PEG-based bowel preparation induces reversible gut microbiota disruption with slower recovery in patients with UC, and probiotic supplementation after colonoscopy was associated with improved microbial diversity and enrichment of beneficial taxa, particularly in patients with UC.
Key Findings
Results
Bowel preparation with PEG significantly reduced alpha diversity and altered beta diversity in healthy controls, with gradual recovery by day 28.
Fecal samples were collected at baseline and on days 2, 14, and 28 post-colonoscopy
16S rRNA gene sequencing was used to assess microbial diversity, composition, and predicted functional pathways
Recovery in healthy controls occurred gradually over the 28-day follow-up period
Both alpha diversity (within-sample diversity) and beta diversity (between-sample compositional differences) were affected
Results
Patients with UC exhibited lower baseline microbial diversity and delayed microbiota recovery compared to healthy controls following bowel preparation.
39 patients with UC were included, compared to 40 healthy controls
UC patients already exhibited baseline dysbiosis and impaired microbial resilience prior to bowel preparation
Recovery trajectory in UC patients was slower than in healthy controls across the 28-day observation period
Lower baseline diversity in UC patients likely reflects pre-existing gut microbiota disruption characteristic of the condition
Results
Probiotic supplementation more substantially improved Shannon diversity and evenness in patients with UC than in healthy individuals.
Probiotics were administered for 28 days following colonoscopy
Improvement in microbial recovery was described as 'modest' in healthy individuals
Improvement was described as 'more substantial' in UC patients, specifically for Shannon diversity and evenness metrics
The trial was a single-center, open-label randomized study (ChiCTR2200064456) with participants randomized to probiotics or no probiotics
Results
Probiotic supplementation was associated with enrichment of beneficial short-chain fatty acid-producing taxa and reductions in potentially harmful bacteria.
Beneficial taxa enriched included Faecalibacterium, Blautia, and Lachnospiraceae, all known short-chain fatty acid producers
Reductions were observed in Proteobacteria and Fusobacteria, taxa associated with gut inflammation and dysbiosis
These compositional shifts were observed across both healthy controls and UC patients, with greater effect in UC
Results
Predicted functional pathways related to energy metabolism and nucleotide biosynthesis were transiently suppressed after bowel preparation and showed only partial recovery over time.
Functional pathway analysis was based on predicted metabolic functions derived from 16S rRNA gene sequencing data
Suppression of these pathways was described as 'transient,' occurring after bowel preparation
Recovery of these functional pathways was characterized as 'partial' over the 28-day study period
Both energy metabolism and nucleotide biosynthesis pathways were affected, suggesting broad functional disruption beyond compositional changes
Methods
The study enrolled 79 participants across a single center in an open-label randomized trial design.
Total sample: 79 participants (40 healthy controls, 39 UC patients)
Trial registration: ChiCTR2200064456
Design: single-center, open-label trial with randomization to probiotics or no probiotics for 28 days post-colonoscopy
Microbial analysis was conducted via 16S rRNA gene sequencing on fecal samples at four time points: baseline, day 2, day 14, and day 28
What This Means
This research suggests that the bowel-cleansing preparation used before colonoscopy — which involves drinking large amounts of a solution called polyethylene glycol (PEG) — temporarily disrupts the community of bacteria living in the gut. In healthy people, this disruption was significant but the gut bacteria gradually recovered over 28 days. However, patients with ulcerative colitis (UC), an inflammatory bowel disease, started with less diverse gut bacteria to begin with and took longer to recover after the bowel prep, suggesting their gut microbiome is less resilient.
The study also tested whether taking probiotics (beneficial live bacteria supplements) for 28 days after the colonoscopy could help restore the gut microbiome more effectively. The findings suggest that probiotics provided modest benefits to healthy individuals but more meaningful improvements in UC patients, including increases in bacterial diversity and greater presence of bacteria known to produce short-chain fatty acids — compounds linked to gut health and reduced inflammation. At the same time, probiotics were associated with reductions in bacterial groups like Proteobacteria and Fusobacteria, which are associated with gut dysfunction and disease.
Beyond the bacteria themselves, the study found that the predicted metabolic functions of the gut microbiome — particularly pathways involved in energy use and DNA building blocks — were also temporarily disrupted by bowel prep and only partially recovered over the study period. This research suggests that colonoscopy preparation has broader effects on gut health than previously appreciated, and that probiotic supplementation afterward may be especially beneficial for UC patients who are already dealing with an imbalanced gut microbiome.
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Ma X, Guan J, Liu G, Tian B, Tong C, Chen X. (2026). Probiotics Accelerate Microbiota and Metabolic Pathway Recovery Following Colonoscopy Bowel Preparation in Ulcerative Colitis.. Medical science monitor : international medical journal of experimental and clinical research. https://doi.org/10.12659/MSM.953589