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)

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General

@ref: 9222

BacDive-ID: 15139

DSM-Number: 40022

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

description: Streptomyces filamentosus 1-C-9 is a spore-forming, mesophilic, Gram-positive 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/bacdive15139.20250331.9.3

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

@refgram stainconfidencemotility
125439positive99.7
12543990.4no
125438positive91.143

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

@refgrowthtypetemperature
19387positiveoptimum28
9222positivegrowth28
67770positivegrowth28

Physiology and metabolism

oxygen tolerance

  • @ref: 125439
  • oxygen tolerance: obligate aerobe
  • confidence: 98.5

spore formation

@refspore formationconfidence
125439yes95.5
125438yes90.671

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
68382alpha-fucosidase-3.2.1.51
68382alpha-mannosidase-3.2.1.24
68382N-acetyl-beta-glucosaminidase-3.2.1.52
68382beta-glucosidase+3.2.1.21
68382beta-glucuronidase-3.2.1.31
68382alpha-glucosidase+3.2.1.20
68382beta-galactosidase+3.2.1.23
68382alpha-galactosidase-3.2.1.22
68382naphthol-AS-BI-phosphohydrolase+
68382acid phosphatase+3.1.3.2
68382alpha-chymotrypsin+3.4.21.1
68382trypsin+3.4.21.4
68382cystine arylamidase+3.4.11.3
68382leucine arylamidase+3.4.11.1
68382valine arylamidase+
68382lipase (C 14)+
68382esterase lipase (C 8)+
68382esterase (C 4)+
68382alkaline phosphatase+3.1.3.1
68368ornithine decarboxylase+4.1.1.17
68368arginine dihydrolase+3.5.3.6
68368gelatinase+
68368tryptophan deaminase-4.1.99.1
68368urease+3.5.1.5
68368lysine decarboxylase+4.1.1.18
68368beta-galactosidase+3.2.1.23

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 sequenceAB122741564nuccore67294
20218Streptomyces filamentosus gene for 16S ribosomal RNA, partial sequence, strain: JCM 4576D44244120nuccore67294
20218Streptomyces filamentosus gene for 16S rRNA, partial sequence, strain: NBRC 12767AB1841301473nuccore67294
20218Streptomyces filamentosus strain NRRL B-2114 16S ribosomal RNA gene, partial sequenceDQ0266321344nuccore67294

Genome sequences

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

Genome-based predictions

predictions

@refmodeltraitdescriptionpredictionconfidencetraining_data
125438gram-positivegram-positivePositive reaction to Gram-stainingyes91.143no
125438anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)no97.32no
125438spore-formingspore-formingAbility to form endo- or exosporesyes90.671no
125438aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)yes81.758no
125438thermophilethermophilicAbility to grow at temperatures above or equal to 45°Cno97.5yes
125438motile2+flagellatedAbility to perform flagellated movementno89.6no
125439BacteriaNetspore_formationAbility to form endo- or exosporesyes95.5
125439BacteriaNetmotilityAbility to perform movementno90.4
125439BacteriaNetgram_stainReaction to gram-stainingpositive99.7
125439BacteriaNetoxygen_toleranceOxygenic conditions needed for growthobligate aerobe98.5

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
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
125438Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg Overmann10.1101/2024.08.12.607695Predicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets
125439Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardyhttps://github.com/GenomeNet/deepGdeepG: Deep Learning for Genome Sequence Data. R package version 0.3.1