Strain identifier

BacDive ID: 16372

Type strain: Yes

Species: Streptomyces bottropensis

Strain history: CIP <- 2001, K. Bouchek, INRA, Le Rheu, France

NCBI tax ID(s): 146820 (species)

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General

@ref: 10587

BacDive-ID: 16372

DSM-Number: 41803

keywords: genome sequence, 16S sequence, Bacteria, mesophilic, Gram-positive, rod-shaped, plant pathogen

description: Streptomyces bottropensis DSM 41803 is a mesophilic, Gram-positive, rod-shaped plant pathogen that was isolated from star-like common scab lesions on potato tubers.

NCBI tax id

  • NCBI tax id: 146820
  • Matching level: species

strain history

@refhistory
10587<- NCPPB
381872001, K. Bouchek, INRA, Le Rheu Cedex, France strain
123307CIP <- 2001, K. Bouchek, INRA, Le Rheu, France

doi: 10.13145/bacdive16372.20230509.8.1

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 bottropensis
  • full scientific name: Streptomyces bottropensis Waksman 1961 (Approved Lists 1980)

  • synonyms

    • @ref: 20215
    • synonym: Streptomyces stelliscabiei

@ref: 10587

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Streptomycetaceae

genus: Streptomyces

species: Streptomyces stelliscabiei

full scientific name: Streptomyces stelliscabiei Bouchek-Mechiche et al. 2000

type strain: yes

Morphology

cell morphology

  • @ref: 123307
  • gram stain: positive
  • cell shape: rod-shaped
  • motility: no

colony morphology

  • @ref: 123307
  • hemolysis ability: 1

multimedia

  • @ref: 10587
  • multimedia content: https://www.dsmz.de/microorganisms/photos/DSM_41803.jpg
  • caption: Medium 252 28°C
  • intellectual property rights: © Leibniz-Institut DSMZ

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
10587GYM 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
38187MEDIUM 57 - for Streptomyces, Nocardioides, Lentzea albidocapillata and Streptoverticillium reticulumyesDistilled water make up to (1000.000 ml);Agar (15.000 g);Glucose (4.000g);Yeast extract (4.000 g);Malt extract (10.000 g);Calcium carbonate (2.000 g)
10587ROLLED OATS MINERAL MEDIUM (DSMZ Medium 84)yeshttps://mediadive.dsmz.de/medium/84Name: ROLLED OATS MINERAL MEDIUM (DSMZ Medium 84) Composition: Agar 20.0 g/l Rolled oats 20.0 g/l ZnSO4 x 7 H2O 0.001 g/l MnCl2 x 4 H2O 0.001 g/l FeSO4 x 7 H2O 0.001 g/l Distilled water
10587STARCH - 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
123307CIP Medium 57yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=57

culture temp

@refgrowthtypetemperaturerange
10587positivegrowth28mesophilic
38187positivegrowth30mesophilic
123307positivegrowth25-37mesophilic
123307nogrowth10psychrophilic
123307nogrowth41thermophilic
123307nogrowth45thermophilic

Physiology and metabolism

halophily

@refsaltgrowthtested relationconcentration
123307NaClpositivegrowth0-2 %
123307NaClnogrowth4 %
123307NaClnogrowth6 %
123307NaClnogrowth8 %
123307NaClnogrowth10 %

metabolite utilization

@refmetaboliteutilization activitykind of utilization testedChebi-ID
68371Potassium 5-ketogluconate-builds acid from
68371Potassium 2-ketogluconate-builds acid from
68371gluconate-builds acid from24265
68371L-arabitol-builds acid from18403
68371D-arabitol-builds acid from18333
68371D-fucose-builds acid from28847
68371D-tagatose-builds acid from16443
68371D-lyxose-builds acid from62318
68371turanose-builds acid from32528
68371gentiobiose-builds acid from28066
68371xylitol-builds acid from17151
68371glycogen-builds acid from28087
68371starch-builds acid from28017
68371raffinose-builds acid from16634
68371melezitose-builds acid from6731
68371inulin-builds acid from15443
68371trehalose-builds acid from27082
68371melibiose-builds acid from28053
68371lactose-builds acid from17716
68371maltose-builds acid from17306
68371cellobiose-builds acid from17057
68371salicin-builds acid from17814
68371esculin+builds acid from4853
68371arbutin-builds acid from18305
68371amygdalin-builds acid from27613
68371methyl alpha-D-glucopyranoside-builds acid from320061
68371methyl alpha-D-mannoside-builds acid from43943
68371D-sorbitol-builds acid from17924
68371D-mannitol-builds acid from16899
68371myo-inositol-builds acid from17268
68371galactitol-builds acid from16813
68371L-rhamnose-builds acid from62345
68371L-sorbose-builds acid from17266
68371D-mannose-builds acid from16024
68371D-fructose-builds acid from15824
68371D-glucose-builds acid from17634
68371D-galactose-builds acid from12936
68371methyl beta-D-xylopyranoside-builds acid from74863
68371ribitol-builds acid from15963
68371L-xylose-builds acid from65328
68371D-xylose-builds acid from65327
68371D-ribose-builds acid from16988
68371L-arabinose-builds acid from30849
68371D-arabinose-builds acid from17108
68371erythritol-builds acid from17113
68371glycerol-builds acid from17754
123307esculin+hydrolysis4853
123307hippurate+hydrolysis606565
123307nitrate+reduction17632
123307nitrite-reduction16301
123307tributyrin+hydrolysis35020
123307nitrate-respiration17632

metabolite production

  • @ref: 123307
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testmethylred-test
12330715688acetoin-
12330717234glucose-

enzymes

@refvalueactivityec
123307oxidase-
123307beta-galactosidase+3.2.1.23
123307alcohol dehydrogenase-1.1.1.1
123307gelatinase+
123307caseinase-3.4.21.50
123307catalase-1.11.1.6
123307gamma-glutamyltransferase+2.3.2.2
123307lecithinase-
123307lipase-
123307lysine decarboxylase-4.1.1.18
123307ornithine decarboxylase-4.1.1.17
123307phenylalanine ammonia-lyase-4.3.1.24
123307tryptophan deaminase-
123307urease+3.5.1.5
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

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
123307-+---+----++--------

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
123307---------------------+/---+-----+/-------------+/------

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
123307+++-+-+++++++--+--+-++-++-+----+++-------------------------++-+--+-------+-----++-----+--+++-++--+-

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
10587star-like common scab lesions on potato tubersBelle de FontenayFranceFRAEurope
123307Solanum tuberosumFranceFRAEurope

isolation source categories

Cat1Cat2Cat3
#Infection#Disease
#Host#Plants#Herbaceous plants (Grass,Crops)
#Host Body-Site#Other#Wound
#Host Body-Site#Plant#Root (Rhizome)

Safety information

risk assessment

@refpathogenicity plantbiosafety levelbiosafety level comment
10587yes1Risk group (German classification)
1233071Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Streptomyces stelliscabiei strain CFBP 4521 clone ITS 16S-23S ribosomal RNA intergenic spacer, partial sequenceAY296989280ena146820
20218Streptomyces stelliscabiei strain CFBP 4521 clone ITS17 16S-23S ribosomal RNA intergenic spacer, partial sequenceAY296990285ena146820
20218Streptomyces stelliscabiei strain CFBP 4521 clone ITS19 16S-23S ribosomal RNA intergenic spacer, partial sequenceAY296991280ena146820
20218Streptomyces stelliscabiei strain CFBP 4521 clone ITS2 16S-23S ribosomal RNA intergenic spacer, partial sequenceAY296992280ena146820
20218Streptomyces stelliscabiei strain CFBP 4521 clone ITS29 16S-23S ribosomal RNA intergenic spacer, partial sequenceAY296993280ena146820
20218Streptomyces stelliscabiei strain CFBP 4521 clone ITS4 16S-23S ribosomal RNA intergenic spacer, partial sequenceAY296994281ena146820
20218Streptomyces stelliscabiei strain CFBP 4521 16S ribosomal RNA gene, partial sequenceFJ0073851441ena146820
10587Streptomyces sp. 16S rRNA gene, isolate CFBP4521AJ0074291478ena146820

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Streptomyces stelliscabiei DSM 41803GCA_014873495contigncbi146820
66792Streptomyces stelliscabiei strain DSM 41803146820.12wgspatric146820
66792Streptomyces stelliscabiei DSM 418032873412701draftimg146820

GC content

  • @ref: 10587
  • GC-content: 71.7

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
motileno93.961no
gram-positiveyes85.475no
anaerobicno99.114no
aerobicyes93.338no
halophileno93.009no
spore-formingyes94.523no
thermophileno99.019yes
glucose-utilyes90.726no
flagellatedno96.887no
glucose-fermentno89.655no

External links

@ref: 10587

culture collection no.: DSM 41803, CFBP 4521, ICMP 13715, NCPPB 4040, CIP 107126

straininfo link

  • @ref: 85426
  • straininfo: 87862

literature

  • topic: Phylogeny
  • Pubmed-ID: 10826791
  • title: DNA relatedness among strains of Streptomyces pathogenic to potato in France: description of three new species, S. europaeiscabiei sp. nov. and S. stelliscabiei sp. nov. associated with common scab, and S. reticuliscabiei sp. nov. associated with netted scab.
  • authors: Bouchek-Mechiche K, Gardan L, Normand P, Jouan B
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/00207713-50-1-91
  • year: 2000
  • mesh: Base Composition, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Genes, rRNA/genetics, Molecular Sequence Data, Nucleic Acid Hybridization, Phylogeny, Plant Diseases/*microbiology, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Solanum tuberosum/*microbiology, Streptomyces/*classification/genetics/isolation & purification/physiology
  • topic2: Genetics

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
10587Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 41803)https://www.dsmz.de/collection/catalogue/details/culture/DSM-41803
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
38187Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/4527
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)
68371Automatically annotated from API 50CH acid
68382Automatically annotated from API zym
85426Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID87862.1StrainInfo: A central database for resolving microbial strain identifiers
123307Curators of the CIPCollection of Institut Pasteur (CIP 107126)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20107126