Strain identifier

BacDive ID: 15338

Type strain: Yes

Species: Streptomyces celluloflavus

Strain Designation: BL904, M338-M1

Strain history: KCC S-0208 <-- M. Hamada M338-M1 <-- H. Umezawa A-9989-A.

NCBI tax ID(s): 1946 (species)

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General

@ref: 9823

BacDive-ID: 15338

DSM-Number: 40819

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

description: Streptomyces celluloflavus BL904 is a mesophilic bacterium that produces antibiotic compounds and was isolated from soil.

NCBI tax id

  • NCBI tax id: 1946
  • Matching level: species

strain history

@refhistory
9823<- H.D. Tresner, BL904 (Streptomyces kasugaensis) <- Bristol Labs, M-338-M1 <- H. Umezawa, A-9989-A
67770KCC S-0208 <-- M. Hamada M338-M1 <-- H. Umezawa A-9989-A.

doi: 10.13145/bacdive15338.20230509.8.1

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 celluloflavus
  • full scientific name: Streptomyces celluloflavus Nishimura et al. 1953 (Approved Lists 1980)

  • synonyms

    • @ref: 20215
    • synonym: Streptomyces kasugaensis

@ref: 9823

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Streptomycetaceae

genus: Streptomyces

species: Streptomyces kasugaensis

full scientific name: Streptomyces kasugaensis Hamada et al. 1995

strain designation: BL904, M338-M1

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram stain
69480no93.656
69480100positive

colony morphology

@refcolony colorincubation periodmedium used
18675Brown beige (1011)10-14 daysISP 2
18675Broom yellow (1032)10-14 daysISP 3
18675Colorless10-14 daysISP 4
18675Colorless10-14 daysISP 5
18675Beige (1001)10-14 daysISP 6
18675Brown beige (1011)10-14 daysISP 7

multicellular morphology

@refforms multicellular complexmedium name
18675noISP 2
18675noISP 3
18675noISP 4
18675noISP 5
18675noISP 6
18675noISP 7

multimedia

  • @ref: 9823
  • multimedia content: https://www.dsmz.de/microorganisms/photos/DSM_40819.jpg
  • caption: Medium 987 28°C
  • intellectual property rights: © Leibniz-Institut DSMZ

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
9823GYM 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
18675ISP 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
18675ISP 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:
18675ISP 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
18675ISP 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
18675ISP 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
18675ISP 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
9823ISP2 MEDIUM (DSMZ Medium 987)yeshttps://www.dsmz.de/microorganisms/medium/pdf/DSMZ_Medium987.pdf
9823GPHF-MEDIUM (DSMZ Medium 553)yeshttps://www.dsmz.de/microorganisms/medium/pdf/DSMZ_Medium553.pdf
9823ROLLED OATS MINERAL MEDIUM (DSMZ Medium 84)yeshttps://www.dsmz.de/microorganisms/medium/pdf/DSMZ_Medium84.pdf

culture temp

@refgrowthtypetemperaturerange
9823positivegrowth28mesophilic
67770positivegrowth28mesophilic

Physiology and metabolism

spore formation

@refspore formationconfidence
18675no
69481yes100
69480yes99.036

compound production

@refcompound
9823kasugamycin
9823thiolutin
18675Kasugamycin

halophily

  • @ref: 18675
  • salt: NaCl
  • growth: positive
  • tested relation: maximum
  • concentration: 2.5 %

observation

  • @ref: 67770
  • observation: quinones: MK-9(H6), MK-9(H8), MK-9(H4)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
1867517234glucose+
1867522599arabinose+
1867517992sucrose+
1867518222xylose-
1867517268myo-inositol+
1867529864mannitol-
1867528757fructose-
1867526546rhamnose-
1867516634raffinose-
1867562968cellulose-
683685291gelatin-hydrolysis
6836827897tryptophan-energy source
6836816199urea+hydrolysis
6836816947citrate+assimilation
6836818257ornithine+degradation
6836825094lysine+degradation
6836829016arginine+hydrolysis

metabolite production

@refChebi-IDmetaboliteproduction
6777081419kasugamycinyes
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
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
18675+-+-++---++-+-+-++-

API 20E

@refONPGADH ArgLDC LysODCCITH2SURETDA TrpINDVPGEL
18675-++++-+----

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
9823soilNara, Nara City, Kasuga shrineJapanJPNAsia
67770SoilKasuga Shrine, Nara CityJapanJPNAsia

isolation source categories

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

taxonmaps

  • @ref: 69479
  • File name: preview.99_2738.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_15;96_103;97_110;98_2124;99_2738&stattab=map
  • Last taxonomy: Streptomyces
  • 16S sequence: AB184530
  • Sequence Identity:
  • Total samples: 181
  • soil counts: 167
  • aquatic counts: 5
  • animal counts: 8
  • plant counts: 1

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
186751German classification
98231Risk group (German classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Streptomyces kasugaensis DNA for 16S ribosomal RNA, strain M338-M1, partial sequenceAB0244411488ena1946
20218Streptomyces kasugaensis gene for 16S rRNA, partial sequence, strain: NBRC 13851AB1845301476ena1946

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Streptomyces kasugaensis strain BCRC 123491946.3wgspatric1946
67770Streptomyces kasugaensis BCRC 12349GCA_002261115scaffoldncbi1946

GC content

@refGC-contentmethod
982370.4
6777070.4high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes100no
motileno93.077no
gram-positiveyes92.369no
anaerobicno99.109no
aerobicyes90.845no
halophileno91.271no
spore-formingyes94.318yes
glucose-utilyes88.94no
flagellatedno98.081no
thermophileno98.079yes
glucose-fermentno86.587no

External links

@ref: 9823

culture collection no.: DSM 40819, ATCC 15714, IFO 13851, JCM 4208, KCC S-0208, NBRC 13851, BCRC 12349, KCTC 1078, KCTC 2113, MTCC 6919, NCIMB 12239, NCIMB 12717

straininfo link

  • @ref: 84431
  • straininfo: 36448

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Enzymology9589071A 7.6kb DNA region from Streptomyces kasugaensis M338-M1 includes some genes responsible for kasugamycin biosynthesis.Ikeno S, Tsuji T, Higashide K, Kinoshita N, Hamada M, Hori MJ Antibiot (Tokyo)10.7164/antibiotics.51.3411998Amino Acid Sequence, *Aminoglycosides, Anti-Bacterial Agents/*biosynthesis, Base Sequence, Cloning, Molecular, DNA, Bacterial/*metabolism, Molecular Sequence Data, Open Reading Frames, Streptomyces/*geneticsGenetics
Enzymology10866219ABC transporter genes, kasKLM, responsible for self-resistance of a kasugamycin producer strain.Ikeno S, Yamane Y, Ohishi Y, Kinoshita N, Hamada M, Tsuchiya KS, Hori MJ Antibiot (Tokyo)10.7164/antibiotics.53.3732000ATP-Binding Cassette Transporters/*genetics, Amino Acid Sequence, *Aminoglycosides, Anti-Bacterial Agents/*biosynthesis, Base Sequence, Cloning, Molecular/methods, DNA, Bacterial/*genetics, Drug Resistance, Microbial, Escherichia coli/*genetics, Gene Expression, Molecular Sequence Data, Open Reading Frames, Plasmids/*genetics, Streptomyces/*genetics, beta-Galactosidase/metabolismGenetics
Metabolism12617515kasT gene of Streptomyces kasugaensis M338-M1 encodes a DNA-binding protein which binds to intergenic region of kasU-kasJ in the kasugamycin biosynthesis gene cluster.Ikeno S, Aoki D, Sato K, Hamada M, Hori M, Tsuchiya KSJ Antibiot (Tokyo)10.7164/antibiotics.55.10532002Amino Acid Sequence, *Aminoglycosides, Anti-Bacterial Agents/*biosynthesis, Bacterial Proteins/*genetics/metabolism, Base Sequence, Binding Sites, Cloning, Molecular, DNA, Intergenic, DNA-Binding Proteins/chemistry/*genetics/*metabolism, Flavin-Adenine Dinucleotide/metabolism, Gene Expression Regulation, Bacterial, Helix-Turn-Helix Motifs, Molecular Sequence Data, Multigene Family, Recombinant Fusion Proteins/genetics/isolation & purification/metabolism, Sequence Analysis, DNA, Sequence Homology, Amino Acid, Streptomyces/*genetics/metabolism, Transcription Factors/chemistry, Transcription Initiation Site, Transcription, GeneticEnzymology
Genetics16568715DNA sequencing and transcriptional analysis of the kasugamycin biosynthetic gene cluster from Streptomyces kasugaensis M338-M1.Ikeno S, Aoki D, Hamada M, Hori M, Tsuchiya KSJ Antibiot (Tokyo)10.1038/ja.2006.42006Amino Acid Sequence, Aminoglycosides/*biosynthesis, Blotting, Northern, DNA/*chemistry/*genetics, Gene Expression Regulation, Fungal, Genes, Fungal/*genetics, Molecular Sequence Data, Multigene Family, Operon/genetics, Plasmids/genetics, RNA, Fungal/biosynthesis/genetics, Reverse Transcriptase Polymerase Chain Reaction, Sequence Analysis, DNA, Streptomyces/*genetics/growth & development/*metabolismTranscriptome
Phylogeny20525811Streptomyces youssoufiensis sp. nov., isolated from a Moroccan phosphate mine.Hamdali H, Virolle MJ, von Jan M, Sproer C, Klenk HP, Ouhdouch YInt J Syst Evol Microbiol10.1099/ijs.0.023036-02010DNA, Bacterial/genetics, Fatty Acids/metabolism, Mining, Molecular Sequence Data, Morocco, Phosphates/analysis, Phylogeny, RNA, Ribosomal, 16S/genetics, *Soil Microbiology, Streptomyces/*classification/genetics/*isolation & purification/metabolismMetabolism
Biotechnology26521251Identification and engineering of regulation-related genes toward improved kasugamycin production.Zhu C, Kang Q, Bai L, Cheng L, Deng ZAppl Microbiol Biotechnol10.1007/s00253-015-7082-32015Aminoglycosides/*biosynthesis, Anti-Bacterial Agents/*biosynthesis, Biosynthetic Pathways/*genetics, Gene Deletion, Gene Expression, Gene Expression Profiling, *Gene Expression Regulation, Bacterial, Genetic Complementation Test, Genetic Loci, *Metabolic Engineering, Multigene Family, Real-Time Polymerase Chain Reaction, Streptomyces/*genetics/*metabolismMetabolism
Phylogeny28476992Actinobacterial-mediated synthesis of silver nanoparticles and their activity against pathogenic bacteria.Wypij M, Golinska P, Dahm H, Rai MIET Nanobiotechnol10.1049/iet-nbt.2016.01122017Actinobacteria/classification/*metabolism, Anti-Bacterial Agents/*administration & dosage/chemistry, Bacterial Physiological Phenomena/*drug effects, Cell Survival/*drug effects/physiology, Dose-Response Relationship, Drug, Materials Testing, Metal Nanoparticles/*administration & dosage/chemistry/ultrastructure, Particle Size, Silver/*administration & dosage/chemistry, Species Specificity, Treatment OutcomePathogenicity

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
9823Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 40819)https://www.dsmz.de/collection/catalogue/details/culture/DSM-40819
18675Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM40819.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)
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
84431Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID36448.1StrainInfo: A central database for resolving microbial strain identifiers