Characterization of the transcriptome interactions between host and gut microbiota in health and disease

The human body is an ecosystem that hosts trillions of bacteria, the vast majority of which live in the gut. In normal conditions, there is an equilibrium in which the different bacterial species (the microbiota) confer several benefits to the host. However, alterations in this equilibrium have been linked to several diseases with a strong inflammatory component, such as inflammatory bowel disease (IBD) and colorectal cancer (CRC).

Cultivation-free genome sequencing (metagenomics) has been applied to identify the species correlating with health and disease, and the genes they encode for. However, this does not provide information regarding which of these genes are active or inactive, which is crucial to understand the interactions between the host and the bacterial community. To address this problem, we will perform metatranscriptomics, a technique to assess which are the active genes in these bacteria, as well as in the host. We will apply this technique to gut biopsies of healthy individuals to understand what is the range of normal interactions, and later we will do the same with biopsies from IBD and CRC patients to understand what are the changes occurring in disorders with a strong inflammatory component. We will also investigate whether the genetic background of the host influences the gene expression of the microbiota in healthy individuals.