Mechanisms of Dysbiosis in the Inflamed Gut

Sparked by the development of next-generation sequencing methods, we have come to appreciate that the human intestinal tract is home to a complexmicrobial ecosystem, termed microbiota. On the species level, the composition of the gut microbiota varies greatly between individuals and is influenced by numerous factors such as diet, immune status, and environmental circumstances. However, the overall composition of themicrobiota, in particular, the dominance of obligate anaerobic bacteria over facultative bacteria is conserved between individuals. In contrast, episodes of intestinal inflammation are accompanied by a severe disruption of the normal bacterial community structure, termed dysbiosis. Inflammation-associated dysbiosis is frequently characterized by a bloom of facultative anaerobic bacteria of the phylum Proteobacteria, in particular, members of the Enterobacteriaceae family, and a relative depletion of obligate anaerobicmembers. While numerous groundbreaking studies have recorded the diversity of the gutmicrobiota, themolecular mechanisms dictating the interaction between the host and microbes residing in the gastrointestinal tract are a medically relevant topic that is still in its infancy. A mechanistic understanding of the complex relationship between the host and its microbiota will significantly contribute to the development of novel intervention strategies targeting the gutmicrobiota and dysbiosis-associated diseases. In this chapter, conceptual advances on molecular mechanisms that influence the structure of gut-associated microbial communities are discussed, with a focus on inflammatory diseases of the intestinal tract.