Check Out Our Seasonal Specials right arrow
(317) 989-8463 Appointment

Blog Center for Fully Functional Health

How To Restore Gut Health After Antibiotics

woman curled up holding her stomach

The Fully Functional® Approach on How To Restore Gut Health

Many of you know that I had a recent appendectomy that was a bit complicated. I thought I had a typical GI bug because my kids were home, sick, so I discounted the possibility of something more serious. Unfortunately, I waited so long and until I had evidence of needing surgery that by the time I presented to the emergency department I had already perforated (‘ruptured’) my appendix. I was told it was necrotic (dead) and that the area around there was inflamed. In this article, I am covering a very comprehensive approach on how to restore gut health.

The issue with the perforation of a part of your intestines is that you now have spillage of fecal material and bacteria into the abdominal cavity. YUCK! This is a true emergency and can be life-threatening. It requires immediate surgery and placement of a drain to remove any remaining infection/bacteria and antibiotics. If it isn’t treated aggressively you can become septic and die. A friend of mine had the same thing happen and ended up spending a month in the hospital and losing 40 pounds.

Traditional vs. Functional Medicine

I was certainly upset that I had a perforated appendix and even more upset with myself for waiting so long to take care of it. One of the benefits of being a board-certified Emergency Medicine is that I understand and am so thankful for what that type of care offers. Many folks consider Traditional Medicine bad and Functional Medicine good and I would tell you that I completely disagree.

Having a respect and understanding of both is best and I believe that a doctor with a healthy understanding and appreciation of both provides the most comprehensive care to their patients. There is an absolute time and place for traditional medicine therapies, and in my case, emergency surgery and antibiotics were required. Thank goodness I had access to them.

I like to describe things in word pictures and sometimes I think traditional medicine therapies are like a fire hose to a house on fire – we need it to put the life-threatening ‘fire’ out. Functional Medicine is like dealing with the smoldering coals underneath. It doesn’t put fires out but rather helps address what might lead to a fire or prevent ‘clean up.’ This is where antibiotics come into play.

If you have a serious infection, such as what happens in a perforated appendix, or something like meningitis or cellulitis (skin infection) antibiotics (and sometimes surgery) become the fire hose and are required to prevent death. No one wants antibiotics, especially not me, but I appreciate their value. I have spent years healing my gut and working on having good gut flora as well as fighting off yeast overgrowth. Did you know that one course of antibiotics has been shown to disrupt the flora in the GI tract even years later?¹

closeup of bottle with antibiotics

First off, why do we want ‘bugs’ (flora) in our GI tract? That just sounds disgusting! The number of bacteria in the gut to the number of cells in the entire body is under debate but what we do know is that there are at least as many bacteria in the body as there as cells in the whole body.² The balance of bacteria is known as the microbiome. Imbalances in the microbiome (dysbiosis) have been associated with numerous diseases, including inflammatory bowel disease, diabetes (types 1 and 2), allergies, asthma, autoimmune diseases, autism, obesity, and cancer.³,⁴

Antibiotic use leads to dysbiosis and thus the risk for serious disease.⁵ So as you can imagine, while I was very fortunate and thankful to have access to antibiotics, I was also very motivated to heal my gut and improve the balance of the flora as quickly as I could. Antibiotics not only have a negative impact on gut health by disrupting the microbiome but have also been linked to intestinal permeability⁶ (leaky gut), immune dysfunction⁷, and decreased numbers of short-chain fatty acids⁸(the fuel that helps heal the gut).⁹

the Antoines walking down a path together

How I Restored My Gut Health Post-Antibiotic Use

My goal for myself and my family as well as for my patients has always been to be one’s most healthy, productive, and joy-filled self. So here’s my Fully Functional® approach to get there and what I specifically did to protect and repair my GI system after antibiotic use:

  • IDENTIFY – underlying root issues and contributing factors – In this case, identifying the underlying root issue as to why I got appendicitis in the first place was relatively easy. Appendicitis is either caused by a fecalith (piece of stool stuck here) or inflammation of the lymphoid tissue leading to obstruction of blood flow and mucus clearing. Since I had several children home with the ‘stomach flu’ and it began as gastroenteritis for me, the suspected cause was infection leading to inflammation. If I’m being honest, I would also have to say that I was running myself ragged and not protecting myself against infection by doing those things I know to be important – sleeping adequately, hydrating enough, practicing stress reduction techniques, etc. It is important to IDENTIFY what led to the health issue to begin with otherwise the likelihood of it presenting itself with some other health concern/disease is high.
  • REDUCE – the negative impact having to take antibiotics has had on my health. I will get into this more below.
  • OPTIMIZE – detoxification. We are detoxifiers by design. We urinate, have bowel movements, sweat, exhale, process toxins through our liver, etc. Optimizing these processes is critically important to achieving optimal health.
  • SUPPORT – your immune system, structural support to bones, muscles, mucus membranes and cell membranes.
  • PERSONALIZE – become empowered by understanding your body better so that you can navigate your health journey differently in the future.
text reading: Fully Functional® 6 R Gut Healing Process

The Fully Functional® 6 R Gut Healing Process (A.K.A. How To Restore Gut Health)

REMOVE: Unhealthy diet – such as sugar, processed items, food additives

  • Foods that contribute to intestinal permeability – gluten¹⁰, common ones that cause adverse reactions¹¹ (soy, wheat, dairy, egg, peanut, shellfish, and tree nuts)¹²
  • Yeast overgrowth as a result of antibiotic use
    • Herbal antifungals
    • Prescription antifungals
    • Yeast-free/sugar-free dietary plan
  • Dysbiosis as a result of antibiotic use
    • Herbal antimicrobials
  • Stressors
    • Work on stress reduction techniques
  • Impact of antibiotics
    • Charcoal has been shown to be an effective binder¹³

REPLACE: Nutrients – magnesium, B vitamins, vitamin C, zinc and fat soluble vitamins (A, E, D, K)¹⁴

  • Many of these nutrients are essential for the production of energy in the mitochondria (Kreb’s Cycle) – this energy is necessary for other biochemical processes in the body – including healing and detoxification
  • Digestive support
    • Digestive enzymes if needed
    • Bile acids¹⁵
  • Short Chain Fatty Acids (SCFAs)¹⁶,¹⁷
    • Through diet – fiber intake
    • Supplementation – Cal-Mag Butyrate

REPAIR: Certain nutrients have been shown to be important in the health of the GI tract

  • Vitamin D¹⁸,¹⁹
  • Essential fatty acids²⁰
  • Glutamine – an amino acid²¹
  • Zinc carnosine²²
  • Aloe²³
  • Cannabinoids²⁴

REINOCULATE: Improve microbiome

  • Probiotics²⁵
  • Beneficial yeast – Saccharomyces boulardii²⁶

REBALANCE: Hormone rebalancing

  • Stress hormones²⁷
    • Stress reduction techniques
  • Thyroid hormones²⁸
    • Replace when necessary/appropriate
  • Sex hormones²⁹
    • Optimizing hormonal health
  • Neurotransmitters³⁰
    • Regulating serotonin and others with 5-HTP³¹
  • Rebalance priorities/stressors in your life

ROTATE: Don’t eat the same thing every day – rotate foods and try to repeat foods no more frequently than once every 4 days

Gut healing can take several months. An unhealthy gut and/or the side effects of antibiotics may not present with any GI symptoms, so you can’t rely on them. It is important to stick with the plan even after you are feeling well.

For more information on gut health, please read our article on ‘How to Heal Your Gut Naturally’.

Some of these gut-healing remedies can be found at The Fully Functional® Shop.

Reach out to our Inventory Manager, Sandy, for any questions you may have. She can be reached at [email protected] 

You can book an appointment by clicking here. We are also happy to speak with you at (317) 989-8463, Monday-Thursday, from 8AM – 5PM Eastern time.


Schedule an Appointment Today.

The Center for Fully Functional Health® is led by a team of award-winning, internationally recognized physicians, committed to providing personalized, life-changing care.

40 North Rangeline Rd. Carmel, IN 46032

Please note: By submitting this information, you agree to be contacted by The Center for Fully Functional Health via text, call, or email. Standard rates may apply. For more details, please read our Privacy Policy.