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
Dear Monica,
Have you ever tried kefir? I’ve had digestive problems for so long, intestinal spazzing, constant diarrhea… crying a lot because the struggles i go through and no one sees or understands why I am SO careful about what I eat. Ironically I was also vegetarian. Kefir always helps me, I switch brands every once in a while to get a different probiotic profile. It stops the spazzing almost immediately.
I could use help. I have been very very sick for almost a year now-cant work anymore:( It first began with nausea every day-it didnt matter what I ate. Then I was diagnosed with IBS constipation and was given a stomach spasm medication which actually helped. Then I got off the medication and began having allergies to food. Anything I put in my mouth I couldn’t breath, couldn’t move, became very tired, depressed, and emotional. I then began getting dizzy and having brain fog for hours at a time every day. I was then diagnosed with leaky gut and heavy metals. I did an all natural heavy metal detox which made me worse. I was crazy in my head and I thought of suicide often (I am a very very happy person and this is unlike me in every way). Then I thought the severe brain fog, depression, etc would go away if I stopped the detox but it didn’t. I was reacting to everything I put in my mouth. Some days it is normal allergy stuff, but more and more it is brain fog every day for hours. I only get relief once I pee, poop, or cry. I do A LOT of crying. I was then diagnosed with Lyme disease where they put me on antibiotics for 5 weeks. Then my internal dr found that I had histamine intolerance and the only thing to do is have a low-histamine diet. I lost 35 lbs due to the lyme, but have gained back about 15 (which is much needed). During my lyme treatment they found candida and another form of yeast in my gut. I have been on meds for almost two weeks now. I feel a little bit different but it is still there. It is very hard because everything is a double-edge sword. For my histamine intolerance I have to do low protein and only certain foods and then for candida I am supposed to do high protein and no sugar, grains, dairy, etc. I only eat a few things right now-meat and about 3 veggies and two fruits. I have been allergy tested and am IGE allergic to the majority of fruits and vegetables. Pretty ironic that I was a vegetarian for 15 years and now HAVE to eat meat. Does anyone have any ideas? I have yet to find a dr who can figure me out. Every morning after my bowel movements I instantly go into brain fog for about 3 hours-I either cry or sleep to feel relief. Has anyone ever heard of this? I feel so helpless. I know if I went to a hospital the would send me packing. But all of this is very real. Yesterday I at grapes and was ok. Today I ate a handful and my stomach is crampy (every day this happens), I want to throw up, im severely depressed and crying, and I am in brain fog. It is terrible and the majority of the day I spend praying to God because I feel like I am being tortured. Any advice? Anyone know of a goo gut dr in Florida? Thank you!
Sara has several guest posts from a chiropractor in Florida that she seems to think knows what he’s doing. Might want to search this site for that Dr. & start from there. Also a good naturopathic doctor (ND as opposed to MD) would help.
Hey Monica, sorry to hear about your condition. If you can look out for MDs who practice functional medicine in your area, they could be of good help. Log onto the Institute for Functional Medicine website or google Dr.Mark Hyman. Hope this helps.
Just read another article (at the link below) before reading your post and someones response sounds pretty much like what you are describing, maybe?
Monica, if I were you, I would get lots of broth from the meat you can eat, that will probably help sooth things, maybe with the veggies you can eat. I would transition to GAPS as you started being able to eat more foods (perhaps even give the intro diet a try, you’re almost there anyway), and at the same time see an NAET practitioner.
I’ve heard really good things from people who have tried it (there was a young girl in a similar situation to yours, allergic to the whole beech tree family which included many stone fruits and things you would never think of, now she can eat it all, and two or three other success stories from support groups. It takes a long time, though), and it seems like a good solution for the vast number of allergies you have.
Dr. Kim Nguyen, naturopath in Tampa.
monica…have your thyroid checked and read everything you can by Dr. Ray Peat.
Hi Monica I too have suffered from Lyme disease. I did two things that helped. Don’t know which is responsible for getting my life back. 1st. Look online for Dr. Theresa Dale. She has a Lyme Detox and Biofilm product that I used for 7 months. It’s homeopathic. You may need to call and speak to someone because the Lyme Detox product isn’t online.
2nd. Dr. Schulze has an incurables program. The book is available online as a free download and it explains how to do the cleanse. I am sorry for what you’re going through. Hope this information helps.
Consider looking into Andrew Cutler protocol for heavy metals. No gut protocol worked for me before orally chelating with his protocol.
NOW brand is a good brand that I have used in the past, but if you have another brand you prefer for that particular strain, that is fine too I’m sure.
Sarah,
Is the source for s. boulardii you link in the blog post one a brand that you recommend?
Thank you!
Beth
*Sigh*…wish I’d known all of this the middle of August when I came home from having emergency surgery for a acute appendicities (perforated appendix). Lots of antibiotics, yup. I went on an all raw organic vegs/fruits/nuts/seeds for 30 days and am still trying to still with it as much as possible. In the last couple of weeks I have added small amounts of lean grassfed organic beef/goat and a little wild caught salmon. And now some organic plain yogurt (I was staying off all dairy) with cut up organic green apple and some cinnamon in it. Nice for a late afternoon snack. I *did* take some good probiotics once I got home (every day for a month, till the bottle ran out) and some enzymes. And some homemade sauerkraut every day or two.
My husband grew up with a father who is Doctor who gave him antibiotics several times a year for all kinds of things that don’t even require antibiotics. His dad would give it to him for EVERYTHING!! Even to this day his dad still tries to give him antibiotics for everything. Last time they were visiting my husband had a little rash on his arm and his dad says “Let’s just give you a routine broad-spectrum course of antibiotics, it might clear it up”. It drives me crazy! Because of all the antibiotic use in his life he has a severe leaky-gut issue which has caused mental problems and fecal-body odor! I used to think he didn’t shower properly. And the fecal body odor has caused many problems in our marriage not to mention the mental issues he has. He is now on GAPS diet and his mental issues are gone and his body odor has 90% cleared up. If he ever cheats and eats wheat or sugar right away there is an odor that comes out of his pores on his body, it’s horrible, and a few days later he will have mental issues. The antibiotics have done so much damage in his life. But we are slowly healing him. It just so clear about the gut-brain connection…and gut- everything connection. I am serious, his face will smell like fecal odor the second he goes off or cheats on the GAPS diet. It’s actually good that he has cheated on it here and there just to prove that the GUT is the problem and it has made him more motivated to stick with the diet and believe in it. He will never take antibiotics again unless there is a life threatening reason.
I’m so glad you mentioned that body odor! I smell it on certain people, and since the majority of people I smelled it on were from a certain demographic, I just assumed that our genetic markers were incompatible or something, that I was the only one that smelled it. Now at least I know what can be done about it, even if I can’t tell them they smell like crap!
Hi Sara,
I just stopped by to say thank you SO much for this post! I just went on antibiotics yesterday for strep throat and my first question was…what should i be doing while I take these and after to maintain my health. And voila! In pops this post! Brilliant! 🙂
Chere, Sarah has a great post on strep throat! Just fyi!
You are welcome Chere! I’m glad the post came at such a good time for you 🙂
Do not Forget about our DOGs …
Connect the DOTs of Canine Allergy to Leaky Gut
85% of our Paw Chewing, Itchy, Gunky Ear / Eye DOGs = Allergy to the Same Pollens, Dust Mites & Molds that We Suffer From.
Canine Allergy = Itching > Open Wounds / Hot Spots > Infection due to Itch & Immune Suppress Pharma > Antibiotic Use > Path Dominated GUT > Leaky Gut / Compromised Health & Quality of Life for Your Dog.
Recognizing that Harmful Pathogenic Bacteria will Re-Occupy / Re-Establish Dominance in Human & Canine GUT’s following Antibiotic Use…
Which not only impairs Daily GUT Functionality, but over time begins to compromise the Integrity of the GUT Lining itself…
To address this suffering population, Healthy GOO under the DVM DACVD Leadership of Dr. Kristin has recently Launched > GOO Gut Rescue.
GOO Gut Rescue’s formulation has been selected to RESCUE > Your Animal’s MicroBiome from Pathogenic BAD Bacteria Dominance / ReStore > Your Animal’s GUT to MicroBiome Health / Flora Balance / Functionality / RETAIN > And Preserves a Healthy & Balanced GUT / GI MicroFlora supporting correct Functionality…
But also to….
REPAIR > Permeability / Porosity of GUT Lining caused by the persistent presence of Pathogenic Bacteria. Restores Integrity of your Animal’s GUT Lining.
As an added Health Focus, GOO Gut Rescue also Sublingually ReSolve > Health / GI Tolerance to 7 everyday FOODs, which often cause Health Issues / Provocations prompted by GUT ImBalance / DysBiosis.
GUT Medicated Immunity is Critical to System Immunity.
Heal the GUT / Seal the GUT / Replenish the GUT .. In Us and our Canine Friends..
http://www.GooGutRescue.com
Are there any good Probiotics for cats too? My kitty has all those allergy symptoms. They put her on an antibiotic & prednisone. It helped her wounds for awhile, but she’s still itching, scratching, biting. Thanks!
Thank you for the info – my puppy Duke thanks you too!
Sarah- What is the reasoning behind taking the probiotics twice daily? Why not take at the same time? Also….when is the best time to take the probiotics (I have heard evening before bed)? Is it better to take on an empty stomach or with food? Thanks!
The reason as I’ve had it described to me by some clinicians is to keep the infusion of probiotics into the gut steady throughout the day as much as possible. Use the probiotic as directed .. whether it says with food or without.
Hi…… I’ve been learning about prebiotics and how important they are to help nourish the good bacteria in your gut and help it regrown after antibiotics. What have you heard about prebiotics ?
Thanks
Yes, feeding our good bacteria what they need to stay strong is very important too! Here are my thoughts on prebiotics. https://www.thehealthyhomeeconomist.com/prebiotics-benefit-gut-health/
Sarah, are supplements warranted if you have a minor yeast/fungal infection being treated with an OTC ointment (Lotrimin)?
Fungal/yeast infections elsewhere in the body originated in the gut. So it would be wise to also make efforts to regain intestinal health which was the source of the external yeast issue to begin with. The guidelines in this article would be a good place to start, but professional advice would also probably be a good idea as these things can be a bit tricky to deal with if they’ve been going on for some time.
Hi Sarah. Can this protocol be used for young children too? How about the sacc.boulardii probiotic? Are there any “rules” as to which probiotics children can or can’t have? If you’re not sure, can you please point me to a source? Thank you!
I would recommend contacting biodynamicwellness.com with your questions as this is the referenced source of this information. This clinic specializes in recovering gut health.