Strain identifier

BacDive ID: 17730

Type strain: Yes

Species: Actinopolyspora erythraea

Strain history: W.-J. Li YIM 90600.

NCBI tax ID(s): 414996 (species)

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General

@ref: 17712

BacDive-ID: 17730

DSM-Number: 45583

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

description: Actinopolyspora erythraea DSM 45583 is a spore-forming, mesophilic bacterium that builds an aerial mycelium and was isolated from soil from a salt field.

NCBI tax id

  • NCBI tax id: 414996
  • Matching level: species

strain history

@refhistory
17712<- W.-J. Li, YIM; YIM 90600
67770W.-J. Li YIM 90600.

doi: 10.13145/bacdive17730.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Pseudonocardiales
  • family: Pseudonocardiaceae
  • genus: Actinopolyspora
  • species: Actinopolyspora erythraea
  • full scientific name: Actinopolyspora erythraea Tang et al. 2011

@ref: 17712

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Actinopolysporaceae

genus: Actinopolyspora

species: Actinopolyspora erythraea

full scientific name: Actinopolyspora erythraea Tang et al. 2011 emend. Nouioui et al. 2018

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram stain
69480no93.914
69480100positive

colony morphology

@refcolony colormedium used
69409Beige (1001), brown beige (1011)ISP 7
69409Beige (1001)ISP 5
69409Basalt grey (7012)suter with tyrosine
69409Basalt grey (7012), ochre yellow (1024)suter without tyrosine
69409Ochre yellow (1024)ISP 2
69409Oyster white (1013)ISP 3

multicellular morphology

@refforms multicellular complexcomplex namecomplex colormedium name
69409yesAerial myceliumCream (9001)ISP 2
69409yesAerial myceliumSignal white (9003)ISP 3
69409yesAerial myceliumCream (9001)ISP 5
69409yesAerial myceliumCream (9001)ISP 7
69409yesAerial myceliumCream (9001)suter with tyrosine
69409yesAerial myceliumCream (9001)suter without tyrosine

pigmentation

@refproductionnamecolor
69409noMelanin
69409yessoluble pigmentOchre brown (8001)

multimedia

@refmultimedia contentcaptionintellectual property rights
17712https://www.dsmz.de/microorganisms/photos/DSM_45583.jpgMedium 1159 28°C© Leibniz-Institut DSMZ
69409DSM_45583_image3.jpegPlates (1240, ISP2, ISP3, ISP4, ISP5, ISP7)Helmholtz-Zentrum für Infektionsforschung GmbH
69409DSM_45583_image4.jpegPlates (1240, ISP2, ISP3, ISP4, ISP5, ISP7)Helmholtz-Zentrum für Infektionsforschung GmbH

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
17712STARCH-MINERAL SALT-AGAR (STMS) + 10%NACL (DSMZ Medium 1240)yeshttps://mediadive.dsmz.de/medium/1240Name: STARCH-MINERAL SALT-AGAR + 10% NACL (DSMZ Medium 1240) Composition: NaCl 100.0 g/l Agar 15.0 g/l Starch 10.0 g/l (NH4)2SO4 2.0 g/l CaCO3 2.0 g/l K2HPO4 1.0 g/l MgSO4 x 7 H2O 1.0 g/l FeSO4 x 7 H2O 0.001 g/l MnCl2 x 4 H2O 0.001 g/l ZnSO4 x 7 H2O 0.001 g/l Distilled water
17712NUTRIENT AGAR (DSMZ Medium 1)yeshttps://www.dsmz.de/microorganisms/medium/pdf/DSMZ_Medium1.pdf
17712GYM STREPTOMYCES MEDIUM 10% NACL (DSMZ Medium 1159)yeshttps://mediadive.dsmz.de/medium/1159Name: GYM STREPTOMYCES MEDIUM 10% NACL (DSMZ Medium 1159) Composition: NaCl 100.0 g/l Agar 15.0 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
17712positivegrowth28mesophilic
67770positivegrowth37mesophilic

Physiology and metabolism

spore formation

@refspore formationconfidence
69481yes100
69480yes99.692

compound production

  • @ref: 67770
  • compound: Erythronolides H and I

halophily

  • @ref: 69409
  • salt: NaCl
  • growth: positive
  • tested relation: growth
  • concentration: 2.5-10 %

observation

  • @ref: 67770
  • observation: quinones: MK-9(H4), MK-9(H2)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
6940922599arabinose+growth
6940962968cellulose+growth
6940928757fructose+growth
6940917234glucose+growth
6940917268inositol-growth
6940937684mannose+growth
6940916634raffinose+growth
6940926546rhamnose+/-growth
6940917992sucrose+/-growth
6940918222xylose+growth
6837917632nitrate-reduction
683794853esculin-hydrolysis
6837916199urea-hydrolysis
683795291gelatin+hydrolysis
6837917634D-glucose-fermentation
6837916988D-ribose-fermentation
6837965327D-xylose-fermentation
6837916899D-mannitol-fermentation
6837917306maltose-fermentation
6837917716lactose-fermentation
6837917992sucrose-fermentation
6837928087glycogen-fermentation

enzymes

@refvalueactivityec
68379gelatinase+
68379urease-3.5.1.5
68379beta-glucosidase-3.2.1.21
68379N-acetyl-beta-glucosaminidase-3.2.1.52
68379alpha-glucosidase+3.2.1.20
68379beta-galactosidase+3.2.1.23
68379beta-glucuronidase-3.2.1.31
68379alkaline phosphatase+3.1.3.1
68379pyrrolidonyl arylamidase-3.4.19.3
68379pyrazinamidase-3.5.1.B15
68382alkaline phosphatase+3.1.3.1
68382leucine arylamidase+3.4.11.1
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
68382alpha-mannosidase-3.2.1.24
68382alpha-fucosidase-3.2.1.51

API coryne

@refNITPYZPYRAPALbeta GURbeta GALalpha GLUbeta NAGESCUREGELGLURIBXYLMANMALLACSACGLYG
69409---+-++---+--------

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
69409++/-+/-+/-++/-------+-+++--

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
17712soil from a salt fieldXinjiang, Baicheng salt fieldChinaCHNAsia
67770Salt fieldXinjiang, north-west ChinaChinaCHNAsia

isolation source categories

Cat1Cat2Cat3
#Engineered#Agriculture#Field
#Environmental#Terrestrial#Soil
#Condition#Saline

taxonmaps

  • @ref: 69479
  • File name: preview.99_5967.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_495;96_2848;97_3502;98_4431;99_5967&stattab=map
  • Last taxonomy: Actinopolyspora erythraea
  • 16S sequence: GQ480939
  • Sequence Identity:
  • Total samples: 13
  • soil counts: 2
  • aquatic counts: 1
  • animal counts: 10

Safety information

risk assessment

  • @ref: 17712
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Actinopolyspora erythraea strain YIM 90600 16S ribosomal RNA gene, partial sequenceEF116937679ena414996
17712Actinopolyspora erythraea strain YIM 90600 culture-collection CCTCC:M208243 16S ribosomal RNA gene, partial sequenceGQ4809391465ena414996

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Actinopolyspora erythraea YIM 90600GCA_002263515completencbi414996
66792Actinopolyspora erythraea YIM90600414996.3wgspatric414996
66792Actinopolyspora erythraea strain YIM 90600414996.4completepatric414996
66792Actinopolyspora erythraea YIM906002630968685draftimg414996
66792Actinopolyspora erythraea YIM 906002773857909completeimg414996
67770Actinopolyspora erythraea YIM 90600GCA_000763095scaffoldncbi414996

GC content

@refGC-contentmethod
1771266.4high performance liquid chromatography (HPLC)
6777068.8genome sequence analysis

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes100no
flagellatedno96.997no
gram-positiveyes90.102no
anaerobicno98.52no
aerobicyes89.995no
halophileyes67.016no
spore-formingyes80.894no
glucose-utilyes89.471yes
thermophileno95.011yes
motileno91.355no
glucose-fermentno89.694no

External links

@ref: 17712

culture collection no.: DSM 45583, CCTCC M 208247, KCTC 19372, YIM 90600, JCM 19144

straininfo link

  • @ref: 86720
  • straininfo: 397362

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny20729305Actinopolyspora alba sp. nov. and Actinopolyspora erythraea sp. nov., isolated from a salt field, and reclassification of Actinopolyspora iraqiensis Ruan et al. 1994 as a heterotypic synonym of Saccharomonospora halophila.Tang SK, Wang Y, Klenk HP, Shi R, Lou K, Zhang YJ, Chen C, Ruan JS, Li WJInt J Syst Evol Microbiol10.1099/ijs.0.022319-02010Actinomycetales/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Molecular Sequence Data, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Salts/chemistry, Sequence Analysis, DNA, *Soil Microbiology, Vitamin K 2/chemistryGenetics
Enzymology21870828Actinopolysporins A-C and tubercidin as a Pdcd4 stabilizer from the halophilic actinomycete Actinopolyspora erythraea YIM 90600.Zhao LX, Huang SX, Tang SK, Jiang CL, Duan Y, Beutler JA, Henrich CJ, McMahon JB, Schmid T, Blees JS, Colburn NH, Rajski SR, Shen BJ Nat Prod10.1021/np200603g2011Actinobacteria/*isolation & purification, Antineoplastic Agents/chemistry/isolation & purification/*pharmacology, Apoptosis Regulatory Proteins/drug effects, Biological Products/chemistry/isolation & purification/*pharmacology, Drug Screening Assays, Antitumor, Humans, Ketones/chemistry/isolation & purification/*pharmacology, Molecular Structure, Polyketides, RNA-Binding Proteins/drug effects, Tubercidin/chemistry/isolation & purification/pharmacologyPhylogeny
Metabolism25250723Identification and characterization of a new erythromycin biosynthetic gene cluster in Actinopolyspora erythraea YIM90600, a novel erythronolide-producing halophilic actinomycete isolated from salt field.Chen D, Feng J, Huang L, Zhang Q, Wu J, Zhu X, Duan Y, Xu ZPLoS One10.1371/journal.pone.01081292014Aryl Hydrocarbon Hydroxylases/genetics/metabolism, Bacterial Proteins/genetics/metabolism, Biosynthetic Pathways, Erythromycin/*analogs & derivatives/metabolism, Genes, Bacterial, Molecular Sequence Data, *Multigene Family, Saccharopolyspora/*genetics/*metabolismGenetics

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
17712Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 45583)https://www.dsmz.de/collection/catalogue/details/culture/DSM-45583
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/
68379Automatically annotated from API Coryne
68382Automatically annotated from API zym
69409Wink, J.https://cdn.dsmz.de/wink/DSM%2045583.pdfCompendium of Actinobacteria. HZI-Helmholtz-Centre for Infection Research, Braunschweig
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
86720Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID397362.1StrainInfo: A central database for resolving microbial strain identifiers