Strain identifier

BacDive ID: 8012

Type strain: Yes

Species: Micromonospora chaiyaphumensis

Strain Designation: MC5-1

Strain history: S. Tanasupawat; Chulalongkorn Univ., Thailand; MC5-1.

NCBI tax ID(s): 307119 (species)

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General

@ref: 15930

BacDive-ID: 8012

DSM-Number: 45246

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

description: Micromonospora chaiyaphumensis MC5-1 is an aerobe, spore-forming, mesophilic bacterium that was isolated from soil.

NCBI tax id

  • NCBI tax id: 307119
  • Matching level: species

strain history

@refhistory
15930<- JCM/RIKEN; JCM 12873 <- S. Tanasupawat; MC5-1
67770S. Tanasupawat; Chulalongkorn Univ., Thailand; MC5-1.

doi: 10.13145/bacdive8012.20230509.8.1

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 chaiyaphumensis
  • full scientific name: Micromonospora chaiyaphumensis Jongrungruangchok et al. 2008

@ref: 15930

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Micromonosporaceae

genus: Micromonospora

species: Micromonospora chaiyaphumensis

full scientific name: Micromonospora chaiyaphumensis Jongrungruangchok et al. 2008

strain designation: MC5-1

type strain: yes

Morphology

cell morphology

@refgram stainmotilityconfidence
32506positiveno
69480positive100

pigmentation

  • @ref: 32506
  • production: yes

multimedia

  • @ref: 15930
  • multimedia content: https://www.dsmz.de/microorganisms/photos/DSM_45246.jpg
  • caption: Medium 65 28°C
  • intellectual property rights: © Leibniz-Institut DSMZ

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
15930N-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
15930GYM 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
15930NUTRIENT AGAR (DSMZ Medium 1)yeshttps://www.dsmz.de/microorganisms/medium/pdf/DSMZ_Medium1.pdf

culture temp

@refgrowthtypetemperaturerange
15930positivegrowth28mesophilic
32506positivegrowth25-45
32506positiveoptimum27.5mesophilic
67770positivegrowth28mesophilic

culture pH

  • @ref: 32506
  • ability: positive
  • type: growth
  • pH: 04-09
  • PH range: alkaliphile

Physiology and metabolism

oxygen tolerance

  • @ref: 32506
  • oxygen tolerance: aerobe

spore formation

@refspore formationconfidence
32506yes
69481yes100
69480yes99.623

halophily

  • @ref: 32506
  • salt: NaCl
  • growth: positive
  • tested relation: growth
  • concentration: <3 %

observation

  • @ref: 67770
  • observation: quinones: MK-10(H8), MK-10(H6), MK-9(H8), MK-9(H6)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3250622599arabinose+carbon source
3250628757fructose+carbon source
3250628260galactose+carbon source
3250617234glucose+carbon source
3250617716lactose+carbon source
3250628053melibiose+carbon source
3250616634raffinose+carbon source
3250617814salicin+carbon source
3250618222xylose+carbon source

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinentgeographic location
15930soilThailandTHAAsia
67770Mountain soilThailandTHAAsiaChaiyaphume Province

isolation source categories

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

Safety information

risk assessment

  • @ref: 15930
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 15930
  • description: Micromonospora chaiyaphumensis gene for 16S rRNA, partial sequence, strain: MC5-1
  • accession: AB196710
  • length: 1436
  • database: ena
  • NCBI tax ID: 307119

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Micromonospora chaiyaphumensis strain DSM 45246307119.5wgspatric307119
66792Micromonospora chaiyaphumensis DSM 452462622736432draftimg307119
67770Micromonospora chaiyaphumensis DSM 45246GCA_900091435scaffoldncbi307119

GC content

@refGC-contentmethod
1593072.8
6777072.8high performance liquid chromatography (HPLC)
6777073.52genome sequence analysis

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes100no
gram-positiveyes90.977no
anaerobicno99.468yes
halophileno94.731no
spore-formingyes93.97no
glucose-utilyes86.787yes
motileno93.927yes
flagellatedno97.324yes
aerobicyes96.417no
thermophileno98.864yes
glucose-fermentno92.04no

External links

@ref: 15930

culture collection no.: DSM 45246, JCM 12873, KCTC 19332, PCU 267, TISTR 1564, CGMCC 4.5707, NBRC 106529, NRRL B-24766

straininfo link

  • @ref: 77442
  • straininfo: 343809

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny18398196Micromonospora chaiyaphumensis sp. nov., isolated from Thai soils.Jongrungruangchok S, Tanasupawat S, Kudo TInt J Syst Evol Microbiol10.1099/ijs.0.65594-02008Carbohydrate Metabolism, Genes, Bacterial, Micromonospora/*classification/genetics/*isolation & purification/metabolism, Microscopy, Electron, Scanning, Molecular Sequence Data, Phenotype, Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Soil Microbiology, Terminology as Topic, ThailandMetabolism
Phylogeny21398502Micromonospora yangpuensis sp. nov., isolated from a sponge.Zhang L, Xi L, Ruan J, Huang YInt J Syst Evol Microbiol10.1099/ijs.0.029439-02011Animals, Bacterial Typing Techniques, Base Composition, China, DNA Gyrase/genetics, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Fatty Acids/analysis, Genes, rRNA, Genotype, Lipids/analysis, Micromonospora/*classification/genetics/isolation & purification/physiology, Molecular Sequence Data, Phenotype, Phylogeny, Porifera/*microbiology, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Species SpecificityGenetics
Phylogeny22634700Micromonospora equina sp. nov., isolated from soil from a racecourse.Everest GJ, Meyers PRInt J Syst Evol Microbiol10.1099/ijs.0.042929-02012Animals, Bacterial Typing Techniques, DNA, Bacterial/genetics, Horses, Micromonospora/*classification/genetics/isolation & purification, Molecular Sequence Data, Nucleic Acid Hybridization, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, South AfricaGenetics
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
Phylogeny33174828Micromonospora fluminis sp. nov., isolated from mountain river sediment.Camacho Pozo MI, Wieme AD, Rodriguez Perez S, Llaurado Maury G, Peeters C, Snauwaert C, Lescaylle Veranes Y, Pena Zamora L, Schumann P, Vandamme PAInt J Syst Evol Microbiol10.1099/ijsem.0.0045542020Bacterial Typing Techniques, Base Composition, Cuba, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Geologic Sediments/*microbiology, Micromonospora/*classification/isolation & purification, *Phylogeny, RNA, Ribosomal, 16S/genetics, Rivers/*microbiology, Sequence Analysis, DNA, Vitamin K 2/chemistryTranscriptome

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
15930Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 45246)https://www.dsmz.de/collection/catalogue/details/culture/DSM-45246
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
32506Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2872628776041
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/
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
77442Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID343809.1StrainInfo: A central database for resolving microbial strain identifiers