Bowel prep and the procedure itself can disrupt your microbiome—here’s how to support recovery with diet and probiotics.
It’s common after a colonoscopy to feel symptoms like gas, bloating, stomach pain, and cramping. For some people, the symptoms can go on for weeks and cause permanent changes to the gut microbiota.
About 40 percent of patients may experience these lingering problems, which tend to be more common in women, patients who have a longer procedure time, and those with pre-existing diseases that already disrupt the microbiota, such as inflammatory bowel disease (IBD).
Changes in the gut microbiota—bacteria, viruses, fungi, and other microorganisms that live mainly in the large intestine—drive general gastrointestinal (GI) discomfort. Colonoscopies can cause negative microbial population shifts, called dysbiosis, though the effects are short-lived for most people.
Colonoscopy timing and microbial recovery efforts, such as eating a healthy diet and taking probiotics, may be key to avoiding or shortening this period of GI distress.
Why Colonoscopies Deplete Microbes
Laxatives, rapid defecation, depletion of the colon’s mucosal layer, and exposure to oxygen during the procedure could all drive changes in a person’s microbiota, according to a review in Clinical Endoscopy.
Diarrhea is associated with dysbiosis secondary to a change in the mucus thickness of the colon. Although thinning of the mucus can offer gastroenterologists—or physicians who diagnose and treat disorders of the gastrointestinal tract—a better view of polyps and problem areas during a colonoscopy, authors of the review noted a thinner mucus results in a decrease of the beneficial bacteria Akkermansia.
Bowel prep can cause a significant alteration of gut microbiota, at least initially.
The review noted specific microbial changes associated with colonoscopies, including:
- Reduction of overall microbial diversity associated with better health
- Decreased Firmicutes and Bacteroidetes normally dominant in the gut
- Having more Firmicutes and less Bacteroidetes, which is also associated with obesity and other health issues
- Increased Proteobacteria, which includes more bacteria that can become pathogenic or disease-causing when present in large numbers
“Most studies have reported that the gut microbiota composition returns to the baseline within two to six weeks after colonoscopy, suggesting the resilience of the gut microbiota,” the authors wrote.
