Strain identifier

BacDive ID: 15129

Type strain: Yes

Species: Streptomyces durhamensis

Strain Designation: 59123

Strain history: KCC S-0291 <-- M. A. Gordon 59123.

NCBI tax ID(s): 68194 (species)

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General

@ref: 9627

BacDive-ID: 15129

DSM-Number: 40539

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

description: Streptomyces durhamensis 59123 is a spore-forming, Gram-positive bacterium that produces antibiotic compounds and was isolated from soil from potted tomato plants.

NCBI tax id

  • NCBI tax id: 68194
  • Matching level: species

strain history

@refhistory
9627<- E.B. Shirling, ISP <- M.A. Gordon, 59123
67770KCC S-0291 <-- M. A. Gordon 59123.

doi: 10.13145/bacdive15129.20240916.9.1

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 durhamensis
  • full scientific name: Streptomyces durhamensis Gordon and Lapa 1966 (Approved Lists 1980)

@ref: 9627

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Streptomycetaceae

genus: Streptomyces

species: Streptomyces durhamensis

full scientific name: Streptomyces durhamensis Gordon and Lapa 1966 emend. Nouioui et al. 2018

strain designation: 59123

type strain: yes

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
9627GYM 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
9627ROLLED OATS MINERAL MEDIUM (DSMZ Medium 84)yeshttps://www.dsmz.de/microorganisms/medium/pdf/DSMZ_Medium84.pdf

culture temp

@refgrowthtypetemperature
18605positiveoptimum28
9627positivegrowth28
67770positivegrowth28

Physiology and metabolism

spore formation

  • @ref: 69481
  • spore formation: yes
  • confidence: 100

compound production

@refcompound
9627durhamycin
20216Durhamycin

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
1860517234glucose+
1860522599arabinose+
1860517992sucrose+
1860518222xylose+/-
1860517268myo-inositol+
1860529864mannitol+
1860528757fructose+
1860526546rhamnose+/-
1860516634raffinose+
1860562968cellulose+
683685291gelatin+hydrolysis
6836827897tryptophan-energy source
6836816199urea+hydrolysis
6836816947citrate+assimilation
6836818257ornithine+degradation
6836825094lysine+degradation
6836829016arginine+hydrolysis

metabolite production

@refmetaboliteproductionChebi-ID
67770durhamycinyes
68368acetoinno15688
68368indoleno35581
68368hydrogen sulfideno16136

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
18605+++-+++--++++-++++-

API 20E

@refONPGADH ArgLDC LysODCCITH2SURETDA TrpINDVPGEL
18605+++++-+---+

Isolation, sampling and environmental information

isolation

@refsample type
9627soil from potted tomato plants
67770Soil of potted tomato plant in Durham, N. C., after spraying of the plants with 2,4-dichlorophenoxyacetic acid

isolation source categories

Cat1Cat2Cat3
#Environmental#Terrestrial#Soil
#Host#Plants#Herbaceous plants (Grass,Crops)

taxonmaps

  • @ref: 69479
  • File name: preview.99_7980.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_15;96_102;97_224;98_253;99_7980&stattab=map
  • Last taxonomy: Streptomyces
  • 16S sequence: AB184405
  • Sequence Identity:
  • Total samples: 787
  • soil counts: 547
  • aquatic counts: 19
  • animal counts: 29
  • plant counts: 192

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
186051German classification
96271Risk group (German classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Streptomyces durhamensis gene for 16S rRNA, partial sequenceAB122732564nuccore68194
20218Streptomyces durhamensis gene for 16S ribosomal RNA, partial sequence, strain: JCM 4747D44331120nuccore68194
20218Streptomyces durhamensis gene for 16S rRNA, partial sequence, strain: NBRC 13441AB1844051432nuccore68194
20218Streptomyces durhamensis strain NRRL B-3309 16S ribosomal RNA gene, partial sequenceAY9997851494nuccore68194

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
67770Streptomyces durhamensis NRRL B-3309GCA_000725475scaffoldncbi68194
67770Streptomyces durhamensis NRRL ISP-5539GCA_000722375scaffoldncbi68194

GC content

  • @ref: 67770
  • GC-content: 71.7
  • method: genome sequence analysis

Genome-based predictions

predictions

@reftraitmodeldescriptionpredictionconfidencetraining_data
69481spore-formingspore-formingAbility to form endo- or exosporesyes100no
69480gram-positivegram-positivePositive reaction to Gram-stainingyes89.953no
69480anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)no96.398no
69480aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)yes89.992no
69480spore-formingspore-formingAbility to form endo- or exosporesyes89.349no
69480thermophilicthermophileAbility to grow at temperatures above or equal to 45°Cno98yes
69480flagellatedmotile2+Ability to perform flagellated movementno87no

External links

@ref: 9627

culture collection no.: DSM 40539, ATCC 23194, CBS 742.72, IFO 13441, ISP 5539, JCM 4291, NBRC 13441, RIA 1402, BCRC 16203, CGMCC 4.1699, HAMBI 1064, IMET 43359, JCM 4747, KCTC 9723, NRRL B-3309, NRRL ISP-5539, VKM Ac-763

straininfo link

  • @ref: 84234
  • straininfo: 125798

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny23959832Streptomyces yaanensis sp. nov., isolated from soil.Zheng J, Zhang X, Xin Y, Han X, Ni S, Zhang JInt J Syst Evol Microbiol10.1099/ijs.0.054734-02013Bacterial Typing Techniques, China, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Molecular Sequence Data, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Streptomyces/*classification/genetics/isolation & purification, Vitamin K 2/analogs & derivatives/chemistryGenetics
Phylogeny30896386Streptomyces fodineus sp. nov., an actinobacterium with antifungal activity isolated from mine area soil.Kim MK, Kang HJ, Roh SG, Park JS, Kim SBInt J Syst Evol Microbiol10.1099/ijsem.0.0033532019Antibiosis, Antifungal Agents, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, *Mining, Peptidoglycan/chemistry, Phospholipids/chemistry, *Phylogeny, Pigmentation, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, *Soil Microbiology, Streptomyces/*classification/isolation & purification, Vitamin K 2/analogs & derivatives/chemistryTranscriptome
Phylogeny33174827Streptomyces phaeolivaceus sp. nov. and Streptomyces broussonetiae sp. nov., isolated from the leaves and rhizosphere soil of Broussonetia papyrifera.Mo P, Liu J, Zhao Y, Xu ZInt J Syst Evol Microbiol10.1099/ijsem.0.0045562020Bacterial Typing Techniques, Base Composition, Broussonetia/*microbiology, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Nucleic Acid Hybridization, *Phylogeny, Plant Leaves, RNA, Ribosomal, 16S/genetics, Rhizosphere, Sequence Analysis, DNA, *Soil Microbiology, Streptomyces/*classification/isolation & purificationTranscriptome

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
9627Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 40539)https://www.dsmz.de/collection/catalogue/details/culture/DSM-40539
18605Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM40539.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
20216Curators of the HKIhttp://www.leibniz-hki.de/de/Collection Description Leibniz-Institut für Naturstoff-Forschung und Infektionsbiologie e. V. Hans-Knöll-Institut (HKI)
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
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
84234Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID125798.1StrainInfo: A central database for resolving microbial strain identifiers