The gastro-intestinal (GI) tract is the primary site of food intake, perception and conversion. It represents one of the most important metabolic organs of the body and is colonised by a myriad of microbes that contribute to nutrient processing, affect immune function, and stimulate a variety of other host activities. Genomes of GI-tract resident microbial species have been sequenced, e.g. the Lactobacillus plantarum WCFS1 genome sequence has been published and an ever improving annotation database is in facilitating ongoing research to provide a model for specific and mechanistically predictable interactions of host and microbe. Bifidobacteria are of particular interest as they are dominantly present in the human GI-tract. The genome of Bifidobacterium longum has been sequenced and its analysis has provided insights into the interactions of Bifidobacteria with their hosts. Research into novel species, such as the recently identified Akkermansia muciniphila, which grows solely on mucin, will help to unravel the species-specific functionality of microbes. This article provides an overview of current research initiatives undertaken to elucidate microbial functionality in the human GI-tract.
