Strain identifier

BacDive ID: 15100

Type strain: Yes

Species: Streptomyces clavifer

Strain history: KCC S-1059 <-- MS 1479 <-- CBS 101.27 <-- W. A. Millard.

NCBI tax ID(s): 68188 (species)

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General

@ref: 9843

BacDive-ID: 15100

DSM-Number: 40843

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

description: Streptomyces clavifer DSM 40843 is a spore-forming, mesophilic, Gram-positive bacterium that was isolated from limed plot and scab on Solanum tuberosum.

NCBI tax id

  • NCBI tax id: 68188
  • Matching level: species

strain history

@refhistory
9843<- NRRL
67770KCC S-1059 <-- MS 1479 <-- CBS 101.27 <-- W. A. Millard.

doi: 10.13145/bacdive15100.20230509.8.1

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 clavifer
  • full scientific name: Streptomyces clavifer (Millard and Burr 1926) Waksman 1953 (Approved Lists 1980)

  • synonyms

    • @ref: 20215
    • synonym: Actinomyces clavifer

@ref: 9843

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Streptomycetaceae

genus: Streptomyces

species: Streptomyces clavifer

full scientific name: Streptomyces clavifer (Millard and Burr 1926) Waksman 1953

type strain: yes

Morphology

cell morphology

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

colony morphology

@refcolony colorincubation periodmedium used
19492Sand yellow10-14 daysISP 2
19492Grey yellow10-14 daysISP 3
1949210-14 daysISP 4
1949210-14 daysISP 5
1949210-14 daysISP 6
1949210-14 daysISP 7

multicellular morphology

@refforms multicellular complexmedium name
19492noISP 2
19492noISP 3
19492noISP 4
19492noISP 5
19492noISP 6
19492noISP 7

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
9843GPHF-MEDIUM (DSMZ Medium 553)yeshttps://mediadive.dsmz.de/medium/553Name: GPHF-MEDIUM (DSMZ Medium 553) Composition: Agar 20.0 g/l Glucose 10.0 g/l Beef extract 5.0 g/l Yeast extract 5.0 g/l Casein peptone 5.0 g/l CaCl2 x 2 H2O 0.74 g/l Distilled water
9843STARCH - MINERAL SALT - AGAR (STMS) (DSMZ Medium 252)yeshttps://mediadive.dsmz.de/medium/252Name: STARCH - MINERAL SALT - AGAR (STMS) (DSMZ Medium 252) Composition: Agar 14.985 g/l Starch 9.99001 g/l (NH4)2SO4 1.998 g/l CaCO3 1.998 g/l K2HPO4 0.999001 g/l MgSO4 x 7 H2O 0.999001 g/l NaCl 0.999001 g/l FeSO4 x 7 H2O 0.000999001 g/l MnCl2 x 4 H2O 0.000999001 g/l ZnSO4 x 7 H2O 0.000999001 g/l Distilled water
19492ISP 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
19492ISP 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:
19492ISP 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
19492ISP 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
19492ISP 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
19492ISP 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
9843GYM STREPTOMYCES MEDIUM (DSMZ Medium 65)yeshttps://www.dsmz.de/microorganisms/medium/pdf/DSMZ_Medium65.pdf

culture temp

@refgrowthtypetemperaturerange
19492positiveoptimum28mesophilic
9843positivegrowth28mesophilic
67770positivegrowth28mesophilic

Physiology and metabolism

spore formation

@refspore formationconfidence
69481yes100
69480yes100

compound production

  • @ref: 19492
  • compound: Melanostatin

halophily

  • @ref: 19492
  • salt: NaCl
  • growth: positive
  • tested relation: maximum
  • concentration: 2.5 %

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
19492++++++++-++++-++---

API 20E

@refONPGADH ArgLDC LysODCCITH2SURETDA TrpINDVPGEL
19492+++++-+--++

Isolation, sampling and environmental information

isolation

  • @ref: 9843
  • sample type: limed plot and scab on Solanum tuberosum
  • host species: Solanum tuberosum

isolation source categories

Cat1Cat2Cat3
#Environmental#Terrestrial
#Host#Plants#Herbaceous plants (Grass,Crops)
#Host Body-Site#Other#Wound
#Host Body-Site#Plant#Fruit (Seed)

taxonmaps

  • @ref: 69479
  • File name: preview.99_135.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_15;96_102;97_109;98_120;99_135&stattab=map
  • Last taxonomy: Streptomyces
  • 16S sequence: AB184649
  • Sequence Identity:
  • Total samples: 4030
  • soil counts: 2441
  • aquatic counts: 286
  • animal counts: 1009
  • plant counts: 294

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
98431Risk group (German classification)
194921Risk group (German classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Streptomyces clavifer strain AS 4.1604 16S ribosomal RNA gene, partial sequenceFJ4059041387ena68188
20218Streptomyces clavifer gene for 16S ribosomal RNA, partial sequence, strain: JCM 5059D44428120ena68188
20218Streptomyces clavifer gene for 16S rRNA, partial sequence, strain: NBRC 15398AB1846491477ena68188
20218Streptomyces clavifer strain NRRL B-2557 16S ribosomal RNA gene, partial sequenceDQ0266701499ena68188

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Streptomyces clavifer DSM 40843GCA_017876255contigncbi68188
66792Streptomyces clavifer JCM 5059GCA_014651175scaffoldncbi68188
66792Streptomyces clavifer strain DSM 4084368188.4wgspatric68188
66792Streptomyces clavifer strain JCM 505968188.3wgspatric68188
66792Streptomyces clavifer DSM 408432918298223draftimg68188

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes100no
flagellatedno97.792no
gram-positiveyes89.522no
anaerobicno99.182no
aerobicyes92.928no
halophileno90.996no
spore-formingyes93.565no
thermophileno99.113yes
glucose-utilyes90.759no
motileno93.297no
glucose-fermentno90.019no

External links

@ref: 9843

culture collection no.: DSM 40843, CBS 101.27, NRRL B-2557, JCM 5059, CGMCC 4.1604, IFO 15398, NBRC 15398

straininfo link

  • @ref: 84207
  • straininfo: 49809

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
9843Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 40843)https://www.dsmz.de/collection/catalogue/details/culture/DSM-40843
19492Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM40843.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
84207Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID49809.1StrainInfo: A central database for resolving microbial strain identifiers