Strain identifier

BacDive ID: 13455

Type strain: Yes

Species: Saccharopolyspora spinosa

Strain history: NRRL 18395 <-- F. P. Mertz A83543.1.

NCBI tax ID(s): 994479 (strain), 60894 (species)

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General

@ref: 11612

BacDive-ID: 13455

DSM-Number: 44228

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

description: Saccharopolyspora spinosa DSM 44228 is a spore-forming, mesophilic bacterium that builds an aerial mycelium and was isolated from soil; sugar mill rum still.

NCBI tax id

NCBI tax idMatching level
994479strain
60894species

strain history

@refhistory
11612<- NRRL <- ? <- F. P. Mertz, A 83543.1
67770NRRL 18395 <-- F. P. Mertz A83543.1.

doi: 10.13145/bacdive13455.20230509.8.1

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 spinosa
  • full scientific name: Saccharopolyspora spinosa Mertz and Yao 1990

@ref: 11612

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Pseudonocardiaceae

genus: Saccharopolyspora

species: Saccharopolyspora spinosa

full scientific name: Saccharopolyspora spinosa Mertz and Yao 1990 emend. Nouioui et al. 2018

type strain: yes

Morphology

colony morphology

@refcolony colorincubation periodmedium used
20023Colorless10-14 daysISP 2
20023Colorless10-14 daysISP 3
20023Colorless10-14 daysISP 4
20023Colorless10-14 daysISP 5
20023Colorless10-14 daysISP 6
20023Colorless10-14 daysISP 7

multicellular morphology

@refforms multicellular complexcomplex namecomplex colormedium name
20023yesAerial MyceliumWhiteISP 2
20023yesAerial MyceliumWhiteISP 3
20023noISP 4
20023noISP 5
20023yesAerial MyceliumWhiteISP 6
20023yesAerial MyceliumWhiteISP 7

multimedia

  • @ref: 11612
  • multimedia content: https://www.dsmz.de/microorganisms/photos/DSM_44228.jpg
  • caption: Medium 65 28°C
  • intellectual property rights: © Leibniz-Institut DSMZ

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
11612GPHF-MEDIUM (DSMZ Medium 553)yeshttps://mediadive.dsmz.de/medium/553Name: GPHF-MEDIUM (DSMZ Medium 553) Composition: Agar 20.0 g/l Glucose 10.0 g/l Beef extract 5.0 g/l Yeast extract 5.0 g/l Casein peptone 5.0 g/l CaCl2 x 2 H2O 0.74 g/l Distilled water
11612GYM 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
20023ISP 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
20023ISP 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:
20023ISP 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
20023ISP 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
20023ISP 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
20023ISP 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
11612positivegrowth28mesophilic
20023positiveoptimum28mesophilic
67770positivegrowth28mesophilic

Physiology and metabolism

spore formation

  • @ref: 20023
  • spore description: Formation of spore chains (spirales)(Sp), spore surface hairy
  • spore formation: yes

halophily

  • @ref: 20023
  • salt: NaCl
  • growth: positive
  • tested relation: maximum
  • concentration: 5 %

observation

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

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2002317234glucose-
2002322599arabinose-
2002317992sucrose-
2002318222xylose-
2002317268myo-inositol-
2002329864mannitol-
2002328757fructose-
2002326546rhamnose-
2002316634raffinose-
2002362968cellulose-
683685291gelatin+hydrolysis
6836827897tryptophan-energy source
6836816199urea+hydrolysis
6836816947citrate+assimilation
6836818257ornithine+degradation
6836825094lysine-degradation
6836829016arginine+hydrolysis

metabolite production

@refChebi-IDmetaboliteproduction
6777039207spinosynyes
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
68382alkaline phosphatase+3.1.3.1
68382esterase (C 4)-
68382esterase lipase (C 8)+
68382lipase (C 14)-
68382leucine arylamidase+3.4.11.1
68382valine arylamidase+
68382cystine arylamidase+3.4.11.3
68382trypsin+3.4.21.4
68382alpha-chymotrypsin-3.4.21.1
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
68382alpha-glucosidase-3.2.1.20
68382beta-glucosidase-3.2.1.21
68382N-acetyl-beta-glucosaminidase+3.2.1.52

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidase
20023+-+-++++-++-----+

API 20E

@refONPGADH ArgLDC LysODCCITH2SURETDA TrpINDVPGEL
20023++-++-+--++

Isolation, sampling and environmental information

isolation

@refsample typecountrycontinentgeographic locationorigin.country
11612soil; sugar mill rum stillVirgin Islands (U.S.)Middle and South America
67770Soil from a sugar mill rum stillUSANorth AmericaVirgin IslandsUSA

isolation source categories

Cat1Cat2Cat3
#Engineered#Industrial#Industrial production
#Environmental#Terrestrial#Soil

taxonmaps

  • @ref: 69479
  • File name: preview.99_2603.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_10;96_1393;97_1660;98_2017;99_2603&stattab=map
  • Last taxonomy: Saccharopolyspora spinosa
  • 16S sequence: LC149867
  • Sequence Identity:
  • Total samples: 1041
  • soil counts: 641
  • aquatic counts: 47
  • animal counts: 206
  • plant counts: 147

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
116121Risk group (German classification)
200231German classification

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Saccharopolyspora spinosa 16S ribosomal RNA gene, partial sequenceAF0028181465ena994479
67770Saccharopolyspora spinosa gene for 16S ribosomal RNA, partial sequence, strain: JCM 9375LC1498671453ena60894

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Saccharopolyspora spinosa NRRL 18395994479.3wgspatric994479
66792Saccharopolyspora spinosa strain DSM 4422860894.4wgspatric60894
66792Saccharopolyspora spinosa DSM 442282634166199draftimg994479
66792Saccharopolyspora spinosa NRRL 183952547132038draftimg994479
67770Saccharopolyspora spinosa NRRL 18395GCA_000194155scaffoldncbi994479
67770Saccharopolyspora spinosa DSM 44228GCA_002846475contigncbi60894

GC content

  • @ref: 67770
  • GC-content: 67.94
  • method: genome sequence analysis

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
motileno93.412no
flagellatedno98.195no
gram-positiveyes91.769no
anaerobicno98.647no
halophileno64.288no
spore-formingyes92.815no
thermophileno96.252no
glucose-utilyes82.935yes
aerobicyes92.018no
glucose-fermentno92.111no

External links

@ref: 11612

culture collection no.: DSM 44228, ATCC 49460, NRRL 18395, JCM 9375, BCRC 16299, CGMCC 4.1365, CPCC 204088, IFO 15153, KACC 20097, NBRC 15153

straininfo link

  • @ref: 82647
  • straininfo: 42489

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Genetics15346767Analysis of a 108-kb region of the Saccharopolyspora spinosa genome covering the obscurin polyketide synthase locus.Zirkle R, Black TA, Gorlach J, Ligon JM, Molnar IDNA Seq10.1080/10425170420002081672004Cloning, Molecular, Conserved Sequence/genetics, *Genome, Bacterial, Guanine Nucleotide Exchange Factors/chemistry/genetics, Molecular Sequence Data, Multienzyme Complexes/*genetics, Muscle Proteins/chemistry/genetics, Saccharopolyspora/*genetics, Sequence Analysis, DNAEnzymology
Phylogeny18450710Saccharopolyspora antimicrobica sp. nov., an actinomycete from soil.Yuan LJ, Zhang YQ, Guan Y, Wei YZ, Li QP, Yu LY, Li WJ, Zhang YQInt J Syst Evol Microbiol10.1099/ijs.0.65532-02008Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Genes, rRNA, Molecular Sequence Data, Nucleic Acid Hybridization, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Saccharopolyspora/*classification/genetics/isolation & purification/physiology, Sequence Analysis, DNA, *Soil Microbiology, Species SpecificityGenetics
Phylogeny19643898Saccharopolyspora tripterygii sp. nov., an endophytic actinomycete isolated from the stem of Tripterygium hypoglaucum.Li J, Zhao GZ, Qin S, Huang HY, Zhu WY, Xu LH, Li WJInt J Syst Evol Microbiol10.1099/ijs.0.011734-02009DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Molecular Sequence Data, Phylogeny, Plant Stems/microbiology, RNA, Ribosomal, 16S/genetics, Saccharopolyspora/*classification/genetics/*isolation & purification, Tripterygium/*microbiologyGenetics
Phylogeny19783611Saccharopolyspora phatthalungensis sp. nov., isolated from rhizosphere soil of Hevea brasiliensis.Duangmal K, Mingma R, Thamchaipenet A, Matsumoto A, Takahashi YInt J Syst Evol Microbiol10.1099/ijs.0.018275-02009DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Fatty Acids/metabolism, Hevea/*microbiology, Molecular Sequence Data, Phylogeny, Plant Roots/microbiology, RNA, Ribosomal, 16S/genetics, Saccharopolyspora/*classification/genetics/*isolation & purification/metabolism, *Soil MicrobiologyMetabolism
Genetics21478350Genome sequence of the Spinosyns-producing bacterium Saccharopolyspora spinosa NRRL 18395.Pan Y, Yang X, Li J, Zhang R, Hu Y, Zhou Y, Wang J, Zhu BJ Bacteriol10.1128/JB.00344-112011Gene Expression Regulation, Bacterial/physiology, *Genome, Bacterial, Macrolides/*metabolism, Molecular Sequence Data, Saccharopolyspora/*genetics/*metabolismMetabolism
Metabolism24786531Switching antibiotics production on and off in actinomycetes by an IclR family transcriptional regulator from Streptomyces peucetius ATCC 27952.Chaudhary AK, Singh B, Maharjan S, Jha AK, Kim BG, Sohng JKJ Microbiol Biotechnol10.4014/jmb.1403.030262014Actinobacteria/*genetics/*metabolism, Anti-Bacterial Agents/*biosynthesis, *Gene Expression Regulation, Bacterial, Pigments, Biological/biosynthesis, Recombinant Proteins/genetics/metabolism, Transcription Factors/*genetics/*metabolismBiotechnology
Metabolism25808914Four-stage dissolved oxygen strategy based on multi-scale analysis for improving spinosad yield by Saccharopolyspora spinosa ATCC49460.Bai Y, Zhou PP, Fan P, Zhu YM, Tong Y, Wang HB, Yu LJMicrob Biotechnol10.1111/1751-7915.122642015Aerobiosis, Biomass, Culture Media/chemistry, Drug Combinations, Fermentation, Glucose/metabolism, Insecticides/*metabolism, Macrolides/*metabolism, Oxygen/*metabolism, Saccharopolyspora/growth & development/*metabolism, Time FactorsBiotechnology
Metabolism26138116Optimization of Culture Medium for Maximal Production of Spinosad Using an Artificial Neural Network - Genetic Algorithm Modeling.Lan Z, Zhao C, Guo W, Guan X, Zhang XJ Mol Microbiol Biotechnol10.1159/0003813122015Culture Media/*chemistry/metabolism, Drug Combinations, Fermentation, Macrolides/*metabolism, Models, Theoretical, Neural Networks, Computer, Saccharopolyspora/chemistry/genetics/*metabolismBiotechnology
Metabolism26260388Characterization of the chromosomal integration of Saccharopolyspora plasmid pCM32 and its application to improve production of spinosyn in Saccharopolyspora spinosa.Chen J, Xia H, Dang F, Xu Q, Li W, Qin ZAppl Microbiol Biotechnol10.1007/s00253-015-6871-z2015Attachment Sites, Microbiological, DNA, Bacterial/chemistry/genetics, Escherichia coli/genetics, Gene Expression, Genetic Vectors, Macrolides/*metabolism, Metabolic Engineering/*methods, Open Reading Frames, Pesticides/*metabolism, *Plasmids, Recombinant Proteins/genetics/metabolism, *Recombination, Genetic, Saccharopolyspora/*genetics/*metabolism, Sequence Analysis, DNA, Transformation, BacterialTranscriptome
Phylogeny27604103Saccharopolyspora griseoalba sp. nov., a novel actinomycete isolated from the Dead Sea.Jiang Y, Wei X, Chen X, Jiang Y, Xue Q, Lai H, Jiang CAntonie Van Leeuwenhoek10.1007/s10482-016-0763-92016Geologic Sediments/microbiology, Molecular Typing, Oceans and Seas, Phylogeny, RNA, Bacterial, RNA, Ribosomal, 16S, Saccharopolyspora/classification/genetics/*isolation & purification/ultrastructure, Soil Microbiology, *Water MicrobiologyEnzymology
Metabolism28166382Saccharopolyspora Species: Laboratory Maintenance and Enhanced Production of Secondary Metabolites.Dhakal D, Pokhrel AR, Jha AK, Thuan NH, Sohng JKCurr Protoc Microbiol10.1002/cpmc.212017Bacteriological Techniques/*methods, Biological Products/*metabolism, Culture Media/chemistry, Metabolic Engineering/*methods, Mutagenesis, Preservation, Biological/methods, Saccharopolyspora/genetics/*growth & development/*metabolismBiotechnology
Phylogeny28785826Saccharopolyspora hattusasensis sp. nov., isolated from soil.Veyisoglu A, Saygin H, Tatar D, Bektas KI, Sahin NAntonie Van Leeuwenhoek10.1007/s10482-017-0921-82017Bacterial Typing Techniques, Metabolomics/methods, Phylogeny, RNA, Ribosomal, 16S/genetics, Saccharopolyspora/chemistry/*classification/genetics/isolation & purification, Sequence Analysis, DNA, *Soil MicrobiologyTranscriptome

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
11612Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 44228)https://www.dsmz.de/collection/catalogue/details/culture/DSM-44228
20023Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM44228.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
68382Automatically annotated from API zym
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
82647Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID42489.1StrainInfo: A central database for resolving microbial strain identifiers