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Gut microbiomics is based on analysis of both live and dead cells in the stool. However, to understand the ecology of gut microbiota and their symbiotic relationships with hosts, spatial distribution of live bacteria must be examined. Here, we analyzed the live composition of luminal microbiota (LM) and mucosa-associated microbiota (MAM) in the ascending and descending colons and the rectums of 10 healthy adults and compared it with the total composition. The abundance of  Lachnospiraceae  in live LM decreased along the gut length and was significantly lower than that in total LM. Contrastingly, the abundance of  Bacteroidaceae  and  Bifidobacteriaceae  in live LM was higher than that in total LM, suggesting differences in death rate during gut migration. Live  Enterobacteriaceae  levels in MAM were significantly higher in rectum than in the ascending and descending colons and in LM. High-performance liquid chromatographic analysis of luminal bile acids revealed that 7α-dehydroxylation occurred towards the rectum. In live LM where a bile acid-inducible gene could be detected ,  7α-dehydroxylation rates were higher than those in the group without the gene. Overall, we showed differences in live bacteria composition among three gut sites and between LM and MAM, highlighting the importance of understanding their spatial distribution.

Spatial distribution of live gut microbiota and bile acid metabolism in various parts of human large intestine