Strain identifier

BacDive ID: 15428

Type strain: Yes

Species: Streptomyces nodosus

Strain history: KCC S-0297 <-- ATCC 14899 <-- SC 2388.

NCBI tax ID(s): 40318 (species)

For citation purpose refer to the digital object identifier (doi) of the current version.
Archive
version 8.1 (current version):
version 8:
version 7.1:
version 7:
version 6:
version 5:
version 4.1:
version 4:
version 3:
version 2.1:
version 2:
version 1:
version 8.1 (current version)

General

@ref: 9320

BacDive-ID: 15428

DSM-Number: 40109

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

description: Streptomyces nodosus DSM 40109 is a spore-forming, mesophilic, Gram-positive bacterium that was isolated from soil.

NCBI tax id

  • NCBI tax id: 40318
  • Matching level: species

strain history

@refhistory
9320<- E.B. Shirling, ISP <- W.H. Trejo, SC 2388
67770KCC S-0297 <-- ATCC 14899 <-- SC 2388.

doi: 10.13145/bacdive15428.20230509.8.1

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 nodosus
  • full scientific name: Streptomyces nodosus Trejo 1961 (Approved Lists 1980)

@ref: 9320

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Streptomycetaceae

genus: Streptomyces

species: Streptomyces nodosus

full scientific name: Streptomyces nodosus Trejo 1961 emend. Nouioui et al. 2018

type strain: yes

Morphology

cell morphology

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

multimedia

  • @ref: 9320
  • multimedia content: https://www.dsmz.de/microorganisms/photos/DSM_40109.jpg
  • caption: Medium 252 28°C
  • intellectual property rights: © Leibniz-Institut DSMZ

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
9320GYM 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
9320STARCH - MINERAL SALT - AGAR (STMS) (DSMZ Medium 252)yeshttps://www.dsmz.de/microorganisms/medium/pdf/DSMZ_Medium252.pdf

culture temp

@refgrowthtypetemperaturerange
18536positiveoptimum28mesophilic
9320positivegrowth28mesophilic
67770positivegrowth28mesophilic

Physiology and metabolism

spore formation

@refspore formationconfidence
69481yes100
69480yes100

compound production

@refcompound
9320amphotericin A
9320amphotericin A, B
9320amphotericin B
20216Amphotericin A (tetraenic)
20216Amphotericin B (heptaenic)

halophily

  • @ref: 18536
  • salt: NaCl
  • growth: positive
  • tested relation: maximum
  • concentration: 2.5 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
1853617234glucose+
1853622599arabinose-
1853617992sucrose-
1853618222xylose+
1853617268myo-inositol+/-
1853629864mannitol+/-
1853628757fructose+
1853626546rhamnose-
1853616634raffinose-
1853662968cellulose-
683685291gelatin+hydrolysis
6836827897tryptophan-energy source
6836816199urea+hydrolysis
6836816947citrate-assimilation
6836818257ornithine+degradation
6836825094lysine+degradation
6836829016arginine-hydrolysis

metabolite production

@refmetaboliteproductionChebi-ID
67770amphotericin Ayes
67770amphotericin Byes
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

API 20E

@refONPGADH ArgLDC LysODCCITH2SURETDA TrpINDVPGEL
18536+-++--+---+

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
9320soil
67770SoilOrinoco River regionVenezuelaVENMiddle and South America

isolation source categories

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

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
185361German classification
93201Risk group (German classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Streptomyces nodosus rrnB operon 16S ribosomal RNA, 23S ribosomal RNA, and 5S ribosomal RNA, complete sequenceAF1140336195ena40318
20218Streptomyces nodosus rrnD operon 16S ribosomal RNA, 23S ribosomal RNA, and 5S ribosomal RNA, complete sequenceAF1140346169ena40318
20218Streptomyces nodosus rrnE operon 16S ribosomal RNA, 23S ribosomal RNA, and 5S ribosomal RNA, complete sequenceAF1140356174ena40318
20218Streptomyces nodosus rrnF operon 16S ribosomal RNA, 23S ribosomal RNA, and 5S ribosomal RNA, complete sequenceAF1140366175ena40318
20218Streptomyces nodosus gene for 16S ribosomal RNA, partial sequence, strain: JCM 4656D44288120ena40318
20218Streptomyces nodosus gene for 16S rRNA, partial sequence, strain: NBRC 12895AB1842261476ena40318
20218Streptomyces nodosus strain NRRL B-2371 16S ribosomal RNA gene, partial sequenceDQ0266611495ena40318

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Streptomyces nodosus ATCC 14899GCA_008704995completencbi40318
66792Streptomyces nodosus ATCC 14899GCA_000819545chromosomencbi40318
66792Streptomyces nodosus DSM 40109GCA_014205035contigncbi40318
66792Streptomyces nodosus ATCC 1489940318.3completepatric40318
66792Streptomyces nodosus strain ATCC 1489940318.10completepatric40318
66792Streptomyces nodosus strain ATCC 1489940318.5wgspatric40318
66792Streptomyces nodosus strain DSM 4010940318.13wgspatric40318
66792Streptomyces nodosus ATCC 148992563366705draftimg40318
66792Streptomyces nodosus ATCC 148992867064541completeimg40318
66792Streptomyces nodosus DSM 401092870767688draftimg40318

GC content

  • @ref: 67770
  • GC-content: 70.9
  • method: genome sequence analysis

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes100no
flagellatedno98.23no
gram-positiveyes91.327no
anaerobicno98.797no
aerobicyes90.374no
halophileno96.247no
spore-formingyes96.029no
thermophileno96.31no
glucose-utilyes89.69yes
motileno94.395no
glucose-fermentno86.865no

External links

@ref: 9320

culture collection no.: DSM 40109, ATCC 14899, ATCC 23942, CBS 926.68, IFO 12895, ISP 5109, JCM 4297, JCM 4656, NBRC 12895, RIA 1123, SC 2388, BCRC 13768, CGMCC 4.1459, KCTC 9035, LMG 19340, NBIMCC 2208, NCIMB 12816, NRRL B-2371, RIA 831, VKM Ac-1224

straininfo link

  • @ref: 84515
  • straininfo: 13350

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Transcriptome10333524Molecular cloning and comparative sequence analyses of rRNA operons in Streptomyces nodosus ATCC 14899.Yap WH, Wang YGene10.1016/s0378-1119(99)00112-21999Base Sequence, Blotting, Southern, *Cloning, Molecular, Molecular Sequence Data, RNA, Bacterial/*genetics, RNA, Ribosomal, 16S/genetics, RNA, Ribosomal, 23S/genetics, RNA, Ribosomal, 5S/genetics, Restriction Mapping, Sequence Alignment, *Sequence Analysis, DNA, Streptomyces/*genetics, *rRNA OperonEnzymology
Enzymology11451671Amphotericin biosynthesis in Streptomyces nodosus: deductions from analysis of polyketide synthase and late genes.Caffrey P, Lynch S, Flood E, Finnan S, Oliynyk MChem Biol10.1016/s1074-5521(01)00046-12001ATP-Binding Cassette Transporters/genetics, Amphotericin B/analogs & derivatives/*biosynthesis, Anti-Bacterial Agents/biosynthesis, Cloning, Molecular, Combinatorial Chemistry Techniques, Cytochrome P-450 Enzyme System/genetics, Genes, Fungal/genetics, Multienzyme Complexes/genetics, Multigene Family/genetics, Protein Engineering, Sequence Analysis, DNA, Streptomyces/enzymology/genetics/*metabolism, Transcription, GeneticTranscriptome
Metabolism33189073Enhanced amphotericin B production by genetically engineered Streptomyces nodosus.Huang K, Zhang B, Shen ZY, Cai X, Liu ZQ, Zheng YGMicrobiol Res10.1016/j.micres.2020.1266232020Acyl Coenzyme A, Amphotericin B/*biosynthesis, Antifungal Agents/metabolism, Base Sequence, Batch Cell Culture Techniques, Bioreactors, Biosynthetic Pathways/genetics, Fermentation, Gene Expression Regulation, Bacterial, Genes, Bacterial/genetics, Genetic Engineering/*methods, Multigene Family, Mutagenesis, Polyketides/metabolism, Secondary Metabolism/genetics, Streptomyces/*genetics/*metabolismBiotechnology
Transcriptome33598451Comparative Transcriptome Analysis of Streptomyces nodosus Mutant With a High-Yield Amphotericin B.Huang K, Zhang B, Chen Y, Liu ZQ, Zheng YGFront Bioeng Biotechnol10.3389/fbioe.2020.6214312021Biotechnology
Biotechnology34194892Enhancing the production of amphotericin B by Strepyomyces nodosus in a 50-ton bioreactor based on comparative genomic analysis.Huang K, Zhang B, Chen Y, Wu ZM, Liu ZQ, Zheng YG3 Biotech10.1007/s13205-021-02844-22021

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
9320Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 40109)https://www.dsmz.de/collection/catalogue/details/culture/DSM-40109
18536Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM40109.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
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)
66794Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg10.1093/nar/gkaa1025BRENDA, the ELIXIR core data resource in 2021: new developments and updatesNucleic Acids Res. 49: D498-D508 202033211880
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
68368Automatically annotated from API 20E
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
84515Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID13350.1StrainInfo: A central database for resolving microbial strain identifiers