Strain identifier

BacDive ID: 8006

Type strain: Yes

Species: Micromonospora chokoriensis

Strain Designation: 2-19(6)

Strain history: I. Ara 2-19(6).

NCBI tax ID(s): 356851 (species)

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General

@ref: 15462

BacDive-ID: 8006

DSM-Number: 45160

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

description: Micromonospora chokoriensis 2-19 is a spore-forming, mesophilic, Gram-positive bacterium that was isolated from sandy soil at a forest-side waterfall.

NCBI tax id

  • NCBI tax id: 356851
  • Matching level: species

strain history

@refhistory
15462<- JCM/RIKEN <- I. Ara; 2-19(6)
67770I. Ara 2-19(6).

doi: 10.13145/bacdive8006.20230509.8.1

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 chokoriensis
  • full scientific name: Micromonospora chokoriensis Ara and Kudo 2007

@ref: 15462

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Micromonosporaceae

genus: Micromonospora

species: Micromonospora chokoriensis

full scientific name: Micromonospora chokoriensis Ara and Kudo 2007

strain designation: 2-19(6)

type strain: yes

Morphology

cell morphology

  • @ref: 69480
  • gram stain: positive
  • confidence: 100

multimedia

@refmultimedia contentintellectual property rightscaption
15462https://www.dsmz.de/microorganisms/photos/DSM_45160-1.jpg© Leibniz-Institut DSMZ
15462https://www.dsmz.de/microorganisms/photos/DSM_45160.jpg© Leibniz-Institut DSMZMedium 65 28°C

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
15462GYM 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
15462BENNETT'S AGAR (DSMZ Medium 548)yeshttps://www.dsmz.de/microorganisms/medium/pdf/DSMZ_Medium548.pdf

culture temp

@refgrowthtypetemperaturerange
15462positivegrowth28mesophilic
67770positivegrowth28mesophilic

Physiology and metabolism

spore formation

@refspore formationconfidence
69481yes100
69480yes100

observation

  • @ref: 67770
  • observation: quinones: MK-10(H4)

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
15462sandy soil at a forest-side waterfallChokoriaBangladeshBGDAsia
67770Sandy soil near a waterfallChokoriaBangladeshBGDAsia

isolation source categories

Cat1Cat2Cat3
#Environmental#Aquatic
#Environmental#Terrestrial#Forest
#Environmental#Terrestrial#Sandy
#Environmental#Terrestrial#Soil

taxonmaps

  • @ref: 69479
  • File name: preview.99_3471.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_94;96_404;97_1111;98_1509;99_3471&stattab=map
  • Last taxonomy: Micromonospora
  • 16S sequence: AB241454
  • Sequence Identity:
  • Total samples: 1419
  • soil counts: 1017
  • aquatic counts: 161
  • animal counts: 219
  • plant counts: 22

Safety information

risk assessment

  • @ref: 15462
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 15462
  • description: Micromonospora chokoriensis gene for 16S rRNA, partial sequence
  • accession: AB241454
  • length: 1503
  • database: ena
  • NCBI tax ID: 356851

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Micromonospora chokoriensis DSM 45160GCA_900091505chromosomencbi356851
66792Micromonospora chokoriensis strain DSM 45160356851.6completepatric356851
66792Micromonospora chokoriensis DSM 451602623620610draftimg356851

GC content

@refGC-contentmethod
1546271
6777071high performance liquid chromatography (HPLC)
6777071.46genome sequence analysis

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes100no
gram-positiveyes92.826no
anaerobicno99.247no
halophileno94.9no
spore-formingyes95.439no
glucose-utilyes87.61no
motileno94.14no
flagellatedno97.718no
thermophileno98.94yes
aerobicyes95.782no
glucose-fermentno90.255no

External links

@ref: 15462

culture collection no.: DSM 45160, JCM 13247, MTCC 8535, NBRC 106572, CGMCC 4.6950, NRRL B-24767

straininfo link

  • @ref: 77436
  • straininfo: 309467

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny17429159Two new species of the genus Micromonospora: Micromonospora chokoriensis sp. nov. and Micromonospora coxensis sp. nov., isolated from sandy soil.Ara I, Kudo TJ Gen Appl Microbiol10.2323/jgam.53.292007Micromonospora/*classification/genetics, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil MicrobiologyTranscriptome
Phylogeny27902235Micromonospora parathelypteridis sp. nov., an endophytic actinomycete with antifungal activity isolated from the root of Parathelypteris beddomei (Bak.) Ching.Zhao S, Liu C, Zheng W, Ma Z, Cao T, Zhao J, Yan K, Xiang W, Wang XInt J Syst Evol Microbiol10.1099/ijsem.0.0016142017Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Micromonospora/*classification/genetics/isolation & purification, Nucleic Acid Hybridization, *Phylogeny, Plant Roots/*microbiology, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Streptophyta/*microbiologyTranscriptome
Phylogeny31630299Micromonospora orduensis sp. nov., isolated from deep marine sediment.Veyisoglu A, Carro L, Cetin D, Igual JM, Klenk HP, Sahin NAntonie Van Leeuwenhoek10.1007/s10482-019-01349-62019*Aquatic Organisms, Bacterial Typing Techniques, Fatty Acids/metabolism, Genome, Bacterial, Genomics/methods, Geologic Sediments/*microbiology, Micromonospora/*classification/genetics/*isolation & purification, Phylogeny, Seawater/microbiology, Soil MicrobiologyGenetics

Reference

@idauthorscataloguedoi/urltitle
15462Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 45160)https://www.dsmz.de/collection/catalogue/details/culture/DSM-45160
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/
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
77436Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID309467.1StrainInfo: A central database for resolving microbial strain identifiers