Effects of bowel preparation on the human gut microbiome and metabolome

Naoyoshi Nagata, Mari Tohya, Shinji Fukuda, Wataru Suda, Suguru Nishijima, Fumihiko Takeuchi, Mitsuru Ohsugi, Tetsuro Tsujimoto, Tomoka Nakamura, Akira Shimomura, Naohiro Yanagisawa, Yuya Hisada, Kazuhiro Watanabe, Koh Imbe, Junichi Akiyama, Masashi Mizokami, Tohru Miyoshi-Akiyama, Naomi Uemura, Masahira Hattori, Naoyoshi Nagata, Mari Tohya, Shinji Fukuda, Wataru Suda, Suguru Nishijima, Fumihiko Takeuchi, Mitsuru Ohsugi, Tetsuro Tsujimoto, Tomoka Nakamura, Akira Shimomura, Naohiro Yanagisawa, Yuya Hisada, Kazuhiro Watanabe, Koh Imbe, Junichi Akiyama, Masashi Mizokami, Tohru Miyoshi-Akiyama, Naomi Uemura, Masahira Hattori

Abstract

Large bowel preparation may cause a substantial change in the gut microbiota and metabolites. Here, we included a bowel prep group and a no-procedure control group and evaluated the effects of bowel prep on the stability of the gut microbiome and metabolome as well as on recovery. Gut microbiota and metabolome compositions were analyzed by 16S rRNA sequencing and capillary electrophoresis time-of-flight mass spectrometry, respectively. Analysis of coefficients at the genus and species level and weighted UniFrac distance showed that, compared with controls, microbiota composition was significantly reduced immediately after the prep but not at 14 days after it. For the gut metabolome profiles, correlation coefficients between before and immediately after the prep were significantly lower than those between before and 14 days after prep and were not significantly different compared with those for between-subject differences. Thirty-two metabolites were significantly changed before and immediately after the prep, but these metabolites recovered within 14 days. In conclusion, bowel preparation has a profound effect on the gut microbiome and metabolome, but the overall composition recovers to baseline within 14 days. To properly conduct studies of the human gut microbiome and metabolome, fecal sampling should be avoided immediately after bowel prep.

Conflict of interest statement

The authors declare no competing interests.

Figures

Figure 1
Figure 1
Gut microbiota α-diversity as measured by the Shannon index before, during, and after bowel preparation. Note: Boxes represent the interquartile range (IQR) and lines inside show the median. Whiskers denote the lowest and highest values within 1.5 times the IQR.
Figure 2
Figure 2
Gut microbial composition across different sampling times in the bowel prep group vs control group. (A) Spearman’s correlation coefficients of gut microbial composition at the genus level. (B) Spearman’s correlation coefficients of gut microbial composition at the species level. (C) Weighted UniFrac distances of gut microbial composition. Note: Boxes represent the interquartile range (IQR) and lines inside show the median. Whiskers denote the lowest and highest values within 1.5 times the IQR.
Figure 3
Figure 3
Principal coordinate analysis (PCoA) plot in microbiome and metabolome. (A) PCoA plot of weighted UniFrac distances for samples between bowel prep group and controls in microbioal analysis. (B) PCoA plot of weighted UniFrac distances for samples in bowel prep group in microbial analysis. (C) PCoA plot, unit variance scaling in bowel prep group in metabolome analysis.
Figure 4
Figure 4
Spearman’s correlation coefficients of fecal metabolome profiles before bowel prep (Day 0), immediately after bowel prep (Day 1), and 14 days after bowel prep (Day 14). Note: Boxes represent the interquartile range (IQR) and lines inside show the median. Whiskers denote the lowest and highest values within 1.5 times the IQR.
Figure 5
Figure 5
Timing of fecal sample collection in the bowel prep group and control group.

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