Strain identifier

BacDive ID: 7192

Type strain: Yes

Species: Methylobacterium phyllosphaerae

Strain Designation: CBMB27, EF 126746

Strain history: KACC 11716 <-- T.-M. Sa CBMB27.

NCBI tax ID(s): 1295137 (strain), 418223 (species)

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General

@ref: 8312

BacDive-ID: 7192

DSM-Number: 19779

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

description: Methylobacterium phyllosphaerae CBMB27 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from leaf of the rice Oryza sativa L. cv. Dong-Jin.

NCBI tax id

NCBI tax idMatching level
418223species
1295137strain

strain history

@refhistory
8312<- T. Sa, Chungbuk Natl. Univ., Republic of Korea; CBMB27 <- M. Madhaiyan
67770KACC 11716 <-- T.-M. Sa CBMB27.

doi: 10.13145/bacdive7192.20230509.8.1

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 phyllosphaerae
  • full scientific name: Methylobacterium phyllosphaerae Madhaiyan et al. 2009

@ref: 8312

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Rhizobiales

family: Methylobacteriaceae

genus: Methylobacterium

species: Methylobacterium phyllosphaerae

full scientific name: Methylobacterium phyllosphaerae Madhaiyan et al. 2009

strain designation: CBMB27, EF 126746

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
28925negative2.25 µm0.64 µmrod-shapedyes
69480yes95.321
69480negative99.999

pigmentation

  • @ref: 28925
  • production: yes

Culture and growth conditions

culture medium

  • @ref: 8312
  • 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

@refgrowthtypetemperaturerange
8312positivegrowth28mesophilic
28925positivegrowth20-30
28925positiveoptimum28mesophilic
67770positivegrowth30mesophilic

culture pH

@refabilitytypepHPH range
28925positivegrowth05-09alkaliphile
28925positiveoptimum6.8

Physiology and metabolism

oxygen tolerance

  • @ref: 28925
  • oxygen tolerance: aerobe

spore formation

@refspore formationconfidence
28925no
69481no100
69480no99.996

halophily

  • @ref: 28925
  • salt: NaCl
  • growth: positive
  • tested relation: growth
  • concentration: <2.0 %

observation

  • @ref: 28925
  • observation: aggregates in clumps

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2892516000ethanolamine+carbon source
28925168082-dehydro-D-gluconate+carbon source
28925370543-hydroxybutyrate+carbon source
28925178794-hydroxybenzoate+carbon source
28925581435-dehydro-D-gluconate+carbon source
2892530089acetate+carbon source
2892517128adipate+carbon source
2892521217L-alaninamide+carbon source
2892516449alanine+carbon source
28925286442-oxopentanoate+carbon source
2892522599arabinose+carbon source
2892522653asparagine+carbon source
2892535391aspartate+carbon source
2892516947citrate+carbon source
2892516236ethanol+carbon source
2892515740formate+carbon source
2892528757fructose+carbon source
2892533984fucose+carbon source
2892524148galactonate+carbon source
2892524175galacturonate+carbon source
2892524265gluconate+carbon source
2892517234glucose+carbon source
2892529987glutamate+carbon source
2892517754glycerol+carbon source
2892528087glycogen+carbon source
2892517240itaconate+carbon source
2892524996lactate+carbon source
2892525115malate+carbon source
2892528053melibiose+carbon source
2892526271proline+carbon source
2892517272propionate+carbon source
2892551850methyl pyruvate+carbon source
2892526546rhamnose+carbon source
2892533942ribose+carbon source
2892517814salicin+carbon source
2892517822serine+carbon source
2892530911sorbitol+carbon source
2892530031succinate+carbon source
2892517992sucrose+carbon source
2892553426tween 80+carbon source
2892516199urea+carbon source
2892518222xylose+carbon source

enzymes

@refvalueactivityec
28925acid phosphatase+3.1.3.2
28925catalase+1.11.1.6
28925cytochrome oxidase+1.9.3.1
28925urease+3.5.1.5

Isolation, sampling and environmental information

isolation

@refsample typehost speciesgeographic locationcountryorigin.countrycontinent
8312leaf of the rice Oryza sativa L. cv. Dong-JinOryza sativaIksan, Ho-namRepublic of KoreaKORAsia
67770Leaf tissues of rice (Oryza sativa L. 'Dong-Jin')Oryza sativa

isolation source categories

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

taxonmaps

  • @ref: 69479
  • File name: preview.99_6957.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_15368;96_285;97_315;98_350;99_6957&stattab=map
  • Last taxonomy: Methylobacterium
  • 16S sequence: EF126746
  • Sequence Identity:
  • Total samples: 3690
  • soil counts: 439
  • aquatic counts: 1020
  • animal counts: 1696
  • plant counts: 535

Safety information

risk assessment

  • @ref: 8312
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 8312
  • description: Methylobacterium phyllosphaerae strain CBMB27 16S ribosomal RNA gene, partial sequence
  • accession: EF126746
  • length: 1367
  • database: ena
  • NCBI tax ID: 418223

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Methylobacterium phyllosphaerae CBMB27GCA_001936175completencbi418223
66792Methylobacterium phyllosphaerae CBMB27GCA_900113465scaffoldncbi418223
66792Methylobacterium phyllosphaerae JCM 16408GCA_001312285contigncbi1295137
66792Methylobacterium phyllosphaerae JCM 164081295137.3wgspatric1295137
66792Methylobacterium phyllosphaerae CBMB272651870129draftimg418223
66792Methylobacterium phyllosphaerae JCM 164082728369718draftimg1295137
66792Methylobacterium phyllosphaerae CBMB272721755615completeimg418223

GC content

@refGC-contentmethod
831266.8
6777066.8high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
flagellatedno76.76no
gram-positiveno97.078yes
anaerobicno98.303yes
halophileno90.493no
spore-formingno93.95yes
glucose-utilyes90.372yes
aerobicyes88.807yes
thermophileno99.566no
motileyes87.867yes
glucose-fermentno87.919no

External links

@ref: 8312

culture collection no.: DSM 19779, KACC 11716, LMG 24361, JCM 16408

straininfo link

  • @ref: 76645
  • straininfo: 360511

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny19126717Methylobacterium phyllosphaerae sp. nov., a pink-pigmented, facultative methylotroph from the phyllosphere of rice.Madhaiyan M, Poonguzhali S, Kwon SW, Sa TMInt J Syst Evol Microbiol10.1099/ijs.0.001693-02009Bacterial Typing Techniques, Carbon-Carbon Lyases/genetics, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Genes, rRNA, Korea, Methylobacterium/*classification/genetics/isolation & purification/physiology, Nucleic Acid Hybridization, Oryza/*microbiology, Phenotype, Phylogeny, Pigmentation, Plant Leaves/*microbiology, RNA, Ribosomal, 16S, Sequence Analysis, DNA, Species SpecificityPhenotype
Phylogeny20127465Methylobacterium dankookense sp. nov., isolated from drinking water.Lee SW, Oh HW, Lee KH, Ahn TYJ Microbiol10.1007/s12275-009-0126-62010Aerobiosis, Bacterial Typing Techniques, Base Composition, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Fresh Water/*microbiology, Hydrogen-Ion Concentration, Methylobacterium/chemistry/*classification/genetics/*isolation & purification, Molecular Sequence Data, Nucleic Acid Hybridization, Phylogeny, Quinones/analysis, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, TemperatureGenetics
Phylogeny23291886Methylobacterium trifolii sp. nov. and Methylobacterium thuringiense sp. nov., methanol-utilizing, pink-pigmented bacteria isolated from leaf surfaces.Wellner S, Lodders N, Glaeser SP, Kampfer PInt J Syst Evol Microbiol10.1099/ijs.0.047787-02013Bacterial Typing Techniques, Caryophyllaceae/*microbiology, DNA, Bacterial/genetics, Fatty Acids/analysis, Germany, Methanol/*metabolism, Methylobacterium/*classification/genetics/isolation & purification, Molecular Sequence Data, Nucleic Acid Hybridization, *Phylogeny, *Pigmentation, Plant Leaves/microbiology, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Trifolium/*microbiologyGenetics
Phylogeny33895889Methylobacterium radiodurans sp. nov., a novel radiation-resistant Methylobacterium.Maeng S, Kim DU, Lim S, Lee BH, Lee KE, Kim M, Srinivasan S, Bai JArch Microbiol10.1007/s00203-021-02293-82021DNA Repair/genetics, *Methylobacterium/classification/genetics/radiation effects, Nucleic Acid Hybridization, Phospholipids/analysis, Phylogeny, RNA, Ribosomal, 16S/genetics, Radiation Tolerance, *Soil Microbiology, Species Specificity

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
8312Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 19779)https://www.dsmz.de/collection/catalogue/details/culture/DSM-19779
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
28925Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2536428776041
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
76645Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID360511.1StrainInfo: A central database for resolving microbial strain identifiers