Understanding the gut ecosystem: bugs, drugs & diseases

The gut microbiota is an ecosystem composed of trillions of microorganisms, including bacteria, fungi, and viruses. Microbes living in our intestine perform crucial functions for us. For example, they help us to digest the food that we eat, synthesize vitamins and protect us from infections. Consequently, severe alterations in the gut microbiota can compromise our health.Inflammatory bowel disease (IBD) is an inflammatory disorder of the gastrointestinal tract, which comprises two main phenotypes: ulcerative colitis and Crohn’s diseases. So far, we do not know what causes the disease: a fact that has increased the interest in understanding the role of the gut microbiota in this disease.In this thesis, we have made use of sequencing techniques to explore the gut microbiota in the context of IBD. We describe which bacterial species and metabolic functions are enriched and depleted in the gut of these patients compared to the normal population. Moreover, we highlight how this information can potentially be used to assist the diagnosis of IBD. We have also investigated the impact of several clinical factors on the gut microbiome composition. One of the most striking findings is the association between the use of proton-pump inhibitors, commonly used drugs against heartburn, and a marked alteration of the gut microbiota.This thesis contributes to understanding the relevance of the gut microbiota in human health, which will pave the future for new therapeutic and diagnostic approaches to IBD