Background: The proliferation and survival of microbial organisms including intestinal microbes are determined by their surrounding environments. Contrary to popular myth, the nutritional and chemical compositions, water contents, O2 contents, temperatures, and pH in the gastrointestinal (GI) tract of a human are very different in a location-specific manner, implying heterogeneity of the microbial composition in a location-specific manner.Results: We first investigated the environmental conditions at 6 different locations along the GI tract and feces of ten weeks’ old male SPF C57BL/6 mice. As previously known, the pH and water contents of the GI contents at the different locations of the GI tract were very different from each other in a location-specific manner, and none of which were not even similar to those of feces. After confirming the heterogeneous nature of the GI contents in specific locations and feces, we thoroughly analyzed the composition of the microbiome of the GI contents and feces. 16S rDNA-based metagenome sequencing on the GI contents and feces showed the presence of 13 different phyla. The abundance of Firmicutes gradually decreased from the stomach to feces while the abundance of Bacteroidetes gradually increased. The taxonomic α-diversities measured by ACE (Abundance-based Coverage Estimator) richness, Shannon diversity, and Fisher’s alpha all indicated that the diversities of gut microbiome at colon and cecum were much higher than that of feces. The diversities of microbiome compositions were lowest in jejunum and ileum while highest in cecum and colon. Interestingly, the diversities of the fecal microbiome were lower than those of the cecum and colon. Beta diversity analyses by NMDS plots, PCA, and unsupervised hierarchical clustering all showed that the microbiome compositions were very diverse in a location-specific manner. Direct comparison of the fecal microbiome with the microbiome of the whole GI tracts by α-and β-diversities showed that the fecal microbiome did not represent the microbiome of the whole GI tractConclusion: The fecal microbiome is different from the whole microbiome of the GI tract, contrary to a baseline assumption of contemporary microbiome research work.

Background: The proliferation and survival of microbial organisms including intestinal microbes are determined by their surrounding environments. Contrary to popular myth, the nutritional and chemical compositions, water contents, O2 contents, temperatures, and pH in the gastrointestinal (GI) tract of human are very different in a location-specific manner, implying heterogeneity of the microbial composition in a location specific manner.Results: We first investigated the environmental conditions at 6 different locations along the along the GI tract and feces of ten weeks’ old male SPF C57BL/6 mice. As previously known, the pH and water contents of the GI contents at the different location of the GI tract were very different from each other in a location-specific manner, and none of which were not even similar to those of feces. After confirming the heterogeneous nature of the GI contents in specific location and feces, we thoroughly analyzed the composition of microbiome of the GI contents and feces. Metagenome sequencing on the GI contents and feces showed presence of 13 different phyla. The abundance of Firmicutes gradually decreased from the stomach to feces while the abundance of Bacteroidetes gradually increased. The taxonomic α-diversities measured by ACE richness, Shannon diversity and Fisher’s alpha all indicated that the diversities of gut microbiota at colon and cecum were much higher than that of feces. The diversities of microbiome compositions were lowest in jejunum and ilium while highest in cecum and colon. Interestingly, the diversities of fecal microbiome were lower than those of cecum and colon. Beta diversity analyses by NMDS plots, PCA, and un-supervised hierarchical clustering all showed that the microbiome compositions were very diverse in location-specific manner. Direct comparison of the fecal microbiome with the microbiome of the whole GI tracts by α-and β-diversities showed that fecal microbiome did not represent the microbiome of the whole GI tractConclusion: The fecal microbiome is different from the whole microbiome of the GI tract, contrary to the baseline assumption in the large majority of contemporary microbiome research work.