Strain identifier

BacDive ID: 15448

Type strain: Yes

Species: Streptomyces olivochromogenes

Strain history: KCC S-0163 <-- IFO 3178 <-- ATCC 3336 <-- S. A. Waksman.

NCBI tax ID(s): 1963 (species)

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General

@ref: 9552

BacDive-ID: 15448

DSM-Number: 40451

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

description: Streptomyces olivochromogenes DSM 40451 is a spore-forming, mesophilic, Gram-positive bacterium that was isolated from soil.

NCBI tax id

  • NCBI tax id: 1963
  • Matching level: species

strain history

@refhistory
9552<- E.B. Shirling, ISP <- ATCC <- S.A. Waksman, IMRU
67770KCC S-0163 <-- IFO 3178 <-- ATCC 3336 <-- S. A. Waksman.

doi: 10.13145/bacdive15448.20230509.8.1

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 olivochromogenes
  • full scientific name: Streptomyces olivochromogenes (Waksman 1923) Waksman and Henrici 1948 (Approved Lists 1980)

  • synonyms

    • @ref: 20215
    • synonym: Actinomyces olivochromogenus

@ref: 9552

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Streptomycetaceae

genus: Streptomyces

species: Streptomyces olivochromogenes

full scientific name: Streptomyces olivochromogenes (Waksman 1923) Waksman and Henrici 1948 emend. Nouioui et al. 2018

type strain: yes

Morphology

cell morphology

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

colony morphology

@refcolony colorincubation periodmedium used
19457Beige10-14 daysISP 2
19457Beige10-14 daysISP 3
19457Beige10-14 daysISP 4
19457Beige10-14 daysISP 5
19457Beige10-14 daysISP 6
19457Beige10-14 daysISP 7

multicellular morphology

@refforms multicellular complexmedium name
19457noISP 2
19457noISP 3
19457noISP 4
19457noISP 5
19457noISP 6
19457noISP 7

multimedia

  • @ref: 9552
  • multimedia content: https://www.dsmz.de/microorganisms/photos/DSM_40451.jpg
  • caption: Medium 65 28°C
  • intellectual property rights: Leibniz-Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
9552GYM 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
19457ISP 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
19457ISP 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:
19457ISP 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
19457ISP 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
19457ISP 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
19457ISP 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
9552ROLLED OATS MINERAL MEDIUM (DSMZ Medium 84)yeshttps://www.dsmz.de/microorganisms/medium/pdf/DSMZ_Medium84.pdf

culture temp

@refgrowthtypetemperaturerange
19457positiveoptimum28mesophilic
9552positivegrowth28mesophilic
67770positivegrowth28mesophilic

Physiology and metabolism

spore formation

@refspore formationconfidence
69481yes100
69480yes100

compound production

  • @ref: 20216
  • compound: Streptomycin

halophily

  • @ref: 19457
  • salt: NaCl
  • growth: positive
  • tested relation: maximum
  • concentration: 2.5 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
1945762968cellulose-
1945716634raffinose-
1945726546rhamnose+
1945728757fructose+
1945729864mannitol+
1945717268myo-inositol+
1945718222xylose-
1945717992sucrose+
1945722599arabinose+
1945717234glucose+
683685291gelatin+hydrolysis
6836827897tryptophan-energy source
6836816199urea-hydrolysis
6836816947citrate-assimilation
6836818257ornithine-degradation
6836825094lysine-degradation
6836829016arginine-hydrolysis

metabolite production

@refChebi-IDmetaboliteproduction
6836815688acetoinyes
6836835581indoleno
6836816136hydrogen sulfideno

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
19457---------++

Isolation, sampling and environmental information

isolation

  • @ref: 9552
  • sample type: soil

isolation source categories

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

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
95521Risk group (German classification)
194571Risk group (German classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Streptomyces olivochromogenes DSM 40451 16S ribosomal RNA gene, partial sequenceAY0943701448ena1963
20218Streptomyces olivochromogenes gene for 16S ribosomal RNA, partial sequence, strain: JCM 4500D44192120ena1963
20218Streptomyces olivochromogenes gene for 16S rRNA, partial sequence, strain: NBRC 13067AB1842891470ena1963
20218Streptomyces olivochromogenes gene for 16S rRNA, partial sequence, strain: NBRC 3178AB1847371471ena1963

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Streptomyces olivochromogenes strain DSM 404511963.3wgspatric1963
66792Streptomyces olivochromogenes DSM 404512775507097draftimg1963
67770Streptomyces olivochromogenes DSM 40451GCA_001514115scaffoldncbi1963

GC content

  • @ref: 67770
  • GC-content: 70.2
  • method: genome sequence analysis

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes100no
motileno94.325no
gram-positiveyes87.215no
anaerobicno99.153no
aerobicyes92.203no
halophileno95.453no
spore-formingyes92.69no
glucose-utilyes89.569no
flagellatedno98.211no
thermophileno98.996yes
glucose-fermentno89.377no

External links

@ref: 9552

culture collection no.: DSM 40451, ATCC 25479, ATCC 3336, CBS 889.69, ETH 11886, ETH 14310, ETH 9517, IFO 13067, IMRU 3336, ISP 5451, KCC S-0163, KCC S-0500, NBRC 13067, NRRL B-1341, RIA 1259, JCM 4163, BCRC 15163, CGMCC 4.2000, IFO 3178, IMET 40352, JCM 4500, KCTC 9064, NBRC 3178

straininfo link

  • @ref: 84536
  • straininfo: 389312

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny15803387Streptomyces roseoalbus sp. nov., an actinomycete isolated from soil in Yunnan, China.Xu LH, Jiang Y, Li WJ, Wen ML, Li MG, Jiang CLAntonie Van Leeuwenhoek10.1007/s10482-004-3720-y2005Bacterial Typing Techniques, Base Sequence, China, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Genes, rRNA, Molecular Sequence Data, Phospholipids/analysis/isolation & purification, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sequence Homology, Nucleic Acid, *Soil Microbiology, Streptomyces/*classification/genetics/*isolation & purification, Vitamin K 2/analysis/isolation & purificationEnzymology
Phylogeny26790712Streptomyces arcticus sp. nov., isolated from frozen soil.Zhang L, Ruan C, Peng F, Deng Z, Hong KInt J Syst Evol Microbiol10.1099/ijsem.0.0009072016
Phylogeny27298302Streptomyces rhizosphaerihabitans sp. nov. and Streptomyces adustus sp. nov., isolated from bamboo forest soil.Lee HJ, Whang KSInt J Syst Evol Microbiol10.1099/ijsem.0.0012362016Bacterial Typing Techniques, DNA, Bacterial/genetics, Fatty Acids/chemistry, *Forests, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sasa/*microbiology, Sequence Analysis, DNA, *Soil Microbiology, Streptomyces/*classification/genetics/isolation & purification, Vitamin K 2/analogs & derivatives/chemistryTranscriptome
Phylogeny33180018Steptomyces fagopyri sp. nov., a novel actinomycete isolated from rhizospheric soil of Fagopyrum dibotrys.Guo Y, Tang X, Hu S, Li K, Zhou M, Jian GInt J Syst Evol Microbiol10.1099/ijsem.0.0045552020Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fagopyrum/*microbiology, Fatty Acids/chemistry, Genome Size, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Rhizosphere, Sequence Analysis, DNA, *Soil Microbiology, Streptomyces/*classification/isolation & purification, Vitamin K 2/analogs & derivatives/chemistryTranscriptome

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
9552Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 40451)https://www.dsmz.de/collection/catalogue/details/culture/DSM-40451
19457Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM40451.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
20216Curators of the HKIhttp://www.leibniz-hki.de/de/Collection Description Leibniz-Institut für Naturstoff-Forschung und Infektionsbiologie e. V. Hans-Knöll-Institut (HKI)
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/
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
84536Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID389312.1StrainInfo: A central database for resolving microbial strain identifiers