Strain identifier

BacDive ID: 15378

Type strain: Yes

Species: Streptomyces litmocidini

Strain Designation: 1823/55

Strain history: KCC S-0394 <-- IFO 12792 <-- SAJ <-- ISP 5164 <-- INA 1823/55.

NCBI tax ID(s): 67318 (species)

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General

@ref: 9360

BacDive-ID: 15378

DSM-Number: 40164

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

description: Streptomyces litmocidini 1823/55 is a spore-forming, mesophilic bacterium that produces antibiotic compounds and was isolated from soil.

NCBI tax id

  • NCBI tax id: 67318
  • Matching level: species

strain history

@refhistory
9360<- E.B. Shirling, ISP <- T.P. Preobrazhenskaya, INA, 1823/55
67770KCC S-0394 <-- IFO 12792 <-- SAJ <-- ISP 5164 <-- INA 1823/55.

doi: 10.13145/bacdive15378.20230509.8.1

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 litmocidini
  • full scientific name: Streptomyces litmocidini (Ryabova and Preobrazhenskaya 1957) Pridham et al. 1958 (Approved Lists 1980)

  • synonyms

    • @ref: 20215
    • synonym: Actinomyces litmocidini

@ref: 9360

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Streptomycetaceae

genus: Streptomyces

species: Streptomyces litmocidini

full scientific name: Streptomyces litmocidini (Ryabova and Preobrazhenskaya 1957) Pridham et al. 1958

strain designation: 1823/55

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram stain
69480no95.395
69480100positive

Culture and growth conditions

culture medium

  • @ref: 9360
  • name: GYM STREPTOMYCES MEDIUM (DSMZ Medium 65)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/65
  • composition: 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

culture temp

@refgrowthtypetemperaturerange
9360positivegrowth28mesophilic
67770positivegrowth28mesophilic

Physiology and metabolism

spore formation

@refspore formationconfidence
69481yes100
69480yes100

compound production

@refcompound
9360litmocidin
9360granaticin
67770Litomocidin

Isolation, sampling and environmental information

isolation

@refsample type
9360soil
67770Soil

isolation source categories

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

taxonmaps

  • @ref: 69479
  • File name: preview.99_490.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_15;96_102;97_109;98_403;99_490&stattab=map
  • Last taxonomy: Streptomyces
  • 16S sequence: AB184149
  • Sequence Identity:
  • Total samples: 9252
  • soil counts: 6254
  • aquatic counts: 336
  • animal counts: 471
  • plant counts: 2191

Safety information

risk assessment

  • @ref: 9360
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Streptomyces litmocidini gene for 16S rRNA, partial sequenceAB122758564ena67318
20218Streptomyces litmocidini gene for 16S ribosomal RNA, partial sequence, strain: JCM 4394D44109120ena67318
20218Streptomyces litmocidini gene for 16S rRNA, partial sequence, strain: NBRC 12792AB1841491461ena67318
20218Streptomyces litmocidini strain NRRL B-3635 16S ribosomal RNA gene, partial sequenceEF6541011487ena67318

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Streptomyces litmocidini JCM 4394GCA_014649755scaffoldncbi67318
66792Streptomyces litmocidini strain JCM 439467318.3wgspatric67318

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes100no
flagellatedno97.581no
gram-positiveyes87.7no
anaerobicno99.316no
aerobicyes91.82no
halophileno95.118no
spore-formingyes94.322no
glucose-utilyes89.253no
thermophileno99.188yes
motileno93.973no
glucose-fermentno88.995no

External links

@ref: 9360

culture collection no.: DSM 40164, ATCC 19914, CBS 533.68, IFO 12792, ISP 5164, JCM 4394, NBRC 12792, RIA 1060, ATCC 19780, BCRC 11866, CGMCC 4.1902, INA 1823/55, NRRL B-3635, VKM Ac-1887, VTT E-072753

straininfo link

  • @ref: 84468
  • straininfo: 37158

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Enzymology3714878Construction and characterization of new cloning vectors derived from Streptomyces griseobrunneus plasmid pBT1 and containing amikacin and sulfomycin resistance genes.Nakanishi N, Oshida T, Yano S, Takeda K, Yamaguchi T, Ito YPlasmid10.1016/0147-619x(86)90040-51986Amikacin/biosynthesis/*pharmacology, *Anti-Bacterial Agents, Cloning, Molecular, DNA, Bacterial/analysis, Drug Resistance, Microbial, Genes, Bacterial, *Genetic Vectors, Kanamycin/*analogs & derivatives, Nucleic Acid Hybridization, Peptide Biosynthesis, Peptides/pharmacology, *Plasmids, Streptomyces/drug effects/*genetics/metabolism, Thiostrepton/pharmacologyPhylogeny
Phylogeny35258449Characterization of Streptomyces nymphaeiformis sp. nov., and its taxonomic relatedness to other polyhydroxybutyrate-degrading streptomycetes.Hix GR, Khan MS, Miller MT, Napier EC, O'Brien AL, White RP, Baron SFInt J Syst Evol Microbiol10.1099/ijsem.0.0052662022Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, *Fatty Acids/chemistry, Nucleic Acid Hybridization, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Streptomyces/geneticsTranscriptome

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
9360Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 40164)https://www.dsmz.de/collection/catalogue/details/culture/DSM-40164
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)
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
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
84468Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID37158.1StrainInfo: A central database for resolving microbial strain identifiers