The human intestine is inhabited by numerous microbes, which form a complex microbial community that deeply affects human physiology. This microbiota is dominated by relatively few divisions that are highly diverse at the strain/subspecies level, which together with its collective genomes (microbiome) provide us with genetic and metabolic attributes we have not been required to evolve on our own. New studies taking advantage of molecular microecological, metagenomic and metabolomic methods are revealing how the gut microbiota has coevolved with us and how it manipulates and complements our biology in ways that are mutually beneficial. However, how certain keystone members of the microbiota operate to maintain the stability and functional adaptability of this microbial organ still need to be answered, which necessitate the combination of high throughput methods and multivariable analysis.