Genomic Characterisation of Starter Cultures and Probiotic Bacteria

The first publicly available genome sequence of a lactic acid bacteria (LAB) strain commonly used as a starter in dairy fermentations is that of Lactococcus lactis subsp. lactis IL1403 (Bolotin et al., 2001). Since then, a huge number of genome sequences of starter and probiotic LAB has been determined. Indeed, genome sequencing has become the starting point of most microbial studies, since it can provide, at a reasonable cost, the framework of the biology of any strain of interest. Comparative genome analyses can provide insights on the genetic make-up, and thus the metabolic potential, of the strains, as well as on many aspects of their genome evolution and divergence. Further, sequencing of genomes can reveal horizontal gene transfer (HGT) events between species and strains of starter and probiotic cultures. Knowledge of the complete genome sequence is not only useful in discovering novel genes and new properties, but also in determining the absence at the genetic level of undesirable traits. In addition, it is of much help in characterizing the variants of modified/improved strains for both cultures with a technological role, i.e., necessary/useful for food fermentation processes, and a functional role, i.e., able to confer health benefits to the consumer/host (FAO/WHO, 2001; Hill et al., 2014). Genome sequencing can further allow precise identification down to the strain level, while providing strategies for its specific detection and quantification, important aspects for commercially-relevant bacteria.