The gut microbiome in inflammatory bowel disease

The role of the gut microbiota in inflammatory bowel disease (IBD), an early focus of microbiome science, is the topic of this chapter. Specifically, we investigate the evidence for the gut microbiota as an integral player in the development and maintenance of IBD, we outline the alterations in community composition ('dysbiosis') that have been reported in the literature and we also describe mechanisms that connect host genotype to a pro-inflammatory dysbiosis, completing a link between disease susceptibility, molecular genetics, microbiome alterations and the subsequent positive feedback cycle between inflammation and dysbiosis. The aim is to highlight how advances in molecular genetics and microbiome science may be brought together to improve our understanding of IBD, while providing a blueprint for developing the next generation of hypotheses, biomarkers, and therapies.