Strain identifier

BacDive ID: 16182

Type strain: Yes

Species: Streptomyces paromomycinus

Strain history: KCC S-0541 <-- IPV 1982 <-- NRRL 2455 <-- Parke, Davis & Co.; PD 04998.

NCBI tax ID(s): 92743 (species)

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General

@ref: 10293

BacDive-ID: 16182

DSM-Number: 41429

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

description: Streptomyces paromomycinus DSM 41429 is a spore-forming, mesophilic bacterium that builds an aerial mycelium and produces antibiotic compounds.

NCBI tax id

  • NCBI tax id: 92743
  • Matching level: species

strain history

@refhistory
10293<- NRRL
67770KCC S-0541 <-- IPV 1982 <-- NRRL 2455 <-- Parke, Davis & Co.; PD 04998.

doi: 10.13145/bacdive16182.20230509.8.1

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 paromomycinus
  • full scientific name: Streptomyces paromomycinus (Coffey et al. 1959) Komaki and Tamura 2019

  • synonyms

    • @ref: 20215
    • synonym: Streptomyces rimosus subsp. paromomycinus

@ref: 10293

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Streptomycetaceae

genus: Streptomyces

species: Streptomyces paromomycinus

full scientific name: Streptomyces paromomycinus (Coffey et al. 1959) Komaki and Tamura 2019

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram stain
69480no93.115
69480100positive

colony morphology

@refcolony colormedium used
69274Beige (1001)ISP 2
69274Beige (1001)ISP 6
69274Beige (1001)suter with tyrosine
69274Beige (1001)suter without tyrosine
69274Ivory (1014)ISP 4
69274Ochre yellow (1024)ISP 5
69274Ochre yellow (1024)ISP 7
69274Sand yellow (1002)ISP 3

multicellular morphology

@refforms multicellular complexcomplex namecomplex colormedium name
69274yesAerial myceliumTraffic white (9016)ISP 2
69274yesAerial myceliumCream (9001)ISP 3
69274yesAerial myceliumTraffic white (9016)ISP 4
69274yesAerial myceliumCream (9001)ISP 5
69274yesAerial myceliumTraffic white (9016)ISP 6
69274yesAerial myceliumCream (9001)ISP 7
69274yesAerial myceliumTraffic white (9016)suter with tyrosine
69274yesAerial myceliumTraffic white (9016)suter without tyrosine

pigmentation

@refproductionnamecolor
69274noMelanin
69274yessoluble pigmentSand yellow (1002)

multimedia

@refmultimedia contentcaptionintellectual property rights
69274DSM_41429_image3.jpegPlates (65, ISP2, ISP3, ISP4, ISP5, ISP7)Helmholtz-Zentrum für Infektionsforschung GmbH
69274DSM_41429_image4.jpegPlates (65, ISP2, ISP3, ISP4, ISP5, ISP7)Helmholtz-Zentrum für Infektionsforschung GmbH

Culture and growth conditions

culture medium

  • @ref: 10293
  • 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
10293positivegrowth28mesophilic
67770positivegrowth28mesophilic

Physiology and metabolism

spore formation

@refspore formationconfidence
69481yes100
69480yes100

compound production

  • @ref: 10293
  • compound: paramomycin

halophily

  • @ref: 69274
  • salt: NaCl
  • growth: positive
  • tested relation: growth
  • concentration: 0-10 %

observation

  • @ref: 67770
  • observation: quinones: MK-9(H6), MK-9(H4), MK-9(H2)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
6927422599arabinose-growth
6927462968cellulose-growth
6927428757fructose+growth
6927417234glucose+growth
6927417268inositol+growth
6927437684mannose+growth
6927416634raffinose+/-growth
6927426546rhamnose-growth
6927417992sucrose-growth
6927418222xylose-growth
6837917632nitrate+reduction
683794853esculin-hydrolysis
6837916199urea-hydrolysis
683795291gelatin+hydrolysis
6837917634D-glucose-fermentation
6837916988D-ribose-fermentation
6837965327D-xylose-fermentation
6837916899D-mannitol-fermentation
6837917306maltose-fermentation
6837917716lactose-fermentation
6837917992sucrose-fermentation
6837928087glycogen-fermentation

metabolite production

  • @ref: 67770
  • Chebi-ID: 7934
  • metabolite: paromomycin
  • production: yes

enzymes

@refvalueactivityec
68379gelatinase+
68379urease-3.5.1.5
68379beta-glucosidase-3.2.1.21
68379N-acetyl-beta-glucosaminidase-3.2.1.52
68379alpha-glucosidase-3.2.1.20
68379beta-galactosidase-3.2.1.23
68379beta-glucuronidase-3.2.1.31
68379alkaline phosphatase+3.1.3.1
68379pyrrolidonyl arylamidase+3.4.19.3
68379pyrazinamidase-3.5.1.B15
68382alkaline phosphatase+3.1.3.1
68382esterase (C 4)+
68382leucine arylamidase+3.4.11.1
68382valine arylamidase+
68382trypsin+3.4.21.4
68382acid phosphatase+3.1.3.2
68382naphthol-AS-BI-phosphohydrolase+
68382alpha-galactosidase+3.2.1.22
68382beta-galactosidase-3.2.1.23
68382beta-glucuronidase-3.2.1.31
68382beta-glucosidase+3.2.1.21
68382N-acetyl-beta-glucosaminidase+3.2.1.52
68382alpha-mannosidase+3.2.1.24
68382alpha-fucosidase-3.2.1.51

API coryne

@refNITPYZPYRAPALbeta GURbeta GALalpha GLUbeta NAGESCUREGELGLURIBXYLMANMALLACSACGLYG
69274+-++------+--------

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
69274+++/-+/-+++/-++/-+++--+/-+++-

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinent
10293soilColombiaCOLMiddle and South America
67770SoilColombiaCOLMiddle and South America

isolation source categories

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

Safety information

risk assessment

  • @ref: 10293
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Streptomyces rimosus subsp. paromomycinus strain CGMCC 4.1760 16S ribosomal RNA gene, partial sequenceJN5660271496ena92743
20218Streptomyces rimosus subsp. paromomycinus 16S rRNA gene, type strain DSM 41429TAJ6216101496ena92743
20218Streptomyces rimosus subsp. paromomycinus gene for 16S rRNA, partial sequence, strain: NBRC 15454AB1846801480ena92743

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Streptomyces rimosus subsp. paromomycinus strain NBRC 1545492743.3wgspatric92743
66792Streptomyces rimosus paromomycinus NRRL 24552582581347draftimg92743
67770Streptomyces paromomycinus NBRC 15454GCA_003865155contigncbi92743

GC content

  • @ref: 67770
  • GC-content: 72
  • method: genome sequence analysis

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes100no
motileno93.49no
flagellatedno97.689no
gram-positiveyes88.992no
anaerobicno98.982no
halophileno94.624no
spore-formingyes95.833no
glucose-utilyes89yes
aerobicyes91.744no
thermophileno98.282no
glucose-fermentno90.758no

External links

@ref: 10293

culture collection no.: DSM 41429, ATCC 14827, IPV 1982, JCM 4541, KCC S-0541, NRRL 2455, CBS 289.60, CGMCC 4.1760, IFO 15454, JCM 4871, NBIMCC 1699, NBRC 15454, VKM Ac-605

straininfo link

  • @ref: 85245
  • straininfo: 44481

literature

  • topic: Phylogeny
  • Pubmed-ID: 31225792
  • title: Reclassification of Streptomyces rimosus subsp. paromomycinus as Streptomyces paromomycinus sp. nov.
  • authors: Komaki H, Tamura T
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijsem.0.003545
  • year: 2019
  • mesh: Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Nucleic Acid Hybridization, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Streptomyces/*classification, Streptomyces rimosus/classification
  • topic2: Transcriptome

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
10293Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 41429)https://www.dsmz.de/collection/catalogue/details/culture/DSM-41429
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/
68379Automatically annotated from API Coryne
68382Automatically annotated from API zym
69274Wink, J.https://cdn.dsmz.de/wink/DSM%2041429.pdfCompendium of Actinobacteria. HZI-Helmholtz-Centre for Infection Research, Braunschweig
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
85245Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID44481.1StrainInfo: A central database for resolving microbial strain identifiers