Strain identifier

BacDive ID: 24174

Type strain: Yes

Species: Methylobacterium brachythecii

Strain Designation: 99b

Strain history: <- A. Tani, Okayama University, Japan; 99b

NCBI tax ID(s): 1176177 (species)

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

@ref: 20649

BacDive-ID: 24174

DSM-Number: 24105

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

description: Methylobacterium brachythecii 99b is an aerobe, mesophilic, Gram-negative bacterium that was isolated from rusty feather-moss Brachythecium plumosum.

NCBI tax id

  • NCBI tax id: 1176177
  • Matching level: species

strain history

  • @ref: 20649
  • history: <- A. Tani, Okayama University, Japan; 99b

doi: 10.13145/bacdive24174.20230509.8.1

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 brachythecii
  • full scientific name: Methylobacterium brachythecii Tani and Sahin 2013

@ref: 20649

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Rhizobiales

family: Methylobacteriaceae

genus: Methylobacterium

species: Methylobacterium brachythecii

full scientific name: Methylobacterium brachythecii Tani and Sahin 2013

strain designation: 99b

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
30947negative2.5 µm1.2 µmrod-shapedyes
69480yes95.666
69480negative99.998

colony morphology

  • @ref: 20649
  • incubation period: 2-3 days

pigmentation

  • @ref: 30947
  • production: yes

Culture and growth conditions

culture medium

  • @ref: 20649
  • 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

  • @ref: 20649
  • growth: positive
  • type: growth
  • temperature: 28
  • range: mesophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 30947
  • oxygen tolerance: aerobe

spore formation

@refspore formationconfidence
30947no
69481no100
69480no99.993

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3094730089acetate+carbon source
3094722599arabinose+carbon source
3094722653asparagine+carbon source
3094735391aspartate+carbon source
3094723652dextrin+carbon source
3094715740formate+carbon source
3094717234glucose+carbon source
3094729987glutamate+carbon source
3094717754glycerol+carbon source
3094728087glycogen+carbon source
3094724996lactate+carbon source
3094715792malonate+carbon source
3094751850methyl pyruvate+carbon source
3094717272propionate+carbon source
3094730031succinate+carbon source
3094717632nitrate+reduction

enzymes

@refvalueactivityec
30947catalase+1.11.1.6
30947cytochrome oxidase+1.9.3.1
30947urease+3.5.1.5

Isolation, sampling and environmental information

isolation

  • @ref: 20649
  • sample type: rusty feather-moss Brachythecium plumosum
  • host species: Brachythecium plumosum
  • geographic location: premises of the Institute of Plant Science and Resources, Okayama University
  • country: Japan
  • origin.country: JPN
  • continent: Asia

isolation source categories

  • Cat1: #Host
  • Cat2: #Plants
  • Cat3: #Moss

Safety information

risk assessment

  • @ref: 20649
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 20649
  • description: Methylobacterium brachythecii gene for 16S rRNA, partial sequence, strain: 99b
  • accession: AB703239
  • length: 1444
  • database: ena
  • NCBI tax ID: 1176177

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Methylobacterium brachythecii DSM 24105GCA_014196345contigncbi1176177
66792Methylobacterium brachythecii strain DSM 241051176177.3wgspatric1176177
66792Methylobacterium brachythecii DSM 241052829871319draftimg1176177

GC content

@refGC-contentmethod
2064966.5thermal denaturation, midpoint method (Tm)
3094766.5

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileyes86.696yes
gram-positiveno98.076yes
anaerobicno98.268no
halophileno94.284no
spore-formingno92.35yes
flagellatedno73.001no
thermophileno99.456yes
glucose-utilyes90.292no
aerobicyes94.158no
glucose-fermentno91.122no

External links

@ref: 20649

culture collection no.: DSM 24105, NBRC 107710

straininfo link

  • @ref: 88129
  • straininfo: 397582

literature

  • topic: Phylogeny
  • Pubmed-ID: 23475343
  • title: Methylobacterium haplocladii sp. nov. and Methylobacterium brachythecii sp. nov., isolated from bryophytes.
  • authors: Tani A, Sahin N
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.048215-0
  • year: 2013
  • mesh: Bacterial Typing Techniques, Base Composition, Bryophyta/*microbiology, DNA, Bacterial/genetics, Fatty Acids/analysis, Japan, Methylobacterium/*classification/genetics/isolation & purification, Molecular Sequence Data, Nucleic Acid Hybridization, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization, Ubiquinone/analogs & derivatives/analysis
  • topic2: Genetics

Reference

@idauthorstitledoi/urlcatalogueID_cross_referencepubmed
20215Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ10.1099/ijsem.0.004332
20649Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-24105Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 24105)
30947Barberan A, Caceres Velazquez H, Jones S, Fierer N.Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information10.1128/mSphere.00237-172727728776041
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)https://diaspora-project.de/progress.html#genomes
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)https://diaspora-project.de/progress.html#genomes
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. MünchPredictions based on the model GenomeNet Sporulation v. 110.21203/rs.3.rs-2527258/v1
88129Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.StrainInfo: A central database for resolving microbial strain identifiers10.60712/SI-ID397582.1