Strain identifier

BacDive ID: 15055

Type strain: Yes

Species: Streptomyces bottropensis

Strain history: CIP <- 1997, IFO <- 1969, SAJ <- OWU: strain ISP 5262

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

@ref: 9416

BacDive-ID: 15055

DSM-Number: 40262

keywords: genome sequence, 16S sequence, Bacteria, obligate aerobe, spore-forming, mesophilic, antibiotic compound production

description: Streptomyces bottropensis DSM 40262 is an obligate aerobe, spore-forming, mesophilic bacterium that produces antibiotic compounds and was isolated from soil.

NCBI tax id

NCBI tax idMatching level
1054862strain
42235species

strain history

@refhistory
9416<- E.B. Shirling, ISP <- J.C. Hoogerheide B-35
67770KCC S-0459 <-- IFO 13023 <-- SAJ <-- ISP 5262 <-- J. C. Hoogerheide B-25.
116900CIP <- 1997, IFO <- 1969, SAJ <- OWU: strain ISP 5262

doi: 10.13145/bacdive15055.20230509.8.1

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: 9416

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Streptomycetaceae

genus: Streptomyces

species: Streptomyces bottropensis

full scientific name: Streptomyces bottropensis Waksman 1961 emend. Nouioui et al. 2018

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram staincell shape
69480no90.344
69480100positive
116900nopositiverod-shaped

colony morphology

  • @ref: 116900

multimedia

@refmultimedia contentintellectual property rightscaption
9416https://www.dsmz.de/microorganisms/photos/DSM_40262-1.JPG© Leibniz-Institut DSMZ
9416https://www.dsmz.de/microorganisms/photos/DSM_40262.jpg© Leibniz-Institut DSMZMedium 65 28°C

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
9416GYM 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
39250MEDIUM 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)
9416STARCH - MINERAL SALT - AGAR (STMS) (DSMZ Medium 252)yeshttps://www.dsmz.de/microorganisms/medium/pdf/DSMZ_Medium252.pdf
116900CIP Medium 236yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=236
116900CIP Medium 57yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=57

culture temp

@refgrowthtypetemperaturerange
18574positiveoptimum28mesophilic
9416positivegrowth28mesophilic
39250positivegrowth30mesophilic
67770positivegrowth28mesophilic
116900positivegrowth25-37mesophilic
116900nogrowth10psychrophilic
116900nogrowth41thermophilic
116900nogrowth45thermophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 116900
  • oxygen tolerance: obligate aerobe

spore formation

@refspore formationconfidence
69481yes100
69480yes100

compound production

  • @ref: 9416
  • compound: bottromycin

halophily

@refsaltgrowthtested relationconcentration
116900NaClpositivegrowth0-2 %
116900NaClnogrowth4 %
116900NaClnogrowth6 %
116900NaClnogrowth8 %
116900NaClnogrowth10 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
1857417234glucose+
1857422599arabinose+
1857417992sucrose+
1857418222xylose-
1857417268myo-inositol+
1857429864mannitol+
1857428757fructose-
1857426546rhamnose+
1857416634raffinose+
1857462968cellulose+
68371Potassium 5-ketogluconate-builds acid from
68371Potassium 2-ketogluconate-builds acid from
6837124265gluconate-builds acid from
6837118403L-arabitol-builds acid from
6837118333D-arabitol-builds acid from
6837128847D-fucose-builds acid from
6837116443D-tagatose-builds acid from
6837162318D-lyxose-builds acid from
6837132528turanose-builds acid from
6837128066gentiobiose-builds acid from
6837117151xylitol-builds acid from
6837128017starch-builds acid from
6837116634raffinose-builds acid from
683716731melezitose-builds acid from
6837115443inulin-builds acid from
6837128053melibiose-builds acid from
6837117716lactose-builds acid from
6837117306maltose-builds acid from
6837117814salicin-builds acid from
683714853esculin-builds acid from
6837118305arbutin-builds acid from
6837127613amygdalin-builds acid from
68371320061methyl alpha-D-glucopyranoside-builds acid from
6837143943methyl alpha-D-mannoside-builds acid from
6837117924D-sorbitol-builds acid from
6837116899D-mannitol-builds acid from
6837117268myo-inositol-builds acid from
6837116813galactitol-builds acid from
6837117266L-sorbose-builds acid from
6837112936D-galactose-builds acid from
6837174863methyl beta-D-xylopyranoside-builds acid from
6837115963ribitol-builds acid from
6837165328L-xylose-builds acid from
6837165327D-xylose-builds acid from
6837116988D-ribose+builds acid from
6837117108D-arabinose-builds acid from
6837117113erythritol-builds acid from
683685291gelatin+hydrolysis
6836827897tryptophan-energy source
6836816199urea+hydrolysis
6836816947citrate+assimilation
6836818257ornithine-degradation
6836825094lysine+degradation
6836829016arginine+hydrolysis
1169004853esculin-hydrolysis
116900606565hippurate-hydrolysis
11690017632nitrate-reduction
11690016301nitrite-reduction
11690017632nitrate-respiration

metabolite production

@refmetaboliteproductionChebi-ID
67770bottromycinyes
68368acetoinyes15688
68368indoleno35581
68368hydrogen sulfideno16136
116900indoleno35581

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testindole testmethylred-test
6836815688acetoin+
6836835581indole-
11690015688acetoin-
11690017234glucose-

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
116900oxidase-
116900beta-galactosidase+3.2.1.23
116900alcohol dehydrogenase-1.1.1.1
116900gelatinase-
116900amylase-
116900DNase-
116900caseinase-3.4.21.50
116900catalase+1.11.1.6
116900tween esterase-
116900gamma-glutamyltransferase-2.3.2.2
116900lecithinase-
116900lipase-
116900lysine decarboxylase-4.1.1.18
116900ornithine decarboxylase-4.1.1.17
116900phenylalanine ammonia-lyase-4.3.1.24
116900tryptophan deaminase-
116900urease-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
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+
68382beta-glucuronidase-3.2.1.31
68382N-acetyl-beta-glucosaminidase+3.2.1.52
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- FucosidaseControl
18574+++-++---++++-++++-
116900+++-+----++-----+---

API 20E

@refONPGADH ArgLDC LysODCCITH2SURETDA TrpINDVPGEL
18574+++-+-+--++

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
116900+/---+/-+-----+/-+/-+/--+/-------+/-----+/----+/-+/-----+/-------+/------

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
116900+++-+-++-+++++-+--++++-++-+----+-+---------------++--+-----++--------++-++----+++-----+--+++-++--+-

Isolation, sampling and environmental information

isolation

@refsample type
9416soil
116900Environment, Soil

isolation source categories

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

taxonmaps

  • @ref: 69479
  • File name: preview.99_1896.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_15;96_102;97_135;98_1456;99_1896&stattab=map
  • Last taxonomy: Streptomyces bottropensis
  • 16S sequence: AB184262
  • Sequence Identity:
  • Total samples: 153
  • soil counts: 120
  • aquatic counts: 1
  • animal counts: 7
  • plant counts: 25

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
94161Risk group (German classification)
185741German classification
1169001Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Streptomyces bottropensis gene for 16S ribosomal RNA, 23S ribosomal RNA, complete and partial sequence, strain:ATCC 25435AB0262171857ena1054862
20218Streptomyces bottropensis strain DSM40262 16S-23S intergenic spacer region, partial sequenceAF363493306ena1054862
20218Streptomyces bottropensis gene for 16S ribosomal RNA, complete sequenceD638681531ena1054862
20218Streptomyces bottropensis ATCC 25435 strain DSM 40262 clone ITS 16S-23S ribosomal RNA intergenic spacer, partial sequenceAY296951283ena1054862
20218Streptomyces bottropensis ATCC 25435 strain DSM 40262 clone ITS11 16S-23S ribosomal RNA intergenic spacer, partial sequenceAY296952273ena1054862
20218Streptomyces bottropensis ATCC 25435 strain DSM 40262 clone ITS29 16S-23S ribosomal RNA intergenic spacer, partial sequenceAY296954274ena1054862
20218Streptomyces bottropensis ATCC 25435 strain DSM 40262 clone ITS3 16S-23S ribosomal RNA intergenic spacer, partial sequenceAY296955285ena1054862
20218Streptomyces bottropensis gene for 16S ribosomal RNA, partial sequence, strain: JCM 4459D44156121ena1054862
20218Streptomyces bottropensis gene for 16S rRNA, partial sequence, strain: NBRC 13023AB1842621476ena42235

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Streptomyces bottropensis ATCC 254351054862.3wgspatric1054862
66792Streptomyces bottropensis ATCC 254351054862.11completepatric1054862
66792Streptomyces bottropensis DSM40262.2582581526draftimg42235
66792Streptomyces bottropensis ATCC 254352517572239draftimg1054862
66792Streptomyces bottropensis ATCC 254352551306667draftimg1054862
67770Streptomyces bottropensis ATCC 25435GCA_000340335scaffoldncbi1054862
67770Streptomyces bottropensis ATCC 25435GCA_000383595scaffoldncbi1054862

GC content

  • @ref: 67770
  • GC-content: 71.2
  • method: genome sequence analysis

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes100no
motileno94.686no
flagellatedno96.995no
gram-positiveyes86.194no
anaerobicno99.018no
aerobicyes92.307no
halophileno94.236no
spore-formingyes95.149no
thermophileno98.329no
glucose-utilyes89.992no
glucose-fermentno88.49no

External links

@ref: 9416

culture collection no.: DSM 40262, ATCC 25435, CBS 163.64, CBS 667.69, ETH 23899, IFO 13023, ISP 5262, JCM 4459, NBRC 13023, RIA 1215, BCRC 12063, CGMCC 4.1669, CIP 105278, KACC 20131, MTCC 4729, NRRL ISP-5262, VKM Ac-1755

straininfo link

  • @ref: 84161
  • straininfo: 45754

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Genetics23516178Draft Genome Sequence of Streptomyces bottropensis ATCC 25435, a Bottromycin-Producing Actinomycete.Zhang H, Zhou W, Zhuang Y, Liang X, Liu TGenome Announc10.1128/genomeA.00019-132013
Phylogeny33871674Streptomyces adelaidensis sp. nov., an actinobacterium isolated from the root of Callitris preissii with potential for plant growth-promoting properties.Kaewkla O, Suriyachadkun C, Franco CMMArch Microbiol10.1007/s00203-021-02308-42021Cupressaceae/*microbiology, Fatty Acids/analysis, Genome, Bacterial, Genotype, Phylogeny, Plant Development, Plant Roots/microbiology, Streptomyces/chemistry/classification/genetics/*isolation & purificationGenetics

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
9416Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 40262)https://www.dsmz.de/collection/catalogue/details/culture/DSM-40262
18574Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM40262.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
39250Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/17280
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
68371Automatically annotated from API 50CH acid
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
84161Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID45754.1StrainInfo: A central database for resolving microbial strain identifiers
116900Curators of the CIPCollection of Institut Pasteur (CIP 105278)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20105278