Strain identifier

BacDive ID: 7201

Type strain: Yes

Species: Methylobacterium soli

Strain history: <- S.-K. Tang, YIM <- Y.-R. Cao

NCBI tax ID(s): 553447 (species)

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

@ref: 16066

BacDive-ID: 7201

DSM-Number: 21955

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

description: Methylobacterium soli DSM 21955 is a mesophilic, motile bacterium that was isolated from forest soil.

NCBI tax id

  • NCBI tax id: 553447
  • Matching level: species

strain history

  • @ref: 16066
  • history: <- S.-K. Tang, YIM <- Y.-R. Cao

doi: 10.13145/bacdive7201.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Alphaproteobacteria
  • order: Hyphomicrobiales
  • family: Methylobacteriaceae
  • genus: Methylobacterium
  • species: Methylobacterium soli
  • full scientific name: Methylobacterium soli Cao et al. 2013

@ref: 16066

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Rhizobiales

family: Methylobacteriaceae

genus: Methylobacterium

species: Methylobacterium soli

full scientific name: Methylobacterium soli Cao et al. 2013

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram stain
69480yes91.926
6948099.999negative

Culture and growth conditions

culture medium

  • @ref: 16066
  • name: ISP2 MEDIUM (DSMZ Medium 987)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/987
  • composition: Name: ISP 2 MEDIUM (DSMZ Medium 987) Composition: Agar 20.0 g/l Malt extract 10.0 g/l Dextrose 4.0 g/l Yeast extract 4.0 g/l Distilled water

culture temp

  • @ref: 16066
  • growth: positive
  • type: growth
  • temperature: 28
  • range: mesophilic

Physiology and metabolism

spore formation

@refspore formationconfidence
69481no99
69480no99.997

Isolation, sampling and environmental information

isolation

  • @ref: 16066
  • sample type: forest soil
  • geographic location: Sichuan Province
  • country: China
  • origin.country: CHN
  • continent: Asia

isolation source categories

Cat1Cat2Cat3
#Environmental#Terrestrial#Forest
#Environmental#Terrestrial#Soil

taxonmaps

  • @ref: 69479
  • File name: preview.99_12118.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_15368;96_6152;97_7385;98_9105;99_12118&stattab=map
  • Last taxonomy: Methylobacterium soli subclade
  • 16S sequence: EU860984
  • Sequence Identity:
  • Total samples: 1114
  • soil counts: 759
  • aquatic counts: 58
  • animal counts: 171
  • plant counts: 126

Safety information

risk assessment

  • @ref: 16066
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 16066
  • description: Methylobacterium soli strain YIM 48816 16S ribosomal RNA gene, partial sequence
  • accession: EU860984
  • length: 1437
  • database: ena
  • NCBI tax ID: 553447

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Methylobacterium soli YIM 48816GCA_008806385scaffoldncbi553447
66792Methylobacterium soli strain YIM 48816553447.3wgspatric553447
66792Methylobacterium soli KCTC 22810GCA_022179555contigncbi553447

GC content

  • @ref: 16066
  • GC-content: 66.2
  • method: high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno99no
flagellatedno68.965no
gram-positiveno98.138no
anaerobicno97.335no
aerobicyes93.272no
halophileno94.397no
spore-formingno95.019no
thermophileno99.182yes
glucose-utilyes83.813no
motileyes89.506no
glucose-fermentno90.058no

External links

@ref: 16066

culture collection no.: DSM 21955, CCTCC AA 208027, KCTC 22810, YIM 48816

straininfo link

  • @ref: 76654
  • straininfo: 403456

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny21222033Methylobacterium soli sp. nov. a methanol-utilizing bacterium isolated from the forest soil.Cao YR, Wang Q, Jin RX, Tang SK, Jiang Y, He WX, Lai HX, Xu LH, Jiang CLAntonie Van Leeuwenhoek10.1007/s10482-010-9535-02011Methanol/*metabolism, Methylobacterium/classification/*genetics/*metabolism, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics, Soil Microbiology, *TreesMetabolism
Phylogeny21908681Methylobacterium oxalidis sp. nov., isolated from leaves of Oxalis corniculata.Tani A, Sahin N, Kimbara KInt J Syst Evol Microbiol10.1099/ijs.0.033019-02011Bacterial Typing Techniques, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Ferns/*microbiology, Locomotion, Methylobacterium/*classification/genetics/*isolation & purification/physiology, Molecular Sequence Data, Nucleic Acid Hybridization, Phylogeny, Pigments, Biological/metabolism, Plant Leaves/microbiology, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNAGenetics
Metabolism31541329Methylobacterium durans sp. nov., a radiation-resistant bacterium isolated from gamma ray-irradiated soil.Kim J, Chhetri G, Kim I, Kim MK, Seo TAntonie Van Leeuwenhoek10.1007/s10482-019-01331-22019Base Composition/genetics, Cardiolipins/metabolism, Fatty Acids/*metabolism, *Gamma Rays, Genotype, Methylobacterium/genetics/*metabolism/*radiation effects, Phosphatidylethanolamines/metabolism, Phosphatidylglycerols/metabolism, Phylogeny, RNA, Ribosomal, 16S/genetics, Soil MicrobiologyPhylogeny
Phylogeny31796988Methylobacterium segetis sp. nov., a novel member of the family Methylobacteriaceae isolated from soil on Jeju Island.Ten LN, Li W, Elderiny NS, Kim MK, Lee SY, Rooney AP, Jung HYArch Microbiol10.1007/s00203-019-01784-z2019Base Composition, Fatty Acids/chemistry, Methylobacterium/*classification/genetics, Nucleic Acid Hybridization, Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, *Soil Microbiology, Species SpecificityTranscriptome
Phylogeny32306065Methylobacterium planium sp. nov., isolated from a lichen sample.Jiang L, An D, Wang X, Zhang K, Li G, Lang L, Wang L, Jiang C, Jiang YArch Microbiol10.1007/s00203-020-01881-42020Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Lichens/*microbiology, Methylobacterium/*classification/genetics/isolation & purification, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Species Specificity, Ubiquinone/metabolismTranscriptome

Reference

@idauthorscataloguedoi/urltitle
16066Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 21955)https://www.dsmz.de/collection/catalogue/details/culture/DSM-21955
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)
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
76654Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID403456.1StrainInfo: A central database for resolving microbial strain identifiers