To understand effectively the role of commensal micro- biota in health and disease, we must be able to describe the complex ecology of the microbiome. Recently developed molecular and metagenomic tools have allowed research- ers to better understand the structure and function of the microbial gut community. Several bacterial phyla are represented in the gut, and commensals exhibit consider- able diversity, with as many as 1000 distinct bacterial species involved [14–16]. The two most prominent phyla are Firmicutes and Bacteroides, accounting for at least 70– 75% of the microbiome [15–17]. Proteobacteria, Actinobac- teria, Fusobacteria, and Verrucomicrobia are also present but in reduced numbers [15]. The dynamic nature and the diversity of the microbiome determined to date extends far beyond what researchers expected