Strain identifier

BacDive ID: 15139

Type strain: Yes

Species: Streptomyces filamentosus

Strain Designation: 1-C-9

Strain history: KCC S-0122 <-- Y. Okami 1-C-9 (NIHJ 256).

NCBI tax ID(s): 67294 (species)

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

@ref: 9222

BacDive-ID: 15139

DSM-Number: 40022

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

description: Streptomyces filamentosus 1-C-9 is a spore-forming, mesophilic bacterium that builds an aerial mycelium and produces antibiotic compounds.

NCBI tax id

  • NCBI tax id: 67294
  • Matching level: species

strain history

@refhistory
9222<- E.B. Shirling, ISP <- Y. Okami, 1-C-9
67770KCC S-0122 <-- Y. Okami 1-C-9 (NIHJ 256).

doi: 10.13145/bacdive15139.20230509.8.1

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 filamentosus
  • full scientific name: Streptomyces filamentosus Okami and Umezawa 1953 (Approved Lists 1980)
  • synonyms

    • @ref: 20215
    • synonym: Streptomyces roseosporus

@ref: 9222

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Streptomycetaceae

genus: Streptomyces

species: Streptomyces filamentosus

full scientific name: Streptomyces filamentosus Okami and Umezawa 1953 emend. Lanoot et al. 2004

strain designation: 1-C-9

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram stain
69480no95.9
69480100positive

colony morphology

@refcolony colorincubation periodmedium used
19387Brown beige10-14 daysISP 2
19387Beige10-14 daysISP 3
19387Beige10-14 daysISP 4
19387Silk grey10-14 daysISP 5
19387Light ivory10-14 daysISP 6
19387Light ivory10-14 daysISP 7

multicellular morphology

@refforms multicellular complexcomplex namemedium namecomplex color
19387yesAerial MyceliumISP 2
19387yesAerial MyceliumISP 3Grey white
19387yesAerial MyceliumISP 4Grey white
19387yesAerial MyceliumISP 5
19387yesAerial MyceliumISP 6
19387yesAerial MyceliumISP 7

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
9222GYM 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
19387ISP 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
19387ISP 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:
19387ISP 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
19387ISP 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
19387ISP 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
19387ISP 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
9222ROLLED OATS MINERAL MEDIUM (DSMZ Medium 84)yeshttps://mediadive.dsmz.de/medium/84Name: ROLLED OATS MINERAL MEDIUM (DSMZ Medium 84) Composition: Agar 20.0 g/l Rolled oats 20.0 g/l ZnSO4 x 7 H2O 0.001 g/l MnCl2 x 4 H2O 0.001 g/l FeSO4 x 7 H2O 0.001 g/l Distilled water

culture temp

@refgrowthtypetemperaturerange
19387positiveoptimum28mesophilic
9222positivegrowth28mesophilic
67770positivegrowth28mesophilic

Physiology and metabolism

spore formation

@refspore formationconfidence
69481yes100
69480yes100

compound production

@refcompound
9222caryomycin
20216Caryomycin

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
1938762968cellulose+/-
1938716634raffinose+/-
1938726546rhamnose+
1938728757fructose+/-
1938729864mannitol+/-
1938717268myo-inositol-
1938718222xylose-
1938717992sucrose+
1938722599arabinose+
1938717234glucose+
683685291gelatin+hydrolysis
6836827897tryptophan-energy source
6836816199urea+hydrolysis
6836816947citrate+assimilation
6836818257ornithine+degradation
6836825094lysine+degradation
6836829016arginine+hydrolysis

metabolite production

@refmetaboliteproductionChebi-ID
67770caryomycinyes
68368acetoinyes15688
68368indoleno35581
68368hydrogen sulfideno16136

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
19387+++++++++++-+-++---

API 20E

@refONPGADH ArgLDC LysODCCITH2SURETDA TrpINDVPGEL
19387+++++-+--++

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
9222soil
67770SoilBeppu, KyushuJapanJPNAsia

isolation source categories

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

taxonmaps

  • @ref: 69479
  • File name: preview.99_4215.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_15;96_102;97_109;98_766;99_4215&stattab=map
  • Last taxonomy: Streptomyces
  • 16S sequence: AB184130
  • Sequence Identity:
  • Total samples: 91
  • soil counts: 45
  • aquatic counts: 8
  • animal counts: 19
  • plant counts: 19

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
92221Risk group (German classification)
193871Risk group (German classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Streptomyces filamentosus gene for 16S rRNA, partial sequenceAB122741564ena67294
20218Streptomyces filamentosus gene for 16S ribosomal RNA, partial sequence, strain: JCM 4576D44244120ena67294
20218Streptomyces filamentosus gene for 16S rRNA, partial sequence, strain: NBRC 12767AB1841301473ena67294
20218Streptomyces filamentosus strain NRRL B-2114 16S ribosomal RNA gene, partial sequenceDQ0266321344ena67294

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Streptomyces filamentosus JCM 4122GCA_014654895contigncbi67294
66792Streptomyces filamentosus strain JCM 412267294.5wgspatric67294

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes100no
gram-positiveyes87.76no
anaerobicno99.086no
halophileno93.793no
spore-formingyes93.84no
glucose-utilyes89.721yes
thermophileno99.134yes
flagellatedno97.216no
motileno93.909no
aerobicyes91.331no
glucose-fermentno84.81no

External links

@ref: 9222

culture collection no.: DSM 40022, ATCC 19753, CBS 492.68, IFO 12767, ISP 5022, NBRC 12767, RIA 1034, JCM 4122, BCRC 13644, CGMCC 4.1656, HAMBI 1010, IFM 1180, IMET 43562, JCM 4576, NCIMB 13018, NRRL B-2114, VKM Ac-1266

straininfo link

  • @ref: 84243
  • straininfo: 45632

literature

  • topic: Phylogeny
  • Pubmed-ID: 27209413
  • title: Streptomyces xinjiangensis sp. nov., an actinomycete isolated from Lop Nur region.
  • authors: Cheng C, Li YQ, Asem MD, Lu CY, Shi XH, Chu X, Zhang WQ, Di An D, Li WJ
  • journal: Arch Microbiol
  • DOI: 10.1007/s00203-016-1234-4
  • year: 2016
  • mesh: Actinobacteria/genetics, Bacterial Typing Techniques, Base Composition/genetics, Cell Wall/chemistry, China, DNA, Bacterial/genetics, Diaminopimelic Acid/analysis, Fatty Acids/analysis, Peptidoglycan/genetics, Phospholipids/analysis, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Streptomyces/*classification/genetics/*isolation & purification
  • topic2: Transcriptome

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
9222Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 40022)https://www.dsmz.de/collection/catalogue/details/culture/DSM-40022
19387Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM40022.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
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
84243Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID45632.1StrainInfo: A central database for resolving microbial strain identifiers