Strain identifier

BacDive ID: 7972

Type strain: Yes

Species: Micromonospora echinospora

Strain history: KCC A-0073 <-- ATCC 15837 <-- Schering Corp. <-- A. Woyciesjes.

NCBI tax ID(s): 1877 (species)

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General

@ref: 11289

BacDive-ID: 7972

DSM-Number: 43816

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

description: Micromonospora echinospora DSM 43816 is a spore-forming, mesophilic bacterium that builds an aerial mycelium and produces antibiotic compounds.

NCBI tax id

  • NCBI tax id: 1877
  • Matching level: species

strain history

@refhistory
11289<- NRRL <- A. Woyciesjes
67770KCC A-0073 <-- ATCC 15837 <-- Schering Corp. <-- A. Woyciesjes.

doi: 10.13145/bacdive7972.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Micromonosporales
  • family: Micromonosporaceae
  • genus: Micromonospora
  • species: Micromonospora echinospora
  • full scientific name: Micromonospora echinospora Luedemann and Brodsky 1964 (Approved Lists 1980)

  • synonyms

    @refsynonym
    20215Micromonospora rhodorangea
    20215Micromonospora purpurea
    20215Micromonospora echinospora subsp. ferruginea

@ref: 11289

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Micromonosporaceae

genus: Micromonospora

species: Micromonospora echinospora subsp. echinospora

full scientific name: Micromonospora echinospora subsp. echinospora Luedemann and Brodsky 1964

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram stain
69480no95.723
69480100positive

colony morphology

@refcolony colorincubation periodmedium used
19959Brown red (3011)10-14 daysISP 2
19959Black red (3007)10-14 daysISP 3
19959Brown red (3011)10-14 daysISP 4
19959Black red (3007)10-14 daysISP 5
19959Orange/black red10-14 daysISP 6
19959Black red (3007)10-14 daysISP 7

multicellular morphology

@refforms multicellular complexmedium namecomplex namecomplex color
19959noISP 2
19959noISP 3
19959noISP 4
19959yesISP 5Aerial MyceliumWhite
19959noISP 6
19959noISP 7

multimedia

@refmultimedia contentintellectual property rightscaption
11289https://www.dsmz.de/microorganisms/photos/DSM_43816-1.jpg© Leibniz-Institut DSMZ
11289https://www.dsmz.de/microorganisms/photos/DSM_43816.jpg© Leibniz-Institut DSMZMedium 554 28°C

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
11289N-Z-AMINE-MEDIUM (DSMZ Medium 554)yeshttps://mediadive.dsmz.de/medium/554Name: N-Z-AMINE-MEDIUM (DSMZ Medium 554) Composition: Starch 20.0 g/l Agar 20.0 g/l Glucose 10.0 g/l N-Z amine 5.0 g/l Yeast extract 5.0 g/l CaCO3 1.0 g/l Distilled water
19959ISP 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
19959ISP 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:
19959ISP 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
19959ISP 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
19959ISP 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
19959ISP 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
11289GYM STREPTOMYCES MEDIUM (DSMZ Medium 65)yeshttps://www.dsmz.de/microorganisms/medium/pdf/DSMZ_Medium65.pdf

culture temp

@refgrowthtypetemperaturerange
11289positivegrowth28mesophilic
19959positiveoptimum28mesophilic
67770positivegrowth28mesophilic

Physiology and metabolism

tolerance

@refcompound
19959Liparmacin A
19959Tiacumicin C

spore formation

@refspore formationconfidence
69481yes100
69480yes100

compound production

@refcompound
11289gentamycin
11289restriction endonuclease MecI

halophily

  • @ref: 19959
  • salt: NaCl
  • growth: positive
  • tested relation: growth
  • concentration: 0 %

observation

  • @ref: 67770
  • observation: quinones: MK-10(H6)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
1995962968cellulose-
1995916634raffinose+
1995926546rhamnose+
1995928757fructose-
1995929864mannitol-
1995917268myo-inositol-
1995918222xylose-
1995917992sucrose+
1995922599arabinose+
1995917234glucose+
683685291gelatin+hydrolysis
6836827897tryptophan-energy source
6836816199urea-hydrolysis
6836816947citrate-assimilation
6836818257ornithine-degradation
6836825094lysine-degradation
6836829016arginine-hydrolysis

metabolite production

@refChebi-IDmetaboliteproduction
6777017833gentamicinyes
6836815688acetoinyes
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
19959+-+-+-++-+--+-+++--

API 20E

@refONPGADH ArgLDC LysODCCITH2SURETDA TrpINDVPGEL
19959---------++

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
11289soil
67770SoilJamesville, NYUSAUSANorth America

isolation source categories

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

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
112891Risk group (German classification)
199591German classification

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Micromonospora echinospora ATCC 15837 16S-23S ribosomal RNA intergenic spacerAY371887361ena1877
11289M.echinospora 16S rRNA gene (isolate DSM 43816)X926071465ena1877
67770Micromonospora echinospora echinospora 16S ribosomal RNA gene sequenceU585321409ena1877

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Micromonospora echinospora DSM 43816GCA_900091495chromosomencbi1877
66792Micromonospora echinospora strain ATCC 158371877.7wgspatric1877
66792Micromonospora echinospora strain DSM 438161877.5completepatric1877
66792Micromonospora echinospora DSM 438162622736613draftimg1877
66792Micromonospora echinospora ATCC 158372855711692draftimg1877
67770Micromonospora echinospora ATCC 15837GCA_002266845scaffoldncbi1877

GC content

@refGC-contentmethod
6777071.7high performance liquid chromatography (HPLC)
6777072.53genome sequence analysis

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes100no
motileno94.333no
gram-positiveyes91.848no
anaerobicno99.244no
aerobicyes96.364no
halophileno95.085yes
spore-formingyes96.042no
glucose-utilyes86.693yes
flagellatedno97.356no
thermophileno98.671yes
glucose-fermentno93.231no

External links

@ref: 11289

culture collection no.: DSM 43816, ATCC 15837, CBS 619.66, IFO 12574, IMET 8211, JCM 3073, NBRC 12574, NRRL 2985, RIA S-420, BCRC 11626, CBS 645.71, CGMCC 4.2102, CGMCC 4.5706, IFO 13149, IMSNU 21292, IMSNU 22043, KCTC 9213, NBRC 13149, NCIMB 12744, VKM Ac-669

straininfo link

  • @ref: 77406
  • straininfo: 36517

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Cultivation10736011Response of Micromonospora echinospora (NCIMB 12744) spores to heat treatment with evidence of a heat activation phenomenon.Hoskisson PA, Hobbs G, Sharples GPLett Appl Microbiol10.1046/j.1472-765x.2000.00680.x2000Colony Count, Microbial, Culture Media, *Hot Temperature, Micromonospora/*physiology, Oxygen Consumption, Spores, Bacterial/physiologyStress
Metabolism11261494Antibiotic production, accumulation of intracellular carbon reserves, and sporulation in Micromonospora echinospora (ATCC 15837).Hoskisson PA, Hobbs G, Sharples GPCan J Microbiol2001Anti-Bacterial Agents/*biosynthesis, Glucans/metabolism, Kinetics, Lipid Metabolism, Micromonospora/growth & development/metabolism/*physiology, *Spores, BacterialEnzymology
Metabolism12680936The importance of amino acids as carbon sources for Micromonospora echinospora (ATCC 15837).Hoskisson PA, Sharples GP, Hobbs GLett Appl Microbiol10.1046/j.1472-765x.2003.01306.x2003Amino Acids/*metabolism, Asparagine/metabolism, Carbon/metabolism, Down-Regulation, Glucose/*metabolism, Micromonospora/classification/growth & development/*metabolismPhylogeny
Metabolism15539926Modulation of glycogen and trehalose levels in Micromonospora echinospora (ATCC 15837).Hoskisson PA, England R, Sharples GP, Hobbs GAntonie Van Leeuwenhoek10.1023/B:ANTO.0000047920.48459.632004Adenosine Triphosphate/metabolism, Asparagine/metabolism, Carbon/metabolism, Glycogen/*metabolism, Kinetics, Micromonospora/*growth & development/metabolism, Nitrogen/metabolism, Trehalose/*metabolismEnzymology
Enzymology16328864Differentiation and protease production in Micromonospora echinospora (ATCC 15837).Hoskisson PA, Sharples GP, Hobbs GAntonie Van Leeuwenhoek10.1007/s10482-005-9001-62005Kinetics, Micromonospora/drug effects/*enzymology/growth & development/physiology, Peptide Hydrolases/*biosynthesis, Serine Proteinase Inhibitors/pharmacology, Spores, Bacterial/drug effects/physiology, Tosyllysine Chloromethyl Ketone/pharmacology, Tosylphenylalanyl Chloromethyl Ketone/pharmacologyPathogenicity
Phylogeny19667372Micromonospora tulbaghiae sp. nov., isolated from the leaves of wild garlic, Tulbaghia violacea.Kirby BM, Meyers PRInt J Syst Evol Microbiol10.1099/ijs.0.013243-02009DNA Gyrase/genetics, DNA, Bacterial/genetics/isolation & purification, Garlic/*microbiology, Micromonospora/classification/genetics/growth & development/*isolation & purification, Molecular Sequence Data, Peas/microbiology, Phylogeny, Plant Leaves/*microbiology, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/geneticsEnzymology

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
11289Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 43816)https://www.dsmz.de/collection/catalogue/details/culture/DSM-43816
19959Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM43816.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
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
77406Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID36517.1StrainInfo: A central database for resolving microbial strain identifiers