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Strain identifier

BacDive ID: 15391

Type strain: Yes

Species: Streptomyces lydicus

Strain history: KCC S-0492 <-- IFO 13058 <-- SAJ <-- ISP 5461 <-- NRRL 2433.

NCBI tax ID(s): 47763 (species)

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

@ref: 9558

BacDive-ID: 15391

DSM-Number: 40461

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

description: Streptomyces lydicus DSM 40461 is a mesophilic bacterium that produces antibiotic compounds and was isolated from soil.

NCBI tax id

  • NCBI tax id: 47763
  • Matching level: species

strain history

doi: 10.13145/bacdive15391.20221219.7.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Streptomycetales
  • family: Streptomycetaceae
  • genus: Streptomyces
  • species: Streptomyces lydicus
  • full scientific name: Streptomyces lydicus De Boer et al. 1956 (Approved Lists 1980)

@ref: 9558

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Streptomycetaceae

genus: Streptomyces

species: Streptomyces lydicus

full scientific name: Streptomyces lydicus De Boer et al. 1956 emend. Nouioui et al. 2018

type strain: yes

Morphology

cell morphology

  • @ref: 69480
  • gram stain: positive
  • confidence: 97.022

multimedia

  • @ref: 9558
  • multimedia content: https://www.dsmz.de/microorganisms/photos/DSM_40461.jpg
  • caption: Medium 65 28°C
  • intellectual property rights: © Leibniz-Institut DSMZ

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
9558STARCH - 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
9558ROLLED 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
9558GYM 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

culture temp

@refgrowthtypetemperaturerange
18594positiveoptimum28mesophilic
9558positivegrowth28mesophilic
67770positivegrowth28mesophilic

Physiology and metabolism

spore formation

  • @ref: 69480
  • spore formation: yes
  • confidence: 95.922

compound production

@refcompound
9558actithiazic acid
9558lydimycin
9558streptolydigin
20216Streptolydigin
20216Lydimycin
20216Actithiaic acid

halophily

  • @ref: 69480
  • halophily level: non-halophilic
  • confidence: 98.629

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
1859417234glucose+/-
1859422599arabinose+
1859417992sucrose+
1859418222xylose+
1859417268myo-inositol+
1859429864mannitol+
1859428757fructose+
1859426546rhamnose-
1859416634raffinose+
683685291gelatin+hydrolysis
6836827897tryptophan-energy source
6836816199urea+hydrolysis
6836816947citrate+assimilation
6836818257ornithine+degradation
6836825094lysine+degradation
6836829016arginine+hydrolysis

metabolite production

@refmetaboliteproductionChebi-ID
67770lydimycinyes
67770mycobacidinyes
67770streptolydiginyes45773
68368acetoinyes15688
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
18594+++++-++-++

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinentgeographic location
9558soilUSAUSANorth America
67770SoilUSAUSANorth AmericaMI

isolation source categories

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

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
185941German classification
95581Risk group (German classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Streptomyces lydicus strain CGMCC 4.1412 16S ribosomal RNA gene, partial sequenceJN5660181365ena47763
20218Streptomyces lydicus gene for 16S ribosomal RNA, partial sequence, strain: JCM 4492D44184121ena47763
9558Streptomyces lydicus gene for 16S rRNA, partial sequence, strain: NBRC 13058AB1842811489ena47763
9558Streptomyces lydicus 16S rRNA gene, strain ATCC 25470Y155071481ena47763

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Streptomyces lydicus strain ATCC 2547047763.31wgspatric47763
66792Streptomyces lydicus NRRL 2433651717112draftimg47763
67770Streptomyces lydicus NRRL ISP-5461GCA_000717345contigncbi47763
67770Streptomyces lydicus ATCC 25470GCA_004125245contigncbi47763

GC content

  • @ref: 67770
  • GC-content: 72.1
  • method: genome sequence analysis

External links

@ref: 9558

culture collection no.: DSM 40461, ATCC 25470, CBS 703.69, IFO 13058, ISP 5461, JCM 4492, NBRC 13058, NRRL 2433, RIA 1250, BCRC 11919, CECT 3163, CGMCC 4.1412, HAMBI 1063, IMET 43531, KCTC 9874, LMG 19331, NCIMB 12977, NRRL ISP-5461, VKM Ac-1869

straininfo link

@refpassport
20218http://www.straininfo.net/strains/55748
20218http://www.straininfo.net/strains/55745
20218http://www.straininfo.net/strains/837854
20218http://www.straininfo.net/strains/55749
20218http://www.straininfo.net/strains/55751
20218http://www.straininfo.net/strains/55752
20218http://www.straininfo.net/strains/334551
20218http://www.straininfo.net/strains/123732
20218http://www.straininfo.net/strains/55757

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Metabolism19875077Deciphering biosynthesis of the RNA polymerase inhibitor streptolydigin and generation of glycosylated derivatives.Olano C, Gomez C, Perez M, Palomino M, Pineda-Lucena A, Carbajo RJ, Brana AF, Mendez C, Salas JAChem Biol10.1016/j.chembiol.2009.09.0152009Aminoglycosides/*biosynthesis/chemistry, Chromatography, High Pressure Liquid, DNA-Directed RNA Polymerases/*antagonists & inhibitors/metabolism, Genetic Engineering, Mass Spectrometry, Multigene Family, Mutagenesis, Insertional, Peptide Synthases/genetics/metabolism, Polyketide Synthases/genetics/metabolism, Streptomyces/chemistry/*genetics/metabolism
Metabolism20176899Involvement of the beta subunit of RNA polymerase in resistance to streptolydigin and streptovaricin in the producer organisms Streptomyces lydicus and Streptomyces spectabilis.Sanchez-Hidalgo M, Nunez LE, Mendez C, Salas JAAntimicrob Agents Chemother10.1128/AAC.01406-092010Amino Acid Sequence, Aminoglycosides/chemistry/*metabolism, Anti-Bacterial Agents/chemistry/*metabolism, Binding Sites/physiology, DNA-Directed RNA Polymerases/*antagonists & inhibitors/genetics/metabolism, Drug Resistance, Bacterial/*physiology, Gene Expression Regulation, Bacterial/physiology, Microbial Sensitivity Tests, Molecular Sequence Data, Mutagenesis, Site-Directed, Protein Structure, Tertiary, RNA Polymerase III/chemistry/genetics/metabolism, Rifampin/metabolism, Streptomyces/genetics/*metabolism, Streptovaricin/chemistry/*metabolismGenetics
Phylogeny21669925Streptomyces staurosporininus sp. nov., a staurosporine-producing actinomycete.Kim BY, Zucchi TD, Fiedler HP, Goodfellow MInt J Syst Evol Microbiol10.1099/ijs.0.031922-02011Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Molecular Sequence Data, Nucleic Acid Hybridization, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Staurosporine/*biosynthesis, Streptomyces/*classification/genetics/isolation & purification, Vitamin K 2/analogs & derivatives/chemistryGenetics
Enzymology22569159Novel compounds produced by Streptomyces lydicus NRRL 2433 engineered mutants altered in the biosynthesis of streptolydigin.Gomez C, Olano C, Palomino-Schatzlein M, Pineda-Lucena A, Carbajo RJ, Brana AF, Mendez C, Salas JAJ Antibiot (Tokyo)10.1038/ja.2012.372012Aminoglycosides/*biosynthesis/pharmacology, Aminoisobutyric Acids/*isolation & purification/pharmacology, Anti-Bacterial Agents/biosynthesis, Genetic Engineering, Mutation, Streptomyces/enzymology/genetics/*metabolism, para-Aminobenzoates/*isolation & purification/pharmacologyPhylogeny
Metabolism22820841Three pathway-specific regulators control streptolydigin biosynthesis in Streptomyces lydicus.Gomez C, Olano C, Mendez C, Salas JAMicrobiology (Reading)10.1099/mic.0.061325-02012Amino Acid Sequence, Aminoglycosides/*biosynthesis, Bacterial Proteins/biosynthesis/genetics/*metabolism, *Gene Expression Regulation, Bacterial, *Genes, Regulator, Molecular Sequence Data, Multigene Family, Reverse Transcriptase Polymerase Chain Reaction, Sequence Alignment, Streptomyces/classification/*genetics/metabolismGenetics
Phylogeny27670691Streptomyces kronopolitis sp. nov., an actinomycete that produces phoslactomycins isolated from a millipede (Kronopolites svenhedind Verhoeff).Liu C, Ye L, Li Y, Jiang S, Liu H, Yan K, Xiang W, Wang XInt J Syst Evol Microbiol10.1099/ijsem.0.0015202016Animals, Arthropods/*microbiology, Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Streptomyces/*classification/genetics/isolation & purification, Vitamin K 2/analogs & derivatives/chemistryTranscriptome
Phylogeny32244447Characterization of Streptomyces piniterrae sp. nov. and Identification of the Putative Gene Cluster Encoding the Biosynthesis of Heliquinomycins.Zhuang X, Wang Z, Peng C, Su C, Gao C, Wang Y, Huang S, Liu CMicroorganisms10.3390/microorganisms80404952020

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
9558Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 40461)https://www.dsmz.de/collection/catalogue/details/culture/DSM-40461
18594Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM40461.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)