Strain identifier

BacDive ID: 7995

Type strain: Yes

Species: Micromonospora sagamiensis

Strain Designation: MK-65

Variant: Isotype of BacDive ID 7978

Strain history: CIP <- 2005, DSMZ <- JCM <- KCC <- NRRL <- Kyowa Hakko Co.: strain MK-65

NCBI tax ID(s): 47875 (species)

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General

@ref: 11263

BacDive-ID: 7995

DSM-Number: 43912

keywords: genome sequence, 16S sequence, Bacteria, obligate aerobe, spore-forming, mesophilic

description: Micromonospora sagamiensis MK-65 is an obligate aerobe, spore-forming, mesophilic bacterium that was isolated from soil.

NCBI tax id

  • NCBI tax id: 47875
  • Matching level: species

strain history

@refhistory
11263<- JCM <- KCC <- NRRL <- Kyowa Hakko Co., MK-65
67770KCC A-0310 <-- NRRL 11334 <-- Kyowa Hakko Kogyo Co., Ltd.; MK-65.
122348CIP <- 2005, DSMZ <- JCM <- KCC <- NRRL <- Kyowa Hakko Co.: strain MK-65

doi: 10.13145/bacdive7995.20230509.8.1

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 sagamiensis
  • full scientific name: Micromonospora sagamiensis Kroppenstedt et al. 2005

@ref: 11263

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Micromonosporaceae

genus: Micromonospora

species: Micromonospora sagamiensis

full scientific name: Micromonospora sagamiensis Kroppenstedt et al. 2005

strain designation: MK-65

variant: Isotype of BacDive ID 7978

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram staincell shape
69480no91.736
69480100positive
122348nopositiverod-shaped

colony morphology

@refcolony colorincubation periodmedium used
19615Coral red10-14 daysISP 2
19615Salmon pink10-14 daysISP 3
19615Antique pink10-14 daysISP 4
19615Tomato red10-14 daysISP 5
19615Antique pink10-14 daysISP 7
122348

multicellular morphology

@refforms multicellular complexmedium name
19615noISP 2
19615noISP 3
19615noISP 4
19615noISP 5
19615noISP 6
19615noISP 7

multimedia

  • @ref: 11263
  • multimedia content: https://www.dsmz.de/microorganisms/photos/DSM_43912.jpg
  • caption: Medium 554 28°C
  • intellectual property rights: © Leibniz-Institut DSMZ

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
11263N-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
11263GYM 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
19615ISP 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
19615ISP 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:
19615ISP 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
19615ISP 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
19615ISP 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
122348CIP Medium 57yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=57

culture temp

@refgrowthtypetemperaturerange
11263positivegrowth28mesophilic
67770positivegrowth28mesophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 122348
  • oxygen tolerance: obligate aerobe

spore formation

@refspore formationconfidence
69481yes100
69480yes100

compound production

@refcompound
11263micronomicin
19615Antibiotic XK 62-6
19615Antibiotic K 144g
19615Antibiotic 477-2h

observation

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

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
1961517234glucose-
1961522599arabinose-
1961517992sucrose-
1961518222xylose-
1961517268myo-inositol-
1961529864mannitol-
1961528757fructose-
1961526546rhamnose-
1961516634raffinose+/-
1961562968cellulose+/-
12234817632nitrate+reduction
12234816301nitrite-reduction

metabolite production

@refChebi-IDmetaboliteproduction
6777081283gentamicin C2byes
12234835581indoleno

enzymes

@refvalueactivityec
122348oxidase+
122348alcohol dehydrogenase-1.1.1.1
122348catalase+1.11.1.6
122348lysine decarboxylase-4.1.1.18
122348ornithine decarboxylase-4.1.1.17
122348urease-3.5.1.5
68382alkaline phosphatase+3.1.3.1
68382esterase lipase (C 8)+
68382leucine arylamidase+3.4.11.1
68382valine arylamidase-
68382alpha-chymotrypsin-3.4.21.1
68382acid phosphatase+3.1.3.2
68382beta-galactosidase+3.2.1.23
68382beta-glucuronidase-3.2.1.31
68382alpha-glucosidase+3.2.1.20
68382beta-glucosidase+3.2.1.21
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- FucosidaseControl
19615+-+-+-+--+-++-+++--
122348+++++--+-++-+-++----

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
11263soil
67770Forest soilSagamihara City, Kanagawa Pref.JapanJPNAsia
122348Environment, Soil

isolation source categories

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

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
112631Risk group (German classification)
196151Risk group (German classification)
1223481Risk group (French classification)

Sequence information

16S sequences

  • @ref: 11263
  • description: Micromonospora sagamiensis 16S rRNA gene, type strain DSM 43912
  • accession: X92624
  • length: 1466
  • database: ena
  • NCBI tax ID: 47875

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Micromonospora sagamiensis DSM 43912GCA_007829995contigncbi47875
66792Micromonospora sagamiensis JCM 3310GCA_014680085completencbi47875
66792Micromonospora sagamiensis strain DSM 4391247875.4wgspatric47875
66792Micromonospora sagamiensis strain JCM 331047875.5completepatric47875
66792Micromonospora sagamiensis MK-652585427560draftimg47875

GC content

  • @ref: 67770
  • GC-content: 72.51
  • method: genome sequence analysis

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes100no
flagellatedno97.129no
gram-positiveyes90.499no
anaerobicno98.849no
aerobicyes94.3no
halophileno94.96no
spore-formingyes95.673no
thermophileno98.462yes
glucose-utilyes83.062yes
motileno93.221no
glucose-fermentno91.195no

External links

@ref: 11263

culture collection no.: DSM 43912, ATCC 21826, CIP 108950, DSM 44886, JCM 3310, KCC A-0310, NBRC 101888, NRRL 11334, KACC 20106, KCTC 9215

straininfo link

  • @ref: 77425
  • straininfo: 37745

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny15997706Eight new species of the genus Micromonospora, Micromonospora citrea sp. nov., Micromonospora echinaurantiaca sp. nov., Micromonospora echinofusca sp. nov. Micromonospora fulviviridis sp. nov., Micromonospora inyonensis sp. nov., Micromonospora peucetia sp. nov., Micromonospora sagamiensis sp. nov., and Micromonospora viridifaciens sp. nov.Kroppenstedt RM, Mayilraj S, Wink JM, Kallow W, Schumann P, Secondini C, Stackebrandt ESyst Appl Microbiol10.1016/j.syapm.2004.12.0112005Carbohydrates/analysis, Diaminopimelic Acid/analysis, Fatty Acids/analysis, Isomerism, Micromonospora/*classification/cytology/genetics/physiology, Nucleic Acid Hybridization, Phospholipids/analysis, Phylogeny, Ribotyping, Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization, Vitamin K 2/analysis
Metabolism23355136Femtosecond laser-based mutagenesis strategy for micronomicin production enhancement of Micromonospora sagamiensis ATCC 21826.Liu P, Wen J, Chen Y, Jia XWorld J Microbiol Biotechnol10.1007/s11274-013-1261-02013Aminoglycosides/*biosynthesis, Anti-Infective Agents/*metabolism, Fermentation, Gentamicins, High-Throughput Screening Assays, *Lasers, Metabolic Engineering/*methods, Micromonospora/*isolation & purification/*metabolism/radiation effects, *MutagenesisBiotechnology
Phylogeny26358439Micromonospora fluostatini sp. nov., isolated from marine sediment.Phongsopitanun W, Kudo T, Mori M, Shiomi K, Pittayakhajonwut P, Suwanborirux K, Tanasupawat SInt J Syst Evol Microbiol10.1099/ijsem.0.0005892015Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Geologic Sediments/*microbiology, Micromonospora/*classification/genetics/isolation & purification, Molecular Sequence Data, Peptidoglycan/chemistry, Phospholipids/chemistry, *Phylogeny, Pigmentation, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Sequence Analysis, DNA, Thailand, Vitamin K 2/chemistryGenetics

Reference

@idauthorscataloguedoi/urltitle
11263Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 43912)https://www.dsmz.de/collection/catalogue/details/culture/DSM-43912
19615Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM43912.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
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/
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
77425Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID37745.1StrainInfo: A central database for resolving microbial strain identifiers
122348Curators of the CIPCollection of Institut Pasteur (CIP 108950)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20108950