Strain identifier

BacDive ID: 13475

Type strain: Yes

Species: Saccharothrix coeruleofusca

Strain history: KCC A-0313 <-- IMET 9602 <-- INA 1335.

NCBI tax ID(s): 33919 (species)

For citation purpose refer to the digital object identifier (doi) of the current version.
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General

@ref: 11242

BacDive-ID: 13475

DSM-Number: 43679

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

description: Saccharothrix coeruleofusca DSM 43679 is a spore-forming, mesophilic bacterium that builds an aerial mycelium and was isolated from soil.

NCBI tax id

  • NCBI tax id: 33919
  • Matching level: species

strain history

@refhistory
11242<- N.S. Agre, INA
67770KCC A-0313 <-- IMET 9602 <-- INA 1335.

doi: 10.13145/bacdive13475.20230509.8.1

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 coeruleofusca
  • full scientific name: Saccharothrix coeruleofusca (Preobrazhenskaya and Sveshnikova 1974) Grund and Kroppenstedt 1990
  • synonyms

    @refsynonym
    20215Nocardiopsis coeruleofusca
    20215Actinomadura coeruleofusca

@ref: 11242

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Pseudonocardiaceae

genus: Saccharothrix

species: Saccharothrix coeruleofusca

full scientific name: Saccharothrix coeruleofusca (Preobrazhenskaya and Sveshnikova 1974) Grund and Kroppenstedt 1990

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram stain
69480no93.195
69480100positive

colony morphology

@refcolony colorincubation periodmedium used
19581Deep orange10-14 daysISP 2
19581Deep orange10-14 daysISP 3
19581Deep orange10-14 daysISP 4
19581Deep orange10-14 daysISP 5
19581Dahlia yellow10-14 daysISP 6
19581Dahlia yellow10-14 daysISP 7

multicellular morphology

@refforms multicellular complexcomplex namecomplex colormedium name
19581yesAerial MyceliumSilver grayISP 2
19581yesAerial MyceliumSilver grayISP 3
19581yesAerial MyceliumWhiteISP 4
19581yesAerial MyceliumWhiteISP 5
19581noISP 6
19581yesAerial MyceliumWhiteISP 7

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
11242GYM+S MEDIUM (DSMZ Medium 214)yeshttps://mediadive.dsmz.de/medium/214Name: GYM+S MEDIUM (DSMZ Medium 214) Composition: Starch 20.0 g/l Agar 12.0 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
19581ISP 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
19581ISP 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:
19581ISP 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
19581ISP 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
19581ISP 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
19581ISP 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
19581positiveoptimum28mesophilic
11242positivegrowth28mesophilic
67770positivegrowth28mesophilic

Physiology and metabolism

spore formation

@refspore descriptiontype of sporespore formationconfidence
19581Formation of spore chains (rectiflixibilis), spore surface smoothsporeyes
69481yes100
69480yes100

halophily

  • @ref: 19581
  • 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
19581+------++++---+-+--

API 20E

@refONPGADH ArgLDC LysODCCITH2SURETDA TrpINDVPGEL
19581+++++-+--++

Isolation, sampling and environmental information

isolation

@refsample type
11242soil
67770Soil

isolation source categories

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

taxonmaps

  • @ref: 69479
  • File name: preview.99_5187.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_10;96_840;97_2407;98_2976;99_5187&stattab=map
  • Last taxonomy: Saccharothrix
  • 16S sequence: AF114805
  • Sequence Identity:
  • Total samples: 72
  • soil counts: 59
  • aquatic counts: 7
  • animal counts: 4
  • plant counts: 2

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
112421Risk group (German classification)
195811Risk group (German classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218S.coeruleofusca (DSM 43679) 16S ribosomal RNA (partial)X769631458ena33919
20218Saccharothrix coeruleofusca strain NRRL B-16115T 16S ribosomal RNA gene, partial sequenceAF1148051512ena33919

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Saccharothrix coeruleofusca DSM 43679GCA_017876325contigncbi33919
66792Saccharothrix coeruleofusca JCM 3313GCA_014648515scaffoldncbi33919
66792Saccharothrix coeruleofusca strain DSM 4367933919.4wgspatric33919
66792Saccharothrix coeruleofusca strain JCM 331333919.3wgspatric33919
66792Saccharothrix coeruleofusca DSM 436792918321734draftimg33919

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes100no
flagellatedno96.991no
gram-positiveyes92.348no
anaerobicno99.095no
aerobicyes95.38no
halophileno88.537no
spore-formingyes95.749yes
thermophileno97.28yes
glucose-utilyes87.195no
motileno91.316no
glucose-fermentno90.469no

External links

@ref: 11242

culture collection no.: DSM 43679, ATCC 35108, INA 1335, JCM 3313, BCRC 13313, CGMCC 4.1356, IFO 14520, IMET 9602, IMSNU 21357, KCTC 9389, NBRC 14520, NRRL B-16115, VKM Ac-855

straininfo link

  • @ref: 82667
  • straininfo: 40874

literature

  • topic: Phylogeny
  • Pubmed-ID: 35212620
  • title: Solihabitans fulvus gen. nov., sp. nov., a member of the family Pseudonocardiaceae isolated from soil.
  • authors: Jin CZ, Jin L, Liu MJ, Lee JM, Park DJ, Kim CJ
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijsem.0.005110
  • year: 2022
  • mesh: Actinobacteria/*classification/isolation & purification, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, *Soil Microbiology, Vitamin K 2/chemistry
  • topic2: Transcriptome

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
11242Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 43679)https://www.dsmz.de/collection/catalogue/details/culture/DSM-43679
19581Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM43679.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
82667Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID40874.1StrainInfo: A central database for resolving microbial strain identifiers