Evolution and transmission dynamics of gut microbiota species.

The intestinal microbiota is composed of multiple species of microorganisms that have important metabolic, immunological and protective functions for the host. Traditionally, the gut microbiota has been studied through the sequencing of DNA (metagenomics), which has permitted identifying what species are present in the community and what functions they encode. However, little is known about the individual species and strains that make up these communities of bacteria. Here, we aim to characterize the global evolutionary trends of major gut bacterial species and to study how they spread between individuals and populations.  For this purpose, we will first develop a framework for population genomic analysis from metagenomic datasets, which we will apply to thousands of gut metagenomes covering the breadth of ecological and geographical origins. Then, we will characterize the distribution of multiple species across different regions and populations and we will determine their evolutionary patterns. Next, we will study the genetic variation within individuals and how it affects the colonization by other bacteria. Finally, we will use epidemiological methods to characterize the transmissibility and migration patterns of these microbiota species. Overall, these analyses will reveal new insights into the evolution and ecology of gut commensal bacteria, and will provide a greater understanding of the transmission of the intestinal microbiota.