Metabolism of carbohydrates by human gut microbiome species

The recent interest in the human gut microbiome stems from associations of its composition to health or disease states.

However, this knowledge still has limited application, since the microbial species that colonize humans remain poorly characterized at the molecular level.

These species are difficult to study with traditional molecular biology approaches, due to a general lack of genetic manipulation tools.

Thus, the mechanisms behind these associations are largely unknown, and even when they are known, we generally lack strategies to manipulate species composition to validate them or use as therapy.In this project, we will apply proteomics, species growth measurements and follow-up biochemical characterization approaches to: (i) determine the proteins responsible for sensing, transporting and metabolizing carbohydrates, allowing data-driven delineation of metabolic pathways in representative bacterial species of the human gut microbiome; (ii) identify growth interactions between pairs of species grown in diverse carbohydrates, allowing defining the principles of bacterial community assembly; (iii) establish and test strategies to manipulate complex microbiome communities by varying media nutrient composition.This integrative approach will pave the way to understand the principles of how stable bacterial communities are formed and maintained, and how these can be used to rationally manipulate microbiome species composition to restore healthy states through diet alterations.