Functional genomics of lactic acid bacteria: from food to health

Abstract

Genome analysis using next generation sequencing technologies has revolutionized the characterization of lactic acid bacteria and complete genomes of all major groups are now available. Comparative genomics has provided new insights into the natural and laboratory evolution of lactic acid bacteria and their environmental interactions. Moreover, functional genomics approaches have been used to understand the response of lactic acid bacteria to their environment. The results have been instrumental in understanding the adaptation of lactic acid bacteria in artisanal and industrial food fermentations as well as their interactions with the human host. Collectively, this has led to a detailed analysis of genes involved in colonization, persistence, interaction and signaling towards to the human host and its health. Finally, massive parallel genome re-sequencing has provided new opportunities in applied genomics, specifically in the characterization of novel non-GMO strains that have potential to be used in the food industry. Here, we provide an overview of the state of the art of these functional genomics approaches and their impact in understanding, applying and designing lactic acid bacteria for food and health.

Figure 1

Overview of LAB associations with plants and animals, human and foods. The estimated time frames of the evolutionary events relating to the emergence of human (top) and domestication (bottom) are indicated - please note their different dimensions. For a further explanation, see text.

Figure 2

A phylogenetic tree of based on sequences of 7 housekeeping genes (recA, rpoD, dnaK, infC, rplA, rpsB and rpmA) from the 36 LAB species. The tree was generated using previously described computational methods [210-219]. Species were colored according to their genus (purple, Leuconostoc spp. ; yellow, Lactobacillus spp. ; blue, Pediococcus spp.; green, Lactococcus spp.; pink, Streptococcus spp. ; orange, Enterococcus spp. ; grey, Oenococcus spp. ). In addition, the presence of isolates in a particular niche are indicated by colored dots (dark green, plant material; green, food products; orange, oral cavity; purple, gastro-intestinal tract; magenta, vaginal cavity and blue, other body sites and clinical isolates). This illustrates the ecological versatility of each species but does not further detail its ecological role, i.e. transient (allochthonous) or endogenous (autochthonous).

Figure 3

Overview of the level of LAB in the different body sites. The estimated LAB fraction is based on several complete and comprehensive phylogenetic and metagenomic datasets and the total number of bacteria per gram of homogenized tissue or fluid or square centimeter of skin [4,94,95,220,221].

Figure 4

Genome, habitat and phenome - a summary overview.