Rapid Identification and Classification of Bacteria Using Ribosomal Protein as Biomarkers by Matrix-Assisted Laser Desorption/Ionization-Mass Spectrometry

The rapid identification of bacteria has become of importance in various fields, such as food industries, biomedical assays, and environmental analyses. In this study, a simple, rapid, and highly reliable method for the identification and classification of bacteria by matrix-assisted laser desorption/ionization-mass spectrometry (MALDI-MS) was developed. In this method, ca. 50 different kinds of ribosomal proteins were used as biomarkers for bacteria characterization. To verify the actual state of sequence information of ribosomal proteins registered in the protein databases, a simple intact protein analysis using only cell lysate without the purification of ribosomal proteins was developed. Through the characterization of ribosomal proteins of genome-sequenced lactic acid bacteria (LAB), a guideline for selecting reliable biomarkers used for the rapid identification of LAB by MALDI-MS was proposed Although the amino acid sequences of ribosomal proteins is highly conserved, slight sequence variations of some ribosomal proteins can occur at the strain level, reflecting different phylogenetic evolution rates. Such sequence variations could be detected as mass differences in the MALDI mass spectra. The profile of the mass differences of ribosomal proteins was processed by cluster analysis, and generating a phylogenetic tree. Using this method, the phylogenetic classification of a total of 16 strains of Pseudomonas pulida was demonstrated. The classification result,of P putida strains was highly comparable to those based on a conventional DNA sequence analysis.