Strain identifier
BacDive ID: 15377
Type strain:
Species: Streptomyces lincolnensis
Strain history: KCC S-0287 <-- NCIB 9413 <-- Upjohn Co., USA; UC 2376.
NCBI tax ID(s): 1915 (species)
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
@ref | history |
---|---|
9478 | <- E.B. Shirling, ISP <- NRRL <- A. Dietz, Upjohn Co. 2376 |
67770 | KCC 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
@ref | name | growth | link | composition |
---|---|---|---|---|
9478 | GYM STREPTOMYCES MEDIUM (DSMZ Medium 65) | yes | https://mediadive.dsmz.de/medium/65 | Name: 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 |
9478 | ROLLED OATS MINERAL MEDIUM (DSMZ Medium 84) | yes | https://www.dsmz.de/microorganisms/medium/pdf/DSMZ_Medium84.pdf |
culture temp
@ref | growth | type | temperature | range |
---|---|---|---|---|
9478 | positive | growth | 28 | mesophilic |
67770 | positive | growth | 28 | mesophilic |
Physiology and metabolism
spore formation
@ref | spore formation | confidence |
---|---|---|
69481 | yes | 100 |
69480 | yes | 100 |
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
@ref | biosafety level | biosafety level comment |
---|---|---|
9478 | 1 | Risk group (German classification) |
19442 | 1 | Risk group (German classification) |
Sequence information
16S sequences
@ref | description | accession | length | database | NCBI tax ID |
---|---|---|---|---|---|
20218 | Streptomyces lincolnensis gene for 16S ribosomal RNA, partial sequence, strain: JCM 4488 | D44182 | 120 | ena | 1915 |
20218 | Streptomyces lincolnensis gene for 16S rRNA, partial sequence, strain: NBRC 13054 | AB184279 | 1471 | ena | 1915 |
20218 | Streptomyces lincolnensis 16S rRNA gene, strain NRRL2936 | X79854 | 1519 | ena | 1915 |
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Streptomyces lincolnensis NRRL 2936 | GCA_001685355 | complete | ncbi | 1915 |
66792 | Streptomyces lincolnensis strain NRRL 2936 | 1915.4 | complete | patric | 1915 |
66792 | Streptomyces lincolnensis NRRL 2936 | 2872777253 | complete | img | 1915 |
66792 | Streptomyces lincolnensis ATCC 25466 | 2563366702 | draft | img | 1915 |
GC content
- @ref: 67770
- GC-content: 71
- method: genome sequence analysis
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
spore-forming | yes | 100 | no |
flagellated | no | 97.507 | no |
gram-positive | yes | 88.994 | no |
anaerobic | no | 99.351 | no |
aerobic | yes | 94.004 | no |
halophile | no | 92.34 | no |
spore-forming | yes | 94.586 | no |
glucose-util | yes | 90.708 | no |
thermophile | no | 98.987 | no |
motile | no | 93.393 | no |
glucose-ferment | no | 90.487 | no |
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
topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
---|---|---|---|---|---|---|---|---|
Metabolism | 813570 | Monophenol monooxygenase and lincomysin biosynthesis in Streptomyces lincolnensis. | Michalik J, Emilianowicz-Czerska W, Switalski L, Raczynska-Bojanowska K | Antimicrob Agents Chemother | 10.1128/AAC.8.5.526 | 1975 | Amino Acids/metabolism, Bacterial Proteins/metabolism, Catechol Oxidase/antagonists & inhibitors/*metabolism, Kinetics, Lincomycin/*biosynthesis, Streptomyces/enzymology/*metabolism, Tyrosine/metabolism | Enzymology |
Metabolism | 6163765 | A family of r-determinants in Streptomyces spp. that specifies inducible resistance to macrolide, lincosamide, and streptogramin type B antibiotics. | Fujisawa Y, Weisblum B | J Bacteriol | 10.1128/jb.146.2.621-631.1981 | 1981 | Anti-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/pharmacology | Phylogeny |
Enzymology | 8577249 | Molecular characterization of the lincomycin-production gene cluster of Streptomyces lincolnensis 78-11. | Peschke U, Schmidt H, Zhang HZ, Piepersberg W | Mol Microbiol | 10.1111/j.1365-2958.1995.tb02338.x | 1995 | ATP-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/metabolism | Genetics |
Metabolism | 11816970 | Putative 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 J | Antonie Van Leeuwenhoek | 10.1023/a:1012034421088 | 2001 | Amino 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/metabolism | Genetics |
Transcriptome | 19085073 | Sequence 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 J | Folia Microbiol (Praha) | 10.1007/s12223-008-0060-8 | 2008 | Anti-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/*metabolism | Metabolism |
19224545 | New carbasugars from Streptomyces lincolnensis. | Sedmera P, Halada P, Pospisil S | Magn Reson Chem | 10.1002/mrc.2408 | 2009 | Benzaldehydes/*chemistry, Magnetic Resonance Spectroscopy, Molecular Structure, Riboflavin/*analogs & derivatives/chemistry, Spectrometry, Mass, Electrospray Ionization, Stereoisomerism, Streptomyces/*chemistry | ||
Metabolism | 19917754 | Mutasynthesis 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 J | Antimicrob Agents Chemother | 10.1128/AAC.00918-09 | 2009 | Anti-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/*metabolism | Pathogenicity |
Phylogeny | 20363928 | Streptomyces caeruleatus sp. nov., with dark blue diffusible pigment. | Zhu HH, Guo J, Yao Q, Yang SZ, Deng MR, Li TH | Int J Syst Evol Microbiol | 10.1099/ijs.0.017392-0 | 2010 | *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/physiology | Genetics |
Phylogeny | 21930680 | Streptomyces 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 GH | Int J Syst Evol Microbiol | 10.1099/ijs.0.029959-0 | 2011 | Bacterial Typing Techniques, DNA, Bacterial/genetics, Molecular Sequence Data, *Phylogeny, *Pigmentation, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sewage, *Soil Microbiology, Streptomyces/*classification/genetics/*isolation & purification | Genetics |
Metabolism | 24324587 | Lincomycin 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 J | PLoS One | 10.1371/journal.pone.0079974 | 2013 | Anti-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/*metabolism | Enzymology |
Metabolism | 28455615 | Enhancement of antibiotic productions by engineered nitrate utilization in actinomycetes. | Meng S, Wu H, Wang L, Zhang B, Bai L | Appl Microbiol Biotechnol | 10.1007/s00253-017-8292-7 | 2017 | Actinobacteria/*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/metabolism | Biotechnology |
Metabolism | 29038257 | The 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 H | J Bacteriol | 10.1128/JB.00447-17 | 2017 | Bacterial Proteins/metabolism, *Gene Expression Regulation, Bacterial, Lincomycin/*biosynthesis, Multigene Family, Saccharopolyspora/genetics, Secondary Metabolism, Streptomyces/*genetics/*metabolism, Transcription Factors/genetics/*metabolism | |
31130942 | LmbU, 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 H | Front Microbiol | 10.3389/fmicb.2019.00989 | 2019 | |||
31708899 | AdpAlin, 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 H | Front Microbiol | 10.3389/fmicb.2019.02428 | 2019 | |||
Biotechnology | 32322696 | Complete 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 H | Synth Syst Biotechnol | 10.1016/j.synbio.2020.03.001 | 2020 | Genetics | |
Phylogeny | 32375929 | Streptomyces montanus sp. nov., a novel actinomycete isolated from soil. | Jiang H, Han L, Li J, Yu M, Zhao J, Guo X, Xiang W, Wang X | Int J Syst Evol Microbiol | 10.1099/ijsem.0.004160 | 2020 | Actinobacteria/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/chemistry | Transcriptome |
35384192 | Developmental 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 H | J Appl Microbiol | 10.1111/jam.15568 | 2022 | |||
Biotechnology | 36453540 | An 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 H | J Basic Microbiol | 10.1002/jobm.202200485 | 2022 |
Reference
@id | authors | catalogue | doi/url | title | journal | pubmed |
---|---|---|---|---|---|---|
9478 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 40355) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-40355 | |||
19442 | Wink, J. | http://www.dsmz.de/microorganisms/wink_pdf/DSM40355.pdf | Compendium of Actinobacteria. HZI-Helmholtz-Centre for Infection Research, Braunschweig | |||
20215 | Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M. | 10.1099/ijsem.0.004332 | List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ | |||
20218 | Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P. | 10.1016/j.syapm.2013.11.002 | StrainInfo introduces electronic passports for microorganisms. | Syst Appl Microbiol. 37: 42-50 2014 | 24321274 | |
66792 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | https://diaspora-project.de/progress.html#genomes | Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | |||
66794 | Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg | 10.1093/nar/gkaa1025 | BRENDA, the ELIXIR core data resource in 2021: new developments and updates | Nucleic Acids Res. 49: D498-D508 2020 | 33211880 | |
67770 | Curators of the JCM | https://jcm.brc.riken.jp/en/ | ||||
69480 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | https://diaspora-project.de/progress.html#genomes | Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | |||
69481 | Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch | 10.21203/rs.3.rs-2527258/v1 | Predictions based on the model GenomeNet Sporulation v. 1 | |||
84467 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID92615.1 | StrainInfo: A central database for resolving microbial strain identifiers |