Host-bacteria homeostasis in the healthy and inflamed gut

Purpose of review We are currently entering an exciting transition period from studying the molecular and cellular bases of the virulence of bacterial pathogens to deciphering the mechanisms of tolerance of the gut commensal flora. This review attempts to delineate the (sometimes thin) border between these two situations that are at the heart of understanding gut homeostasis and its possible rupture. Recent findings Essential issues are examined, such as metagenomic analysis of gut microbiota, the control of inflammation leading to tolerance, the molecular bases of regulation and rupture, and the way pathogens themselves regulate inflammation. Summary Breakthroughs in understanding how gut homeostasis can be established, maintained or disrupted in the presence of microbes should be sources of new therapeutic targets and drugs (i.e. anti-inflammatory, immunomodulatory and anti-infectious molecules).