Our bodies are colonized by a multitude of microorganisms whose collective genome, the microbiome, complements and enhances our own genome. From this perspective, we are “supraorganisms” coated with a number of microbial cells that is 10 times greater than the sum of all our cells. The intestine contains the largest collection of microbes among all of our body “habitats”. In the colon, for example, bacteria reach densities of 1011 cells per gram of luminal contents. Together, gut microbes form a community, or microbiota, that has a major impact on health through interactions with host cells, through extractions of nutrients and energy from the diet, and through complex biotransformations of a variety of ingested compounds, including potential carcinogens.
Long-standing questions abound concerning this ecosystem. How is the microbiota assembled and maintained over a lifetime? How personal is each individual’s microbiota? How does its composition contribute to well-being or disease predisposition and pathogenesis? The answers to these and other questions are starting to emerge with the application of next generation sequencing to characterize the composition and gene content of the gut microbial community. The advances in sequencing technology are concordant with advances in computational methodology which is used to analyze the vast amount of data emanating from studies of the gut microbiota, coupled with the application of principles gleaned from the fields of ecology, evolutionary biology, and population genetics, are illuminating the properties and operations of this remarkable microbial “organ”.
