Strain identifier

BacDive ID: 23092

Type strain: Yes

Species: Methylobacterium oxalidis

Strain Designation: 35a

Strain history: <- A. Tani, Okayama University, Institute of Plant Science and Resources, Japan; strain 35a

NCBI tax ID(s): 944322 (species)

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

@ref: 19152

BacDive-ID: 23092

DSM-Number: 24028

keywords: genome sequence, 16S sequence, Bacteria, aerobe, mesophilic, Gram-negative, motile, rod-shaped

description: Methylobacterium oxalidis 35a is an aerobe, mesophilic, Gram-negative bacterium that was isolated from leaves of the sorrel Oxalis corniculata.

NCBI tax id

  • NCBI tax id: 944322
  • Matching level: species

strain history

  • @ref: 19152
  • history: <- A. Tani, Okayama University, Institute of Plant Science and Resources, Japan; strain 35a

doi: 10.13145/bacdive23092.20230509.8.1

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 oxalidis
  • full scientific name: Methylobacterium oxalidis Tani et al. 2012

@ref: 19152

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Rhizobiales

family: Methylobacteriaceae

genus: Methylobacterium

species: Methylobacterium oxalidis

full scientific name: Methylobacterium oxalidis Tani et al. 2012

strain designation: 35a

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
30303negative1.8 µm1.3 µmrod-shapedyes
69480yes92.828
69480negative100

colony morphology

  • @ref: 19152
  • incubation period: 3-7 days

pigmentation

  • @ref: 30303
  • production: yes

Culture and growth conditions

culture medium

  • @ref: 19152
  • name: R2A MEDIUM (DSMZ Medium 830)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/830
  • composition: Name: R2A MEDIUM (DSMZ Medium 830) Composition: Agar 15.0 g/l Casamino acids 0.5 g/l Starch 0.5 g/l Glucose 0.5 g/l Proteose peptone 0.5 g/l Yeast extract 0.5 g/l K2HPO4 0.3 g/l Na-pyruvate 0.3 g/l MgSO4 x 7 H2O 0.05 g/l Distilled water

culture temp

@refgrowthtypetemperaturerange
19152positivegrowth28mesophilic
30303positivegrowth28-35mesophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 30303
  • oxygen tolerance: aerobe

spore formation

@refspore formationconfidence
30303no
69481no99
69480no99.998

halophily

  • @ref: 30303
  • salt: NaCl
  • growth: positive
  • tested relation: growth
  • concentration: <2 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3030330089acetate+carbon source
3030315740formate+carbon source
3030328757fructose+carbon source
3030329987glutamate+carbon source
3030324996lactate+carbon source
3030315792malonate+carbon source
3030351850methyl pyruvate+carbon source
3030317272propionate+carbon source
3030330031succinate+carbon source

enzymes

  • @ref: 30303
  • value: catalase
  • activity: +
  • ec: 1.11.1.6

Isolation, sampling and environmental information

isolation

  • @ref: 19152
  • sample type: leaves of the sorrel Oxalis corniculata
  • host species: Oxalis corniculata
  • country: Japan
  • origin.country: JPN
  • continent: Asia

isolation source categories

Cat1Cat2Cat3
#Host#Plants#Herbaceous plants (Grass,Crops)
#Host Body-Site#Plant#Leaf (Phyllosphere)

taxonmaps

  • @ref: 69479
  • File name: preview.99_62296.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_15368;96_6152;97_28745;98_44137;99_62296&stattab=map
  • Last taxonomy: Methylobacterium oxalidis subclade
  • 16S sequence: AB607860
  • Sequence Identity:
  • Total samples: 6895
  • soil counts: 3583
  • aquatic counts: 701
  • animal counts: 1775
  • plant counts: 836

Safety information

risk assessment

  • @ref: 19152
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 19152
  • description: Methylobacterium oxalidis gene for 16S ribosomal RNA, partial sequence
  • accession: AB607860
  • length: 1446
  • database: ena
  • NCBI tax ID: 944322

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Methylobacterium oxalidis NBRC 107715GCA_007992195contigncbi944322
66792Methylobacterium oxalidis strain NBRC 107715944322.3wgspatric944322
66792Methylobacterium oxalidis DSM 24028GCA_022179505contigncbi944322

GC content

@refGC-contentmethod
1915270.2thermal denaturation, midpoint method (Tm)
3030370.2

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno99no
motileyes88.071yes
flagellatedno83.604no
gram-positiveno97.135yes
anaerobicno98.155yes
halophileno90.496no
spore-formingno94.083no
glucose-utilyes82.199no
aerobicyes92.232yes
thermophileno98.559yes
glucose-fermentno91.053no

External links

@ref: 19152

culture collection no.: DSM 24028, NBRC 107715

straininfo link

  • @ref: 87330
  • straininfo: 380589

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
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
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

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
19152Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 24028)https://www.dsmz.de/collection/catalogue/details/culture/DSM-24028
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
30303Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2664428776041
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
87330Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID380589.1StrainInfo: A central database for resolving microbial strain identifiers