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How to Rebuild Your Child’s Gut After Antibiotics

medicines pills antibiotics

For centuries, we’ve had relationships with other organisms to keep us healthy – it used to be external beasts like leeches, now we’re learning that it’s all about the internal relationship with our bugs and bacteria. The big question lately is what to do after we go nuclear on our own healthy bacteria with a round of antibiotics – how to fix the gut after that, especially for our kids? 

A walk through medical history can be funny, yet alarming: the practice of blood-letting, with or without leeches, that persisted for 2,000 years; shock treatments for psychiatric patients; cocaine as a pain killer; and even trying to cure everything from scrapes to constipation to syphilis with mercury. Sources: 1, 2, 3

I certainly hope that in a hundred years, people don’t look back on our era and laugh at how ridiculous some of the cures of our day were. There’s a lot of research behind things like chemotherapy and antibiotics, and they have helped many people – but there are folks who question the real benefit vs. the risk.

Because there is a risk.

The new frontier of modern medicine and research, now that we’ve catalogued the human genome, is studying the human microbiome – the 3 trillion or so bacteria (and even viruses) that live inside our bodies, co-existing with us and likely playing a large role in our continued existence.

That’s a work in process. In other words, we don’t know what we don’t know.

And just like the docs giving shock therapy, the doctors of today can only prescribe treatments based on what they do know. It’s a “give it your best shot” kind of healing, which is all any of us can do.

This post is sponsored by WellFuture. I am not a doctor, naturopath, or trained clinician, and even if I was, this information would not be intended to diagnose, treat, or advise away any symptoms of your health. That’s not how the Internet works…

How Do Antibiotics Harm the Gut?

Since we have so much to learn about our gut and other bacteria, we surely don’t quite understand the full ramifications of taking an antibiotic.

But we do know some things:

  • Antibiotics do damage gut bacteria/intestinal flora, causing an imbalance called dysbiosis.
  • The gut houses about 80% of the body’s immune cells.
  • Antibiotics can cause a reduced immune response (one known symptom is diarrhea).
  • Antibiotics in infancy have also been tied to an increased risk for infectious diseases, allergies and other autoimmune disorders, and even obesity, later in life.
  • Antibiotics may create an “obese environment” that causes people to gain weight; probiotics may reverse it.
  • Sources: 1, 2, 3, 4

I try to avoid anyone in my family taking antibiotics at all costs, and 3 of my children have never had them in their lives. In the last 10 years, I had one regimen (10 years ago) and I think my husband has had one or two in that time as well. Unfortunately my oldest son has had about four rounds, including at birth and then for strep and some ear infections, but not for about 3 years.

You could say I’m anti-antibiotics. Winking smile

And since I’ve learned more about essential oils that have antibacterial properties without contributing to antibiotic resistance and superbugs, I’m a fan of always trying natural remedies first.

But I realize that sometimes, antibiotic drugs are the only thing that will keep you alive (or get you through a certain infection) and I’m not going to judge folks who accept them.

What you do after a round of antibiotics is really important though, and you can do a lot of good for your kids if you are careful to rebuild what has been lost.

How to Rebuild Gut Health After Antibiotics children and adults need to fix their gut bacteria

I get a LOT of questions about taking probiotics after a regimen of antibiotics, including:

  • What can I do after antibiotics to help build gut health again?
  • Can I take probiotics at the same time as my antibiotics or will it just cancel out?
  • How long should my child take probiotics after completing a round of antibiotics (if it’s not something we take regularly anyway)?

Let’s dig in!

What can I do after antibiotics to help build gut health again?

There are lots of things anyone can do to help heal their gut at any time – in fact, I listed 100 of them not too long ago!

I’m not going to reinvent that wheel here, but I would like to say that because antibiotics harm the gut’s flora, not the gut lining necessarily (as in other issues like leaky gut), taking probiotics and eating fermented foods are the most important steps to repair any damage from the medicine. Just beware the dangers of soil based probiotics. They are not the same thing!

The antibiotics are going to wipe out both good and bad bacteria in your gut, so you need to replenish it with the good guys, lest the bad guys take hold.

Can I take probiotics at the same time as my antibiotics or will it just cancel out?

When on antibiotics, the NIH recommends taking probiotics twice a day, two hours away from the prescription to avoid killing the supplemented probiotics.

This recommendation seems to be based on common sense of digestion timing rather than specific research that I can source. Whether there’s been any official research on whether the antibiotics just wipe out all the probiotics the next time you take them – and therefore you should take a break from probiotics during your actual abx regiment – I am not sure.

But my own common sense says that we’re only talking about a 5-10 day period, and that’s not very much probiotics to “waste” if it’s going to be wasted anyway. If it doesn’t bother your stomach, I’d keep taking them right through the prescription.

A reader shared that taking them at the exact same time caused her extreme digestive distress (maybe a battle of the bugs inside her?) so do follow the 2-hour guidelines and listen to your body. Again, it’s only 5-10 days, so skipping probiotics during that time isn’t going to set you back so far that you can’t recover.

How long should my child take probiotics after completing a round of antibiotics?

This is the big one!

If you don’t regularly take probiotics (and you really should, but I understand they can be expensive), at the very least please please please give your gut a chance to bounce back after antibiotics by taking a probiotic supplement.

But for how long, minimum, if you’re not going to continue taking them regularly?WellBelly probiotics

I asked this question of Catherine Clinton, naturopath and founder of WellFuture and the WellBelly probiotic that our 2-year-old has been taking since he started food:

“A disturbed flora from antibiotics can onset several weeks after completing a course of antibiotics, and the microbial ecosystem in your post-antibiotic gut is shifting dynamically for weeks, so a general guideline of continuing probiotic supplementation a week or two after completing the round of antibiotics is common.”

I responded and said I was surprised to hear “weeks,” as I had always thought it was at least two months. Her reply:

“Actually the advice does say weeks to months but I just hesitate because I’m the lady who sells probiotics so it makes me uncomfortable if there is no hard research. It is certainly clear that the damage from antibiotics can be quite long term.”

That’s great honesty and transparency from “the lady who sells probiotics” if you ask me!

Here’s some research to back all this up:

  • Probiotics cut chances of getting antibiotic-induced diarrhea by 20-50% (5, 6, 7).
  • Exciting! Probiotics may indeed reduce the need for antibiotics and fight superbugs if used regularly (more research needed though). (8)
  • Doses of probiotics should be more than 5 billion daily to help with antibiotic damage. (9)
  • A great overview of antibiotics, probiotics, and prebiotics – and questions that still need to be researched, such as what is the best delivery system for probiotics. (10)
  • What are prebiotics? Food for the good guys! There’s a little bit of info on that in this big ol’ post to start you off. 

WellBelly is allergen-free, designed especially for infants and children, and you can check out the ingredients for yourself right HERE.

NEW! WellBelly has been reformulated since we shared about it last – not the active part, but the carrier. I’ll let Catherine explain:

“Our new and improved WellBelly is a unique blend of nine different non-dairy probiotics that target intestinal, digestive and immune health in infants and children, although adults love it too! We are proud to offer the first organic, whole food based probiotic blend that contains no solvent derived probiotic carriers.

While probiotic carriers accompany probiotics in very small amounts, we believe every bit counts when it comes to our children.

We wanted an organic, whole food option that avoided a daily exposure to a chemically derived carrier. Our probiotics are grown on a hypoallergenic yeast to avoid common food allergens. Our probiotics do not produce the D form of lactic acid that can irritate digestive tracts, especially in young ones, and are wonderful for diets that avoid histamine and SIBO issues.”

The new carrier is organic banana and apple fruit powder, and it’s just a little bit different looking, off-white instead of the pure white powder it used to be when made from non-GMO corn. This is a wonderful change many have been asking for!

But don’t worry – it still blends easily and seamlessly into yogurt or juice. We call it Gabe’s “special yummies” and he has it every day at lunch.

The Only Consistent Thing is Change!

The last thing Catherine threw out in our emails is something I just have to share with you, because it blows my mind and intrigues me (and underscores my first point about how quickly medical research and knowledge changes!):

So much neat info coming out about the length of prescriptions for antibiotics and stopping a prescription before it is over. Seems the old wisdom of never stopping a course of antibiotics to avoid superbugs is wrong. Longer regimens of antibiotics seem more at fault than the shorter ones or even stopping prescriptions early. Go figure.

I wish they would research how to put the gut back together again after antibiotics and start prescribing shorter courses of antibiotics like the research finally shows as super important.

Me too, Catherine, me too!!

RELATED: Seed Synbiotic Probiotic Review & Side Effects From Antibiotics.

Cheat Sheet Summary

The bottom line on antibiotics and probiotics is this:

  • You should definitely take probiotics after a prescription of antibiotics.
  • At least two weeks – but more likely two months.
  • Taking them during the prescription may help you avoid antibiotic induced diarrhea, and it definitely won’t hurt.
Do you take probiotics regularly? Why or why not? Do you have a family philosophy about antibiotics?

If you need a probiotic for your children, you can buy WellBelly right here.

For All Ages…

Some Quality Probiotics

Some of these I’ve used, some I’m planning to use, and some have been recommended by friends and professionals alike. It’s good to remember a few things about probiotics: 1. People should get different colonies of probiotics, so switching brands/strains every so often (6 weeks?) is good practice. 2. What works great for one person’s needs doesn’t always work for another.  I’ve personally tried:
  • Just Thrive Probiotics – this one can be taken during antibiotics and not be rendered ineffective, which almost all other probiotics are! It’s the top-recommended probiotic overall by Paleo Mom Sarah Ballantyne. 😮 (Be sure to use the code Katie15 for 15% off; also found on Amazon and from Perfect Supplements where you can use the coupon KS10 for 10% off!)
  • Seed Daily Synbiotic – the new player in the field but recommended by superstars like Chris Kresser for its unique probiotic/prebiotic synergy. Here’s my full review including a number of surprises for my thinking and a 15% off code!
  • Note: If you’re struggling with digestion, especially constipation, or you feel like you really need to populate your gut with healthy probiotics, I would recommend Saccharomyces Boulardii in addition to any other you choose (except any above which include this strain). Saccharomyces Boulardii is research-proven to get through the digestive tract without being killed, which is rare. 
  • Balance One probiotics with a unique time-release formula (use the code KITCHENS15 at either Balance One’s site or even Amazon to save 15% either place! Wow! Use the code at checkout on Amazon btw.)

For Little Ones (we use all of these):

  • Mary Ruth’s liquid probiotic is a liquid probiotic that doesn’t need to be refrigerated and tastes like…nothing! It’s my new favorite for administering to kids! (Use code KCRF15 for 15% off!)
  • WellBelly by WellFuture (9 strains of probiotics in apple and banana carrier – it’s a powder)
  • Buddies in my Belly probiotic powder (2 strains of probiotics + potato starch carrier and prebiotics) or chewable tablets
Recommended by experts I trust:

Unless otherwise credited, photos are owned by the author or used with a license from Canva or Deposit Photos.
Category: Natural Health

39 thoughts on “How to Rebuild Your Child’s Gut After Antibiotics”

  1. I was on antibiotic daily.. Doubled when i was sick which was monthly. For 9 years for Rheumatic Fever. Ended at 19 years old.
    I was thin til age 35. I gained, cant lise, add in depression, chronic stress. moid swings. anxiety, headaches, brain fog, pcos, sweet cravings, and then a full hysterectomy. Now at 47 ive been on probiitics for a year. Everything is gone but the weight.

    Amazing what a bad gut can do to you!!!

  2. Hello! Thanks for this post, it’s a topic I’ve been wondering about since becoming a mother because I’ve reluctantly had to give my daughter antibiotics twice. One thing I’ve noticed, however, is that when she does start back up on probiotics, she becomes constipated. All her bms during and after her receiving probiotics come out very hard and like pellets and I can tell she’s having a difficult time passing them. When she isn’t taking probiotics she seems to have fine bms otherwise… Have you heard of this happening to other kids? (She’s currently 15 months old.)

  3. I have been sporadic with probiotics and I know I need to be more consistent. It’s been over a year since my two oldest have had antibiotics (something I know I could’ve treated on my own now), but my youngest just recently had his first round due to serious pneumonia (that required an ambulance ride). It’s been tough trying to afford probiotics for all 5 of us (though the hubby would eat sourkraut everyday if I had it). My main question is at what point does a “kid” need to take an “adult” probiotic? Is it all weight based or simply age? I think I may have found a good probiotic that is safe for whole family, but still would like to have my options. And for that matter, should doses be different based on weight (or age) anyway? Thanks for this and all other posts!!!

    1. Hi Shalimar, I am really not qualified to answer that question, but I do know that recommended dosages are different on the WellBelly probiotic based on age/weight and I always give my bigger kids more around here. We use a food-based probiotic so they can’t get too much, and I don’t really worry as long as they’re getting some. Maybe your goal should be to be more regular about making sauerkraut and/or dairy kefir as that’s certainly the least expensive option? 🙂 Katie

    2. Catherine Clinton ND

      Hi Shalimar, great question! The strains of probiotics in WellBelly were chosen for two reasons. First, the strains promote digestive, immune and neurological health which is especially important for littles. Second, the strains produce little to no D lactic which can irritate sensitive digestive tracts of any age but, again, especially in infants and children. There is no real answer to your question because each digestive system is different. Many adults love and use WellBelly because it is compatible with their SIBO or low histamine diets while others do ok on probiotics that produce D lactic acid. As far as the age and weight affecting serving size, once a child is 4 or 5 years old the metabolic needs are similar to that of an adult. And Katie makes a great point about supplementing with homemade sauerkraut or other fermented foods, inexpensive and so good for the gut. Hope this helps! -Catherine Clinton ND

  4. I take probios for a month after antibios. Would take them daily, rotating in n off, but cant afford it and i use Vitacost ones lol.
    Try to eat yogurt or kefir daily for some strains of probios at least. If i could get a better place, I d ferment veggies too but as it is, i use my crockpot on the floor (no little kids here!).

  5. My Dr has always said if the abx don’t seem to be helping in a couple of days, stop taking them. My husband and I both had a round once. I stopped mine after it didn’t help. No problem. Thankfully so far the kids haven’t had them. My mother always had us eat yogurt when we were on abx as kids. And that was often, seems like. I don’t think it helped as much as it could have if it were probiotics, but we never got thrush and I don’t recall diarrhea. As an adult, my gut is shot. I think lots of abx as a kid was a contributing factor.

    1. Interesting. If the abx isnt wkg in 24 hrs, you need to switch, not just stop altogether. I’d call the MD for another type of abx if i had made the extreme decision to take the things in the first place.

    2. Oh man Tracy…you are probably right about the abx in childhood affecting you now. 🙁 You should still be able to rebuild though! It will just take a more pointed effort. Be sure to follow our journey on Gut Thrive – step 2 to come this week…

  6. What other probiotics do you recommend for a 6yog who is taking a round of antibiotics for (suspected) Lymes disease???

    1. Hey Janell,
      Lyme is sooooo scary, hit it hard with abx! That’s one of the few things I’d take abx for without even thinking about it, even if I didn’t know I had it for sure. 🙁 There are lots of good probiotics – WellBelly is great for kids, and we take Miessence (the liquid is easy to give kids). I’d just make it a permanent part of her life from here on out. Blessings on a full recovery! Katie

      1. You can do the probios after the antibios are done. I would wham the lyme hard with antibios too!

  7. What about for newborns. I am very very anti antibiotic as well but after dosing myself up to pass through my breastmilk, focusing on healing my own gut prior to conception and pregnancy bub (6 weeks) has a throat infection so I have made the decision for him to take an antibiotic. I already have some probiotics for him but as he is not on solids and the issue of the virgin gut would you recommend anything else. My plan is to hope to hold off till over 6 months before solids and also follow GAPS when he does start solids.

    1. Hi Hannah,
      I think just making sure he gets probiotics regularly will be the best thing you can do. Here are a few newer posts that may give you some insight too:

      Hope he feels better now!
      🙂 Katie

  8. taking antibiotics and probiotics at the same time can actually be very harmful. That’s why they recommend two hours apart, but i found even that bothered me. It can cause extreme gas and swelling, i.e. the good bacteria and bad bacteria actually clash and fight with each other when taken at the same time and cause severe abdominal pain. Trust me I made this mistake twice before figuring out taking a strong probiotic with a medication such as zithromax at the same time.

    I was drinking a fermented bio-k to wash down my antibiotic thinking i was helping myself. Boy oh boy did I pay for that with hours of agony!
    Just something you might want to change in this post where it says “it can’t do any harm”.

  9. After giving an ear infection a month to clear up on its own (next time I’ll be more proactive with your natural remedies of getting rid of ear infections!) it’s time to do antibiotics for my one year old. The other ear is infected now too. My question is… My Wellbelly arrives tomorrow… I’m hoping to hold out on starting antibiotics until I get the Probiotics. (Please note that my son shows no sign of being in pain so I thought antibiotics could wait a day). Anyway, is waiting unnecessary? Is getting him on the probiotic the second day suffice? I want to wait but I’m feeling guilty that I have medicine to make the infection go away but I’m just letting it sit there!

    1. Lindsay,
      Well I’m sure not a doctor or even researcher and can’t give medical advice, but the antibiotics are going to fight with the probiotics anyway, so as long as you’re going with antibiotics, there’s no reason to wait — hope LO feels better! 🙂 Katie

  10. My little boy had his spleen removed after cancer of the liver. As a result he is on 10mls of antibiotics a day they say for the rest of his life. What can I do to help his gut repair without stopping the antibiotics? Or is there something that could replace the antibiotics?

    1. Phew, what a journey you’ve been on already, ! Praise be to God that your little guy is ok! This is definitely something to bring up with your docs – the microbiome, gut health and probiotics are becoming more and more mainstream and researched, so s/he should know a bit about it. From what I understand, probiotics DO still help in the midst of antibiotics, just space out the consumption during the day.

      Good luck with this issue! 🙂 Katie

      1. Thanks Katie
        I notice his immune system is not strong so he picks up virus like Molluscum contagiosum. I’m worried to stop the antibiotics in case he picks up a serious infection – docs say that could be fatal. I’ll try and strengthen his immune system by promoting a good gut. Many thanks Ann

    2. I wud seriouly look into alternative treatment. Daily abx for life starting as a child makes me shudder at the thot. Cant hurt to investigate on ur own further (or with an ND, etc), right?

    1. Hi Anna,
      From what I understand, yogurt is a great start, but the sheer number of live bacteria in a probiotic puts yogurt to shame. Many people say dairy kefir has about 8x the strains vs. yogurt, so if you want a food source that will pack a punch, kefir and other fermented foods are better. Hope that makes sense! 🙂 Katie

      1. Thank you for the info. I make yogurt, Kefir, kombucha, and I haven’t made any fermented veggies for a while, but I’ll eat Bubbies Sauerkraut straight out of the jar. I’d hate to take something else, even something as beneficial as a probiotic pill, if I could get what I needed by eating real food.

  11. Nana Phyllis

    Having had a knee replacement, I do have to take antibiotics when I have any type of surgery, including oral. I drink water kefir, about 16 oz./day, most every day. I also eat organic yogurt most mornings. I hope this puts enough probiotics into my system to counteract antibiotics. I haven’t had antibiotics for several years.

      1. Kefir has alot of strains, fermented veggies are good sources too. But yogurt is one, maybe 3 strains. I take a supplement that has 15 strains, 35 billion cfu.
        Make sure to eat prebiotic containing foods too. The probiotics are critters and the prebiotics are their food. Need to feed them to keep them around. Probios often contain prebios to help with this.

  12. Thanks for the info!

    I was curious, are you aware of any research that shows that the method of getting antibiotics changes the effect on the gut flora? I was specifically thinking about injections/IV antibiotics vs. oral ones. After a c-section with my firstborn (and corresponding IV antibiotics) I wondered if there was a chance I (or he) would be less affected than having all those antibiotics go straight to the gut to wreak havok. We both did probiotics anyway, but I still wonder…

      1. I’ve wondered about this too as I had IV antibiotics during labor with all four of my kids.

        With my first I didn’t know to use probiotics and he had more issues with digestion and skin than the others.

        I enjoyed this post because it removes some of the fear of giving your kids antibiotics. I avoid them like the plague, but last year my daughter had pneumonia and was having trouble breathing; I knew she needed them and so we moved forward. I sometimes get annoyed with the extreme view of some natural blogs, acting like antibiotics are NEVER necessary and making you feel guilty for using them. We used tons of probiotics during and after and her health has not seemed to suffer at all from using antibiotics.

        Another point is that beneficial yeasts (like s. boullardi) are not killed by antibiotics and can be great for keeping candida at bay during a round of antibiotics.

  13. We were fortunate when our kids were small to find out about colloidal silver as an antibiotic. Thus not so hard on system, although we did give them yogurt after 3 hours of a dose of silver to keep that going right.

    1. Janet, If you have time would love to hear how (how much, what ages, how long?) you use silver as an antibiotic! Pam

  14. I’d want to see the citation on the research for not finishing a round of antibiotics. I don’t think it’s a good idea to just put that out there without a citation because it could be encouraging people to stop their antibiotic regimen because Catherine heard it somewhere. I’m not necessarily saying she’s wrong, but a citation seems like common sense for such a huge statement.

    Otherwise, great post!

    1. Catherine Clinton ND

      Hi Sonja! Great point, we should all be digging deeper for the actual research! Here’s a great article from Discover magazine that explains the shift in thinking about antibiotics with links to the research at the bottom:

      This is not say that antibiotics are horrible, they are a necessary and important pieces of modern medicine but they have been woefully over-prescribed and this is leading to major problems.

      Thanks Sonja!

      1. It seems antibios/virals are now very short duration. I have been the only one my whole life who ever finished a Script of them anyway, i swear. My friends always took only about half to 2/3s of theirs in spite of me imploring them to stop creating superbugs!

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