Strain identifier

BacDive ID: 13458

Type strain: Yes

Species: Saccharopolyspora flava

Strain Designation: 07

Strain history: <- JCM

NCBI tax ID(s): 95161 (species)

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General

@ref: 12076

BacDive-ID: 13458

DSM-Number: 44771

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

description: Saccharopolyspora flava 07 is an aerobe, spore-forming, mesophilic bacterium that was isolated from garden soil.

NCBI tax id

  • NCBI tax id: 95161
  • Matching level: species

strain history

@refhistory
12076<- CGMCC <- Z. Liu; 07
67770Z. Liu 07.
67771<- JCM

doi: 10.13145/bacdive13458.20230509.8.1

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 flava
  • full scientific name: Saccharopolyspora flava Lu et al. 2001

@ref: 12076

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Pseudonocardiaceae

genus: Saccharopolyspora

species: Saccharopolyspora flava

full scientific name: Saccharopolyspora flava Lu et al. 2001 emend. Nouioui et al. 2018

strain designation: 07

type strain: yes

Morphology

cell morphology

@refgram stainmotilityconfidence
67771positive
69480no95.332
69480positive100

Culture and growth conditions

culture medium

  • @ref: 12076
  • name: GYM STREPTOMYCES MEDIUM (DSMZ Medium 65)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/65
  • composition: Name: 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

culture temp

@refgrowthtypetemperaturerange
12076positivegrowth28mesophilic
67770positivegrowth28mesophilic
67771positivegrowth28mesophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 67771
  • oxygen tolerance: aerobe

spore formation

@refspore formationconfidence
69481yes100
69480yes100

observation

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

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
6836925115malate+assimilation
6836927689decanoate-assimilation
6836924265gluconate+assimilation
6836917306maltose+assimilation
6836959640N-acetylglucosamine+assimilation
6836916899D-mannitol+assimilation
6836916024D-mannose+assimilation
6836917634D-glucose+assimilation
683695291gelatin+hydrolysis
683694853esculin+hydrolysis
6836916199urea+hydrolysis
6836929016arginine-hydrolysis
6836917634D-glucose-fermentation
6836927897tryptophan-energy source
6836917632nitrate-reduction

metabolite production

  • @ref: 68369
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

  • @ref: 68369
  • Chebi-ID: 35581
  • metabolite: indole
  • indole test: -

enzymes

@refvalueactivityec
68369gelatinase+
68369beta-glucosidase+3.2.1.21
68369urease+3.5.1.5
68369arginine dihydrolase-3.5.3.6
68382alkaline phosphatase+3.1.3.1
68382esterase (C 4)-
68382lipase (C 14)-
68382leucine arylamidase+3.4.11.1
68382valine arylamidase+
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
68382alpha-fucosidase-3.2.1.51

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
12076-+-+/--+++/-+/--++---++++/--

API 20NE

@refNO3TRPGLU_ FermADH ArgUREESCGELPNPGGLU_ AssimARAMNEMANNAGMALGNTCAPADIMLTCITPAC
12076----++++++/-+++++-+/-+++

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
12076garden soilBeijing, Xishan MountainChinaCHNAsia
67770Garden soilXishan Mountain, BeijingChinaCHNAsia
67771From grassland soilChinaCHNAsia

isolation source categories

Cat1Cat2Cat3
#Environmental#Terrestrial#Soil
#Engineered#Agriculture#Garden

taxonmaps

  • @ref: 69479
  • File name: preview.99_149139.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_10;96_1393;97_7142;98_98630;99_149139&stattab=map
  • Last taxonomy: Saccharopolyspora flava subclade
  • 16S sequence: AF154128
  • Sequence Identity:
  • Total samples: 327
  • soil counts: 142
  • aquatic counts: 35
  • animal counts: 136
  • plant counts: 14

Safety information

risk assessment

  • @ref: 12076
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 20218
  • description: Saccharopolyspora flava 16S ribosomal RNA, partial sequence
  • accession: AF154128
  • length: 1443
  • database: ena
  • NCBI tax ID: 95161

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Saccharopolyspora flava strain DSM 4477195161.3wgspatric95161
66792Saccharopolyspora flava DSM 447712599185150draftimg95161
67770Saccharopolyspora flava DSM 44771GCA_900116135scaffoldncbi95161

GC content

@refGC-contentmethod
6777073.1thermal denaturation, midpoint method (Tm)
6777070.8genome sequence analysis

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes100no
motileno91.29no
flagellatedno97.618no
gram-positiveyes90.094yes
anaerobicno99.01no
halophileno51.998no
spore-formingyes86.19no
thermophileno96.764yes
glucose-utilyes86.927yes
aerobicyes90.993no
glucose-fermentno91.37yes

External links

@ref: 12076

culture collection no.: DSM 44771, AS 4.1520, IFO 16345, JCM 10665, KCTC 19905, NBRC 16345, CGMCC 4.1520

straininfo link

  • @ref: 82650
  • straininfo: 100940

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny11321076Saccharopolyspora flava sp. nov. and Saccharopolyspora thermophila sp.nov., novel actinomycetes from soil.Lu Z, Liu Z, Wang L, Zhang Y, Qi W, Goodfellow MInt J Syst Evol Microbiol10.1099/00207713-51-2-3192001Bacterial Typing Techniques, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Molecular Sequence Data, RNA, Ribosomal, 16S/genetics, Saccharopolyspora/*classification/cytology/metabolism, *Soil Microbiology, Terminology as TopicGenetics
Phylogeny18929936Saccharopolyspora endophytica sp. nov., an endophytic actinomycete isolated from the root of Maytenus austroyunnanensis.Qin S, Li J, Zhao GZ, Chen HH, Xu LH, Li WJSyst Appl Microbiol10.1016/j.syapm.2008.08.0012008Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/analysis/isolation & purification, DNA, Ribosomal/analysis, Fatty Acids/analysis, Genes, rRNA, Maytenus/*microbiology, Medicine, Chinese Traditional, Nucleic Acid Hybridization, Phenotype, Phylogeny, Plant Roots/*microbiology, Plants, Medicinal/microbiology, RNA, Ribosomal, 16S/genetics, Saccharopolyspora/*classification/genetics/*isolation & purification/physiology, Species SpecificityEnzymology
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
Phylogeny30789325Saccharopolyspora rhizosphaerae sp. nov., an actinomycete isolated from rhizosphere soil in Thailand.Intra B, Euanorasetr J, Take A, Inahashi Y, Mori M, Panbangred W, Matsumoto AInt J Syst Evol Microbiol10.1099/ijsem.0.0033072019Bacterial Typing Techniques, Base Composition, Colocasia/*microbiology, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Nucleic Acid Hybridization, Peptidoglycan/chemistry, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, *Rhizosphere, Saccharopolyspora/*classification/isolation & purification, Sequence Analysis, DNA, *Soil Microbiology, Thailand, Vitamin K 2/analogs & derivatives/chemistryTranscriptome
35855324Psi-Footprinting approach for the identification of protein synthesis inhibitor producers.Handel F, Kulik A, Wex KW, Berscheid A, Saur JS, Winkler A, Wibberg D, Kalinowski J, Brotz-Oesterhelt H, Mast YNAR Genom Bioinform10.1093/nargab/lqac0552022

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
12076Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 44771)https://www.dsmz.de/collection/catalogue/details/culture/DSM-44771
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/
67771Curators of the KCTChttps://kctc.kribb.re.kr/En/Kctc
68369Automatically annotated from API 20NE
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
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
82650Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID100940.1StrainInfo: A central database for resolving microbial strain identifiers