Will Colonoscopy Change Your Gut Flora?

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.) The value of this procedure has been established for more than a decade. A study in The New England Journal of Medicine (Feb. 23, 2012) demonstrated it conclusively. 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, mostly in the preparation. However, 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 (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 might help restore the natural balance ( Advanced Biomedical Research, June 25, 2018).

You are not the only person to ask about this possible change in gut flora. Other readers have also expressed concern.

Could Probiotics Restore the Gut Flora?

Q. I just completed a colonoscopy. I was relieved that the gastroenterologist gave me a good bill of health, but I was disappointed that he said nothing about post-procedure recovery.

When you use the prep you probably disrupt the microbiome of your digestive tract. I expected some suggestion about probiotics. All I got was crickets.

When you flush out most of the beneficial bacteria in your colon, isn’t there some way to help restore a good balance? I am still suffering from some abdominal discomfort.

A. You should let your doctor know about any symptoms you are experiencing. Sadly, though, there is not much research bearing on the topic of post-colonoscopy probiotic use. An article in the journal Medical Sciences (June 9, 2025) asked a similar question: “Is It Advisable to Use Probiotics Routinely After a Colonoscopy? A Rapid Comprehensive Review of the Evidence.” The investigators wrote that more research is needed to answer their question.

They concluded:

“Therefore, we are still far from being able to suggest a routine probiotics treatment after colonoscopy.”

One consideration is that changes in the gut flora following a colonoscopy don’t always persist more than a few weeks or months (Scientific Reports, March 1, 2019). But a review of the research found that probiotics might be helpful in treating post-colonoscopy symptoms, especially for those who had digestive difficulties before the procedure (Clinical Endoscopy, Jan. 2025). The investigators suggest that we need more research on the topic of whether and when people might benefit from probiotics following a colonoscopy.

Their conclusion was:

“Therefore, probiotic administration immediately after a colonoscopy may be a viable option for certain patients, particularly those predisposed to persistent gastrointestinal disturbances.”

Will Probiotics Restore Gut Flora?

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. 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, it seems reasonable to try to replace them. Many probiotic supplements do offer a few strains of Lactobacillus. This is, however, just one type of the many thousands of varieties of microbes that normally inhabit the gut. Although colonoscopy preparation requires a low-fiber diet, returning to a high-fiber diet soon after the procedure might also be helpful in re-establishing the normal microbiome.

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 next 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. Our interview with them is Show 1156: How the Microbiota in the Good Gut Takes Care of You. 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.