Strain identifier

BacDive ID: 16597

Type strain: Yes

Species: Streptosporangium violaceochromogenes

Strain Designation: MK-49

Strain history: KCC A-0281 <-- ATCC 21807 <-- Kyowa Hakko Kogyo Co., Ltd.; MK-49.

NCBI tax ID(s): 46188 (species)

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General

@ref: 11331

BacDive-ID: 16597

DSM-Number: 43849

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

description: Streptosporangium violaceochromogenes MK-49 is a spore-forming, mesophilic bacterium that builds an aerial mycelium and produces antibiotic compounds.

NCBI tax id

  • NCBI tax id: 46188
  • Matching level: species

strain history

@refhistory
11331<- ATCC <- Kyowa Ferm. Ind. Co., Ltd., MK-49
67770KCC A-0281 <-- ATCC 21807 <-- Kyowa Hakko Kogyo Co., Ltd.; MK-49.

doi: 10.13145/bacdive16597.20250331.9.3

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Streptosporangiales
  • family: Streptosporangiaceae
  • genus: Streptosporangium
  • species: Streptosporangium violaceochromogenes
  • full scientific name: Streptosporangium violaceochromogenes Kawamoto et al. 1975 (Approved Lists 1980)

@ref: 11331

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Streptosporangiaceae

genus: Streptosporangium

species: Streptosporangium violaceochromogenes

full scientific name: Streptosporangium violaceochromogenes Kawamoto et al. 1975

strain designation: MK-49

type strain: yes

Morphology

cell morphology

@refgram stainconfidencemotility
125439positive99.4
12543991.6no

colony morphology

@refcolony colorincubation periodmedium used
19604Yellow orange10-14 daysISP 2
19604Yellow10-14 daysISP 3
19604Yellow10-14 daysISP 4
19604Orange red10-14 daysISP 5
19604Yellow10-14 daysISP 6
19604Orange10-14 daysISP 7

multicellular morphology

@refforms multicellular complexcomplex namecomplex colormedium name
19604yesAerial MyceliumWhiteISP 2
19604yesAerial MyceliumWhiteISP 3
19604yesAerial MyceliumWhiteISP 4
19604yesAerial MyceliumWhiteISP 5
19604yesAerial MyceliumWhiteISP 6
19604yesAerial MyceliumWhiteISP 7

multimedia

@refmultimedia contentintellectual property rightscaption
11331https://www.dsmz.de/microorganisms/photos/DSM_43849-1.jpg© Leibniz-Institut DSMZ
11331https://www.dsmz.de/microorganisms/photos/DSM_43849-2.jpg© Leibniz-Institut DSMZ
11331https://www.dsmz.de/microorganisms/photos/DSM_43849.jpg© Leibniz-Institut DSMZMedium 548 28°C

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
11331BENNETT'S AGAR (DSMZ Medium 548)yeshttps://mediadive.dsmz.de/medium/548Name: BENNETT'S AGAR (DSMZ Medium 548) Composition: Agar 15.0 g/l Glucose 10.0 g/l N-Z amine 2.0 g/l Yeast extract 1.0 g/l Beef extract 1.0 g/l Distilled water
11331GYM 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
19604ISP 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
19604ISP 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:
19604ISP 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
19604ISP 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
19604ISP 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
19604ISP 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
11331GPHF-MEDIUM (DSMZ Medium 553)yeshttps://www.dsmz.de/microorganisms/medium/pdf/DSMZ_Medium553.pdf

culture temp

@refgrowthtypetemperature
11331positivegrowth28
19604positiveoptimum30
67770positivegrowth28

Physiology and metabolism

oxygen tolerance

  • @ref: 125439
  • oxygen tolerance: obligate aerobe
  • confidence: 95.7

spore formation

@refspore descriptiontype of sporespore formationconfidence
19604Formation of sporangia, spore surface smoothsporeyes
125438yes90.127

compound production

@refcompound
11331antibiotic XK-49-1-B-2
67770Victomycin

halophily

  • @ref: 19604
  • salt: NaCl
  • growth: positive
  • tested relation: maximum
  • concentration: 5 %

observation

  • @ref: 67770
  • observation: quinones: MK-9(H2), MK-9(III,VIII-H4), MK-9

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
1960417234glucose+
1960422599arabinose+
1960417992sucrose+
1960418222xylose-
1960417268myo-inositol+
1960429864mannitol-
1960428757fructose+
1960426546rhamnose-
1960416634raffinose-
1960462968cellulose-
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
68382alpha-mannosidase-3.2.1.24
68382N-acetyl-beta-glucosaminidase-3.2.1.52
68382alpha-glucosidase+3.2.1.20
68382beta-glucosidase-3.2.1.21
68382alpha-galactosidase-3.2.1.22
68382naphthol-AS-BI-phosphohydrolase+
68382alpha-chymotrypsin-3.4.21.1
68382acid phosphatase+3.1.3.2
68382cystine arylamidase+3.4.11.3
68382trypsin+3.4.21.4
68382leucine arylamidase-3.4.11.1
68382valine arylamidase+
68382lipase (C 14)+
68382esterase (C 4)+
68382esterase lipase (C 8)+
68382alkaline phosphatase+3.1.3.1
68368lysine decarboxylase+4.1.1.18
68382alpha-fucosidase-3.2.1.51
68382beta-glucuronidase-3.2.1.31
68382beta-galactosidase+3.2.1.23
68368gelatinase+
68368tryptophan deaminase-4.1.99.1
68368urease+3.5.1.5
68368ornithine decarboxylase+4.1.1.17
68368arginine dihydrolase+3.5.3.6
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
19604++++-+++-++-+-+----

API 20E

@refONPGADH ArgLDC LysODCCITH2SURETDA TrpINDVPGEL
19604+++++-+--++

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinentgeographic location
11331soil swampJapanJPNAsia
67770SoilJapanJPNAsiaYoshioka, Gunma Pref.

isolation source categories

Cat1Cat2Cat3
#Environmental#Terrestrial#Soil
#Environmental#Terrestrial#Wetland (Swamp)

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
113311Risk group (German classification)
196041Risk group (German classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218S.violaceochromogenes DNA for 16S ribosomal RNA gene (strain DSM43849T)X899511456nuccore46188
20218Streptosporangium violaceochromogenes 16S rRNA geneU489971423nuccore46188

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Streptosporangium violaceochromogenes JCM 3281GCA_014654615scaffoldncbi46188
66792Streptosporangium violaceochromogenes strain JCM 328146188.3wgspatric46188

Genome-based predictions

predictions

@refmodeltraitdescriptionpredictionconfidencetraining_data
125438gram-positivegram-positivePositive reaction to Gram-stainingyes86.261no
125438anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)no93.698no
125438aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)yes85.692no
125438spore-formingspore-formingAbility to form endo- or exosporesyes90.127yes
125438thermophilethermophilicAbility to grow at temperatures above or equal to 45°Cno89.488no
125438motile2+flagellatedAbility to perform flagellated movementno84.5no
125439BacteriaNetspore_formationAbility to form endo- or exosporesyes84.6
125439BacteriaNetmotilityAbility to perform movementno91.6
125439BacteriaNetgram_stainReaction to gram-stainingpositive99.4
125439BacteriaNetoxygen_toleranceOxygenic conditions needed for growthobligate aerobe95.7

External links

@ref: 11331

culture collection no.: DSM 43849, ATCC 21807, JCM 3281, KCC A-0281, CGMCC 4.2064, IFO 15560, IMSNU 22054, KCTC 9439, MTCC 1523, NBRC 15560, NRRL B-16784

straininfo link

  • @ref: 85624
  • straininfo: 297052

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny24760800Streptosporangium jomthongense sp. nov., an actinomycete isolated from rhizospheric soil and emendation of the genus Streptosporangium.Intra B, Matsumoto A, Inahashi Y, Omura S, Panbangred W, Takahashi YInt J Syst Evol Microbiol10.1099/ijs.0.061978-02014Actinomycetales/*classification/genetics/isolation & purification, Araceae, Bacterial Typing Techniques, DNA, Bacterial/genetics, Fatty Acids/chemistry, Molecular Sequence Data, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, *Rhizosphere, Sequence Analysis, DNA, *Soil Microbiology, Thailand, Vitamin K 2/analogs & derivatives/chemistryGenetics
Phylogeny25256952Streptosporangium subfuscum sp. nov., isolated from the rhizosphere of marigold (Tagetes erecta L.).Zhou Y, Liu C, Zhang Y, Li C, Xing J, Li L, Zhou S, Wang X, Xiang WAntonie Van Leeuwenhoek10.1007/s10482-014-0293-22014Actinobacteria/*classification/genetics/*isolation & purification/physiology, Bacterial Typing Techniques, China, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Microscopy, Electron, Scanning, Molecular Sequence Data, Nucleic Acid Hybridization, Phylogeny, RNA, Ribosomal, 16S/genetics, *Rhizosphere, Sequence Analysis, DNA, *Soil Microbiology, Tagetes/*microbiologyGenetics

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
11331Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 43849)https://www.dsmz.de/collection/catalogue/details/culture/DSM-43849
19604Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM43849.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
85624Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID297052.1StrainInfo: 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