Fecal microbiome does not represent whole gut microbiome

The current gut microbiome research relies on the fecal microbiome under the assumption that the fecal microbiome represents the microbiome of the entire gastrointestinal (GI) tract. However, there have been growing concerns about using feces as a proxy to study the gut microbiome. Here, we comprehensively analyzed the composition of microbiome and metabolites in the feces and at 14 different locations of GI tracts of genetically homogenous sibling pigs to evaluate the validity of using feces as a proxy to the whole gut microbiome. The fluctuation in the composition of the microbiome in stomach and the small intestine became stabilized from the large intestine to feces and were able to be categorized into 3 groups. The highly independent intestinal microbes in stomach and the small intestine became flourished in the large intestine and converged into a community with tightly connected networks. Comparative analysis of the gut microbiome at each location suggested that fecal microbiome is insufficient to represent the whole gut microbiome.