How To Recover Gut Health After Antibiotics


The same infectious diseases that would have impaired or killed us in past generations are now easily halted through a simple course of antibiotic medication.

While I’m not in favor of contaminating our food supply with antibiotics, using them wisely in order to stop the progress of acute disease is extremely valuable.

One of their unfortunate side effects, however, is that antibiotic drugs are not selective in choosing which bacteria to kill. All the good bacterial colonies in the gut die along with the bad. Because of that, readers often write to me asking how to recover their gut health after a round of antibiotics.

Why is the balance of bacteria in the gut important?

More than 1000 trillion bacteria live in our digestive systems, which it needs to maintain a good balance in order to be healthy. (Did you know you have 10 times more bacterial cells in your body than you do human?) Toxins produced by an imbalance of good and bad bacteria can lead to inflammation and disorders such as leaky gut syndrome.

These disorders have a huge impact on your metabolism and overall health.

They can:

  • weaken immune function
  • cause hormonal imbalance
  • lead to eczema
  • cause insomnia
  • and even create mood disorders such as anxiety.

With these symptoms of poor gut health in mind, it’s imperative you take immediate action to restore gut health after a round of antibiotic treatment.

But, before you begin…

Understanding your digestive health is crucial to repairing your gut effectively after a course of antibiotics.

If you follow the guidelines in this post but have a chronic diet of processed, refined, industrialized dead foods, you may not be able to repair your gut because it’s “normal” state may be one of disrepair.

A traditional real food diet can make a huge difference in how healthy your intestinal tract is, so reviewing these principles is a necessary first step.


The one-two punch for restoring gut health.

If you already follow a traditional real food diet, but suffered intestinal damage due to a course of antibiotics, the obvious solution is to: first, repair what has been damaged, and second, re-introduce beneficial bacteria into the digestive process.

The three best ways to do this have been proven through experience.

1. Eat more bone broth.

Your grandmother or great-grandmother may have offered real chicken soup (not the stuff you buy in cans) to anyone who was sick with the flu or a cold.

This was not just a gesture to offer comfort to someone who is ill, but real chicken soup contained bone broth which introduced lots of minerals and beneficial amino acids, including glutamine, into the body.

Studies have shown that there is a significant link between glutamine and the repair of the epithelial lining of the gut.

If you can’t make bone broth at home, you may want to consider buying bone broth from pasture-raised or grass-fed animals online.

(Where to buy real bone broth online.)

2. Eat more fermented foods.

Fermented foods can help to re-introduce beneficial bacteria into your digestive system.

Cultures around the world have been consuming living, active fermented foods for millennia, and reaping the benefits.

The primary benefit of fermentation is that it introduces living, vital probiotics into the digestive system. Lacto-bacillus bacteria cultures produce lactic acid, which acts as an agent to increase the nutrients that are present, as well as improving the taste and preserving foods for safe consumption.

Eating more fermented foods doesn’t just help repopulated gut flora, but helps keep your intestinal tract strong. The carbohydrates and sugars in living foods turns into alcohol and beneficial acids that can protect the immune system and balance the metabolism.

Homemade, craft fermented pickle relish, chutneys, homemade sauerkraut and fermented dairy products like buttermilk, kefir, sour cream, and homemade raw yogurt can all help to repopulate gut flora and restore your digestive system to its optimal health.

Living cultures contain the beneficial bacteria that your body needs in order to stay in balance. Traditional cultures throughout history on every continent have known this, but it has gradually been forgotten in our culture of processed dead food that is robbed of its nutritional value.

Need an Easy Guide to Get Started Eating More Fermented Foods?

I’ve created a nifty, print-friendly, easy-to-follow collection of 7 naturally probiotic recipes your kids (and you!) will love.


3. Take therapeutic grade probiotics.

Lastly, you may want to guide the process of recovering your gut health by implementing high-quality probiotics.

I rarely recommend supplements to a real food lifestyle, but this is an exception. Good probiotics can aid in the introduction of good bacteria into your digestive system, and many report that they improve their overall health in a much shorter period of time.

(This is the brand of probiotic I take.)

I would also recommend consuming fermented cod liver oil because of its capacity to reduce inflammation.

Listen to your body!

If antibiotics have helped you to recover from infectious disease, it’s critical to continue your recovery.

Whatever you do, don’t ignore your gut, whether you have had to take a course of antibiotics or not.

The importance of your digestive system as a “second brain” in maintaining physical and mental health is vital to maintaining a healthy diet.

(photo credit: adossphoto)


  1. says

    I took too many courses of antibiotics growing up, and I can personally say all of the above has helped me regain my health. Kudos Kristen to sharing this article with everyone. I think this is a very common situation that many are not aware of.

  2. Rrebecca says

    I have read that manufactured probiotics should be kept cold, as the heating of them to unite them in a vitamin kills them.
    Is this what your research has told you?

    • says

      It depends on the specific probiotic in question. For example, the one that I take doesn’t require refrigeration, but does require that it be stored below 72F.

      Some probiotics don’t require refrigeration because they are activated by your digestive environment and are shelf-stable until then.

  3. says

    The more I learn about bone broth, the more I love it. In fact my crock pot on the countertop is bubbling away right now, full of bone broth, hooray! I just wrote a blog post about it but I could have written a book. Great stuff!

  4. Peggy says

    I was on three rounds of antibiotics a year, every year, as a child. I was able to restore my health to a point, then got to be “a certain age” and the doctors started up again with more rounds. I am working very hard to avoid them now, building my immune system and trying very hard to build back the health I lost. My suggestion to my children is always: do everything else first. Seek medical treatment as a course of last resort. I wish it weren’t that way. But my husband, who goes to the doctor first is now on 12 prescriptions, each for the side effects of the previous. I want better.

  5. Carrie says

    I was on antibiotics for breast abscess/mastitis when my baby was two months old. Despite the fact that I took strong probiotics, she has developed eczema along with other digestive issues. She is four months now and exclusively breastfeeding. I tried to give her infant probiotics in powder form but she wont take a bottle. Also, I am allergic to bovine casein and many probiotics contain it making me hesitant to give it to my baby who already shows signs of an impaired gut. Any advice?

    • sy says

      Hi Carrie, I have a similar issue – my 3 month old was given antibiotics and 2 weeks later developed eczema. I’ve been giving him probiotics but the eczema is getting worse. How is your little one getting along?

  6. says

    Great advice, though I usually prescribe a “synbiotic” such as Bio-Immersion’s Original or even Supernatant probiotic. The prebiotics enhance the viability of the pro-biotics, and both have often been diminished if not wiped out by the antibiotics. The broth is magic, and the fermented foods are wonderful!

  7. Beth says

    Wonderful info. I might add Saccharomyces boulardii to the protocol to ward off yeast overgrowth from antibiotics, as well as oil of oregano, a safe and natural ‘antibiotic’.

  8. JenCan says

    Two and half years ago I had to have my spleen and tail of my pancreas removed due to a benign mass. I was on a lot of antibiotics. The surgeon and my infectious disease doctor both advised against taking a probiotic supplement while I was on the antibiotics, but said that probiotic food would be a good idea. Kefir, yogurt and saurkraut really helped restore my good gut health. This also answers why I crave bone broth.

  9. Anna B says

    Yes to all! I always like to remind people that there is no point in starting even the healthiest food until diarrhea caused by antibiotics (or anything really) stops. How can the gut repopulate if the contents are eliminated rapidly? The bone broth is a great start to recovery, then slowly introduce probiotics and fermented foods.

  10. Sarah Jane Johnson Stevens via Facebook says

    I know this all too well. I had c-diff when I was 18 because of antibiotics. It was really bad because they thought it was the flu. For two months I suffered until I almost went into kidney failure. My stomach has never been right since. It is weird, though, that you cure an antibiotic illness with another antibiotic (flagyl).

  11. Sarah says

    Thanks for the advice, I’m on two antibiotics for a nasty cat bite, and my gut is a MESS.

    And thanks for the tip on Garden of Life probiotics. I’ve taken their multivitamin, and I know they make quality products.

    One question: should I start taking probiotics before I finish the antibiotic course, or would that be ineffective — will the antibiotics just kill off the probiotics before they have a chance to do any good?

  12. becky says

    My 16 month old is on a daily antibiotic for a kidney condition to prevent uti’s from traveling up into her kidneys. She has had 2 breakthrough uti’s, so the antibiotic isn’t working. To treat her initial uti caused by psuedmonas (sp?), she was on a VERY aggressive antibiotic. Is it possible that she’s more susceptible to additional uti’s since the strong antibiotic wiped everything out? Also, should I be using an infant specific probiotic? She’s on a twice daily dose of Culterelle although it may not be effective in conjunction with her daily, preventative antibiotic. Dealing with diarrhea, lack of appetite and fussiness. She is exclusively breastfed, but does eat a small amount of food.

  13. says

    I eat organic InLiven probiotic superfood, the only probiotic made from fermented organic whole foods. I eat this daily. When In need a boost, such as after antibiotics, illness, etc I take Fast Tract organic liquid probiotic. Two of the best organic probiotics on the market.

  14. Howard Gray via Facebook says

    Step 4, feed your gut bacteria resistant starch. It’s incredibly easy and super cheap – supplement your diet with unmodified potato starch, plantain starch, and also supplement with inulin and FOS.

  15. says

    ever hear of nature senses? I came up with it. It’s what God has given humans to understand nature through their senses I feel this so. Their instinct or critical thinking makes it possible to come up with conclusions and such of nature through nature sensing.

  16. says

    Thanks so much for this post! I thought I’d add a comment about my own progress with healing from antibiotic use. In December 2014, I had to/chose to take antibiotics, for the first time since I was about 17. (Im 36 now). I eat a whole foods-based diet, with a heavy influence from Sally Fallon’s Nourishing Traditions. I was AMAZED at how violently the antibiotics effected me, esp my usually near-perfect digestion. After I stopped the antibiotics, I went on a “bone broth” fast for about 4 days ( also taking probiotics and eating a few well-cooked veggies). This turned me around! My digestion was back to better than normal, just after 4 days. Im continuing the daily bone broth and probiotics, and still have some lingering effects from the antibiotics (namely, my skin is really dry and reactive to foods and stress.) Thanks again for a great post, it was useful to find when I was freaking out about my health post-antibiotics =) jennifer.

  17. Robyn says

    What do you recommend for an ebf 6 month old. She is battling an ear infection and I know they can get better on their own but after it got progressively worse we decided to go with a round of amoxicillin. She already is on a probiotic and I take one too. Anything else I can do? We were going to introduce foods this week but with this illness I’m now uncertain about doing that.

  18. Ruth says

    After 3 months of antibiotics for the treatment of Lyme Disease my stomach and digestive system was totally shot out. The antibiotics caused a terrible bout of Gerd Reflux. That was mid December and I am still struggling to regain my stomach health. I have totally changed my diet to lots of veggies and lean meats. I also have a fruit smoothie for breakfast every morning. I took DGL licorice and Madtic Gum for the first month. Now I take a daily probiotic along with digestive enzymes and ginger in lozenges form several times a day. Also for lunch a large salad with ACV each day. I’m am somewhat better but still not good. I just want this to be over with and would caution anyone who is put on a long term antibiotic. Sometimes they can do more damage than good. I just wish I knew how long this will take to heal.

  19. says

    I would add that other healing protocols would be helpful for everyone with gut problems, including guided (by an herbalist so there are no
    misundertandings and mistakes) use of a comfrey/marshmallow leaf/ soothing tissue rebuilding formula, and a small amount of ashwaganda as an overall adaptogen. Comfrey (root and leaf), calendula, and other herbs rebuild damaged tissue. I feel judicial use of a high quality coconut oil is also
    helpful. for vegans who will not consume bone broth, Beet kvass as well as nutritional yeast flakes can help supply helpful nourishment and constituents .

  20. says

    Hi. I find that the capsules have to be triple encapsulated to get past the stomach acid. I’m not seeing VitaCoast has this. Shaklee’s are proven to get the lower intestine. The piece about fermented foods is awesome. I started a recent client on the fermented foods and she lost 2 lbs. in a week where as before, her weight loss was stubborn. I have one who will not eat fermented foods and she has stubborn weight loss. Really interesting area of research, especially with metabolic syndrome and probiotics. It’s sad to see what is happening to all these patients I see who are given antibiotics. A tv evangelist came to me fatigued and depressed. He was given heavy antibiotics for a condition he just got over.

  21. Ann says

    I have been on 6-7 antibiotics since january2015 it was one thing after another. Twice I’ve been on flagyl. I just finished 2nd round of flagyl last week. 5 days later I got hit with a terrible gastrointestinal ‘bug’ or something. It’s been 6 days since it hit me and I’m still having abdominal cramps off and on and frequent loose stools. Probably (2 )every hour. I’m extremely exhausted – been in bed most of the time. Not eating because of cramping so when I go it’s liquid and mucous. How should I start? I’ve been taking 4 dr Ohhiras probiotics a day and sticking to water,ginger ale, mint tea. Ate some yogurt with applesauce but I keep getting cramps. Do you have any suggestions?

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