High-throughput identification and screening of novel methylobacterium species using whole-cell MALDI-TOF/MS analysis

Akio Tani, Nurettin Sahin, Yumiko Matsuyama, Takashi Enomoto, Naoki Nishimura, Akira Yokota, Kazuhide Kimbara

Research output: Contribution to journalArticle

33 Citations (Scopus)

Abstract

Methylobacterium species are ubiquitous α-proteobacteria that reside in the phyllosphere and are fed by methanol that is emitted from plants. In this study, we applied whole-cell matrix-assisted laser desorption/ionization time-of-flight mass spectrometry analysis (WC-MS) to evaluate the diversity of Methylobacterium species collected from a variety of plants. The WC-MS spectrum was reproducible through two weeks of cultivation on different media. WC-MS spectrum peaks of M. extorquens strain AM1 cells were attributed to ribosomal proteins, but those were not were also found. We developed a simple method for rapid identification based on spectra similarity. Using all available type strains of Methylobacterium species, the method provided a certain threshold similarity value for species-level discrimination, although the genus contains some type strains that could not be easily discriminated solely by 16S rRNA gene sequence similarity. Next, we evaluated the WC-MS data of approximately 200 methylotrophs isolated from various plants with MALDI Biotyper software (Bruker Daltonics). Isolates representing each cluster were further identified by 16S rRNA gene sequencing. In most cases, the identification by WC-MS matched that by sequencing, and isolates with unique spectra represented possible novel species. The strains belonging to M. extorquens, M. adhaesivum, M. marchantiae, M. komagatae, M. brachiatum, M. radiotolerans, and novel lineages close to M. adhaesivum, many of which were isolated from bryophytes, were found to be the most frequent phyllospheric colonizers. The WC-MS technique provides emerging high-throughputness in the identification of known/novel species of bacteria, enabling the selection of novel species in a library and identification without 16S rRNA gene sequencing.

Original languageEnglish
Article numbere40784
JournalPLoS One
Volume7
Issue number7
DOIs
Publication statusPublished - Jul 12 2012

Fingerprint

Methylobacterium
matrix-assisted laser desorption-ionization mass spectrometry
Matrix-Assisted Laser Desorption-Ionization Mass Spectrometry
rRNA Genes
Screening
Genes
Throughput
screening
ribosomal RNA
Hepatophyta
Bryophyta
Proteobacteria
Ribosomal Proteins
cells
phyllosphere
Libraries
Ionization
Mass spectrometry
Methanol
Desorption

ASJC Scopus subject areas

  • Agricultural and Biological Sciences(all)
  • Biochemistry, Genetics and Molecular Biology(all)
  • Medicine(all)

Cite this

High-throughput identification and screening of novel methylobacterium species using whole-cell MALDI-TOF/MS analysis. / Tani, Akio; Sahin, Nurettin; Matsuyama, Yumiko; Enomoto, Takashi; Nishimura, Naoki; Yokota, Akira; Kimbara, Kazuhide.

In: PLoS One, Vol. 7, No. 7, e40784, 12.07.2012.

Research output: Contribution to journalArticle

Tani, Akio ; Sahin, Nurettin ; Matsuyama, Yumiko ; Enomoto, Takashi ; Nishimura, Naoki ; Yokota, Akira ; Kimbara, Kazuhide. / High-throughput identification and screening of novel methylobacterium species using whole-cell MALDI-TOF/MS analysis. In: PLoS One. 2012 ; Vol. 7, No. 7.
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