Colonoscopy Worry: Missing Microbiome? - Ask Dr. Weil (2023)

I have to prepare for a colonoscopy by taking cleansing agents to clean out my colon. I am worried this will affect the populations of healthy bacteria in my digestive tract. What should I do to restore the bacteria wiped out by the cleansing process?

Andrew Weil, M.D. |November 26, 2015

Colonoscopy Worry: Missing Microbiome? - Ask Dr. Weil (1)

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Preparing for a colonoscopy involves both fasting and taking strong laxatives to clean out your GI tract. You’re correct in assuming that this process will remove much of the gut microbiota – the approximately 100 trillion microbes (bacteria, viruses and fungi) that live within us. This is a valid concern that is seldom discussed. We have begun to recognize that the microbiome is an important influence on our health, so it should be a priority to re-establish it after a colonoscopy.

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I discussed your question with Justin Sonnenberg, Ph.D., assistant professor of microbiology and immunology at Stanford University and one of the world’s leading microbiome researchers. He notes that recovery from removing part of the microbiome in preparation for colonoscopy and the factors that can improve its recovery have not been studied in detail. We know more about recovery after antibiotic treatment, Dr. Sonnenberg says. “We know that probiotics, either found in fermented foods like yogurt, kefir, or kimchi, or in supplement form, can serve as ‘placeholders’ after microbiota disruption and can reduce the incidence and duration of antibiotic-associated diarrhea. We also know that diverse sources of dietary fiber found in vegetables, legumes, whole grains, and nuts can help foster the re-growth of beneficial community members,” Dr. Sonnenberg tells me.

Several studies have shown that daily consumption of fermented foods (or probiotic bacteria derived from fermented foods) can have a variety of beneficial health effects, including protection from colds and flu as well as quicker recovery from antibiotic-associated diarrhea. Dr. Sonnenberg says that while it is difficult to know which fermented food is best for you and your microbiota, it is important to use trial and error to find ones that agree with your digestive system and affect bowel habits in a desired way.

If you want to know more about the care and feeding of your microbiome, I recommend the book Dr. Sonnenburg and his wife and fellow researcher Erica Sonnenburg Ph.D., have written, The Good Gut: Taking Control of Your Weight, Your Mood, and Your Long Term Health, published in April 2015. The book includes recipes and a menu plan to help nourish your microbiota plus safe alternatives to antibiotics and sound dietary and lifestyle advice.

(Video) Microbiome Talk with Dr. Sabine Hazan

Andrew Weil, M.D.


How do I fix my microbiome after a colonoscopy? ›

A colon cleanse can wipe out the healthy and the unhealthy microbes, so you may want to consider taking probiotics after a colonoscopy. Probiotics can help rebuild colonies of beneficial gut flora to help your intestines reestablish the balance of your digestive system (Source: Livestrong).

Does a colonoscopy wipe out your microbiome? ›

A. Preparing for a colonoscopy requires clearing the bowel with fasting, a laxative drink and, in some cases, an enema. While such preparation can alter the microbiome, the rich array of microbes that are present in the gut, research suggests that the microbiome bounces back in about two to four weeks.

Are gut microbiome tests worth it? ›

Taking care of the microbes in the gut that take care of us is certainly a good idea, but experts caution that at-home gut-health tests won't provide anything more insightful than advice to eat more vegetables, exercise, and reduce stress. “The bottom line: I do not recommend home gut-health tests,” says Lacy.

Does a colonoscopy get rid of good gut bacteria? ›

Cleansing the bowel in preparation for a colonoscopy may deplete the digestive tract of many types of beneficial bacteria. Probiotics might restore them.

How long does it take to repair microbiome? ›

Building a healthy microbiome can take up to 6 months if the correct healthy habits are adopted (diet, exercise, sleep and stress management - and also supplements if needed) however it really is a lifelong journey because you need to continue these habits to maintain a healthy microbiome.

What is the fastest way to restore gut microbiome? ›

Here are 9 science-based ways to improve your gut bacteria.
  1. Eat a diverse range of foods. ...
  2. Eat lots of vegetables, legumes, beans, and fruit. ...
  3. Eat fermented foods. ...
  4. Eat prebiotic foods. ...
  5. If you can, breastfeed for at least 6 months. ...
  6. Eat whole grains. ...
  7. Eat a plant-based diet. ...
  8. Eat foods rich in polyphenols.

What happens if your microbiome is off? ›

When your body doesn't have enough good bacteria, bad bacteria can thrive. The following can be signs of a gut bacteria imbalance: Autoimmune problems, such as thyroid issues, rheumatoid arthritis and type 1 diabetes. Digestive issues, such as irritable bowel syndrome, constipation, diarrhea, heartburn or bloating.

What happens if you lose your microbiome? ›

Your microbiome helps keep your skin healthy. An imbalanced microbiome can lead to skin problems. For instance, too many pimple-causing bacteria can lead to acne. The allergic skin condition eczema is linked to another type of bacteria.

How do you restore good bacteria in the colon? ›

How to Restore Your Gut Bacteria Naturally
  1. Take probiotics.
  2. Eat fermented foods.
  3. Increase your vegetable and fruit intake.
  4. Cut out sugar.
  5. Take time to relax and reduce stress levels.
  6. Only take medication – especially antibiotics – if necessary.
  7. Have an adequate amount of sleep.
  8. Take exercise regularly.
Mar 1, 2022

How reliable are microbiome tests? ›

The FDA has not approved home microbiome tests, meaning that it has not tested them for accuracy or safety. Microbiome tests cannot diagnose health conditions. People should only purchase these products if they are interested in finding out which bacteria are in their stool.

Are stool microbiome tests accurate? ›

Scientists have not yet defined a healthy or normal gut microbiome that can reliably predict whether a person will develop a particular disease. Relying on stool samples for studying the gut microbiome is inaccurate as the microbiome in stool does not faithfully reflect the microbiome at the intestinal mucosa.

Does insurance cover microbiome testing? ›

If you believe you have a medical need for microbiome testing, please talk to your healthcare provider about microbiome testing for medical purposes. Microbiome tests may be covered by insurance, depending on your insurance policy, and indication for testing.

Does a colonoscopy damage your gut biome? ›

Recently, several studies have shown that bowel preparation for colonoscopy could change the fecal microbial diversity and composition, and these effects could last up to 1 month [13-15]. Bowel preparation also affects the change of gut metabolome but this is recovered within 14 days [16].

Should you be concerned about bacterial growth in the colon? ›

All of these bacteria exist in the colon normally and generally aren't harmful there, says DePaolo. The problem seems to occur when the bacteria change or expand, releasing toxins into the body that cause inflammation and damage DNA in the colon. They may combine forces and contribute to tumor growth.

Do probiotics heal your colon? ›

Probiotics can help to restore gut microbial balance and improve gut health. Probiotics do this by inhibiting the growth of harmful bacteria, producing antimicrobial substances, stimulating the immune system, and improving intestinal motility.

Can microbiome be restored? ›

However, the gut microbiome is very adaptable and responds to positive lifestyle choices. So if you eat a diet with lots of fiber-rich whole foods (something scientists like to call prebiotics) and add some probiotic foods or supplements, you can speed up your gut biome restoration.

How do I reset my microbiome? ›

Gut resets aim to restore the balance of the microbiome by:
  1. removing foods that feed harmful bacteria and cause inflammation.
  2. introducing plenty of prebiotic foods, which feed beneficial bacteria.
  3. encouraging healthful practices, such as getting enough sleep and exercise and staying hydrated.
Oct 26, 2020

Can you live without your microbiome? ›

Humans have evolved to live with microbes for millions of years. During this time, microbes have learned to play very important roles in the human body. In fact, without the gut microbiome, it would be very difficult to survive.

What foods repair gut microbiome? ›

Probiotic foods contain beneficial live microbiota that may further alter one's microbiome. These include fermented foods like kefir, yogurt with live active cultures, pickled vegetables, tempeh, kombucha tea, kimchi, miso, and sauerkraut.

What destroys the gut microbiome? ›

Diet and lifestyle factors, including poor sleep quality, alcohol consumption and inactivity, can harm your gut bacteria. Alternatively, living a healthy lifestyle characterized by regular physical activity, low stress and a variety of whole foods is the best way to ensure a healthy gut flora.

What diseases are microbiome related? ›

Nowadays, gut microbiota deviations are linked with many diseases including obesity, type 2 diabetes, hepatic steatosis, intestinal bowel diseases (IBDs) and several types of cancer. Thus, suggesting that various pathways involved in immunity, energy, lipid and glucose metabolism are affected.

Can stress change your microbiome? ›

Exposure to stress impacts colonic motor activity, which can alter gut microbiota profiles, including lower numbers of potentially beneficial Lactobacillus (Lutgendorff et al., 2008). Thus, stress may interact with diet to contribute to IBS.

Can you replace microbiome? ›

Can you reset your microbiome? Yes, it is possible to restore your gut to a healthy state after taking antibiotics. A healthy diet and certain supplements can help re-establish healthy gut flora and prevent the common side effects of antibiotic use such as antibiotic-associated diarrhea.

How can I improve my gut microbiome in a day? ›

Here are some tips to get your gut going:
  1. Increase your fibre intake. ...
  2. Eat as many types of fruit and veg as possible, and try to eat seasonally. ...
  3. Pick high-fibre vegetables. ...
  4. Choose food and drinks with high levels of polyphenols. ...
  5. Avoid snacking. ...
  6. Eat plenty of fermented foods containing live microbes. ...
  7. Drink a bit of alcohol.
Feb 10, 2020

How long does it take for probiotics to restore good bacteria? ›

The short answer: It takes most people 2 to 3 weeks to feel significant benefits when they start taking probiotics. That's because probiotics need time to accomplish their three key goals: increase your good bacteria count, decrease your bad bacteria count, and reduce inflammation.

Which microbiome test is best? ›

The best microbiome tests of 2023:
  • Best overall. ViomeGo to review. $249 on Viome. $249 on Viome.
  • Best follow-up care. BiohmGo to review. From $130 on Amazon. From $130 on Amazon.
  • Best subscription. FloréGo to review. $169 on Floré $169 on Floré
  • Best budget. OmbreGo to review. $99.99 on Ombre. $99.99 on Ombre.
6 days ago

What does a gut microbiome test tell you? ›

Gut microbiome tests can tell you what types of bacteria, archaea, viruses, and fungi are in your gut and how they might be affecting your health. In most cases, you can do the test from the comfort of your home by simply collecting a stool sample and sending it to a specialized lab.

Is your microbiome in your colon? ›

Ninety-five percent of the body's microbiota reside in the gut, primarily in the colon where microbial cells outnumber the total cells in the human body (4). Using available sequencing methods, it is now possible to determine the presence of healthy or disarrayed microbiomes.

What is the most accurate stool test? ›

Fecal immunochemical test (FIT)

Studies show that FITs can be nearly 80% accurate in detecting colorectal cancer.

Can you use feces to cure infections in the gut microbiome? ›

Fecal transplantation is a procedure to collect feces, also called stool or poop, from a healthy donor and introduce them into a patient's gastrointestinal tract. The procedure can control an infection called Clostridium difficile, or C. diff, by adding healthy bacteria into the recipient's intestines.

How much does a gut microbiome test cost? ›

How do our top recommended tests compare?
Current price$139$129
Approx wait time after shipping back2-3 weeks4-6 weeks
Tests for bacteriaYesYes
Tests for fungiYesYes
5 more rows
Jan 4, 2023

How do I prepare for a microbiome test? ›

How to prepare for the test? You don't have to change your diet. Keep eating the way you normally do — this will allow us to get an accurate picture of your “normal” microbiome and provide recommendations on how to improve or maintain it.

Do the benefits of a colonoscopy outweigh the risks? ›

While there are risks associated with even the most routine medical procedures, the benefits of a colonoscopy significantly outweigh the associated risks for people ages 45 to 75.

How long does it take to restore gut biome? ›

For most people, the composition of the gut microbiome returns almost completely to baseline in one to two months. But for a few, things may not go back to the way they were for quite a long period of time. Which is when we may see the long term side effects of antibiotic use.

What probiotics to take after colonoscopy? ›

Another probiotic mixture containing strains of Lactobacillus plantarum Lactobacillus lactis subspecies cremoris and Lactobacillus delbrueckiidiminished the presence and the severity of intestinal symptoms and improved stool form when given to a large outpatient group for 4 weeks after colonoscopy.

Can you see bacterial overgrowth in a colonoscopy? ›

Examination of the tissue of the GI tract itself with an upper endoscopy or colonoscopy may be obtained. Some of the material from the jejunum, the middle part of the small intestine, may be obtained to analyze. The number of bacteria present in this sample can determine if there is overgrowth.

What are the symptoms of bacteria in the bowel? ›

Bacterial gastroenteritis is a digestive problem caused by bacteria. Symptoms include nausea, vomiting, fever, diarrhea, abdominal cramping, and pain. In severe cases, you may become dehydrated and have an electrolyte imbalance. Bacterial gastroenteritis is sometimes treated with antibiotics.

What causes disruption of bacteria in colon? ›

Any interruption in the balance of microbiota can cause dysbiosis. When dysbiosis happens in your GI tract, it's typically the result of: a dietary change that increases your intake of protein, sugar, or food additives. accidental chemical consumption, such as lingering pesticides on unwashed fruit.

How do I restore my gut microbiome after a colonoscopy? ›

Here are a few steps that you can take to gently and naturally replenish your gut flora through probiotics:
  1. Eat yogurt and kefir that is high in probiotics for several days after your colonoscopy. ...
  2. Take a probiotic supplement in the morning on an empty stomach. ...
  3. Eat a diet rich in prebiotics.
Oct 19, 2015

What is the difference between microbiome and probiotics? ›

Probiotics are live microorganisms that offer a health benefit—for example, by helping to enhance or restore health to our gut microbiome. Many of the microorganisms that naturally live in our bodies are similar to microorganisms found in probiotic foods, drinks and dietary supplements.

What kills probiotics in your gut? ›

Foods That Interfere with Probiotics
  • Carbonated Drinks. Whether you are binging on regular or diet sodas, neither are good for your gut health. ...
  • Processed Foods and Probiotics. ...
  • GMO Products. ...
  • Red Meat. ...
  • Gluten-Rich Foods and Probiotics. ...
  • Refined Oils. ...
  • Dairy Foods and Probiotics. ...
  • Tap Water.
Feb 4, 2020

How do I restore my gut after a colonoscopy? ›

Building of the intestinal flora after colonoscopy with a balanced diet. Immediately after the colonoscopy low-fat and easily digestible foods spare the still empty digestive tract. Tea, still water and vegetable juices are well suited to compensate for the loss of fluid.

How long does it take for gut to recover after colonoscopy? ›

Recently, several studies have shown that bowel preparation for colonoscopy could change the fecal microbial diversity and composition, and these effects could last up to 1 month [13-15]. Bowel preparation also affects the change of gut metabolome but this is recovered within 14 days [16].

Which yogurt has the most probiotics? ›

Kefir contains more probiotics than any yogurt. With up to 61 different strains of microbes, it can be an excellent source of probiotics.

How do you heal your colon lining? ›

A balanced diet, complete with all the necessary macronutrients and micronutrients (vitamins and minerals) can help fortify your gut. Vitamin D and an amino acid called L-glutamine may specifically help repair your gut lining.

Can you regrow intestinal lining? ›

The inner lining of the intestines is one of the most-often renewed surfaces in the human body, replenishing itself every 2 to 4 weeks. Lining replacement depends on stem cells stored within indentations called crypts, which are densely scattered across the intestine's inner wall.

What is a good first meal after a colonoscopy? ›

Since the colon's lining may be irritated, your doctor may recommend that you drink generous amounts of fluids and eat soft, mild foods for the first day or two. Foods you can eat after the procedure include: Scrambled eggs. Applesauce.

What is the most common complication after colonoscopy? ›

Bleeding is one of the most common complications of colonoscopy, accounting for 0.3-6.1% of cases[35,36].

Is yogurt good after colonoscopy? ›

Fatty, rich foods and those with a high fiber content, for instance, should be avoided. These foods are healthy options to enjoy for about a day after your procedure: Applesauce. Yogurt.

How do I restore my electrolytes after a colonoscopy? ›

The preparations you went through to prepare for the colonoscopy are dehydrating, so putting fluids and electrolytes back into your system is vital.
Foods and drinks to have the day after your colonoscopy include:
  1. drinks with electrolytes.
  2. water.
  3. fruit juice.
  4. vegetable juice.
  5. herbal tea.
  6. saltine crackers.
  7. graham crackers.
  8. soup.

Can you have digestive issues after colonoscopy? ›

As with any invasive procedure, complications may occur. Complications related to colonoscopy include, but are not limited to, the following: Continued bleeding after biopsy (tissue sample) or polyp removal. Nausea, vomiting, bloating or rectal irritation caused by the procedure or by the preparatory bowel cleansing.

What are the best foods to feed the gut microbiome? ›

Probiotic foods contain beneficial live microbiota that may further alter one's microbiome. These include fermented foods like kefir, yogurt with live active cultures, pickled vegetables, tempeh, kombucha tea, kimchi, miso, and sauerkraut.


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