The Genomic Basis of Lactobacilli as Health-Promoting Organisms

Abstract

Lactobacilli occupy a unique position in human culture and scientific history. Like brewer's and baker's yeast, lactobacilli have been associated with food production and preservation for thousands of years. species are used in mixed microbial cultures, such as the classical/ inoculum for yogurt fermentation, or combinations of diverse lactobacilli/yeasts in kefir grains. The association of lactobacilli consumption with greater longevity and improved health formed the basis for developing lactobacilli as probiotics, whose market has exploded worldwide in the past 10 years. The decade that followed the determination of the first genome sequence of a food-associated species, , saw the application to lactobacilli of a full range of functional genomics methods to identify the genes and gene products that govern their distinctive phenotypes and health associations. In this review, we will briefly remind the reader of the range of beneficial effects attributed to lactobacilli, and then explain the phylogenomic basis for the distribution of these traits across the genus. Recognizing the strain specificity of probiotic effects, we review studies of intraspecific genomic variation and their contributions to identifying probiotic traits. Finally we offer a perspective on classification of lactobacilli into new genera in a scheme that will make attributing probiotic properties to clades, taxa, and species more logical and more robust.

Comparative Genomics of the Genus Lactobacillus Reveals Robust Phylogroups That Provide the Basis for Reclassification

“…One of the overall aims of this study was to stop the never-ending expansion of Lactobacillus as a heterogeneous clade (1,3,4,11,12,20). We used two methods with a phylogenetic component (MLSA of ribosomal proteins and a set of housekeeping genes) and two which were phylogeny independent (AAI and POCP analysis).…”

A Sensitive and Rapid Method to Determine the Adhesion Capacity of Probiotics and Pathogenic Microorganisms to Human Gastrointestinal Mucins

“…The E. coli strain, Nissle 1917, has proven to be efficient in the treatment for maintaining remission in ulcerative colitis [ 32 ] and helps to stop acute diarrhea in infants and toddlers [ 33 ]. Lactobacilli have long been considered to be good for health and due to their beneficial and protechnological properties, numerous Lactobacillus species are used as probiotics with recognized effects in the treatment of gastrointestinal disease [ 34 ]. Members of the Lactobacillus plantarum species have been found to reduce the concentration of cholesterol and fibrinogen and reduce the risk of cardiovascular disease and atherosclerosis [ 35 ].…”

Phylotype-Level Profiling of Lactobacilli in Highly Complex Environments by Means of an Internal Transcribed Spacer-Based Metagenomic Approach

“…Thus, they are extensively used in the food industry, in particular in fermented foods, due to their high performance in lactic acid fermentation coupled with a high tolerance for low pH, preservative and organoleptic properties, and the production of exopolysaccharides that contribute to the texture of foods (2,7). In this context, members of the genus Lactobacillus have in recent years gained significant scientific and commercial interest as health-promoting microorganisms, as evidenced by the fact that 22 species encompass strains patented as probiotics in Europe (8).…”

“…The retrieved genomic data have been exploited for comparative genomic analyses and has allowed the identification of many shared or distinct genetic features of this genus. Furthermore, this genomic information has permitted the reconstruction of their metabolic potential, has shed light on host-microbe interactions (such as adhesion to the mucus layer and modulation of the immune system of the host), and has revealed particular microbemicrobe interactions with other commensals or (opportunistic) pathogens (1,7,8).…”