and throughoutour lives, humans serve as reservoirs forextremely complex and dynamic communitiesof microorganisms of varying origins. These microbesinclude archaea, bacteria, viruses, bacteriophage, andeukaryotes (uni- and multicellular parasites). Althoughconstituting a potential threat to health and well-beingthrough parasitism, these microbial communities haveco-evolved over millions of years with the healthyhuman host to provide a range of beneficial, and oftenessential, services. Although still rudimentary, ourunderstanding of the beneficial roles played by thehuman microbiome has grown appreciably in recentyears,as high-throughput,culture-independenttechnol-ogyandrelatedmoleculartechnologieshavebeenadap-ted to complement the role of traditional microbiologiccultures to facilitate the study of the human ecosystem.Most studies identify individuals within complex popu-lations by focusing on molecular characterization ofDNA from bacterial 16S ribosomal genes, a sequencethat distinguishes each organism by its phylum, genus,and even species, depending on the length of the se-quence. By studying communities in their native habi-tats, rather than in liquid broth or on Petri plates, wehave gained significant insight into the dynamic, multi-factorial interactions that occur among host, pathogen,commensal community, and environment. Undernormal, healthy circumstances, these interactions occuracross both the integument and mucosal surfaces(eg, airways, intestinal, reproductive tracts, mouth),the surfaces of the human body exposed to the environ-ment that are the primary sites of microbial residence.As thoughtfully reviewed in this issue of TranslationalResearch, the authors consider the microbial ecologyof the intestine,