Populations of gut microorganisms change across the whole GI tract

The concept that the intestinal microbiota modulates numerous physiologic processes, including immune development and function, nutrition and metabolism, and pathogen exclusion, is relatively well established in the scientific community. The molecular mechanisms driving these various effects and the events leading to the establishment of a “healthy” microbiome are slowly emerging. This review brings into focus important aspects of microbial/host interactions in the intestine and discusses key molecular mechanisms controlling health and disease states. We discuss the evidence of how microbes interact with the host and one another and their impact on intestinal homeostasis.