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

Daisuke Chinda,Kenji Oishi,Shinsaku Fukuda,Kensuke Shimizu,Kosuke Oana,Yusuke Nagara,Tetsu Arai,Hirotake Sakuraba,Tatsuya Mikami,Toshihiko Takada,Daichi Fujii,Miyuki Katto,Kazuki Akitaya,Hiroshi Makino

doi:10.1038/s41598-022-07594-6

Daisuke Chinda, Kenji Oishi + Show 12 more

Open Access

https://doi.org/10.1038/s41598-022-07594-6

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Abstract

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.

Highlights

Gut microbiomics is based on analysis of both live and dead cells in the stool
Propidium monoazide (PMA) binds to the DNA of dead cells, as the cell membrane in live cells is impermeable to PMA; the PMA-bound DNA is not amplified by PCR, and only the DNA from live cells is detected
Tian et al (2017) reported a correlation between the results of an approach involving a combination of PMA and MiSeq (PMA-MiSeq) and ATP activity of bacteria inhabiting sludge, suggesting that PMA-MiSeq is useful for analyzing live b acteria[18]

Summary

Introduction

Gut microbiomics is based on analysis of both live and dead cells in the stool. to understand the ecology of gut microbiota and their symbiotic relationships with hosts, spatial distribution of live bacteria must be examined. Ever since Eckburg et al.[10] reported their colon site-specific analysis of microbiota via 16S rRNA, many researchers have analyzed the composition of the microbiota collected from various parts of the gut These studies showed that the gut microbiota in healthy people varies more among individuals than among parts of the gut. Using 16S rRNA meta-analysis of PMA-treated and untreated samples, Fu et al (2018) reported site differences (foregut vs hindgut) in the proportion and composition of microbiome of total versus live bacteria in the gut of rex rabbits[17]. Tian et al (2017) reported a correlation between the results of an approach involving a combination of PMA and MiSeq (PMA-MiSeq) and ATP activity (an indicator of viability) of bacteria inhabiting sludge, suggesting that PMA-MiSeq is useful for analyzing live b acteria[18]

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