Fecal Microbiome Does Not Represent Whole Gut Microbiome

The current gut microbiome research relies on the fecal under assumption that represents of entire gastrointestinal (GI) tract. However, there have been growing concerns about using feces as a proxy to study microbiome. Here, we comprehensively analyzed composition and metabolites in at 14 different locations GI tracts genetically homogenous sibling pigs evaluate validity whole intestinal microbes constituting each content their metabolic compositions were thoroughly investigated through metagenome sequencing an ultraperformance LC-MS/MS, respectively. fluctuation stomach small intestine became stabilized from large was able be categorized into 3 groups. taxonomic α-diversities measured by ACE (abundance-based coverage estimator) richness Shannon diversity indicated much more diverse than those feces. highly independent flourished converged community with tightly connected networks. β-Diversity analyses NMDS plots, PCA, unsupervised hierarchical clustering all showed diversities lowest while highest intestine. In accordance along tract, also completely differed location-specific manner Comparative analysis tract is insufficient represent