Guide to repairing the gut when a round of antibiotics is necessary, including specific probiotics and supplements to take along with the meds and the proper protocol to follow for 30-60 days afterward.
Antibiotics are truly a wonder of modern medicine. Never in a million years did the scientists who developed them think that a century later, people would desperately need to take action to repair the massive microbiome damage taking these medications caused.
History of Antibiotics
Beginning with the discovery of penicillin by Alexander Fleming in 1928, the pure magic of antibiotics with their rapid resolution of bacterial infections of all kinds caused many in the medical profession to become completely enamored with the drug-based approach to illness.
By 1940, antibiotics had come into widespread use, causing both doctors and people to gradually forget about tried and true natural antibiotics used for millennia.
This change in the medical paradigm has led in recent decades to abuse of these magical meds and the growing threat of antibiotic-resistant bacterial strains.
It has also caused an epidemic of people with compromised gut function due to an imbalanced intestinal environment resulting from excessive exposure to antibiotics via industrially produced foods, medicine, pesticides, and more recently, groundwater contamination.
Cure to Curse
While antibiotics clearly have their place in treating life-threatening bacterial infections, their overuse has led to a plethora of modern-day health challenges and the curse of rampant autoimmunity in young and old alike.
While complete avoidance of all antibiotic exposure would be ideal, it is simply not practical in the majority of cases.
Sometimes, antibiotics are necessary, and when such a situation arises, it is imperative to protect the gastrointestinal tract from fungal or yeast overgrowth during treatment and to replenish beneficial gut bacteria when the course of antibiotics is complete.
While antibiotics effectively kill both pathogenic and beneficial bacterial strains with the exception of antibiotic-resistant species of streptococcus and other strains, they do not affect the many forms of yeast such as Candida albicans naturally found in the body in a non-dominant role. They also have no effect on the super fungus Candida auris.
As beneficial bacteria lining the gut wall are eliminated, yeasts like Candida albicans have the opportunity to overgrow and become dominant by attaching to the gut wall. Once attached to the gut wall, yeast has the ability to create lesions in the cell membranes.
This can lead to the syndrome referred to as “leaky gut”, which increases the likelihood of foreign proteins entering the bloodstream, resulting in inflammation, food intolerances, a myriad of digestive problems, autoimmune disease, and other associated imbalances.
If you or a loved one find yourself in a situation where antibiotics are critically necessary and cannot be avoided with holistic therapies, the following recommendations and protocol for support during and after antibiotic treatment can help minimize the damage to the gut environment and quickly rebuild gut flora at the conclusion of treatment.
Repair of the Gut is Essential
The protocol and suggestions below are provided to patients of Biodynamic Wellness, a clinic that specializes in helping people recover and maintain optimal balance of the intestinal environment to encourage vibrant health that is free of chronic disease. I was given permission by the founder, Kim Schuette CN, to share this important protocol.
Please note that these recommendations are helpful whether the antibiotic treatment came from oral medication or IV treatment.
Contrary to popular belief, IV antibiotics heavily damage gut flora despite the fact that the medication does not make its way directly through the intestinal environment like oral meds do.
Note that birth control medications and colonoscopies also devastate the gut microbiome in the same way antibiotics do.
Thus, there are other medically induced reasons for using the diet and protocol below for repair of the microbiome.
Dietary Suggestions
These dietary suggestions are recommended to protect the gut microbiome from damage while the antibiotics are being taken and for at least 30-60 days afterward.
- Include generous servings of fermented dairy and cultured vegetables during and after antibiotics, whether oral or from an IV treatment. One tablespoon to half a cup of 24-hour yogurt, kefir, kimchi, sauerkraut, and beet kvass, two to three times daily is advisable. Dozens of fermented food recipes and cultured beverage recipes are available on this blog to meet whatever dietary needs you may have.
- Include gelatin-rich foods such as homemade meat stocks and bone broths daily along with abundant vegetables, animal fats, coconut oil, and cod liver oil after antibiotics are completed. Powdered gelatin can be used to further boost homemade soups and sauces.
- Avoid all refined carbohydrates, sugar, and fruit juices.
Probiotic Support During Antibiotics
The probiotic strain Saccharomyces boulardii (this brand or this brand is suggested) is very important to take along with your antibiotics. S. boulardii maintains gut wall integrity and keeps Candida from overgrowing.
Dosage: Take one capsule Saccharomyces boulardii daily to discourage yeast overgrowth during antibiotic treatment when beneficial gut flora is compromised.
Post Antibiotics Repair Protocol
Note the following probiotic supplements to take and how long to take each to give the gut its best chance to repair quickly.
- After antibiotics (or a colonoscopy), make sure to take a high-quality, multi-strain, therapeutic probiotic that includes soil-based organisms (SBOs). Suggested brands are listed on my Shopping Guide, which I often re-vet for ingredient changes and company buyouts. This is my favorite brand for this purpose, and I used it successfully myself to rebuild my gut after surgery/IV antibiotics from a serious injury. Take twice daily for 60 days, ideally after meals.
- Saccharomyces boulardii: Increase your dosage to one capsule twice daily to discourage yeast overgrowth during the gut microbiome recovery phase. Be sure to continue for 30 days.
This short video summarizes the protocol.
More Information
Are Antibiotics Always Necessary for Strep Throat?
The 11 Best Natural Antibiotics and How to Use Them
Why Antibiotics Today Could Threaten Your Life Tomorrow
How to Kick Strep Throat Faster and Better Without Antibiotics
Today I was prescribed Ciprofloxacin 500mg twice daily for a UTI that had spread to my kidney. This was after attempting multiple home remedies over the last 2 days to treat the UTI including D-Mannose, cranberry extract, apple cider vinegar, raw garlic, sarsparilla and a few others.
The infection moved very quickly and at the end of the second day of symptoms I was so miserable with the back and side pain from my kidneys aching, as well as the normal urgency and burning from UTI, that I was desperate enough to consider taking antibiotics, which I have not done in years.
I was hospitalized for a severe kidney infection as a small child, and was given daily antibiotics for about 5 years after, to which I attribute the majority of my gut issues as an adult. I definitely do not take antibiotics lightly, but remembering how sick I was as a child made me afraid enough to get a prescription.
Now upon coming home from the pharmacy, I took my first dose right away as instructed by my doctor, after reading the information included. Then I did a little research.
Apparently Cipro and other antibiotics in that class contain fluoride. Cipro and these other antibiotics can also cause severe reactions including blindness, psychosis, and central nervous system damage in a large percentage of people. This damage is known as fluoroquinolone toxicity.
Frankly, even though I have only taken one dose, I’m a little terrified and more than a little upset that my doctor not only prescribed me this, but did not warn me of any of these potential side effects.
I’m not sure I feel comfortable continuing to take this medication, but I don’t want my kidney infection to get worse.
My doctor said to call back if I was feeling worse or did not start feeling better in 2 days, and she would prescribe something else. I’m just wondering if Sarah or anyone else here knows any more about this antibiotic, has taken it, or has any advice for me.
I too have had to take Cipro for stubborn, painful UTI’s that don’t respond to holistic approaches and it was noticeably different than any other type of antibiotic I have been given over the years. At age 65, I can look back on antibiotics, the different types and how my body felt. With Cipro, I felt mentally very strange and it really ripped my gut up. I have sworn with the next UTI to ask for an “old fashioned” antibiotic, the type you took for 7-10 days. I still recall as a child needing antibiotics for an infection being given a shot of penicillin and then a week of pills. Times have changed, but I think the new stronger, shorter doses are even worse for our bodies than the old types. Anyone else have experience with these too. I really felt psychotic on Cipro! Oh, I have been UTI free since discovering D-mannose with Cranactin. I take one a day, plus lots of homemade yogurt and other lacto-fermented foods.
i use a otc called azo yeast for yeast infections.. they put me on cepolactin or however you spell iit. i ended up with yeast infection in mouth and down south. i had a remarkable on day 3. only itching left was in my mouth and it was just light
Hi there,
Do you have specific recommendations for how to repair the gut following 2 rounds of antibiotics (flagyl) to fight c diff?
Thanks,
-Pam
This is perfect timing as I just came off some antibiotics a few weeks ago and haven’t been feeling myself lately. I forgot about taking probiotic pills for some reason so thanks for the reminder! Hopefully it doesn’t take too long to feel back to normal.
Sarah, I have been diagnosed with SIBO, which you probably know about. I have been to a couple different doctors including an integrative medicine guy and they all recommended antibiotics. I did a round, reluctantly, but it did nothing to change my condition. They want me to do another round but I don’t know what to do. Is there another way. Please help me. My symptoms are so embarrassing and it’s ruining my life!
@ Amelia…SIBO is caused by slowed digestion due to hypothyroidism. Try eating a raw grated carrot made into a salad with apple cider vinegar, salt and coconut oil or MCT oil EVERY DAY. It sweeps bad bacteria out of you small intestine.
I took enteric coated oregano oil and mine eventually went away. I was in a lot of pain before I tried the vitamins . They work like anti biotics.
This is a very helpful article. I’m surprised to see some of the supplements being sold on Amazon, like Klaire Labs. They are usually only sold to healthcare professionals. How does Amazon do that?
A great way to clear out the wrong pathogens and clear the slate for the good bacteria is to take Immunoglobulin Y which is the antibodies found in chicken egg yolk. While fighting off pathogens a hen’s immune system generates millions of antibodies and also puts them into the developing egg yolk for the chick to have when it’s born. Chicks obviously don’t breastfed and need an aggressive defense right away. The antibodies are also effective for roughly 450 different human related pathogens. This is another reason why eggs are good for you. However when eaten with the rest of the egg most of the antibodies are digested in the stomach.
There is a unique and new consumer product available which is capsule of purified Immunoglobulin Y, it’s called Vector450 made by IGY Immune Technologies & Life Sciences. Because it’s in a capsule and not combined with the rest of the egg components, when taken on an empty stomach the capsule passes quickly to the small intestine and the antibodies go to work binding to and eliminating pathogens. You can take probiotics with it since the antibodies will not bind to the good bacteria!
Crikeys! My doc just had me on 2 of these pacs, then had to take a 3rd stronger anti bee as I was still so sick. So 3 lots of gut killing stuff in a row, plus about 3 loads last year. I have to fix this. Sarah, I love your blog. Thanks. I believe that one pack of anti bees made shut down my cat’s health too and then led to her death shortly afterwards from sudden onset of thyroid and kidney disorder. I believe it was routine anti bees that did her in, and I’m not blaming the vet, but vets just shake their head when I bring this up…
Have you tried GUTPRO from Organic3? I just ordered it online and wondering whether this is a good probiotic.
Yoshi!
she also needs to be concerned with sustaining or rebuilding her bladder lining in my experience… Ashley Deason