Antibiotics, Colonoscopies and Your Gut Microbiome 
August 6, 2019


In recent years, the health and diversity of the trillions of bacteria living in the human gut have been recognized as an important component relevant to overall wellness. While several factors can influence gut health, today I’m going to address two common occurrences that may disrupt the gut microbiome: antibiotic use and colonoscopy prep.


Antibiotics are live savers designed to kill bacterial infections. Broad-spectrum antibiotics kill a wide variety of bacteria, both good and bad, while narrow-spectrum antibiotics target specific bacteria. Unfortunately, we have all become familiar with the overuse and misuse of antibiotics and the proliferation of antibiotic resistant strains of destructive bacteria. 


Perhaps in response to the overuse of antibiotics, fear of taking antibiotics has become a concern among some people. In particular, some are concerned about disrupting or destroying their unique strains of gut bacteria and as a result, may resist taking a course of prescribed antibiotics. 


What actually happens to your gut when you complete a course of broad-spectrum antibiotics? According to Drs. Justin and Erica Sonnenburg, orally administered, broad-spectrum antibiotics cause significant destruction to the gut microbiota. One course of antibiotics can require months to recover from – with some studies suggesting the microbiome may not recover completely. Long lasting destruction absolutely occurs when just two courses of broad-spectrum antibiotics are taken within a single year, altering the pre-antibiotic microbiome permanently. 


It’s critical to avoid overuse of antibiotics – particularly for illnesses that are not bacterial in nature, such as a cold or flu. Don’t be afraid to discuss your concerns about the type of antibiotic treatment being recommended with your doctor. However, it’s also important to remember that several things, not just antibiotic use, can alter the bacteria in the gut. Stress, diet, gastrointestinal illness, overuse of antibacterial products, constipation and diarrhea can impact the balance of good and bad gut bacteria. While the vast majority of our gut bacteria should reside in the large intestine, sometimes bacteria overpopulate the small intestine, causing an undesirable condition called Small Intestinal Bacteria Overgrowth (SIBO). 


Sometimes our microbiome may not be as healthy as it could be. Destroying or crowding out some of the undesirable bacteria and tipping the scale in favor of the good bacteria have many advantages to overall health. In fact, research in Japan has just begun to link the presence of certain types of undesirable gut bacteria with colon cancer. 


Colonoscopies are procedures that require a complete clearing of the contents of the bowel. Remember that the bowel, aka large intestine, is home to the vast majority of our gut bacteria. Artificially cleansing the colon with strong laxatives has an impact on the bacteria living there. Early research indicates that the gut microbiome is impacted after a colonoscopy, but recovery most likely occurs within a month or so. However, there is much more to learn about the impact colonoscopy prep has on the health of the gut microbiome. 


Our gut bacteria are constantly evolving. Studies have shown that those we live with influence our gut bacteria strains. Diet and lifestyle play an important role in the health and variety of our microbiome. We need a diverse mix of bacteria to keep us healthy, with a focus on keeping the good bacteria happy. Probiotics allow us the opportunity to populate our guts with desirable strains of good bacteria. 


There are several pro-active steps you can do to support your gut flora during and after completing a course of antibiotics or recovering from colonoscopy prep.

  • Eat a diet rich in fermented foods.

  • Include plenty of fiber rich foods in your diet which act as prebiotics to your gut bacteria. Prebiotics are essentially food that feed your bacteria.

  • Avoid sugar and artificial sweeteners.

  • Avoid overuse of antibacterial cleaners.

  • Hug your pets – they have good bacteria.

  • Dig in the garden.

  • Take a high quality probiotic. See my recommendations below.


When I recently completed a course of broad-spectrum antibiotics, I supported by system with four products: 


  • Saccharomyces Boulardii + MOS by Jarrow Formulas is supportive to take during antibiotic treatment and during times of potential digestive distress – such as traveling. 

  • Flora 300-14 7 Day Intensive by Innate Response is an excellent product to inoculate your system with desirable, diverse and beneficial bacteria after completing a course of antibiotics or colonoscopy bowel cleansing.

  • Fem-Dophilus by Jarrow Formulas supports vaginal and urinary health. After a course of antibiotics, the delicate vaginal flora can be disrupted. 

  • Ther-Biotic Metabolic Formula by Klaire Labs is my choice to regulate and improve energy, weight, and glucose metabolism. Lactobacillus gasseri has been shown to be effective in promoting weight loss.


Remember we are all unique, what works for one may not work for another. Listen to your body. Of course, always discuss your concerns with your doctor.


Please visit my Online Dispensary to learn more about the recommended products.




The Good Gut: Taking Control of Your Weight, Your Mood, and Your Long-Term Health; Justin and Erica Sonnenburg, PhDs


“Stress may harm gut health as much as junk food”  Medical News Today, 17 October 2017, Honor Whiteman


“The effects of bowel cleansing for colonoscopies on our microbiome”  American Microbiome Institute, January 8, 2015


“A gut feeling: Microbiome changes may mean early detection of colorectal cancer”  Science Daily, June 12, 2019 


The Microbiome Diet: The scientifically Proven Way to Restore Your Gut Health and Achieve Permanent Weight Loss; Raphael Kellman, MD


Colleen Forgus is a professional chef and certified holistic nutritional therapy consultant. 


As a Certified Nutritional Therapy Consultant, I am not licensed or certified by any state.  I have received a certificate of completion from the Nutritional Therapy Association, Inc.  A license to practice Nutritional Therapy is not required in the state of Arizona.  Laws and regulations regarding certification and licensure requirements differ from state to state.  Nutritional Therapy is not meant to diagnosis, treat or cure.  If you have any questions, always consult your physician.