Get a FREE copy of my report The 7 Most Shocking Things the Health Food Industry
Will Never Tell You
+ my newsletter AND special health deals!

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.

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)

Print Friendly
Sharing Is Rebellious! ENJOY.

The following two tabs change content below.
I am a passionate advocate for REAL FOOD -- food that's sustainable, organic, local, and traditionally-prepared according to the wisdom of our ancestors. I'm also an author and a nutrition educator. I enjoy playing in the rain, a good bottle of Caol Ila scotch, curling up with a page-turning book, sunbathing on my hammock, and watching my three children explore their world.
STANDARD FTC DISCLOSURE: In order for me to support my blogging activities, I may receive monetary compensation or other types of remuneration for my endorsement, recommendation, testimonial and/or link to any products or services from this blog. Please note that I only ever endorse products that are in alignment with Food Renegade's ideals and that I believe would be of value to my readers. You may read my full disclosure statements here.

24 Responses to How To Recover Gut Health After Antibiotics
  1. Vanessa
    November 22, 2013 | 8:57 pm

    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
    November 23, 2013 | 11:48 am

    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?

    • Kristen
      November 24, 2013 | 6:08 pm

      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. Amy
    November 25, 2013 | 5:09 pm

    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
    November 25, 2013 | 11:40 pm

    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
    November 26, 2013 | 12:23 am

    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
      March 17, 2014 | 12:22 pm

      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. Deborah Gordon
    November 26, 2013 | 11:17 am

    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
    November 26, 2013 | 1:19 pm

    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
    November 26, 2013 | 7:45 pm

    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
    December 1, 2013 | 3:51 pm

    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. Thyroid Nation via Facebook
    January 16, 2014 | 8:11 pm

    Thanks for this post…so necessary!

  11. Lacy Lewis via Facebook
    January 16, 2014 | 8:32 pm

    Perfect timing as I’m having a c section next week and really want to avoid thrush and yeast rashes for my little one.

  12. Sarah Jane Johnson Stevens via Facebook
    January 17, 2014 | 2:07 pm

    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).

  13. Kelly
    April 22, 2014 | 6:02 pm

    What type of probiotics do you use? Your link doesn’t work any longer. Thanks.

  14. Shellie
    May 21, 2014 | 6:42 pm

    How long does it take to heal your gut after taking 2 rounds of antibiotics?

  15. Sarah
    June 16, 2014 | 5:12 pm

    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?

  16. becky
    June 17, 2014 | 6:43 pm

    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.

  17. Angela Haeder via Facebook
    July 18, 2014 | 12:50 am

    Natalia This is a good read.

  18. Your Organic Life via Facebook
    July 18, 2014 | 1:24 am

    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.

  19. Howard Gray via Facebook
    July 19, 2014 | 12:08 am

    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.

  20. Omar Ayyash via Facebook
    July 20, 2014 | 7:32 am

    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.

  21. Marjorie Winship Durbrow via Facebook
    September 9, 2014 | 7:09 pm

    Good article! Thanks :-)

  22. Anette
    October 1, 2014 | 7:07 am

    Eating plenty of fermentable fibers will help.

Leave a Reply

Wanting to leave an <em>phasis on your comment?

Who Am I?

My name is Kristen Michaelis. I'm a nutrition educator, author, and mother of three. I adore hats, happy skirts, horizons full of storm clouds, the full-bodied feel of wind as I ride motorcylces, reading in my hammock, and a hearty shot of Caol Ila scotch. I'm also a rebel with a cause.
Food Renegade October Giveaway