Strain identifier

BacDive ID: 13454

Type strain: Yes

Species: Saccharopolyspora hordei

Strain Designation: A54, A735

Strain history: NCIMB 12824 <-- J. Lacey A735 (M. Goodfellow A54).

NCBI tax ID(s): 1838 (species)

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General

@ref: 11466

BacDive-ID: 13454

DSM-Number: 44065

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

description: Saccharopolyspora hordei A54 is a spore-forming, thermophilic, Gram-positive bacterium that was isolated from hay.

NCBI tax id

  • NCBI tax id: 1838
  • Matching level: species

strain history

@refhistory
11466<- F. Korn-Wendisch, TH Darmstadt <- M. Goodfellow, A54 <- J. Lacey, A735
67770NCIMB 12824 <-- J. Lacey A735 (M. Goodfellow A54).

doi: 10.13145/bacdive13454.20230509.8.1

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 hordei
  • full scientific name: Saccharopolyspora hordei Goodfellow et al. 1989

@ref: 11466

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Pseudonocardiaceae

genus: Saccharopolyspora

species: Saccharopolyspora hordei

full scientific name: Saccharopolyspora hordei Goodfellow et al. 1989

strain designation: A54, A735

type strain: yes

Morphology

cell morphology

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

colony morphology

@refcolony colorincubation periodmedium used
19993Pastel yellow (1034)10-14 daysISP 2
19993Pastel yellow (1034)10-14 daysISP 3
19993Pastel yellow (1034)10-14 daysISP 4
19993Pastel yellow (1034)10-14 daysISP 5
19993Pastel yellow (1034)10-14 daysISP 6
19993Pastel yellow (1034)10-14 daysISP 7

multicellular morphology

@refforms multicellular complexmedium name
19993noISP 2
19993noISP 3
19993noISP 4
19993noISP 5
19993noISP 6
19993noISP 7

multimedia

@refmultimedia contentintellectual property rightscaption
11466https://www.dsmz.de/microorganisms/photos/DSM_44065-1.jpg© Leibniz-Institut DSMZ
11466https://www.dsmz.de/microorganisms/photos/DSM_44065.jpg© Leibniz-Institut DSMZMedium 65 45°C

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
11466CYC-MEDIUM (modified following Cross and Attwell,1973) (DSMZ Medium 550)yeshttps://mediadive.dsmz.de/medium/550Name: CYC-MEDIUM (modified following Cross and Attwell,1973) (DSMZ Medium 550) Composition: Czapek Dox agar 48.0 g/l Agar 20.0 g/l Casamino acids 6.1 g/l Yeast extract 2.0 g/l Tryptophan 0.02 g/l Distilled water
11466GYM 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
19993ISP 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
19993ISP 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:
19993ISP 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
19993ISP 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
19993ISP 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
19993ISP 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
11466positivegrowth45thermophilic
19993positiveoptimum37mesophilic
67770positivegrowth40thermophilic

Physiology and metabolism

spore formation

@refspore formationconfidence
69481yes100
69480yes100

halophily

  • @ref: 19993
  • salt: NaCl
  • growth: positive
  • tested relation: maximum
  • concentration: 2.5 %

observation

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

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

@refChebi-IDmetaboliteproduction
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
68382alpha-mannosidase-3.2.1.24
68382alpha-fucosidase-3.2.1.51

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
19993+-+++++++++---+----

API 20E

@refONPGADH ArgLDC LysODCCITH2SURETDA TrpINDVPGEL
19993+++++-+--++

Isolation, sampling and environmental information

isolation

  • @ref: 11466
  • sample type: hay

isolation source categories

Cat1Cat2Cat3
#Host#Plants#Herbaceous plants (Grass,Crops)
#Host Body Product#Plant#Straw

taxonmaps

  • @ref: 69479
  • File name: preview.99_10629.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_10;96_5246;97_6339;98_7909;99_10629&stattab=map
  • Last taxonomy: Saccharopolyspora
  • 16S sequence: KC139251
  • Sequence Identity:
  • Total samples: 2838
  • soil counts: 1276
  • aquatic counts: 198
  • animal counts: 987
  • plant counts: 377

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
114661Risk group (German classification)
199931German classification

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Saccharopolyspora hordei partial 16S rRNA gene, type strain DSM 44065TFN1792751503ena1838
20218Saccharopolyspora hordei strain NBRC 15046 16S ribosomal RNA gene, partial sequenceKC1392511471ena1838
67770Saccharopolyspora hordei 16S rRNA (part.)X531971340ena1838

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Saccharopolyspora hordei strain DSM 440651838.3wgspatric1838
66792Saccharopolyspora hordei DSM 440652856425837draftimg1838
67770Saccharopolyspora hordei DSM 44065GCA_013410345contigncbi1838

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes100no
motileno93.357no
gram-positiveyes89.56no
anaerobicno98.611no
aerobicyes89.481no
halophileyes61.728no
spore-formingyes88.375no
glucose-utilyes87.365no
flagellatedno98.009no
glucose-fermentno90.81no
thermophileno81.229no

External links

@ref: 11466

culture collection no.: DSM 44065, ATCC 49856, IFO 15046, JCM 8090, NBRC 15046, NCIB 12824, IMSNU 20124, KCTC 9485, NCIMB 12824, NRRL B-16507

straininfo link

  • @ref: 82646
  • straininfo: 42721

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
11466Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 44065)https://www.dsmz.de/collection/catalogue/details/culture/DSM-44065
19993Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM44065.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)
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
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
82646Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID42721.1StrainInfo: A central database for resolving microbial strain identifiers