Secretomes of lactobacilli and enterococci and their impact on bacterial adaptation and human health

Lactic acid bacteria belonging to the genera Lactobacillus and Enterococcus are normal inhabitants of fermented food products and of the human gastrointestinal tract. The impact of these bacteria on human health varies from beneficial to harmful. We will conduct genome-wide studies of surface-located and secreted proteins (secretomes) of lactobacilli and enterococci, including comparative analyses (by experiment and bioinformatics) of two lactobacilli with different genome sizes (L. plantarum WCFS1, 3.31 Mb, and L. salivaricus, 2.13 Mb) and of enterococci displaying varying degrees of pathogenicity (E. faecalis and E. faecium). The bacteria will be grown under various conditions selected to resemble elements of the human ecosystem (bile salts, intestinal extracts, epithelial cells) and bacterial responses will be studied using transcriptomics and proteomics. In particular, we will analyze how the secretome is affected by growth conditions and how species differ in their adaptive behaviour. These studies w ill be complemented by phenotypic studies (e.g. immunomodulation, adhesion, survival), using e.g. knock-out mutants, over-expression of selected genes, and/or in vivo monitoring of labelled bacterial cells. In some cases, further insight will be obtained through detailed studies of target proteins emerging from the genome-wide work. The project involves two major European Research Centers (in Cork, Ireland and in Wageningen, The Netherlands) working on lactobacilli, and an Italian group that recently has developed new techniques for LC-MS/MS-based analysis of proteins displayed on the surfaces of Gram-positive bacteria. By conducting this systematic, partly comparative functional genomics analysis of bacterial secretomes, we hope to identify and understan d mechanisms that are crucial for bacterial behaviour during interaction with the human ecosystem.