Strain identifier

BacDive ID: 13482

Type strain: Yes

Species: Saccharothrix espanaensis

Strain history: IFO 15066 <-- NRRL 15764 <-- Lederle Labs.; LL-C19004.

NCBI tax ID(s): 1179773 (strain), 103731 (species)

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General

@ref: 11491

BacDive-ID: 13482

DSM-Number: 44229

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

description: Saccharothrix espanaensis DSM 44229 is a spore-forming, mesophilic bacterium that was isolated from soil.

NCBI tax id

NCBI tax idMatching level
1179773strain
103731species

strain history

@refhistory
11491<- NRRL <- ? <- D. P. Labeda, LL-C19004-NS 29
67770IFO 15066 <-- NRRL 15764 <-- Lederle Labs.; LL-C19004.

doi: 10.13145/bacdive13482.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Pseudonocardiales
  • family: Pseudonocardiaceae
  • genus: Saccharothrix
  • species: Saccharothrix espanaensis
  • full scientific name: Saccharothrix espanaensis Labeda and Lechevalier 1989

@ref: 11491

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Pseudonocardiaceae

genus: Saccharothrix

species: Saccharothrix espanaensis

full scientific name: Saccharothrix espanaensis Labeda and Lechevalier 1989

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram stain
69480no93.243
69480100positive

multimedia

@refmultimedia contentintellectual property rightscaption
11491https://www.dsmz.de/microorganisms/photos/DSM_44229-1.jpg© Leibniz-Institut DSMZ
11491https://www.dsmz.de/microorganisms/photos/DSM_44229.jpg© Leibniz-Institut DSMZMedium 65 28°C

Culture and growth conditions

culture medium

  • @ref: 11491
  • 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
11491positivegrowth28mesophilic
67770positivegrowth28mesophilic

Physiology and metabolism

spore formation

@refspore formationconfidence
69481yes100
69480yes100

compound production

@refcompound
11491antibiotic LL-C19004
67770Antibiotic LL-C19004

observation

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

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
6836817632nitrate-reduction
6836830849L-arabinose-fermentation
6836827613amygdalin-fermentation
6836828053melibiose-fermentation
6836817992sucrose-fermentation
6836862345L-rhamnose-fermentation
6836830911sorbitol-fermentation
6836817268myo-inositol-fermentation
6836816899D-mannitol-fermentation
6836817634D-glucose-fermentation
683685291gelatin+hydrolysis
6836827897tryptophan-energy source
6836816199urea-hydrolysis
6836816947citrate-assimilation
6836818257ornithine-degradation
6836825094lysine-degradation
6836829016arginine-hydrolysis

metabolite production

@refChebi-IDmetaboliteproduction
6836817997dinitrogenno
6836816301nitriteno
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
68382cystine arylamidase-3.4.11.3
68382alpha-chymotrypsin+3.4.21.1
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
68382alpha-mannosidase+3.2.1.24
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
11491-+---++/--+/-++/-----+-+/-+-

API 20E

@refONPGADH ArgLDC LysODCCITH2SURETDA TrpINDVPGELGLUMANINOSorRHASACMELAMYARANO2N2
11491---------++-----------

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
11491soilPuerto LlanoSpainESPEurope
67770SoilPuerto LlanoSpainESPEurope

isolation source categories

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

taxonmaps

  • @ref: 69479
  • File name: preview.99_7679.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_10;96_840;97_2407;98_2976;99_7679&stattab=map
  • Last taxonomy: Saccharothrix
  • 16S sequence: AF114807
  • Sequence Identity:
  • Total samples: 507
  • soil counts: 337
  • aquatic counts: 49
  • animal counts: 83
  • plant counts: 38

Safety information

risk assessment

  • @ref: 11491
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 20218
  • description: Saccharothrix espanaensis strain NRRL 15764 16S ribosomal RNA gene, partial sequence
  • accession: AF114807
  • length: 1510
  • database: ena
  • NCBI tax ID: 103731

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Saccharothrix espanaensis DSM 44229 type strain: DSM 44229GCA_000328705completencbi1179773
66792Saccharothrix espanaensis DSM 442291179773.3completepatric1179773
66792Saccharothrix espanaensis DSM 442292540341184completeimg1179773

GC content

  • @ref: 11491
  • GC-content: 72.2
  • method: thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes100no
motileno92.216no
flagellatedno97.379no
gram-positiveyes91.073no
anaerobicno99.293no
aerobicyes93.309no
halophileno91.844no
spore-formingyes95.848no
thermophileno97.464yes
glucose-utilyes86.91no
glucose-fermentno92.679yes

External links

@ref: 11491

culture collection no.: DSM 44229, ATCC 51144, IFO 15066, JCM 9112, NBRC 15066, NRRL 15764, CGMCC 4.1714, IMSNU 21342, KCTC 9392, VKM Ac-1969

straininfo link

  • @ref: 82674
  • straininfo: 46138

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny21892613Saccharothrix yanglingensis sp. nov., an antagonistic endophytic actinomycete isolated from cucumber plant.Yan X, Huang LL, Tu X, Gao XN, Kang ZSAntonie Van Leeuwenhoek10.1007/s10482-011-9631-92011Actinomycetales/chemistry/*classification/genetics/*isolation & purification, Bacterial Typing Techniques, Cell Wall/chemistry, Cluster Analysis, Cucumis sativus/*microbiology, Cytosol/chemistry, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Diaminopimelic Acid/analysis, Fatty Acids/analysis, Molecular Sequence Data, Nucleic Acid Hybridization, Phospholipids/analysis, Phylogeny, Plant Roots/microbiology, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Vitamin K 2/analysisGenetics
Genetics22958348Complete genome sequence of Saccharothrix espanaensis DSM 44229(T) and comparison to the other completely sequenced Pseudonocardiaceae.Strobel T, Al-Dilaimi A, Blom J, Gessner A, Kalinowski J, Luzhetska M, Puhler A, Szczepanowski R, Bechthold A, Ruckert CBMC Genomics10.1186/1471-2164-13-4652012Actinomycetales/*genetics/metabolism, Anti-Bacterial Agents/metabolism, Genome, Bacterial/*genetics, Multigene Family/geneticsMetabolism
Phylogeny26674086Saccharothrix stipae sp. nov., an actinomycete isolated from the rhizosphere of Stipa grandis.Bing Lin Y, Qing Guo Y, Hui Di X, Chun Fan M, Hong Dong D, Hong Wei GInt J Syst Evol Microbiol10.1099/ijsem.0.0008272015
Phylogeny27915411Saccharothrix ghardaiensis sp. nov., an actinobacterium isolated from Saharan soil.Bouznada K, Bouras N, Mokrane S, Chaabane Chaouch F, Zitouni A, Potter G, Sproer C, Klenk HP, Sabaou NAntonie Van Leeuwenhoek10.1007/s10482-016-0812-42016Actinomycetales/*classification/genetics/*isolation & purification/physiology, Africa, Northern, Algeria, Cell Wall/chemistry, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Diaminopimelic Acid/analysis, Fatty Acids/analysis, Micromonosporaceae/genetics, Phenotype, Phospholipids/analysis, Phylogeny, RNA, Ribosomal, 16S/genetics, Sodium Chloride/metabolism, Soil/chemistry, *Soil Microbiology, Species Specificity, Temperature, Vitamin K 2/analogs & derivatives/analysisPhenotype
33800500Activation of a Cryptic Manumycin-Type Biosynthetic Gene Cluster of Saccharothrix espanaensis DSM44229 by Series of Genetic Manipulations.Gorniakova D, Petricek M, Kahoun D, Grabic R, Zelenka T, Chronakova A, Petrickova KMicroorganisms10.3390/microorganisms90305592021
Phylogeny35960652Saccharothrix obliqua sp. nov., isolated from soil of Sichang Island, Thailand.Azad MAK, Chunhacha P, Suriyachadkun C, Sripreechasak P, Tanasupawat S, Phongsopitanun WInt J Syst Evol Microbiol10.1099/ijsem.0.0054792022*Actinomycetales, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Glycolipids/analysis, Phospholipids/analysis, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil, Soil Microbiology, ThailandTranscriptome

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
11491Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 44229)https://www.dsmz.de/collection/catalogue/details/culture/DSM-44229
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
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
82674Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID46138.1StrainInfo: A central database for resolving microbial strain identifiers