Antibiotics are truly a wonder of modern medicine. Never in a million years did the scientists that developed them think that nearly 100 years later, people would desperately need to take action to repair the gut after antibiotics are taken.
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 techniques for preventing illness such as the age-old remedy cod liver oil.
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, and more recently, groundwater contamination.
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 autoimmune diseases.
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 newly emerging 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 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.
Repairing the Gut After Antibiotics
These recommendations are provided to patients of the clinic Biodynamic Wellness which specializes in helping people recover and maintain the optimal balance of the intestinal environment to encourage vibrant health free of chronic disease stemming from a compromised gut. The owner of Biodynamic Wellness, Kim Schuette CN, generously gave permission to share the recommendations listed below.
Please note that these recommendations are helpful whether the antibiotic treatment came from oral medication or IV treatment.
Contrary to popular belief, IV antibiotics also 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 colonoscopies devastate gut flora in the same way. Hence, the protocol below is helpful to utilize if you must endure one for whatever reason.
Diet During and After Antibiotics
- Include generous servings of Lacto-fermented dairy and cultured vegetables during and after antibiotics whether oral or from an IV treatment. One tablespoon to half a cup of yogurt, kefir, kimchi, sauerkraut, beet kvass, etc. two to three times daily is advisable.
- Include gelatin-rich foods such as homemade meat stocks and bone broths daily along with abundant vegetables, animal fats, coconut oil, and skate or cod liver oil after antibiotics are completed. Powdered gelatin can be used to further boost homemade soups and sauces.
- Avoid all refined carbohydrates and fruit juices.
Support During Antibiotics
- Saccharomyces boulardii: one capsule twice daily to discourage yeast overgrowth during antibiotic treatment when beneficial gut flora is being compromised.
This particular strain is very important to maintaining gut wall integrity throughout a round of meds and keep Candida in check.
Gut Replenishing Supplements
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 probiotic. Suggested brands are listed on my Shopping Guide which I often re-vett for ingredient changes. Take twice daily for 60 days ideally after meals.
- Saccharomyces boulardii: one capsule twice daily to discourage yeast overgrowth during the gut flora recovery phase. Be sure to continue for 30 days.
- Note that not all beneficial bacteria are created equal for repairing the gut. Be sure to match specific probiotic strains to the function you wish it to perform and the ailments you are working to resolve.
This one-minute 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
This is a great article.
How do we help a leaky gut to heal? I know my colitis developed after a round a strong antibiotics, then a terrible yeast infection.
What is the protocol for healing a leaky gut?
I also have extreme food intolerance now…can only eat 6 foods!
Thanks!
Do you think it is possible overcome the damage done by 10 years of continuous use of antibiotics and prednisone, laxatives, tranquillizers and anti diarrhoea medication as a child (I am a Münchhausen by proxy survivor). I’m at a loss on how to become healthier. I’ve been eating WAPF for about 10 years now. It helped a bit. In that time I have done GAPS and Body Ecology and other protocols, without any change. Changing to WAPF has had the biggest effect. I have seen many health care professionals over the last 25 years. Mainly alternative, as my digestive issues are not recognised by conventional health care professionals.
You might want to consider a fecal transplant. See posts on this by Sarah and others.
Also check out homeopathics that can boost GAPS healing. See Joette Calabrese’s website for this.
I have been looking into a fecal transplant. It is on my wishlist, but unfortunately it seems only available in the US for the moment and i do not live there. I will check out Joette Calabrese’s website.
Diana, I am so sorry you had to endure all that. I can’t answer your question, but I will pray for your god health and that you can find something to undo at least some of that damage and that you will see progress.
Hi Sarah,
What would you recommend for a breastfeeding newborn & mom who were given antibiotics in the hospital? Should anything be given straight to the newborn, or should it all come from mom’s diet via the breast milk? My 2 month old is suffering from sleep disturbances (restless, wakes up after just a few minutes of napping), very gassy, cries for no apparent reason. Thanks!
Thoughts for your Consideration…
Pre & Probiotic Blend Before / During & After Antibiotics.
It takes 10 Days for Stool to regain normalcy after Anti’s.
Probiotics direct to Newborn as well ..and will receive extra Immune help via Mother’s Milk
2 Yr Old ..
If Mother is genetically predisposed to Allergy / Asthma ..
sounds like early GI Issues caused by Allergy March .. typically early Symptom of Allergy March is a reaction to Cow Milk.
Use of Anti’s in Mother / Child w/o Pre & Probiotic increase likelihood of Allergy to Asthma incidence.
Unfortunately, the only way to Stop progression of Allergy to possible Asthma is Sublingual Immunotherapy
To Confirm presence of Allergy March in Infant ..
suggest ImmuneTech Home IgE Heel Stick Blood Test for Top 10 Allergy Troublemaker’s ( 3 Food & 7 Enviro ) .. Test is $65 ..
And the Only FDA IgE Allergy Blood Test that can be Purchased Without a Dr’s Prescription.
Then once IgE Confirms presence of Allergy MARCH .. show Dr and because it is FDA Approved.. must take Seriously and he / she must take further .. if Allergist .. find an Allergist that does Sublingual Immuno-Allergy Drops based on IgE Blood Test .. not Skin !
Do not allow Infant’s Symptoms to be Masked by Pharma ..
You must Stop & Melt Allergy March SnowBall before it Rolls Bigger / Faster to possibly Allergic Asthma.
Be on Allergy Alert to further Signs of Allergy MARCH.
Do not be Fooled into believing that your Child will Out Grow early FOOD Allergy Signs of Allergy March .. some do .. others not … the OutGrow is typically that the progression of Allergy March has Re-Invented itself from early Food Allergy to Respiratory on its way to possibly Allergic Asthma.
Allergy is Cumulative, progressive, LifeTime, Chronic Disease that begins in the Womb.. and sets into motion a LifeTime Slippery Slope of Multi Diseases and compromised Quality of Life.
ALLERGIES are Nothing to Sneeze At !
We have a young child who has been on long term antibiotics. How can we best support her while on them and between use? When should she take her probiotic in relation to the antibiotic. I struggle with the timing of everything.
What is the protocol when having to take an anti-fungal antibiotic like Diflucan?
I believe there are many so called “life threatening” situations where antibiotics are not necessary or warranted. I can’t remember the name of the book I read, but it gives an actual account of a woman from the civil war era who had intestinal surgery in some of the nastiest conditions, after her body was ravaged by starvation for months, and she survived and went on to live a healthy life. More and more doctors and surgeons are administering antibiotics for minor surgeries and procedures, b/c of hospital protocol initiated for liability reasons. On occasion you might be able to persuade a doctor, say if your doing a procedure such as a DNC, to forego antibiotics. I would discuss this with the doctor far in advance of course. Not sure how long this will last however as it seems the cases I run across are fewer and fewer.
I had surgery a few weeks ago and they put me on an antibiotic (Keflex I think). Daily I’ve been taking FCLO with homemade raw kefir already for several months. I then went on vacation to NYC/Boston with my husband where every meal there was plenty of white bread and dessert after. Didn’t have my kefir so have drank a little Synergy Kombucha to hopefully help while away from home. Then I found the Lindt store. Bad news. I rarely eat any sweets at all but I found myself indulging a little too much on the chocolate and now I’m paying for it. Lots of regrets at this moment. I also suffer from an overgrowth of candida and have been maintaining my symptoms with kefir for the time being. Whole family of 6 has issues and have felt too overwhelmed to get on the right diet at the moment. Was preparing for GAPS a few months back and truly believe it could help but just prepping for it caused major issues within my family so I’ve unfortunately had to let it go.
Anyway, b/c of the last few weeks I now have a UTI which normally I’ve been able to kick with topically applying DoTerra Geranium EO. For some reason it didn’t work this time. I was flying back home and couldn’t get any EO until later in the day so thinking I didn’t catch it soon enough to stay on top of it even after using several times in the first couple of days. Anyway, went to the health store and they suggested a Solar Ray probiotic with 30 bill CFU and CranActin with D-Mannose. After a few days (which seems like forever when having a UTI) still no relief. So after talking with an osteopathic doctor who understands gut health (and is even familiar with GAPS)) he said Macrobid is one antibiotic they’re not afraid to use because it doesn’t effect the gut like other antibiotics (skips the intestinal tract maybe?). I’ve been under a lot of stress and didn’t feel like mentally I could fight this naturally any longer so I caved and got it. I know it’s a temporary fix but that’s what I need at the moment to keep going. In survival mode with my life right now.
Back to the health food store. They said stay off sugar of any kind natural or not b/c yeast will feed off of it regardless (also no starches, anything refined, etc.) They even included staying off ALL dairy fermented or not b/c of the high sugar content. B/c I’ve seen the positive effects of raw kefir that’s been so hard for me to accept. I know their perspective on good health is different from mine so I’ve been questioning their info since but at the same time I wondered if they were right. I noticed on the suggested regimen here fermented dairy was a go. Why the differing perspectives? Why is sugar in dairy acceptable?
After starting Macrobid a couple days ago I decided to get back on my kefir. I was starving trying to follow the no sugar from anywhere mindset and just couldn’t do it anymore regardless of it being harmful or not. So that’s where I’m at for better or worse but would love thoughts.
Also while I’m here mine as well ask if you have any thoughts on the Dr. Whitings Oxy Aloe Flush recommended as a detox for candida. Again I understand GAPS is going to be the first choice for gut issues but I just can’t do it in my situation so looking for alternatives. Thank you so much for all of the amazing info shared on this site. I’ve come along way in my understanding real health and appreciate the support offered here!
I have read that honey can also get rid of candida. May have been manuka, or maybe just any honey.
We are a very fermented family. I also supplement with Klaire Labs Therbiotic when I feel its needed. We take our FCLO, drink raw dairy, eat very clean, dont vax. The whole nine yards so to speak. It does happen that once in a blue moon one will get quite ill. We have used a product called Pleo Not. While not perfect in every way it seems pretty decent. Does anyone have any opinions on Pleo Not?
The problem is with antibiotics the slightest thing wrong with someone and the doctors prescribe antibiotics when they could of just let them fight the less serious things off them selves. This then leads to antibiotics been useless against many viruses now its our own doing.