Gastrointestinal Microbiology in the Normal Host

This article updates information about gastrointestinal (GI) microbiota in the normal host. The human GI microbiota is complex that the dominant bacteria in different parts (esophagus, stomach, small intestine and colon) differ significantly from each other and there is a large inter-individual variation among population. More than 1000 culturable GI microbial species have been identified up to 2014 and more the remaining are expected to be cultured in the future. Next generation sequencing (NGS) technologies become mainstreams in the studies of GI microbiota with the advantage of being culture-independent and high-throughput. Other "omics" technologies (such as metabolomics, metatranscriptomics and metaproteomics), are combined with metagenomics to facilitate functional studies. Many statistical methods and bioinformatic tools emerge to improve the quality of the metagenomic study, whose resolution can even reach at strain-level. Despite that a large number of large-scale epidemiologic investigations have been performed to define a healthy human gut microbiome, there has no uniformly recognized "core microbiome" for healthy populations yet. Drug/diet targeted clinical interventions have been developed to understand the features of functional microbiota and provide promising solution to chronic diseases such as obesity and type 2 diabetes.