Strain identifier

BacDive ID: 15205

Type strain: Yes

Species: Streptomyces fragilis

Strain history: KCC S-0187 <-- M. Hamada <-- Y. Okami (NIHJ 415) <-- Parke, Davis & Co.; PD 04926.

NCBI tax ID(s): 67301 (species)

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General

@ref: 9123

BacDive-ID: 15205

DSM-Number: 40044

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

description: Streptomyces fragilis DSM 40044 is a spore-forming, mesophilic bacterium that was isolated from soil.

NCBI tax id

  • NCBI tax id: 67301
  • Matching level: species

strain history

@refhistory
9123<- E.B. Shirling, ISP <- L. Anderson, Res. Lab., Parke, Davis and Co., PD 04926
67770KCC S-0187 <-- M. Hamada <-- Y. Okami (NIHJ 415) <-- Parke, Davis & Co.; PD 04926.

doi: 10.13145/bacdive15205.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Kitasatosporales
  • family: Streptomycetaceae
  • genus: Streptomyces
  • species: Streptomyces fragilis
  • full scientific name: Streptomyces fragilis Anderson et al. 1956 (Approved Lists 1980)

@ref: 9123

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Streptomycetaceae

genus: Streptomyces

species: Streptomyces fragilis

full scientific name: Streptomyces fragilis Anderson et al. 1956

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram stain
69480no94.926
69480100positive

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
9123GYM 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
9123STARCH - MINERAL SALT - AGAR (STMS) (DSMZ Medium 252)yeshttps://mediadive.dsmz.de/medium/252Name: STARCH - MINERAL SALT - AGAR (STMS) (DSMZ Medium 252) Composition: Agar 14.985 g/l Starch 9.99001 g/l (NH4)2SO4 1.998 g/l CaCO3 1.998 g/l K2HPO4 0.999001 g/l MgSO4 x 7 H2O 0.999001 g/l NaCl 0.999001 g/l FeSO4 x 7 H2O 0.000999001 g/l MnCl2 x 4 H2O 0.000999001 g/l ZnSO4 x 7 H2O 0.000999001 g/l Distilled water

culture temp

@refgrowthtypetemperaturerange
18471positiveoptimum28mesophilic
9123positivegrowth37mesophilic
67770positivegrowth28mesophilic

Physiology and metabolism

spore formation

@refspore formationconfidence
69481yes100
69480yes99.646

compound production

@refcompound
9123azaserine
20216Azaserine

observation

  • @ref: 67770
  • observation: quinones: MK-9(H6), MK-9(H8)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
1847117234glucose+
1847122599arabinose+
1847117992sucrose+
1847118222xylose-
1847117268myo-inositol-
1847129864mannitol-
1847128757fructose-
1847126546rhamnose-
1847116634raffinose-
1847162968cellulose-
683685291gelatin+hydrolysis
6836827897tryptophan-energy source
6836816199urea-hydrolysis
6836816947citrate-assimilation
6836818257ornithine-degradation
6836825094lysine-degradation
6836829016arginine-hydrolysis

metabolite production

@refChebi-IDmetaboliteproduction
6777074846azaserineyes
6836815688acetoinno
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

API 20E

@refONPGADH ArgLDC LysODCCITH2SURETDA TrpINDVPGEL
18471+------+--+

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinent
9123soilArgentinaARGMiddle and South America
67770SoilArgentinaARGMiddle and South America

isolation source categories

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

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
184711German classification
91231Risk group (German classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Streptomyces fragilis gene for 16S ribosomal RNA, partial sequence, strain: JCM 4638D44280120ena67301
20218Streptomyces fragilis gene for 16S rRNA, partial sequence, strain: NBRC 12862AB1842001474ena67301
20218Streptomyces fragilis strain NRRL 2424 16S ribosomal RNA gene, partial sequenceAY9999171500ena67301

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Streptomyces fragilis strain NBRC 1286267301.3wgspatric67301
66792Streptomyces fragilis NBRC 128622862407089draftimg67301
67770Streptomyces fragilis NBRC 12862GCA_003112515contigncbi67301

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes100no
gram-positiveyes90.63no
anaerobicno98.949no
halophileno89.405no
spore-formingyes96.793no
glucose-utilyes90.447yes
thermophileno98.96yes
flagellatedno98.055no
aerobicyes90.833no
glucose-fermentno87.887no
motileno96.22no

External links

@ref: 9123

culture collection no.: DSM 40044, ATCC 23908, CBS 804.68, IFO 12862, ISP 5044, NBRC 12862, NRRL 2424, RIA 1111, PD 04926, JCM 4187, BCRC 13654, CGMCC 4.1955, HAMBI 1083, HAMBI 1090, IMET 43575, JCM 4638, NCIMB 9795, VKM Ac-1773

straininfo link

  • @ref: 84303
  • straininfo: 38285

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny23011007Streptomyces bullii sp. nov., isolated from a hyper-arid Atacama Desert soil.Santhanam R, Rong X, Huang Y, Andrews BA, Asenjo JA, Goodfellow MAntonie Van Leeuwenhoek10.1007/s10482-012-9816-x2012Bacterial Typing Techniques, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, *Desert Climate, Microscopy, Electron, Scanning, Molecular Sequence Data, Nucleic Acid Hybridization, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Streptomyces/*classification/genetics/*isolation & purificationGenetics
Phylogeny23291893Streptomyces chilikensis sp. nov., a halophilic streptomycete isolated from brackish water sediment.Ray L, Suar M, Pattnaik AK, Raina VInt J Syst Evol Microbiol10.1099/ijs.0.046284-02013Bacterial Typing Techniques, DNA, Bacterial/genetics, Diaminopimelic Acid/analysis, Fatty Acids/analysis, Geologic Sediments/*microbiology, India, Lakes/*microbiology, Molecular Sequence Data, Nucleic Acid Hybridization, Phospholipids/analysis, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Streptomyces/*classification/genetics/isolation & purification, Vitamin K 2/analogs & derivatives/analysisGenetics
Metabolism31853029Diversity of PKS and NRPS gene clusters between Streptomyces abyssomicinicus sp. nov. and its taxonomic neighbor.Komaki H, Sakurai K, Hosoyama A, Kimura A, Trujilo ME, Igarashi Y, Tamura TJ Antibiot (Tokyo)10.1038/s41429-019-0261-12019Bridged Bicyclo Compounds, Heterocyclic, Gene Expression Regulation, Bacterial/*physiology, Gene Expression Regulation, Enzymologic/*physiology, Multigene Family, Peptide Synthases/genetics/*metabolism, Polyketide Synthases/genetics/*metabolism, Streptomyces/*enzymology/geneticsPhylogeny

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
9123Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 40044)https://www.dsmz.de/collection/catalogue/details/culture/DSM-40044
18471Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM40044.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
20216Curators of the HKIhttp://www.leibniz-hki.de/de/Collection Description Leibniz-Institut für Naturstoff-Forschung und Infektionsbiologie e. V. Hans-Knöll-Institut (HKI)
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
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
84303Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID38285.1StrainInfo: A central database for resolving microbial strain identifiers