Strain identifier

BacDive ID: 13441

Type strain: Yes

Species: Saccharopolyspora rectivirgula

Strain history: KCC A-0057 <-- N. S. Agre 683.

NCBI tax ID(s): 1283279 (strain), 28042 (species)

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General

@ref: 11244

BacDive-ID: 13441

DSM-Number: 43747

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

description: Saccharopolyspora rectivirgula DSM 43747 is a spore-forming, thermophilic, Gram-positive bacterium that builds an aerial mycelium and was isolated from soil.

NCBI tax id

NCBI tax idMatching level
1283279strain
28042species

strain history

@refhistory
11244<- N.S. Agre, INMI, 683 (Micropolyspora rectivirgula)
67770KCC A-0057 <-- N. S. Agre 683.

doi: 10.13145/bacdive13441.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Pseudonocardiales
  • family: Pseudonocardiaceae
  • genus: Saccharopolyspora
  • species: Saccharopolyspora rectivirgula
  • full scientific name: Saccharopolyspora rectivirgula (Krassilnikov and Agre 1964) Korn-Wendisch et al. 1989

  • synonyms

    @refsynonym
    20215Micropolyspora faeni
    20215Thermopolyspora rectivirgula
    20215Micropolyspora rectivirgula
    20215Faenia rectivirgula

@ref: 11244

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Pseudonocardiaceae

genus: Saccharopolyspora

species: Saccharopolyspora rectivirgula

full scientific name: Saccharopolyspora rectivirgula (Krassilnikov and Agre 1964) Korn-Wendisch et al. 1989 emend. Nouioui et al. 2018

type strain: yes

Morphology

cell morphology

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

colony morphology

@refcolony colorincubation periodmedium used
19949Beige10-14 daysISP 2
19949Beige10-14 daysISP 3
19949Colorless10-14 daysISP 4
19949Beige10-14 daysISP 5
19949Yellow10-14 daysISP 6
19949Beige10-14 daysISP 7

multicellular morphology

@refforms multicellular complexmedium namecomplex namecomplex color
19949noISP 2
19949noISP 3
19949noISP 4
19949noISP 5
19949noISP 6
19949yesISP 7Aerial MyceliumWhite

multimedia

  • @ref: 11244
  • multimedia content: https://www.dsmz.de/microorganisms/photos/DSM_43747.jpg
  • caption: Medium 65 45°C
  • intellectual property rights: © Leibniz-Institut DSMZ

Culture and growth conditions

culture medium

@refnamegrowthcompositionlink
19949ISP 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
19949ISP 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:
19949ISP 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
19949ISP 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
19949ISP 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
19949ISP 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
11244GYM STREPTOMYCES MEDIUM (DSMZ Medium 65)yesName: 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 waterhttps://mediadive.dsmz.de/medium/65

culture temp

@refgrowthtypetemperaturerange
19949positivemaximum55thermophilic
19949positiveminimum40thermophilic
19949positiveoptimum45thermophilic
11244positivegrowth45thermophilic
67770positivegrowth50thermophilic

Physiology and metabolism

spore formation

@refspore formationconfidence
69481yes100
69480yes99.999

halophily

  • @ref: 19949
  • salt: NaCl
  • growth: positive
  • tested relation: maximum
  • concentration: 10 %

observation

  • @ref: 67770
  • observation: quinones: MK-9(H4), MK-10(H4), MK-9(H4), MK-9(II,III-H4)

metabolite utilization

@refChebi-IDmetaboliteutilization activity
1994962968cellulose+
1994916634raffinose+
1994926546rhamnose+
1994928757fructose+
1994929864mannitol+
1994917268myo-inositol+
1994918222xylose+
1994917992sucrose+
1994922599arabinose+
1994917234glucose+

Isolation, sampling and environmental information

isolation

@refsample typecountrycontinentgeographic location
11244soilUSSRAsia
67770SoilUSSRPamir

isolation source categories

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

taxonmaps

  • @ref: 69479
  • File name: preview.99_2681.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_10;96_1427;97_1703;98_2078;99_2681&stattab=map
  • Last taxonomy: Saccharopolyspora rectivirgula subclade
  • 16S sequence: JN010255
  • Sequence Identity:
  • Total samples: 6825
  • soil counts: 2203
  • aquatic counts: 522
  • animal counts: 3502
  • plant counts: 598

Safety information

risk assessment

@refbiosafety levelbiosafety level commentpathogenicity human
199491German classification
112441Risk group (German classification)yes, in single cases

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Saccharopolyspora rectivirgula strain ATCC 33515 16S ribosomal RNA gene, partial sequenceM203871246ena28042
20218Saccharopolyspora rectivirgula strain DSM 43747 16S ribosomal RNA gene, partial sequenceJN0102551507ena1283279
67770S.rectivirgula 16S rRNAX531941427ena28042

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Saccharopolyspora rectivirgula DSM 437471283279.3wgspatric1283279
66792Saccharopolyspora rectivirgula DSM 437472579778685draftimg1283279
67770Saccharopolyspora rectivirgula DSM 43747GCA_000497205contigncbi1283279

GC content

  • @ref: 67770
  • GC-content: 68.9
  • method: genome sequence analysis

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes100no
motileno93.977no
gram-positiveyes89.001no
anaerobicno96.632no
aerobicyes87.367no
halophileyes56.265no
spore-formingyes77.407no
thermophileyes84.882no
glucose-utilyes86.431no
flagellatedno98.054no
glucose-fermentno92.034no

External links

@ref: 11244

culture collection no.: DSM 43747, ATCC 33515, BKM A-810, INMI 683, KCC A-0057, VKM A-810, VKM Ac-810, JCM 3057, CGMCC 4.1362, IFM 0101, IFM 10562, IFM 1130, IFO 12464, IMSNU 20125, KACC 20055, KCTC 9487, MTCC 1547, NBRC 12464, NCIMB 12296, NRRL B-16280

straininfo link

  • @ref: 82633
  • straininfo: 40534

literature

  • topic: Phylogeny
  • Pubmed-ID: 21511892
  • title: Detection of Saccharopolyspora rectivirgula by quantitative real-time PCR.
  • authors: Schafer J, Kampfer P, Jackel U
  • journal: Ann Occup Hyg
  • DOI: 10.1093/annhyg/mer018
  • year: 2011
  • mesh: *Air Microbiology, Air Pollutants, Occupational/*analysis, Animal Husbandry, Animals, Blotting, Southern, Cloning, Molecular, DNA Primers, DNA, Bacterial/analysis/genetics, Ducks, Environmental Monitoring/methods, Farmer's Lung/microbiology, Housing, Animal, Humans, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics, *Real-Time Polymerase Chain Reaction, Saccharopolyspora/classification/genetics/*isolation & purification, Sensitivity and Specificity, Sequence Analysis/methods, Soil, rRNA Operon
  • topic2: Enzymology

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
11244Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 43747)https://www.dsmz.de/collection/catalogue/details/culture/DSM-43747
19949Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM43747.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/
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
82633Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID40534.1StrainInfo: A central database for resolving microbial strain identifiers