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Will Colonoscopy Change Your Gut Flora?

Colonoscopy is a life-saving procedure to detect and prevent colon cancer. Does the stringent colon cleansing process result in changes to the gut flora?
Will Colonoscopy Change Your Gut Flora?
Doctor gastroenterologist with probe to perform gastroscopy and colonoscopy

Colonoscopy, in which the gastroenterologist uses a scope to examine the colon for signs of polyps or other growths, can save lives. (Learn more here.) A study in The New England Journal of Medicine (Feb. 23, 2012) demonstrated pretty conclusively that the effort is worthwhile. The National Polyp Study involved seven clinical research centers in the U.S. Patients who had a colonoscopy between 1980 and 1990 were included in the long-term follow-up. Those who had their polyps removed were only half as likely as people in the general population to die of colon cancer over the next 20 years. The investigators conclude that the polyps removed during colonoscopy include some that would otherwise have become cancerous. This procedure is generally considered to involve short-term unpleasantness, but some individuals may end up with changes in their gut flora (the bacteria that inhabit the colon) that may be long-lasting.

For people at normal risk, colonoscopy should be done at age 50 and every 10 years thereafter. Higher-risk individuals may need more frequent colonoscopies and may need to start at a younger age. The preparation for this procedure entails a really thorough cleansing of the colon by drinking a highly laxative solution of polyethylene glycol. Could this cleaning be too strong? Might it affect the microbial ecology of the digestive tract?

Can Colonoscopy Affect Gut Flora?

Q. My 60-year-old husband had his colonoscopy two years ago. All was normal.

Shortly thereafter he started experiencing many bouts of constipation and occasional loose stools. He rarely has a normal evacuation.

The gastroenterologist performed another colonoscopy this year and found nothing abnormal. My husband has had a breath test to rule out an infection with H. pylori. It was normal. He’s been checked for allergies (none) and has lost weight. Crohn’s and celiac disease have also been ruled out.

We believe his gut flora has been compromised and are at a loss as to what can be done to remedy his situation. Can you suggest a course of action for a six-foot, one hundred seventy-five-pound man who takes no medication and is otherwise healthy?

Evidence That Colonoscopy Can Change the Microbiome:

A. There is some evidence to suggest that the cleansing process in preparation for a colonoscopy can disrupt the balance of intestinal microbes (Drago et al, European Journal of Gastroenterology & Hepatology, May, 2016). Species in the family that includes Lactobacillus genera appear especially depleted.

Your husband’s physician may wish to order a stool analysis to detect whether there is microbial imbalance. Organizations such as uBiome.com or Verisana.com do this type of analysis. If there is alteration of the microbial ecology, probiotics may help restore the natural balance (Khodadoostan et al, Advanced Biomedical Research, June 25, 2018).

You are not the first person to ask about this possible change in gut flora. Another reader wrote:

Q. I will be undergoing a colonoscopy next month. It seems like cleaning out the colon gets rid of lots of beneficial bacteria. Should I take probiotics afterwards?

A. Your question is insightful. The more we learn about the microbes that live in us and on us, the more important they appear. It seems logical that washing them out might have consequences. Indeed, one recent study showed a change in the balance of bacteria after the polyethylene glycol prep (European Journal of Gastroenterology & Hepatology, May, 2016). So far, however, there is not much research to show whether these shifts in the types of bacteria found in the colon have any implications for our health.

Should You Take Probiotics?

The concept of replacing bacteria with probiotic supplements is intriguing, but again, we could find very little research to answer it. Since the family of Lactobacillus bacteria are depleted, according to the study we cite above, it seems reasonable to try to replace them. Many probiotic supplements do offer a few strains of Lactobacillus.

One randomized controlled trial found that people who took probiotics after colonoscopy had less discomfort than those on placebo (ANZ Journal of Surgery, online, July 17, 2015). So far as we know, the risk is low, so you might want to try it.

Deloris also had diarrhea following a colonoscopy:

“I just had my second colonoscopy four weeks ago. While I recovered from the first one quickly and easily, the second one has caused diarrhea that I can’t seem to overcome. I’ve been taking several kinds of probiotic supplements and eating all the fermented foods I can think of, but the diarrhea keeps returning and then I’m back on Imodium for a day or two of relief. I’m glad I don’t have to have another colonoscopy for another 10 years, but I may put it off for longer.”

Karl reported his experience with rectal bleeding:

“About 12 years ago, at age 70, I experienced an episode of minor rectal bleeding which was similar to a brief episode 2 years prior in summer as a result of over-consumption of ice cream and cheese. On my internist’s advice, I scheduled a colonoscopy for 4 weeks later. However, the bleeding stopped after about a week.

“About 4-5 days AFTER the colonoscopy – which was totally unremarkable – I began to experience heavy rectal bleeding and I returned to the colon specialist. He prescribed sulfasalazine, which had no effect. His response was that I would simply “have to learn to live with it” which meant going to the bathroom every 50-60 minutes 24/7. Over the net several months, I became anemic, lost weight, and was constantly fatigued.

“I searched the Internet and learned that depletion of the intestinal flora was a common side effect. I stopped the medication and began to consume yogurt, sour kraut, pickle juice, lactobacillus and any other probiotics I could find. In about 3 weeks, everything was back to normal. I have not experienced any recurrence and I no longer eat ice cream or excessive amounts of cheese.”

We hope that future research will demonstrate the type of probiotics and the appropriate doses to help restore the gut flora to a healthy balance. In the meantime, indulging in the fermented foods you enjoy, whether that means kombucha, yogurt, sauerkraut or kimchi, makes sense as part of your post-colonoscopy plan.

Learn More:

You may be interested in this New York Magazine profile of microbiota researchers Justin and Erica Sonnenberg. This article from The New York Times details the connections between gut flora and brain function. You might also wish to listen to our interview on fecal (stool) transplants as a means of overcoming C. diff infections that cause severe, chronic diarrhea. It is Show 935: Stool Transplants Can Save Lives.

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About the Author
Terry Graedon, PhD, is a medical anthropologist and co-host of The People’s Pharmacy radio show, co-author of The People’s Pharmacy syndicated newspaper columns and numerous books, and co-founder of The People’s Pharmacy website. Terry taught in the Duke University School of Nursing and was an adjunct assistant professor in the Department of Anthropology. She is a Fellow of the Society of Applied Anthropology. Terry is one of the country's leading authorities on the science behind folk remedies. .
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