Strain identifier

BacDive ID: 16027

Type strain: Yes

Species: Streptomyces spectabilis

Strain history: KCC S-0308 <-- T. Furumai <-- NRRL 2494 <-- Upjohn Co., USA.

NCBI tax ID(s): 68270 (species)

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General

@ref: 9610

BacDive-ID: 16027

DSM-Number: 40512

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

description: Streptomyces spectabilis DSM 40512 is a spore-forming, mesophilic bacterium that builds an aerial mycelium and produces antibiotic compounds.

NCBI tax id

  • NCBI tax id: 68270
  • Matching level: species

strain history

@refhistory
9610<- E.B. Shirling, ISP <- NRRL <- Upjohn Co
67770KCC S-0308 <-- T. Furumai <-- NRRL 2494 <-- Upjohn Co., USA.

doi: 10.13145/bacdive16027.20230509.8.1

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 spectabilis
  • full scientific name: Streptomyces spectabilis Mason et al. 1961 (Approved Lists 1980)

@ref: 9610

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Streptomycetaceae

genus: Streptomyces

species: Streptomyces spectabilis

full scientific name: Streptomyces spectabilis Mason et al. 1961

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram stain
69480no91.053
69480100positive

colony morphology

@refcolony colorincubation periodmedium used
19469Red10-14 daysISP 2
19469Orange10-14 daysISP 3
19469Orange10-14 daysISP 4
19469Red10-14 daysISP 5
19469Yellow10-14 daysISP 6
19469Red10-14 daysISP 7

multicellular morphology

@refforms multicellular complexcomplex namecomplex colormedium name
19469yesAerial MyceliumWhite/ redISP 2
19469yesAerial MyceliumSparse whiteISP 3
19469yesAerial MyceliumWhiteISP 4
19469yesAerial MyceliumWhite/ redISP 5
19469noISP 6
19469yesAerial MyceliumWhite/ redISP 7

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
9610GYM 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
19469ISP 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
19469ISP 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:
19469ISP 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
19469ISP 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
19469ISP 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
19469ISP 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
9610ROLLED OATS MINERAL MEDIUM (DSMZ Medium 84)yeshttps://www.dsmz.de/microorganisms/medium/pdf/DSMZ_Medium84.pdf

culture temp

@refgrowthtypetemperaturerange
9610positivegrowth28mesophilic
19469positiveoptimum30mesophilic
67770positivegrowth28mesophilic

Physiology and metabolism

spore formation

@refspore descriptiontype of sporespore formationconfidence
19469Formation of spore chains (rectiflixibilis), spore surface smoothsporeyes
69481yes100
69480yes100

compound production

@refcompound
9610actinospectacin
9610prodigiosine
9610streptovaricin complex
9610lincomycin sulfoxides
19469Spectinomycin
19469Spectomycin
19469Streptovaricin

halophily

  • @ref: 19469
  • salt: NaCl
  • growth: positive
  • tested relation: maximum
  • concentration: 5 %

observation

  • @ref: 67770
  • observation: quinones: MK-9(H6), MK-9(H8)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
683685291gelatin+hydrolysis
6836827897tryptophan-energy source
6836816199urea+hydrolysis
6836816947citrate+assimilation
6836818257ornithine+degradation
6836825094lysine+degradation
6836829016arginine+hydrolysis

metabolite production

@refmetaboliteproductionChebi-ID
67770spectinomycinyes
67770streptovaricinyes
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
19469+++++-++-++

Isolation, sampling and environmental information

isolation

  • @ref: 67770
  • sample type: Soil
  • geographic location: Dallas, TX
  • country: USA
  • origin.country: USA
  • continent: North America

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
96101Risk group (German classification)
194691Risk group (German classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Streptomyces spectabilis gene for 16S ribosomal RNA, partial sequence, strain: JCM 4832D44395121ena68270
20218Streptomyces spectabilis gene for 16S rRNA, partial sequence, strain: NBRC 13424AB1843931470ena68270
20218Streptomyces spectabilis gene for 16S rRNA, partial sequence, strain: NBRC 15441AB1846771451ena68270
20218Streptomyces spectabilis strain NRRL 2494 16S ribosomal RNA gene, partial sequenceAY9999261317ena68270
20218Streptomyces exfoliatus strain NRRL B-2924 16S ribosomal RNA gene, partial sequenceDQ0266471482ena1905

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Streptomyces spectabilis ATCC 27465GCA_008704795completencbi68270
66792Streptomyces spectabilis CECT 3146GCA_014203475scaffoldncbi68270
66792Streptomyces spectabilis JCM 4308GCA_014649235scaffoldncbi68270
66792Streptomyces spectabilis strain ATCC 2746568270.5completepatric68270
66792Streptomyces spectabilis strain CECT 314668270.8wgspatric68270
66792Streptomyces spectabilis strain JCM 430868270.9wgspatric68270
66792Streptomyces spectabilis CECT 31462863231158draftimg68270
66792Streptomyces spectabilis KCTC9218GCA_022698305contigncbi68270

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes100no
motileno91.961no
flagellatedno97.689no
gram-positiveyes89.563no
anaerobicno99.387no
aerobicyes90.212no
halophileno91.966no
spore-formingyes93.798yes
thermophileno99.245no
glucose-utilyes89.999no
glucose-fermentno86.539no

External links

@ref: 9610

culture collection no.: DSM 40512, ATCC 27465, CBS 725.72, IFO 13424, ISP 5512, JCM 4308, NBRC 13424, NRRL 2494, RIA 1385, BCRC 12648, CECT 3146, IFO 15441, JCM 4832, KCTC 9218, LMG 5986, NBIMCC 70, NBRC 15441, NCAIM B.01936, NCIMB 9733

straininfo link

  • @ref: 85100
  • straininfo: 92721

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny19090420Isolation and identification of alpha,alpha-trehalose and glycerol from an arctic psychrotolerant Streptomyces sp. SB9 and their possible role in the strain's survival.Ivanova V, Lyutskanova D, Stoilova-Disheva M, Kolarova M, Aleksieva K, Raykovska V, Peltekova V, Laatsch HPrep Biochem Biotechnol10.1080/108260608025895852009Arctic Regions, Cell Survival, Glycerol/*isolation & purification/*metabolism, *Soil Microbiology, Species Specificity, Streptomyces/*classification/*metabolism, Trehalose/*isolation & purification/*metabolismMetabolism
Metabolism20176899Involvement of the beta subunit of RNA polymerase in resistance to streptolydigin and streptovaricin in the producer organisms Streptomyces lydicus and Streptomyces spectabilis.Sanchez-Hidalgo M, Nunez LE, Mendez C, Salas JAAntimicrob Agents Chemother10.1128/AAC.01406-092010Amino Acid Sequence, Aminoglycosides/chemistry/*metabolism, Anti-Bacterial Agents/chemistry/*metabolism, Binding Sites/physiology, DNA-Directed RNA Polymerases/*antagonists & inhibitors/genetics/metabolism, Drug Resistance, Bacterial/*physiology, Gene Expression Regulation, Bacterial/physiology, Microbial Sensitivity Tests, Molecular Sequence Data, Mutagenesis, Site-Directed, Protein Structure, Tertiary, RNA Polymerase III/chemistry/genetics/metabolism, Rifampin/metabolism, Streptomyces/genetics/*metabolism, Streptovaricin/chemistry/*metabolismGenetics
Phylogeny28005517Streptomyces lasiicapitis sp. nov., an actinomycete that produces kanchanamycin, isolated from the head of an ant (Lasius fuliginosus L.).Ye L, Zhao S, Li Y, Jiang S, Zhao Y, Li J, Yan K, Wang X, Xiang W, Liu CInt J Syst Evol Microbiol10.1099/ijsem.0.0017562017Animals, Ants/*microbiology, Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Fatty Acids/chemistry, Genes, Bacterial, Nucleic Acid Hybridization, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Streptomyces/*classification/genetics/isolation & purificationTranscriptome
29387049Growth Promotion and Disease Suppression Ability of a Streptomyces sp. CB-75 from Banana Rhizosphere Soil.Chen Y, Zhou D, Qi D, Gao Z, Xie J, Luo YFront Microbiol10.3389/fmicb.2017.027042018
Phylogeny30302648Streptomyces monticola sp. nov., a novel actinomycete isolated from soil.Li D, Han L, Zhao J, Ju H, Jiang S, Guo X, Wang X, Xiang WAntonie Van Leeuwenhoek10.1007/s10482-018-1177-72018China, Cluster Analysis, Cytosol/chemistry, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Multilocus Sequence Typing, Nucleic Acid Hybridization, Phospholipids/analysis, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Streptomyces/*classification/*isolation & purification, Vitamin K 2/analysisTranscriptome
Phylogeny32372105Antimicrobial and Antioxidant Effects of a Forest Actinobacterium V002 as New Producer of Spectinabilin, Undecylprodigiosin and Metacycloprodigiosin.Gacem MA, Ould-El-Hadj-Khelil A, Boudjemaa B, Wink JCurr Microbiol10.1007/s00284-020-02007-12020Algeria, *Anti-Infective Agents, *Antioxidants, DNA, Bacterial, Fatty Acids, Forests, Phylogeny, Prodigiosin/analogs & derivatives, Pyrones, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Soil Microbiology, StreptomycesTranscriptome
Transcriptome35996099Whole-genome sequencing and analysis of Streptomyces strains producing multiple antinematode drugs.Yi JS, Kim JM, Kang MK, Kim JH, Cho HS, Ban YH, Song MC, Son KH, Yoon YJBMC Genomics10.1186/s12864-022-08847-42022Animals, *Antinematodal Agents/pharmacology, Multigene Family, Nematoda/drug effects, *Secondary Metabolism, Sequence Analysis, DNA, *Streptomyces/genetics/metabolism, Whole Genome SequencingGenetics

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
9610Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 40512)https://www.dsmz.de/collection/catalogue/details/culture/DSM-40512
19469Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM40512.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)
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
85100Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID92721.1StrainInfo: A central database for resolving microbial strain identifiers