For health and disease, the gut microbial community of humans has received significant attention from researchers. The application of 16S rRNA-based molecular technology enables researchers to study the microbial composition in the gut ecosystem. Developments in “omics” approaches have made it possible to reveal the function of microbes in the gastrointestinal tract. In this paper, combined with our own findings, we summarized advances in molecular ecology applied to studying gastrointestinal tract microorganism.