Systems solutions by lactic acid bacteria: from paradigms to practice

Abstract

Lactic acid bacteria are among the powerhouses of the food industry, colonize the surfaces of plants and animals, and contribute to our health and well-being. The genomic characterization of LAB has rocketed and presently over 100 complete or nearly complete genomes are available, many of which serve as scientific paradigms. Moreover, functional and comparative metagenomic studies are taking off and provide a wealth of insight in the activity of lactic acid bacteria used in a variety of applications, ranging from starters in complex fermentations to their marketing as probiotics. In this new era of high throughput analysis, biology has become big science. Hence, there is a need to systematically store the generated information, apply this in an intelligent way, and provide modalities for constructing self-learning systems that can be used for future improvements. This review addresses these systems solutions with a state of the art overview of the present paradigms that relate to the use of lactic acid bacteria in industrial applications. Moreover, an outlook is presented of the future developments that include the transition into practice as well as the use of lactic acid bacteria in synthetic biology and other next generation applications.

Multifactorial diversity sustains microbial community stability

“…Starter culture communities may face several (a)biotic selective pressures during back-slopping regimes. Despite this environmental uncertainty, mixed-strain undefined cultures are more resilient and display a more robust performance as compared with defined low-strain-diversity cultures in dairy processes (de Vos, 2011).…”

Comparative Genomic and Functional Analysis of Lactobacillus casei and Lactobacillus rhamnosus Strains Marketed as Probiotics

“…Many LAB are traditionally used as culture starters in industrial dairy fermentations of raw materials, such as milk, vegetables, and meat. However, in recent years, specific LAB strains have been associated with health benefits and are marketed as probiotics in a highly successful way, reaching market volumes of over $100 billion (2,3). Most of these marketed strains belong to the genus Lactobacillus, which represents the largest group of LAB, encompassing more than 100 cultivable bacterial species (4).…”

“…To demonstrate their health-promoting abilities, a number of Lactobacillus strains, including L. rhamnosus GG, have been successfully used in human interventions with subjects suffering from GI disorders and atopic dermatitis (7,8). Comparative studies have shown that probiotic features and their associated health properties are strain specific and cannot be generalized, indicating that it is essential to characterize the Lactobacillus strains at the genome level, as has been done for a limited number of paradigm probiotics (2). This has promoted rapid insights into the diversity, evolution, and molecular basis underlying the health benefits of these strains, resulting in a research area that has been termed probiogenomics (9).…”

Functional Identification of Conserved Residues Involved in Lactobacillus rhamnosus Strain GG Sortase Specificity and Pilus Biogenesis

“…However, the recent genome sequencing and analysis of Lactobacillus rhamnosus strain GG revealed the presence of a genomic island encoding three structural LPXTGlike pilin proteins called SpaC, SpaB, and SpaA and a pilin-specific sortase SrtC1 (4). L. rhamnosus GG 2 is globally marketed in probiotic products and has been among the best studied lactic acid bacteria (5)(6)(7)(8). In GG, the discovery that mucus-binding pili signal the intestinal cells has generated new insights into the mechanisms involved in host interactions and underlines the potential contribution of pili in probiotic response (9).…”