Strain identifier

BacDive ID: 15216

Type strain: Yes

Species: Streptomyces gardneri

Strain history: KCC A-0004 <-- T. Yamaguchi (IAM 0105) <-- ATCC 9604 <-- NCTC 6531.

NCBI tax ID(s): 66892 (species)

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General

@ref: 9265

BacDive-ID: 15216

DSM-Number: 40064

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

description: Streptomyces gardneri DSM 40064 is a spore-forming, mesophilic bacterium that produces antibiotic compounds and was isolated from air contamination.

NCBI tax id

  • NCBI tax id: 66892
  • Matching level: species

strain history

@refhistory
9265<- E.B. Shirling, ISP <- S.A. Waksman, IMRU
67770KCC A-0004 <-- T. Yamaguchi (IAM 0105) <-- ATCC 9604 <-- NCTC 6531.

doi: 10.13145/bacdive15216.20230509.8.1

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 gardneri
  • full scientific name: Streptomyces gardneri (Waksman 1942) Waksman 1961 (Approved Lists 1980)

  • synonyms

    • @ref: 20215
    • synonym: Proactinomyces gardneri

@ref: 9265

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Streptomycetaceae

genus: Streptomyces

species: Streptomyces gardneri

full scientific name: Streptomyces gardneri (Waksman 1942) Waksman 1961

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram stain
69480no94.038
69480100positive

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
9265GYM 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
9265STARCH - MINERAL SALT - AGAR (STMS) (DSMZ Medium 252)yeshttps://www.dsmz.de/microorganisms/medium/pdf/DSMZ_Medium252.pdf

culture temp

@refgrowthtypetemperaturerange
18476positiveoptimum28mesophilic
9265positivegrowth28mesophilic
67770positivegrowth28mesophilic

Physiology and metabolism

spore formation

@refspore formationconfidence
69481yes98
69480yes100

compound production

@refcompound
9265proactinomycin A, B, C
9265proactinomycin B
9265proactinomycin C
9265proactinomycin A
67770Proactinomycins A, B and C

observation

  • @ref: 67770
  • observation: quinones: MK-8(H4)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
1847617234glucose+
1847622599arabinose+
1847617992sucrose+
1847618222xylose-
1847617268myo-inositol-
1847629864mannitol-
1847628757fructose+
1847626546rhamnose+
1847616634raffinose+
1847662968cellulose+
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
18476+++++++++++++-++++-

API 20E

@refONPGADH ArgLDC LysODCCITH2SURETDA TrpINDVPGEL
18476+++++-+--++

Isolation, sampling and environmental information

isolation

@refsample type
9265air contamination
67770Air contamination

isolation source categories

Cat1Cat2Cat3
#Engineered#Laboratory#Contaminant
#Environmental#Air

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
184761German classification
92651Risk group (German classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Actinomyces israeli serotype 1 partial 16S rRNAX532281386ena1659
20218Streptomyces gardneri gene for 16S rRNA, partial sequenceAB122713564ena66892
20218Streptomyces gardneri gene for 16S ribosomal RNA, partial sequence, strain: JCM 4375D44091120ena66892
20218Streptomyces gardneri gene for 16S rRNA, partial sequence, strain: NBRC 12865AB2499081451ena66892
20218Streptomyces gardneri gene for 16S rRNA, partial sequence, strain: NBRC 3385AB1847541470ena66892
20218Streptomyces gardneri strain NRRL B-5615T 16S ribosomal RNA gene, partial sequenceDQ4425001442ena66892

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Streptomyces gardneri JCM 4375GCA_014655085contigncbi66892
66792Streptomyces gardneri strain JCM 437566892.4wgspatric66892
66792Streptomyces gardneri strain NBRC 1286566892.3wgspatric66892
67770Streptomyces gardneri NBRC 12865GCA_006539185contigncbi66892

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes98no
gram-positiveyes87.627no
anaerobicno99.418no
halophileno93.656no
spore-formingyes94.318no
glucose-utilyes90.227no
thermophileno99.158no
flagellatedno97.335no
motileno94.159no
aerobicyes92.249no
glucose-fermentno84.942no

External links

@ref: 9265

culture collection no.: DSM 40064, ATCC 23911, ATCC 9604, CBS 832.68, DSM 43020, ETH 28347, IFO 12865, IFO 13974, IFO 3385, IMET 7182, IMRU 3834, ISP 5064, JCM 3004, JCM 4375, KCC A-0004, KCC S-0375, NBRC 12865, NBRC 13974, NBRC 3385, RIA 1117, RIA 634, BCRC 12346, BCRC 13687, BCRC 13731, CGMCC 4.1956, NCTC 6531, NRRL B-5615, VKM Ac-1829

straininfo link

  • @ref: 84314
  • straininfo: 35082

literature

  • Pubmed-ID: 6968019
  • title: Polyclonal B cell activation by cell wall preparations of gram-positive bacteria. In vitro responses of spleen cells obtained from Balb/c, nu/nu, nu/+, C3H/He, C3H/HeJ and hybrid (DBA/N x Balb/c)F1 mice.
  • authors: Saito-Taki T, Tanabe MJ, Mochizuki H, Matsumoto T, Nakano M, Takada H, Tsujimoto M, Kotani S, Kusumoto S, Shiba T, Yokogawa K, Kawata S
  • journal: Microbiol Immunol
  • DOI: 10.1111/j.1348-0421.1980.tb00580.x
  • year: 1980
  • mesh: Animals, B-Lymphocytes/*immunology, Bacteria/*immunology, Cell Wall/immunology, Female, *Lymphocyte Activation, Male, Mice, Mice, Inbred Strains/immunology, Mice, Nude/immunology, Spleen/cytology

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
9265Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 40064)https://www.dsmz.de/collection/catalogue/details/culture/DSM-40064
18476Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM40064.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
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
84314Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID35082.1StrainInfo: A central database for resolving microbial strain identifiers