Clin Endosc.  2025 Jan;58(1):25-39. 10.5946/ce.2024.147.

Alteration in gut microbiota after colonoscopy: proposed mechanisms and the role of probiotic interventions

• Jo HH
• Lee MY
• Ha SE
• Yeom DH
• Kim YS

• KMID: 2564015
• DOI: http://doi.org/10.5946/ce.2024.147

Abstract

Colonoscopy, a widely used procedure for diagnosing and treating colonic diseases, induces transient gastrointestinal symptoms and alterations in the gut microbiota. This review comprehensively examines the evidence on alterations in the gut microbiota following colonoscopy and their possible mechanisms. Factors such as rapid colonic evacuation, increased osmolality, and mucus thinning caused by bowel preparation and exposure to oxygen during the procedure contribute to these alterations. Typically, the alterations revert to the baseline within a short time. However, their long-term implications remain unclear, necessitating further investigation. Split-dose bowel preparation and CO2 insufflation during the procedure result in fewer alterations in the gut microbiota. Probiotic administration immediately after colonoscopy shows promise in reducing alterations and gastrointestinal symptoms. However, the widespread use of probiotics remains controversial due to the transient nature of both the symptoms and gut microbial alterations following a colonoscopy. Probiotics may offer greater benefits to individuals with preexisting gastrointestinal symptoms. Thus, probiotic administration may be a viable option for selected patients.

Keyword

Colonoscopy; Dysbiosis; Microbiota; Probiotics

Figure

• 

  Fig. 1. Postulated mechanisms of gut microbiota alterations after colonoscopy. Bowel preparation using osmotic laxatives, such as polyethylene glycol, facilitates the rapid evacuation of colonic contents, including fecal matter and nutrients, while increasing osmolality within the gastrointestinal tract. This process induces significant changes in the gut microbiota. It precipitates mucus depletion and alterations in epithelial cells, leading to modifications in submucosal immune responses, thereby further influencing the gut microbiota composition. Moreover, exposure to oxygen during the colonoscopy exacerbates the disruption of gut microbiota induced by bowel preparation. These combined effects usually result in an increased relative abundance of Proteobacteria. If anaerobic bacteria and fiber decrease in the colonic lumen after colonoscopy, butyrate production may be reduced, causing colonic epithelial cells to consume less oxygen. This may result in increased levels of oxygen released from the epithelial surface, further inducing a shift in the microbial community from obligate to facultative anaerobic bacteria. While individuals with a healthy gut microbiota typically return to the baseline shortly after colonoscopy, individuals with underlying gastrointestinal disorders, such as inflammatory bowel disorders or irritable bowel syndrome with antibiotic exposure, and those with baseline dysbiosis may experience sustained alterations in the gut microbiota. Split-dose bowel preparation and CO2 insufflation during the procedure have been found to be less disruptive to the gut microbiota. Furthermore, administering probiotics immediately after colonoscopy may reduce post-procedural gastrointestinal symptoms and microbiota alterations, particularly in individuals with preexisting gastrointestinal symptoms.

Reference

1. Lynch SV, Pedersen O. The human intestinal microbiome in health and disease. N Engl J Med. 2016; 375:2369–2379.

2. Berg G, Rybakova D, Fischer D, et al. Microbiome definition re-visited: old concepts and new challenges. Microbiome. 2020; 8:103.

3. Wei L, Singh R, Ghoshal UC. Enterochromaffin cells-gut microbiota crosstalk: underpinning the symptoms, pathogenesis, and pharmacotherapy in disorders of gut-brain interaction. J Neurogastroenterol Motil. 2022; 28:357–375.

4. Collatuzzo G, Boffetta P, Radaelli F, et al. Incidence, risk and protective factors of symptoms after colonoscopy. Dig Liver Dis. 2022; 54:1698–1705.

5. Ko CW, Riffle S, Shapiro JA, et al. Incidence of minor complications and time lost from normal activities after screening or surveillance colonoscopy. Gastrointest Endosc. 2007; 65:648–656.

6. Vajravelu RK, Shapiro JM, Ni J, et al. Risk for post-colonoscopy irritable bowel syndrome in patients with and without antibiotic exposure: a retrospective cohort study. Clin Gastroenterol Hepatol. 2022; 20:e1305–e1322.

7. Drago L, Valentina C, Fabio P. Gut microbiota, dysbiosis and colon lavage. Dig Liver Dis. 2019; 51:1209–1213.

8. Cohen SM, Wexner SD, Binderow SR, et al. Prospective, randomized, endoscopic-blinded trial comparing precolonoscopy bowel cleansing methods. Dis Colon Rectum. 1994; 37:689–696.

9. Mai V, Greenwald B, Morris JG, et al. Effect of bowel preparation and colonoscopy on post-procedure intestinal microbiota composition. Gut. 2006; 55:1822–1823.

10. Harrell L, Wang Y, Antonopoulos D, et al. Standard colonic lavage alters the natural state of mucosal-associated microbiota in the human colon. PLoS One. 2012; 7:e32545.

11. Gorkiewicz G, Thallinger GG, Trajanoski S, et al. Alterations in the colonic microbiota in response to osmotic diarrhea. PLoS One. 2013; 8:e55817.

12. O'Brien CL, Allison GE, Grimpen F, et al. Impact of colonoscopy bowel preparation on intestinal microbiota. PLoS One. 2013; 8:e62815.

13. Jalanka J, Salonen A, Salojärvi J, et al. Effects of bowel cleansing on the intestinal microbiota. Gut. 2015; 64:1562–1568.

14. Shobar RM, Velineni S, Keshavarzian A, et al. 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. Clin Transl Gastroenterol. 2016; 7:e143.

15. Drago L, Toscano M, De Grandi R, et al. Persisting changes of intestinal microbiota after bowel lavage and colonoscopy. Eur J Gastroenterol Hepatol. 2016; 28:532–537.

16. Shaw AG, Black N, Rushd A, et al. Assessing the colonic microbiota in children: effects of sample site and bowel preparation. J Pediatr Gastroenterol Nutr. 2017; 64:230–237.

17. Chen HM, Chen CC, Chen CC, et al. Gut microbiome changes in overweight male adults following bowel preparation. BMC Genomics. 2018; 19:904.

18. Kim JH, Choi YJ, Kwon HJ, et al. Effect of gut microbiome on minor complications after a colonoscopy. Intest Res. 2021; 19:341–348.

19. Batista L, Robles V, Manichanh C, et al. Colonic bacterial diversity and dysbiosis in active microscopic colitis as compared to chronic diarrhoea and healthy controls: effect of polyethylene glycol after bowel lavage for colonoscopy. BMC Gastroenterol. 2022; 22:320.

20. Nalluri-Butz H, Bobel MC, Nugent J, et al. A pilot study demonstrating the impact of surgical bowel preparation on intestinal microbiota composition following colon and rectal surgery. Sci Rep. 2022; 12:10559.

21. Powles ST, Gallagher KI, Chong LWL, et al. Effects of bowel preparation on intestinal bacterial associated urine and faecal metabolites and the associated faecal microbiome. BMC Gastroenterol. 2022; 22:240.

22. Zou Y, Zeng S, Chen M, et al. Gut microbiota in children with split-dose bowel preparations revealed by metagenomics. Front Cell Infect Microbiol. 2023; 13:1202007.

23. Bacsur P, Rutka M, Asbóth A, et al. Effects of bowel cleansing on the composition of the gut microbiota in inflammatory bowel disease patients and healthy controls. Therap Adv Gastroenterol. 2023; 16:17562848231174298.

24. Human Microbiome Project Consortium. Structure, function and diversity of the healthy human microbiome. Nature. 2012; 486:207–214.

25. Shin NR, Whon TW, Bae JW. Proteobacteria: microbial signature of dysbiosis in gut microbiota. Trends Biotechnol. 2015; 33:496–503.

26. Litvak Y, Byndloss MX, Bäumler AJ. Colonocyte metabolism shapes the gut microbiota. Science. 2018; 362:eaat9076.

27. Toro Monjaraz EM, Ignorosa Arellano KR, Loredo Mayer A, et al. Gut microbiota in mexican children with acute diarrhea: an observational study. Pediatr Infect Dis J. 2021; 40:704–709.

28. Dinleyici EC, Martínez-Martínez D, Kara A, et al. Time series analysis of the microbiota of children suffering from acute infectious diarrhea and their recovery after treatment. Front Microbiol. 2018; 9:1230.

29. Pop M, Walker AW, Paulson J, et al. Diarrhea in young children from low-income countries leads to large-scale alterations in intestinal microbiota composition. Genome Biol. 2014; 15:R76.

30. Chen SY, Tsai CN, Lee YS, et al. Intestinal microbiome in children with severe and complicated acute viral gastroenteritis. Sci Rep. 2017; 7:46130.

31. Li YD, Liu BN, Zhao SH, et al. Changes in gut microbiota composition and diversity associated with post-cholecystectomy diarrhea. World J Gastroenterol. 2021; 27:391–403.

32. Min YW, Rezaie A, Pimentel M. Bile acid and gut microbiota in irritable bowel syndrome. J Neurogastroenterol Motil. 2022; 28:549–561.

33. Kim YS, Choi SC. The long and winding road to the best clinical research and personalized therapy with probiotics: do not forget host physiology. J Neurogastroenterol Motil. 2023; 29:129–131.

34. Tropini C, Moss EL, Merrill BD, et al. Transient osmotic perturbation causes long-term alteration to the gut microbiota. Cell. 2018; 173:1742–1754.

35. Pockros PJ, Foroozan P. Golytely lavage versus a standard colonoscopy preparation. Effect on normal colonic mucosal histology. Gastroenterology. 1985; 88:545–548.

36. Rejchrt S, Bures J, Siroký M, et al. A prospective, observational study of colonic mucosal abnormalities associated with orally administered sodium phosphate for colon cleansing before colonoscopy. Gastrointest Endosc. 2004; 59:651–654.

37. Bucher P, Gervaz P, Egger JF, et al. Morphologic alterations associated with mechanical bowel preparation before elective colorectal surgery: a randomized trial. Dis Colon Rectum. 2006; 49:109–112.

38. Jiang W, Wu J, Zhu S, et al. The role of short chain fatty acids in irritable bowel syndrome. J Neurogastroenterol Motil. 2022; 28:540–548.

39. Yang X, Xiu WB, Wang JX, et al. CO2 is beneficial to gut microbiota homeostasis during colonoscopy: randomized controlled trial. J Clin Med. 2022; 11:5281.

40. Menees S, Higgins P, Korsnes S, et al. Does colonoscopy cause increased ulcerative colitis symptoms? Inflamm Bowel Dis. 2007; 13:12–18.

41. Otake-Kasamoto Y, Shinzaki S, Hiyama S, et al. Carbon dioxide insufflation reduces the relapse of ulcerative colitis after colonoscopy: a randomized controlled trial. PLoS One. 2023; 18:e0290329.

42. Imai A, Kato M, Ono S, et al. Efficacy of carbon dioxide-insufflating colonoscopy in patients with irritable bowel syndrome: a randomized double-blind study. J Gastroenterol Hepatol. 2012; 27:1623–1628.

43. Lee H, Kim YH, Kim JH, et al. A feasibility study of probiotics pretreatment as a bowel preparation for colonoscopy in constipated patients. Dig Dis Sci. 2010; 55:2344–2351.

44. D'Souza B, Slack T, Wong SW, et al. Randomized controlled trial of probiotics after colonoscopy. ANZ J Surg. 2017; 87:E65–E69.

45. Mullaney TG, Lam D, Kluger R, et al. Randomized controlled trial of probiotic use for post-colonoscopy symptoms. ANZ J Surg. 2019; 89:234–238.

46. Deng X, Tian H, Yang R, et al. Oral probiotics alleviate intestinal dysbacteriosis for people receiving bowel preparation. Front Med (Lausanne). 2020; 7:73.

47. Liu H, Zhang K, Liu P, et al. Improvement effect of Bifidobacterium animalis subsp. lactis MH-02 in patients receiving resection of colorectal polyps: a randomized, double-blind, placebo-controlled trial. Front Immunol. 2022; 13:940500.

48. Labenz J, Borkenstein DP, Heil FJ, et al. Application of a multispecies probiotic reduces gastro-intestinal discomfort and induces microbial changes after colonoscopy. Front Oncol. 2022; 12:1078315.

49. Son D, Choi YJ, Son MY, et al. Benefits of probiotic pretreatment on the gut microbiota and minor complications after bowel preparation for colonoscopy: a randomized double-blind, placebo-controlled pilot trial. Nutrients. 2023; 15:1141.

50. Aragona SE, Spada C, DE Luca L, et al. Probiotics for managing patients after bowel preparation for colonoscopy: an interventional, double-arm, open, randomized, multi-center, and national study (COLONSTUDY). Minerva Gastroenterol (Torino). 2024; 70:187–196.

51. Tremblay A, Auger J, Alyousif Z, et al. Total transit time and probiotic persistence in healthy adults: a pilot study. J Neurogastroenterol Motil. 2023; 29:218–228.

52. Quigley EM. Clinical trials of probiotics in patients with irritable bowel syndrome: some points to consider. J Neurogastroenterol Motil. 2022; 28:204–211.

53. Khodadoostan M, Shavakhi A, Sherafat Z, et al. Effect of probiotic administration immediately and 1 month after colonoscopy in diarrhea-predominant irritable bowel syndrome patients. Adv Biomed Res. 2018; 7:94.

54. Mai V, Stine OC. Bowel preparation for colonoscopy: relevant for the gut's microbiota? Gut. 2015; 64:1504–1505.