Bowel preparation may affect gut microbiota composition and affect the results of experiments

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Kristina Campbell – IBD, Research & Practice

Bowel preparation is a necessary, but sometimes ‘invisible’, part of a successful colonoscopy. The question of how bowel preparation procedures affect the normal gut microbiota is so far unanswered, since existing data are conflicting.

Two recent studies supported the idea that bowel preparation significantly affects the gut microbiota. The first study, by Italian researchers (Drago, et al.), profiled the fecal samples of ten middle-aged patients one week before colonoscopy, between the bowel preparation and colonoscopy, and one month after colonoscopy. Patients were asked to adhere to a Mediterranean diet during the study period. All patients used a four-litre polyethylene glycol-based bowel lavage.

In general, the gut microbiota of these patients showed significant differences after bowel prep and colonoscopy; some of these differences were normalized one month later and some were not. Immediately after the bowel preparation and one month after the procedure, researchers observed an increase in Proteobacteria abundance and a decrease in Firmicutes. At the class level, they found a significant increase in both γ-Proteobacteria and α-Proteobacteria immediately after the colonoscopy and a significant decrease in these bacterial classes one month afterward. They also found changes at the family level, including a striking reduction in Lactobacillaceae and increase in Enterobacteriaceae after colonoscopy. Rikenellaceae and Eubacteriaceae were significantly higher in samples collected after the bowel preparation, while Streptococcaceae were significantly increased one month later.

The authors say this shows, in healthy individuals, a high-volume polyethylene glycol bowel cleansing preparation can have a long-lasting effect on gut microbiota composition—especially a decrease in the abundance of Lactobacillaceae, a population of bacteria with putative protective effects. Although the study included a sample size of only ten and offered no control group, it offers preliminary evidence that bowel preparation can alter the gut microbiota for at least a month.

The next study, by American researchers (Shobar, et al.), looked at two different groups of middle-aged subjects. The study aimed to determine how bowel preparation procedures affected the mucosa-associated and luminal colonic microbiota in ten healthy subjects and eight subjects with inflammatory bowel disease (IBD). They collected both biopsy and fecal samples, before and after a prepped colonoscopy. Subjects used either a sodium phosphate-based or a polyethylene glycol-based preparation. (The pre-bowel-prep biopsy was collected through a limited unprepped flexible sigmoidoscopy to 20–25 cm from the anal verge.) Subjects were instructed not to alter their diet between the two procedures.

The results showed bowel preparation affected the composition and diversity of the fecal and luminal microbiota in the short term; there was an overall trend toward reduced richness. After the procedure, Bacteroidetes and its subtypes increased in both the luminal and mucosal compartments. In the healthy individuals, the gut microbiota differences after bowel preparation were most apparent in biopsy samples and in rare taxa; in those with IBD, however, the differences were mostly observed in the fecal samples and affected both abundant and rare taxa. The observed effects of bowel preparation were more pronounced in subjects with IBD.

Together, these studies support the notion that bowel preparation affects the gut microbiota in specific ways, potentially for weeks after the procedure. Bowel preparation may affect fecal and biopsy samples differently. It remains to be seen whether these changes have any clinical consequences; however, Shobar, et al. noted the importance of taking a careful patient history that includes bowel preparation procedures. Above all, these results show caution is warranted when interpreting any gut microbiota study that includes a bowel preparation procedure for its subjects.


Drago L, Toscano M, De Grandi R, Casini V, & Pace F. (2016) Persisting changes of intestinal microbiota after bowel lavage and colonoscopy. Eur J Gastroenterol Hepatol. doi: 10.1097/MEG.0000000000000581.

Shobar RM, Velineni S, Keshavarzian A, Swanson G, DeMeo MT, Melson JE, Losurdo J, Engen PA, Sun Y, Koenig L, & Mutlu EA. (2016) The Effects of Bowel Preparation on Microbiota-Related Metrics Differ in Health and in Inflammatory Bowel Disease and for the Mucosal and Luminal Microbiota Compartments. Clinical and Translational Gastroenterology. 7(143) doi:10.1038/ctg.2015.54]

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