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

Abstract

OBJECTIVES:Bowel preparations (BPs) taken before colonoscopy may introduce a confounding effect on the results of gastrointestinal microbiota studies. This study aimed to determine the effect of bowel preparation on the mucosa-associated and luminal colonic microbiota in healthy subjects (HC) and inflammatory bowel disease (IBD) patients.METHODS:Biopsy samples (n=36) and fecal samples (n=30) were collected from 10 HC and 8 IBD subjects pre- and post-BP. 16S rRNA gene was pyrosequenced using 454 Titanium protocols. We compared the differences between the pre- and post-BP samples (i.e., comparisons-across-bowel-prep); we examined the effect of BP on the expected separation of the mucosal vs. the luminal compartments (i.e., comparisons-across-compartments). Last, we compared the baseline differences between the HC vs. IBD groups (a secondary analysis), and examined whether the differences between the HC vs. IBD changed after BP.RESULTS:In comparisons-across-bowel-prep, the Shannon's index (SI) decreased only in the biopsy samples of IBD subjects post-BP (P=0.025) and phylogenetic diversity-whole tree (PD-WT) metric decreased in biopsy samples of HC subjects post-BP (P=0.021). In secondary comparisons, the subtle differences between the fecal samples of the HC vs. IBD groups, in terms of evenness and the SI, were not apparent post-BP. In terms of β-diversity, in comparisons-across-bowel-prep, the proportion of shared operational taxonomic units (OTUs) in pre- and post-BP samples was low (~30%) and unweighted Unifrac distances between pre- and post-BP specimens ranged from 0.52 to 0.66. HC biopsies were affected more than IBD biopsies with BP (P=0.004). In comparisons-across-compartments, the proportion of shared OTUs between biopsy and fecal samples increased and Unifrac distances decreased post-BP in IBD subjects, reducing the differences between the mucosal and luminal compartments of the gut microbiota. Interindividual differences in Unifrac distances were preserved even with BP effects, although the effects were greater on weighted Unifrac distances. Bacteroidetes and its subtypes increased post-BP in both the luminal and mucosal compartments.CONCLUSIONS:Bowel preparations affect the composition and diversity of the fecal and luminal microbiota in the short term, introducing potential bias into experiments examining the gut microbiota. The magnitude of the effect of BP is not greater than that of interindividual variation. Both the luminal and mucosal compartments of the gut microbiota get affected, and samples from controls and IBD subjects may get affected differently. Studies of the colonic microbiota should take into account the direction and the magnitude of the change introduced by BP during the design stage of the experiments, and consider sample sizes so that potential bias is minimized.

Extending colonic mucosal microbiome analysis—assessment of colonic lavage as a proxy for endoscopic colonic biopsies

“…The study demonstrated that bowel prep affected the composition and diversity of the microbiota in the short term differently between sample types with differences also noted between controls and IBD patients. Biopsies from healthy subjects showed greater changes due to bowel prep compared to IBD patients [40]. …”

Nutraceuticals as modulators of gut microbiota: Role in therapy

“…Only longitudinal studies with sampling at multiple time points can aid in making this distinction. Diet, likely to be altered in many disease states, can significantly modify the microbiome (in both the long and short terms) and has not been accounted for in many of studies. For obvious reasons of convenience, most human studies have been based on the analysis of faecal samples, an approach that disregards variations in bacterial populations along the length of the gastrointestinal tract and may fail to represent those bacterial populations that reside close to or adherent to the mucosa. Though more challenging in terms of access, studies of the juxta‐mucosal microbiome in the colon have revealed significant difference in health and disease from those studies where microbiome analyses were based on stool samples (Parthasarathy et al, ; Ringel et al, ; Shobar et al, ). Even more logistically challenging are studies of the small intestinal microbiome; here also, new data are appearing (Saffouri et al, ).…”

“…Though more challenging in terms of access, studies of the juxtamucosal microbiome in the colon have revealed significant difference in health and disease from those studies where microbiome analyses were based on stool samples (Parthasarathy et al, 2016;Ringel et al, 2015;Shobar et al, 2016). Even more logistically challenging are studies of the small intestinal microbiome; here also, new data are appearing (Saffouri et al, 2019).…”

Novel insight into the role of microbiota in colorectal surgery

“…Drago et al 50 compared the microbiota composition immediately and 1 month after MBP; contrary to most other studies, they found that MBP has long-lasting effects on the gut microbiota composition and homeostasis, particularly in terms of a decrease in the abundance of Lactobacillaceae , a population of protective bacteria (figure 3). Shobar et al 51 conducted one of the most thorough studies, which simultaneously analysed the composition of the microbiota at the levels of the mucosal and luminal compartments, differentiating between healthy subjects and patients with IBD and using a high-resolution technique.…”

“…In addition, the initial composition of the gut microbiota might already be dysbiotic and therefore not ‘normal’ because of the specific disease to be treated. However, there is no doubt, for example, that the microbiota in patients with IBD suffers from significant changes in its bacterial composition 51. Even though data are scarce for the moment, we can presume that other diseases that will finally point towards a colorectal surgery such as repeated diverticulitis or colorectal cancer are also characterised by changes in the microbial diversity also leading to a chronic inflammatory status, as recently shown by Barbara et al68 All these changes threaten the microbiota diversity and allow pathogenic bacteria that contribute to postsurgical complications to thrive.…”