Update on Basic and Applied Aspects of Genome Analysis of Lactic Acid-Producing Bacteria, Including Bifidobacteria

The rapidly increasing number of genome sequences provides an important resource to study the genetics, physiology and biochemical capabilities of lactic acid bacteria (LAB) and bifidobacteria. Despite the fact that they are phylogenitally unrelated, bifidobacteria are usually included under the term of LAB, as they are found within the same natural environments and are frequently used for the same purpose, i.e. as probiotics to exert health-promoting effects on the gastrointestinal and/or genitourinary tracts of animals and humans. The most updated sequence information (GOLD genome online database; http://www.genomesonline.org) summarizes 280 completed LAB genomes (14 Lactococcus, 165 Lactobacillus, 18 Leuconostoc, 6 Streptococcus thermophilus, 13 Oenococcus, 6 Pediococcus, 4 Weissella, and 54 Bifidobacterium) and more than 500 in progress. The typical LAB genome is relatively small (from 1.7 Mb in the case of S. thermophilus to 3.9 Mb for Lactobacillus pentosus), thus harboring a limited assortment of genes (from around 1,600 to over 3,000). These small genomes code for a broad array of transporters for efficient carbon and nitrogen assimilation from the nutritionally-rich niches they usually inhabit, and specify a rather limited range of biosynthetic and catabolic capabilities. The variation in the number of genes even within strains of the same species suggests that the genome of LAB is rather plastic and dynamic. The genome diversification of LAB from their ancestors is thought to be driven by niche adaptation through extensive gene loss, gene duplication, and acquisition of key functions via lateral gene transfer. The availability of genome sequences is expected to revolutionize the exploitation of the metabolic potential of LAB, improving their use in bioprocessing and their utilization in biotechnological and health-related applications.

Keywords: Adjunct cultures, bifidobacteria, Bifidobacterium, Bifidobacterium, animalis, Bifidobacterium lactis, Bifidobacterium longum, cheese, dairy cultures, dairy microbiology, dairy products, fermented dairy products, gastrointestinal tract, genome analysis, genome sequencing, genomics, intestinal microbiology, LAB, lactic acid bacteria, lactobacilli, Lactobacillus, Lactobacillus delbrueckii, Lactobacillus helveticus, Lactobacillus plantarum, lactococci, Lactococcus, Lactococcus lactis, Leuconostoc, probiotics, starters, Streptococcus thermophilus, yogurt.