Strain identifier

BacDive ID: 7222

Type strain: Yes

Species: Methylopila capsulata

Strain history: <- VKM (Methylomicrobium capsulatus) <- N. V. Doronina, IM1, IBPhM

NCBI tax ID(s): 61654 (species)

For citation purpose refer to the digital object identifier (doi) of the current version.
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General

@ref: 2496

BacDive-ID: 7222

DSM-Number: 6130

keywords: genome sequence, 16S sequence, Bacteria, mesophilic, motile

description: Methylopila capsulata DSM 6130 is a mesophilic, motile bacterium that was isolated from soil.

NCBI tax id

  • NCBI tax id: 61654
  • Matching level: species

strain history

  • @ref: 2496
  • history: <- VKM (Methylomicrobium capsulatus) <- N. V. Doronina, IM1, IBPhM

doi: 10.13145/bacdive7222.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Alphaproteobacteria
  • order: Hyphomicrobiales
  • family: Methylocystaceae
  • genus: Methylopila
  • species: Methylopila capsulata
  • full scientific name: Methylopila capsulata Doronina et al. 1998

@ref: 2496

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Rhizobiales

family: Methylocystaceae

genus: Methylopila

species: Methylopila capsulata

full scientific name: Methylopila capsulata Doronina et al. 1998

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram stain
69480yes92.869
6948099.998negative

Culture and growth conditions

culture medium

  • @ref: 2496
  • name: NUTRIENT AGAR (DSMZ Medium 1)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/1
  • composition: Name: NUTRIENT AGAR (DSMZ Medium 1; with strain-specific modifications) Composition: Agar 15.0 g/l Methanol 10.0 g/l Peptone 5.0 g/l Meat extract 3.0 g/l Distilled water

culture temp

  • @ref: 2496
  • growth: positive
  • type: growth
  • temperature: 30
  • range: mesophilic

Physiology and metabolism

spore formation

@refspore formationconfidence
69481no100
69480no99.997

Isolation, sampling and environmental information

isolation

  • @ref: 2496
  • sample type: soil
  • geographic location: Uzbekistan, Tashkent
  • country: USSR
  • origin.country: UZB
  • continent: Asia

isolation source categories

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

taxonmaps

  • @ref: 69479
  • File name: preview.99_1985.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_5;96_1101;97_1289;98_1553;99_1985&stattab=map
  • Last taxonomy: Methylopila
  • 16S sequence: AF004844
  • Sequence Identity:
  • Total samples: 274
  • soil counts: 79
  • aquatic counts: 89
  • animal counts: 81
  • plant counts: 25

Safety information

risk assessment

  • @ref: 2496
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 20218
  • description: Methylopila capsulata 16S ribosomal RNA gene, partial sequence
  • accession: AF004844
  • length: 1331
  • database: ena
  • NCBI tax ID: 61654

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Methylopila capsulata DSM 6130GCA_016907975contigncbi61654
66792Methylopila capsulata strain DSM 613061654.3wgspatric61654
66792Methylopila capsulata DSM 61302901030786draftimg61654

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
gram-positiveno98.332no
anaerobicno98.663no
halophileno93.368no
spore-formingno94.771no
glucose-utilyes91.167no
thermophileno95.092no
flagellatedno74.892no
aerobicyes94.845no
motileyes80.144no
glucose-fermentno90.872no

External links

@ref: 2496

culture collection no.: DSM 6130, VKM B-1606

straininfo link

  • @ref: 76674
  • straininfo: 44100

literature

  • topic: Phylogeny
  • Pubmed-ID: 9828432
  • title: Methylopila capsulata gen. nov., sp. nov., a novel non-pigmented aerobic facultatively methylotrophic bacterium.
  • authors: Doronina NV, Trotsenko YA, Krausova VI, Boulygina ES, Tourova TP
  • journal: Int J Syst Bacteriol
  • DOI: 10.1099/00207713-48-4-1313
  • year: 1998
  • mesh: Base Composition, DNA, Bacterial/chemistry, Fatty Acids/analysis, Genes, rRNA, Gram-Negative Aerobic Bacteria/*classification/genetics/*isolation & purification/physiology, Molecular Sequence Data, Nucleic Acid Hybridization, Phospholipids/analysis, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Serine/metabolism, *Soil Microbiology, Terminology as Topic
  • topic2: Genetics

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
2496Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 6130)https://www.dsmz.de/collection/catalogue/details/culture/DSM-6130
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)
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
76674Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID44100.1StrainInfo: A central database for resolving microbial strain identifiers