The People's Perspective on Medicine

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?
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 or 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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Very interesting. If people have so many problems afterward, is it worth having one done?

It is definitely worthwhile, at least in the big picture. When colonoscopy rates are higher, colon cancer rates are lower.

I had a colonoscopy about 4 weeks ago. I’ve had loose stools ever since. I’m here on the internet looking for answers. I’m going to take probiotics regularly and eat yogurt, and hopefully that’ll solve the problem. Also I’m going to check out fermented food. I’m 72, and I’m supposed to get a colonoscopy every 5 years because my mother had colon cancer. I have not had a post-colonoscopy problem with previous colonoscopies. I guess as a person gets older they don’t bounce back as quickly.

I am your age. I had no problems with the colonoscopy prep 10 yrs ago but this time the prep was much stronger and more “violent.” 2 polyps were found so I have to retest in 5 yrs. I’m having the same issues 2 months after this colonoscopy as you are.

Today I started taking probiotics and buying lots of yogurt. I will cross my fingers this works for both of us💕

Instead of a colonoscopy, why not ask for a fecal blood test (Cologard). Fast, easy, and requires no prep. Doctors go straight for the colonoscopy and never mention alternatives.

The effect of multi-strain probiotics is not always beneficial. See:

I would highly recommend the Heidelberg Test. Seems the “main stream” medical community do not want to do this test as it doesn’t make the money. However, the Heidelberg test is basically a small capsule that is swallowed and then monitored, measuring the pH content in the stomach. Afterward, the doctor adjusts the pH level with digestive enzymes as needed. This test has been around since the 1960s and would help so many people if the “main stream” medical community would use.

You ‘don’t learn to live’ with constipation/diarrhea; you correct it! My daughter was told the same ‘lie’ (which basically says they don’t want to deal with you). The gastroenterologist she was seeing told her she needed her gall bladder removed. Even after surgery she still had problems, and he told her she’d have to live with it!! She found another doctor who did the Heidelberg test, found her stomach pH levels were out-of-whack; that doctor corrected with digestive enzymes (at dose levels that would help her), and she has not had any problems since. A simple procedure, yet the medical community acts as if they’ve never heard of this.

My sister and I never had hemorrhoids until after we had colonoscopies. When I asked my doctor about this, he said that colonoscopies do not cause hemorrhoids. I’m not so sure. I wonder if anyone else has had this happen.

Whether after a colonoscopy or after a stomach bug, bad gut bacteria return first. We’ve had luck with a 2-step process. First, start with a probiotic supplement, not yogurt. A capsule contains significantly more good bacteria. We use Culturelle products, which contain Lactobacillus GG, the most researched probiotic in the world. Step #2, at the same time boost your immunity quickly with a zinc supplement. This can hold bad bacteria at bay while good bacteria multiply. We adopted the latter after reading that international health organizations in third world countries are fighting infant diarrhea with IV zinc, as the bad bacteria in third world water has become resistant to antibiotics. They are achieving quick and lasting remission with the process. We use Coldeeze lozenges (which contain zinc), as they seem to be absorbed well vs. a clunky pill with hardening agents in them. Take 1/2 a lozenge at lunch and 1/2 at dinner (with meals) over 4-5 days and then stop. On day #1, consider starting with a whole zinc lozenge. If no improvement, see your GI person ASAP. FYI: I have no financial interest in either of the two products noted above.

Because of polyp issues I get to have colonoscopies more often than I like (hate the prep). But after the procedure, and before I leave the facility, I eat the yogurt I brought with me. I want to get my gut back to normal as quickly as I can, and so far this has helped.

I suffered with Ulcerative colitis for about 10 years and had yearly colonoscopies. Each time polyps were detected; they removed partial polyps to check for cancerous cells but they were clear. The doctor said that didn’t mean there was no cancer in the ones left behind. The powders they gave to clean the system were very harsh, and I had many side effects. Then I read that the powders contain Aspartame. I refused to take them, as I will not allow that poison into my body. After that I had different powders, which I took over 3 days with no side effects. I eventually had 15 polyps totally removed and have not had colitis since .

Doctors know how to do fecal implants from someone with a healthy gut to someone who has a problem. How about taking a sample prior to the prep and then putting it back into the same patient as a standard part of the colonoscopy? Some enterprising person or company could develop a standard kit to make it easy and relatively inexpensive.

My previous comment was used above, and I’m happy to report that I overcame the bouts of diarrhea I had but it took a good month. Next time I have a colonoscopy (if there is one), I’ll ask if there’s something other than polyethylene glycol that I can take to prepare. As I get older, it gets harder to deal with such nasty aftereffects.

I had a colonoscopy in the spring 2014 with normal results. Shortly after I changed my diet to lower my cholesterol eating oatmeal daily. While on the diet, I was prescribed antibiotics for an infection. By fall, I noticed unpleasant gut changes particularly bloating and gas. By Thanksgiving, I was having regular diarrhea and losing weight. All tests came back normal. With a shrug the gastro NP diagnosed IBS and told me to learn to live with it. A search of the internet (because where else could I go?), suggested that all 3–colonoscopy prep, high fiber diet, and antibiotics contributed to my unhealthy gut. Unfortunately, all I can do is avoid foods that cause diarrhea–most raw fruits, seeds, high fiber grains and coffee–all foods that otherwise I would be eating for good health. I also take probiotics daily. I would like to find a doctor who could help me heal my gut.

Hi Linda,

I just watched a summit on fasting. Two of the doctors talked about studies that showed that an extended water fast resets the microbiome and immune system. Maybe look into that, and see what you think? It gives your gut time to rest and repair. During the fast both good and bad bacteria are reduced, and afterwards the good comes back at a higher percentage. Cutting out processed foods and grains and adding fermented foods might help too, and prebiotics to feed the probiotics. Hope you find a doctor you like. Functional medicine doctors or naturopaths might be a good place to start.

I had a colonoscopy – all was well. After I returned home and a couple of days later I had extreme diarrhea – gastroenterologist took a sample and turned out I was positive for C. Difficile. Put on antibiotics and became steadily worse so I stopped taking them and started taking Probiotics (capsules) 3 times a day. Gradually the flora in my intestines returned to normal. It took a year for me to regain my strength and my physician informed me C.Difficle is life threatening.

On a Friday in January, 2010 I had a colonoscopy, everything was fine. Went to work that Monday and couldn’t keep anything down. Went home and called my Gastroenterologist and he said I could go to the ER to be checked out. I did. I had an appendectomy that afternoon. I had no prior problems. He said he had never heard of anyone needing an appendectomy post colonoscopy. Guess I’m special!

After a routine colonoscopy, I experienced very bad cramps, stomach spasms, weight loss of 14 lbs, sleeplessness, fatigue, gas, eczema and seldom left the house. All symptoms I have never had before. My dr said it was not the result of the procedure.

It took 6 to 7 months to feel better and my new gastroenterologist told me the risk was small but it could happen again after my next colonoscopy (in 5 years). I thought colonoscopies were safe.

My Grandfather had colon cancer so that made me a candidate for having colonoscopies every 4-5 years for the past 20 years. Every colonoscopy, multiple polyps (some are precancerous) are removed. I am now 72 yoa.
After the last two procedures I came down with pneumonia within 4 days.
I have moderate COPD which makes me vulnerable to respiratory infections. But is my colon bacteria vital to the health of my immune system? This gut protection would be lost during the clean out prep perhaps? Or am I catching pneumonia in the colonoscopy facility? I had respiratory infection every 8 weeks for the next year after the last colonoscopy which may indicate that my immune system was
not in good shape. I take probiotics erratically–must improve.

Autologous fecal transplant post colonoscopy would restore your microbiome.

I wonder if the instruments used in colonoscopy might also be to blame. Sites that perform colonoscopy do many per day, with perhaps not enough sterilization time for the instruments between patients. Could the instruments themselves introduce bacteria from other patients that then upsets the flora balance?

I don’t understand why a procedure that is risky on every level has become the “Gold Standard”. The cleanse that can ruin your gut microbiome, the anesthetic that can adversely affect your brain & memory, the possibility of colon perforation, and the difficulty of sterilizing the flexible instrument. Why put people through all this when there is a non-invasive test you can perform in your home: Cologuard? There are also the non-invasive FOBT tests. If those tests have positive results, a colonoscopy can be scheduled. Sometimes I wonder if the “gold standard” refers to the amazing profits to be made on them, all the buildings being erected solely for gastrointestinal diagnostic tests.

Colonoscopy equipment CAN NOT be sterilized, it can only be disinfected. Human debris is always left behind, placing one at risk for I fevtion.

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