Strain identifier

BacDive ID: 16180

Type strain: Yes

Species: Streptomyces lomondensis

Strain history: KCC S-0866 <-- Upjohn Co., USA; UC 5022.

NCBI tax ID(s): 68229 (species)

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General

@ref: 10292

BacDive-ID: 16180

DSM-Number: 41428

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

description: Streptomyces lomondensis DSM 41428 is a spore-forming, mesophilic bacterium that builds an aerial mycelium and was isolated from soil.

NCBI tax id

  • NCBI tax id: 68229
  • Matching level: species

strain history

@refhistory
10292<- NRRL <- ATCC <- A. Dietz, UC 5022
67770KCC S-0866 <-- Upjohn Co., USA; UC 5022.

doi: 10.13145/bacdive16180.20230509.8.1

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 lomondensis
  • full scientific name: Streptomyces lomondensis Johnson and Dietz 1969 (Approved Lists 1980)

@ref: 10292

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Streptomycetaceae

genus: Streptomyces

species: Streptomyces lomondensis

full scientific name: Streptomyces lomondensis Johnson and Dietz 1969

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram stain
69480no91.12
69480100positive

colony morphology

@refcolony colorincubation periodmedium used
19497Orange10-14 daysISP 2
19497Red10-14 daysISP 3
19497Brown10-14 daysISP 4
19497Brown10-14 daysISP 5
19497Brown10-14 daysISP 6
19497Black10-14 daysISP 7

multicellular morphology

@refforms multicellular complexcomplex namecomplex colormedium name
19497yesAerial MyceliumBlue grey (7031)ISP 2
19497yesAerial MyceliumBlue grey (7031)ISP 3
19497yesAerial MyceliumBlue grey (7031)ISP 4
19497yesAerial MyceliumBlue grey (7031)ISP 5
19497yesAerial MyceliumBlue grey (7031)ISP 7
19497noISP 6

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
10292GYM 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
19497ISP 2yesName: ISP 2 / Yeast Malt Agar (5265); 5265 Composition Malt extract 10.0 g/l Yeast extract 4.0 g/l Glucose 4.0 g/l Agar 15.0 g/l Preparation: Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.0 Usage: Maintenance and Taxonomy Organisms: All Actinomycetes
19497ISP 3yesName: ISP 3; 5315 Composition Dog oat flakes 20.0 g/l Trace element solution (5314) 2.5 ml/l Agar 18.0 g/l Preparation: Oat flakes are cooked for 20 minutes, trace element solution and agar are added (in the case of non rolled oat flakes the suspension has to bee filtrated). Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.8 Usage: Maintenance and taxonomy (e.g. SEM As liquid medium for metabolite production) Organisms: All Actinomycetes Trace element solution 5314 Name: Trace element solution 5314; 5314 Composition CaCl2 x H2O 3.0 g/l Fe-III-citrate 1.0 g/l MnSO4 0.2 g/l ZnCl2 0.1 g/l CuSO4 x 5 H2O 0.025 g/l Sodium tetra borate 0.2 g/l CoCl2 x 6 H2O 0.004 g/l Sodium molybdate 0.01 g/l Preparation: Use double destillated water. Sterilisation: 20 minutes at 121°C pH before sterilisation: Usage: Trace element solution for different media Organisms:
19497ISP 4yesName: ISP 4; DSM 547 Solution I: Difco soluble starch, 10.0 g. Make a paste of the starch with a small amount of cold distilled water and bring to a volume of 500 ml. Solution II: CaCO3 2.0 g K2HPO4 (anhydrous) 1.0 g MgSO4 x 7 H2O 1.0 g NaCl 1.0 g (NH4)2SO4 2.0 g Distilled water 500.0 ml Trace salt solution (see below) 1.0 ml The pH should be between 7.0 and 7.4. Do not adjust if it is within this range. Mix solutions I and II together. Add 20.0 g agar. Liquify agar by steaming at 100°C for 10 to 20 min. Trace element solution: FeSO4 x 7 H2O 0.1 g MnCl2 x 4 H2O 0.1 g ZnSO4 x 7 H2O 0.1 g Distilled water 100.0 ml
19497ISP 5yesName: ISP 5 (5323) Composition L-Asparagine 1.0 g/l Glycerol 10.0 g/l K2HPO4 1.0 g/l Salt solution (see preparation) 1.0 ml/l Agar 20.0 g/l Preparation: Salt solution 1.0 g FeSO4 x 7 H2O 1.0 g MnCl2 x 4 H2O 1.0 g ZNSO4 x 7 H2O in 100 ml water Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.2 Usage: Maintenance and taxonomy Organisms: All Actinomycetes
19497ISP 6yesName: ISP 6 (5318) Composition Peptone 15.0 g/l Proteose peptose 5.0 g/l Ferric ammonium citrate 0.5 g/l Sodium glycerophosphate 1.0 g/l Sodium thiosulfate 0.08 g/l Yeast extract 1.0 g/l Agar 15.0 g/l Sterilisation: 20 minutes at 121°C pH before sterilisation: Usage: Production of melanoid pigments Organisms: All Actinomycetes
19497ISP 7yesName: ISP 7 (5322) Composition Glycerol 15.0 g/l L-Tyrosine 0.5 g/l L-Asparagine 1.0 g/l K2HPO4 0.5 g/l NaCl 0.5 g/l FeSO4 x 7 H2O 0.01 g/l Trace element solution 5343 1.0 ml/l Agar 20.0 Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.3 Usage: Production of melanoid pigments Organisms: All Actinomycetes

culture temp

@refgrowthtypetemperaturerange
10292positivegrowth28mesophilic
19497positiveoptimum28mesophilic
67770positivegrowth28mesophilic

Physiology and metabolism

spore formation

@refspore descriptiontype of sporespore formationconfidence
19497Formation of spore chains (retinaculiapetri)(hook), spore surface wartysporeyes
69481yes100
69480yes100

compound production

@refcompound
10292lomofungin
19497Phenazine antibiotic

halophily

  • @ref: 19497
  • salt: NaCl
  • growth: positive
  • tested relation: maximum
  • concentration: 5 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
1949762968cellulose-
1949716634raffinose+
1949726546rhamnose+
1949728757fructose-
1949729864mannitol+
1949717268myo-inositol+
1949718222xylose-
1949717992sucrose+
1949722599arabinose+
1949717234glucose+
683685291gelatin+hydrolysis
6836827897tryptophan-energy source
6836816199urea+hydrolysis
6836816947citrate+assimilation
6836818257ornithine-degradation
6836825094lysine-degradation
6836829016arginine+hydrolysis

metabolite production

@refmetaboliteproductionChebi-ID
67770lomofunginyes
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
19497++--+-++-++

Isolation, sampling and environmental information

isolation

@refsample type
10292soil
67770Soil

isolation source categories

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

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
102921Risk group (German classification)
194971Risk group (German classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Streptomyces lomondensis gene for 16S ribosomal RNA, partial sequence, strain: JCM 4866D44415121ena68229
20218Streptomyces lomondensis gene for 16S rRNA, partial sequence, strain: NBRC 15426AB1846731440ena68229
67770Streptomyces lomondensis 16S rRNA gene, type strain LMG 20088AJ7813521467ena68229

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Streptomyces lomondensis JCM 4866GCA_014651035scaffoldncbi68229
66792Streptomyces lomondensis strain JCM 486668229.3wgspatric68229
66792Streptomyces lomondensis DSM 41428GCA_021440105contigncbi68229

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes100no
flagellatedno97.971no
gram-positiveyes89.363no
anaerobicno98.803no
aerobicyes91.636no
halophileno93.332no
spore-formingyes96.63no
thermophileno97.854yes
glucose-utilyes90.051yes
motileno93.578no
glucose-fermentno88.928no

External links

@ref: 10292

culture collection no.: DSM 41428, ATCC 25299, JCM 4866, KCC S-0866, NCIB 10094, NRRL 3252, BCRC 12208, CGMCC 4.1746, IFO 15426, NBRC 15426, NCIMB 10094

straininfo link

  • @ref: 85243
  • straininfo: 265482

literature

  • topic: Phylogeny
  • Pubmed-ID: 22080411
  • title: Streptomyces deserti sp. nov., isolated from hyper-arid Atacama Desert soil.
  • authors: Santhanam R, Okoro CK, Rong X, Huang Y, Bull AT, Andrews BA, Asenjo JA, Weon HY, Goodfellow M
  • journal: Antonie Van Leeuwenhoek
  • DOI: 10.1007/s10482-011-9672-0
  • year: 2011
  • mesh: Carbon/metabolism, Chile, Culture Media, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, *Desert Climate, Humidity, Molecular Sequence Data, Nitrogen/metabolism, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Ribotyping, Sequence Alignment, Sequence Homology, Nucleic Acid, *Soil Microbiology, Species Specificity, Streptomyces/classification/genetics/growth & development/*isolation & purification/metabolism
  • topic2: Metabolism

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
10292Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 41428)https://www.dsmz.de/collection/catalogue/details/culture/DSM-41428
19497Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM41428.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)
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)
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
85243Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID265482.1StrainInfo: A central database for resolving microbial strain identifiers