Strain identifier

BacDive ID: 15377

Type strain: Yes

Species: Streptomyces lincolnensis

Strain history: KCC S-0287 <-- NCIB 9413 <-- Upjohn Co., USA; UC 2376.

NCBI tax ID(s): 1915 (species)

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

@ref: 9478

BacDive-ID: 15377

DSM-Number: 40355

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

description: Streptomyces lincolnensis DSM 40355 is a spore-forming, mesophilic, Gram-positive bacterium that produces antibiotic compounds and was isolated from soil.

NCBI tax id

  • NCBI tax id: 1915
  • Matching level: species

strain history

@refhistory
9478<- E.B. Shirling, ISP <- NRRL <- A. Dietz, Upjohn Co. 2376
67770KCC S-0287 <-- NCIB 9413 <-- Upjohn Co., USA; UC 2376.

doi: 10.13145/bacdive15377.20230509.8.1

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 lincolnensis
  • full scientific name: Streptomyces lincolnensis Mason et al. 1963 (Approved Lists 1980)

@ref: 9478

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Streptomycetaceae

genus: Streptomyces

species: Streptomyces lincolnensis

full scientific name: Streptomyces lincolnensis Mason et al. 1963 emend. Nouioui et al. 2018

type strain: yes

Morphology

cell morphology

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

multimedia

  • @ref: 9478
  • multimedia content: https://www.dsmz.de/microorganisms/photos/DSM_40355.jpg
  • caption: Medium 65 28°C
  • intellectual property rights: © Leibniz-Institut DSMZ

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
9478GYM 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
9478ROLLED OATS MINERAL MEDIUM (DSMZ Medium 84)yeshttps://www.dsmz.de/microorganisms/medium/pdf/DSMZ_Medium84.pdf

culture temp

@refgrowthtypetemperaturerange
9478positivegrowth28mesophilic
67770positivegrowth28mesophilic

Physiology and metabolism

spore formation

@refspore formationconfidence
69481yes100
69480yes100

compound production

  • @ref: 9478
  • compound: lincomycin

metabolite production

  • @ref: 67770
  • Chebi-ID: 6472
  • metabolite: lincomycin
  • production: yes

Isolation, sampling and environmental information

isolation

  • @ref: 9478
  • sample type: soil
  • country: USA
  • origin.country: USA
  • continent: North America

isolation source categories

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

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
94781Risk group (German classification)
194421Risk group (German classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Streptomyces lincolnensis gene for 16S ribosomal RNA, partial sequence, strain: JCM 4488D44182120ena1915
20218Streptomyces lincolnensis gene for 16S rRNA, partial sequence, strain: NBRC 13054AB1842791471ena1915
20218Streptomyces lincolnensis 16S rRNA gene, strain NRRL2936X798541519ena1915

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Streptomyces lincolnensis NRRL 2936GCA_001685355completencbi1915
66792Streptomyces lincolnensis strain NRRL 29361915.4completepatric1915
66792Streptomyces lincolnensis NRRL 29362872777253completeimg1915
66792Streptomyces lincolnensis ATCC 254662563366702draftimg1915

GC content

  • @ref: 67770
  • GC-content: 71
  • method: genome sequence analysis

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes100no
flagellatedno97.507no
gram-positiveyes88.994no
anaerobicno99.351no
aerobicyes94.004no
halophileno92.34no
spore-formingyes94.586no
glucose-utilyes90.708no
thermophileno98.987no
motileno93.393no
glucose-fermentno90.487no

External links

@ref: 9478

culture collection no.: DSM 40355, ATCC 25466, CBS 630.70, DSM 2013, IFO 13054, ISP 5355, JCM 4287, JCM 4488, KCC S-0287, NBRC 13054, NCIB 9413, NRRL 2936, RIA 1246, UC 2376, BCRC 11173, CBS 699.69, CCM 4150, KCTC 1868, KCTC 9088, KCTC 9089, NBIMCC 1526, NCIMB 9413, VKM Ac-727

straininfo link

  • @ref: 84467
  • straininfo: 92615

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Metabolism813570Monophenol monooxygenase and lincomysin biosynthesis in Streptomyces lincolnensis.Michalik J, Emilianowicz-Czerska W, Switalski L, Raczynska-Bojanowska KAntimicrob Agents Chemother10.1128/AAC.8.5.5261975Amino Acids/metabolism, Bacterial Proteins/metabolism, Catechol Oxidase/antagonists & inhibitors/*metabolism, Kinetics, Lincomycin/*biosynthesis, Streptomyces/enzymology/*metabolism, Tyrosine/metabolismEnzymology
Metabolism6163765A family of r-determinants in Streptomyces spp. that specifies inducible resistance to macrolide, lincosamide, and streptogramin type B antibiotics.Fujisawa Y, Weisblum BJ Bacteriol10.1128/jb.146.2.621-631.19811981Anti-Bacterial Agents/*pharmacology, Drug Resistance, Microbial, Erythromycin/pharmacology, Leucomycins/pharmacology, Methylation, RNA, Bacterial/metabolism, RNA, Ribosomal/metabolism, Species Specificity, Streptomyces/*drug effects/genetics/metabolism, Virginiamycin/pharmacologyPhylogeny
Enzymology8577249Molecular characterization of the lincomycin-production gene cluster of Streptomyces lincolnensis 78-11.Peschke U, Schmidt H, Zhang HZ, Piepersberg WMol Microbiol10.1111/j.1365-2958.1995.tb02338.x1995ATP-Binding Cassette Transporters/chemistry/genetics, Amino Acid Sequence, Base Sequence, Blotting, Southern, Cloning, Molecular, Conserved Sequence/genetics, DNA Probes, Electrophoresis, Gel, Pulsed-Field, Gene Expression Regulation, Bacterial, Genes, Bacterial, Lincomycin/*biosynthesis/chemistry, Molecular Sequence Data, Molecular Structure, *Multigene Family, Operon/genetics, Promoter Regions, Genetic, Sequence Alignment, Sequence Analysis, Streptomyces/chemistry/*genetics/metabolismGenetics
Metabolism11816970Putative lmbI and lmbH genes form a single lmbIH ORF in Streptomyces lincolnensis type strain ATCC 25466.Janata J, Najmanova L, Novotna J, Hola K, Felsberg J, Spizek JAntonie Van Leeuwenhoek10.1023/a:10120344210882001Amino Acid Sequence, Bacterial Proteins/chemistry/*genetics/metabolism, *Escherichia coli Proteins, Gene Expression Regulation, Bacterial, Genes, Bacterial, Lincomycin/*biosynthesis, Molecular Sequence Data, Multigene Family, Open Reading Frames/*genetics, *Protein Biosynthesis, Sequence Analysis, DNA, Streptomyces/*genetics/metabolismGenetics
Transcriptome19085073Sequence analysis and heterologous expression of the lincomycin biosynthetic cluster of the type strain Streptomyces lincolnensis ATCC 25466.Koberska M, Kopecky J, Olsovska J, Jelinkova M, Ulanova D, Man P, Flieger M, Janata JFolia Microbiol (Praha)10.1007/s12223-008-0060-82008Anti-Bacterial Agents/*biosynthesis/chemistry, Bacterial Proteins/genetics/*metabolism, Biotechnology, Cosmids, Gene Library, Lincomycin/*biosynthesis/chemistry, *Multigene Family, Point Mutation, *Sequence Analysis, DNA, Streptomyces/*genetics/growth & development/metabolism, Streptomyces coelicolor/genetics/*metabolismMetabolism
19224545New carbasugars from Streptomyces lincolnensis.Sedmera P, Halada P, Pospisil SMagn Reson Chem10.1002/mrc.24082009Benzaldehydes/*chemistry, Magnetic Resonance Spectroscopy, Molecular Structure, Riboflavin/*analogs & derivatives/chemistry, Spectrometry, Mass, Electrospray Ionization, Stereoisomerism, Streptomyces/*chemistry
Metabolism19917754Mutasynthesis of lincomycin derivatives with activity against drug-resistant staphylococci.Ulanova D, Novotna J, Smutna Y, Kamenik Z, Gazak R, Sulc M, Sedmera P, Kadlcik S, Plhackova K, Janata JAntimicrob Agents Chemother10.1128/AAC.00918-092009Anti-Bacterial Agents/chemistry/*metabolism/*pharmacology, Bacterial Proteins/genetics/metabolism, Humans, Lincomycin/analogs & derivatives/chemistry/*metabolism/*pharmacology, Microbial Sensitivity Tests, Molecular Structure, Proline/analogs & derivatives/metabolism, Staphylococcal Infections/microbiology, Staphylococcus/*drug effects, Streptomyces/genetics/*metabolismPathogenicity
Phylogeny20363928Streptomyces caeruleatus sp. nov., with dark blue diffusible pigment.Zhu HH, Guo J, Yao Q, Yang SZ, Deng MR, Li THInt J Syst Evol Microbiol10.1099/ijs.0.017392-02010*Antibiosis, China, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Lycopersicon esculentum, Molecular Sequence Data, Nucleic Acid Hybridization, Phylogeny, Pigments, Biological/*metabolism, RNA, Ribosomal, 16S/genetics, Rhizosphere, Sequence Analysis, DNA, Soil Microbiology, Streptomyces/*classification/genetics/*isolation & purification/physiologyGenetics
Phylogeny21930680Streptomyces shaanxiensis sp. nov., a blue pigment-producing streptomycete from sewage irrigation soil.Lin YB, Wang XY, Fang H, Ma YN, Tang J, Tang M, Wei GHInt J Syst Evol Microbiol10.1099/ijs.0.029959-02011Bacterial Typing Techniques, DNA, Bacterial/genetics, Molecular Sequence Data, *Phylogeny, *Pigmentation, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sewage, *Soil Microbiology, Streptomyces/*classification/genetics/*isolation & purificationGenetics
Metabolism24324587Lincomycin biosynthesis involves a tyrosine hydroxylating heme protein of an unusual enzyme family.Novotna J, Olsovska J, Novak P, Mojzes P, Chaloupkova R, Kamenik Z, Spizek J, Kutejova E, Mareckova M, Tichy P, Damborsky J, Janata JPLoS One10.1371/journal.pone.00799742013Anti-Bacterial Agents/*biosynthesis, Bacterial Proteins/genetics/*metabolism, Chromatography, High Pressure Liquid, Circular Dichroism, Dihydroxyphenylalanine/metabolism, Escherichia coli/enzymology/genetics, Gene Expression, Heme/chemistry/metabolism, Hemeproteins/genetics/*metabolism, Hydroxylation, Iron/chemistry/metabolism, Lincomycin/*biosynthesis, Multigene Family, Recombinant Proteins/genetics/metabolism, Streptomyces/*enzymology/genetics, Tyrosine/metabolism, Tyrosine 3-Monooxygenase/genetics/*metabolismEnzymology
Metabolism28455615Enhancement of antibiotic productions by engineered nitrate utilization in actinomycetes.Meng S, Wu H, Wang L, Zhang B, Bai LAppl Microbiol Biotechnol10.1007/s00253-017-8292-72017Actinobacteria/*genetics/metabolism, Anion Transport Proteins/genetics, Anthraquinones/metabolism, Anti-Bacterial Agents/*biosynthesis/metabolism, Bacterial Proteins/genetics, Gene Expression Regulation, Bacterial, Lincomycin/*biosynthesis, Nitrates/*metabolism, Nitrogen/metabolism, Pyrans/metabolism, Streptomyces/*genetics/metabolism, Streptomyces coelicolor/genetics, Trans-Activators/genetics/metabolismBiotechnology
Metabolism29038257The Novel Transcriptional Regulator LmbU Promotes Lincomycin Biosynthesis through Regulating Expression of Its Target Genes in Streptomyces lincolnensis.Hou B, Lin Y, Wu H, Guo M, Petkovic H, Tao L, Zhu X, Ye J, Zhang HJ Bacteriol10.1128/JB.00447-172017Bacterial Proteins/metabolism, *Gene Expression Regulation, Bacterial, Lincomycin/*biosynthesis, Multigene Family, Saccharopolyspora/genetics, Secondary Metabolism, Streptomyces/*genetics/*metabolism, Transcription Factors/genetics/*metabolism
31130942LmbU, a Cluster-Situated Regulator for Lincomycin, Consists of a DNA-Binding Domain, an Auto-Inhibitory Domain, and Forms Homodimer.Hou B, Zhu X, Kang Y, Wang R, Wu H, Ye J, Zhang HFront Microbiol10.3389/fmicb.2019.009892019
31708899AdpAlin, a Pleiotropic Transcriptional Regulator, Is Involved in the Cascade Regulation of Lincomycin Biosynthesis in Streptomyces lincolnensis.Kang Y, Wang Y, Hou B, Wang R, Ye J, Zhu X, Wu H, Zhang HFront Microbiol10.3389/fmicb.2019.024282019
Biotechnology32322696Complete genome sequence of high-yield strain S. lincolnensis B48 and identification of crucial mutations contributing to lincomycin overproduction.Wang R, Kong F, Wu H, Hou B, Kang Y, Cao Y, Duan S, Ye J, Zhang HSynth Syst Biotechnol10.1016/j.synbio.2020.03.0012020Genetics
Phylogeny32375929Streptomyces montanus sp. nov., a novel actinomycete isolated from soil.Jiang H, Han L, Li J, Yu M, Zhao J, Guo X, Xiang W, Wang XInt J Syst Evol Microbiol10.1099/ijsem.0.0041602020Actinobacteria/genetics, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Genes, Bacterial, Multilocus Sequence Typing, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Streptomyces/*classification/isolation & purification, Vitamin K 2/analogs & derivatives/chemistryTranscriptome
35384192Developmental regulator RamRsl controls both morphological development and lincomycin biosynthesis in Streptomyces lincolnensis.Wang R, Cao Y, Kong F, Hou B, Zhao J, Kang Y, Ye J, Wu H, Zhang HJ Appl Microbiol10.1111/jam.155682022
Biotechnology36453540An alternative sigma factor sigma(L) (sl) regulates lincomycin production in Streptomyces lincolnensis.Tu B, Mao Y, Wang R, Kang Y, Ye J, Zhang H, Wu HJ Basic Microbiol10.1002/jobm.2022004852022

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
9478Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 40355)https://www.dsmz.de/collection/catalogue/details/culture/DSM-40355
19442Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM40355.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)
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/
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
84467Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID92615.1StrainInfo: A central database for resolving microbial strain identifiers