCC 4.1664, ICMP 12538, KCTC 9020, NCIMB 12827, NRRL ISP-5141, VKM Ac-1091, VTT E-072673

straininfo link

  • @ref: 84172
  • straininfo: 298106

literature

  • topic: Phylogeny
  • Pubmed-ID: 24091604
  • title: Streptomyces fukangensis sp. nov., a novel alkaliphilic actinomycete isolated from a saline-alkaline soil.
  • authors: Zhang YG, Wang HF, Liu Q, Hozzein WN, Wadaan MA, Cheng J, Chen YJ, Zhang YM, Li WJ
  • journal: Antonie Van Leeuwenhoek
  • DOI: 10.1007/s10482-013-0045-8
  • year: 2013
  • mesh: Amino Acids/analysis, Bacterial Typing Techniques, Base Composition, Carbohydrates/analysis, China, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Desert Climate, Fatty Acids/analysis, Microscopy, Electron, Scanning, Molecular Sequence Data, Phospholipids/analysis, Phylogeny, Quinones/analysis, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Streptomyces/*classification/genetics/*isolation & purification/physiology
  • topic2: Genetics

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
9343Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 40141)https://www.dsmz.de/collection/catalogue/details/culture/DSM-40141
18543Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM40141.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
84172Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID298106.1StrainInfo: A central database for resolving microbial strain identifiers