Genomic analysis of lactic acid bacteria and their applications

Abstract

Lactic acid bacteria (LABs) comprise a group of Gram-positive, rod- or cocci-shaped, and low G + C content bacteria with common metabolic and physiological characteristics. The association of LAB with food fermentation can be traced back to the early nineteenth century. As the "milk-souring organisms," they produce lactic acid as one of their main metabolic end products (Orla-Jensen, The lactic acid bacteria, (D Kgl danske vidensk Selsk Skrifter Naturv og mathematisk Afd, 8 Række, vol 2). A. F. Høst, Københaven, 1919). The classical phenotype-based identification of LAB is not always reliable because the phenotype could be subject to the environmental variations. As a more reliable identification method, nucleic acid probe was applied for genotypic tests (Salama M, Sandine W, Giovannoni S, Appl Environ Microbiol 57(5):1313-1318, 1991). The 16 s or 23 s rRNA probes with specific sequences on a phylogenetic basis were both practical and reliable approach to identify LAB in the 1990s (Schleifer KH, Ehrmann M, Beimfohr C, Brockmann E, Ludwig W, Amann R, Int Dairy J 5(8):1081-1094. https://doi.org/10.1016/ 0958-6946(95)00047-X, 1995). With the advancement of sequencing technology and sequence database, LAB genome analyses using sequencing technologies and bioinformatics have not only revolutionized the characterization of lactic acid bacteria but also had a huge impact on interpreting its functional and ecological diversity. This chapter will focus on new development of DNA sequencing, gene-based technologies, and its implication on LAB for the scientific and industry fields.