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5 Reasons Your Baby Might Need Probiotics (& isn’t getting them from food)

She needs baby probiotics! Breastmilk sometimes isn't enough.

When my first was born, I was adamant that not only was “breast best,” but that it had to be sufficient, 100%.

There was no way my baby could need supplementation, I thought.

Breastmilk was nature’s perfect food, and my body was created to produce it for my baby.

I cried and cried, wracking sobs, when we were told we “had” to supplement with formula.

I was so stubborn.

I think I only gave him an ounce and a half or so, not even enough to drag his skinny little body anywhere near back to his birth weight, and I just kept nursing, and nursing, and nursing.

I didn’t even realize that he was napping more than nursing, comforting more than sucking.

Looking back, I’m probably lucky that he made it through and that my body and his finally got in sync on the whole nourishment equation.

He’s still the skinniest kid you’ll ever see (at age ten, the bathing suit he put on today is a size 6-7) but is healthy and has a great appetite for both healthy and, much to his mother’s chagrin, unhealthy foods.

It’s a good thing my own mother wasn’t so stubborn, and that a neighbor had the guts to tell her she was worried about newborn Katie’s health – when she finally took me in, I was nearly starved and suffering from water intoxication from the bottles of water my mom had been instructed to give me after each nurse. (Sigh.)

She kept trying for a while along with the formula, but it wasn’t meant to be.

How to Get the Best Start with Babies’ Gut Health

Key Steps You Can Take Today to Heal Your Gut

We talk a lot about healing the gut for adults, but here at Kitchen Stewardship®, we prefer prevention whenever possible. If you are expecting or will be someday, try to focus on these strategies to give baby the best gut health start possible:

RELATED: Breastfeeding a Baby with Food Allergies


Genevieve from Mama Natural offers great week 2 week pregnancy updates. I wish I had these when I was pregnant!

I’m so happy to introduce you to Genevieve from Mama Natural. I loved her video series for years before I met her and I’m proud now that our families have become dear friends. She’s such a sweet, genuine woman!

Not only do I love her weekly pregnancy updates, but she is now offering a Natural Baby Care Course. I wish I had this with mine!

Imagine having access to a team of expert health professionals in your home, whenever you need them, as you raise your newborn.

  • A holistic pediatrician to give you tips on what to feed your baby.
  • A board certified lactation consultant to help you master breastfeeding.
  • And a firefighter / CPR instructor to make you aware and prepared.

This is a masterclass in everyday baby care. You’ll be supported for ALL the challenges that come up with baby in this program.

  • It’s easy to access. Watch the classes on your own schedule. No traveling across town after a long day at work.
  • It’s comfortable. Learn in the privacy of your own home—no sterile classrooms filled with rows of uncomfortable chairs. Simply curl up in your favorite spot and soak it all in.
  • It’s fast, but comprehensive. Other baby care courses speed through the most important topics to cover it all. We don’t do that. Instead, we unpack all of the issues that come up postpartum, but we do so in small chunks so you can squeeze the education into your busy life.
  • It’s affordable. Our course is priced lower than in-person classes and less than most online alternatives as well.

More of a book person? You must check out Genevieve’s week-by-week Guide to Pregnancy & Childbirth. It’s the natural answer to “What to Expect” and soooo comprehensive and beautiful!!

What About Vitamins for Babies?

Beyond “supplementing” with formula, which hopefully is a last resort but necessary for many mamas (even though I still hate that ounce and a half my eldest consumed, that’s just my mommy guilt ringing in heavy), do babies need supplemental vitamins or nutrients that aren’t available in breastmilk? (By the way, when formula is necessary, some are able to use a homemade baby formula, but it’s a big commitment.)

The most commonly recommended by pediatricians is Vitamin D, and I was also stubbornly opposed to that for my first three children.

Whether I’ve been beaten down or just convinced at this point, Gabe IS receiving a Vitamin D drop (nearly) daily for a couple of reasons:

  • My new family doctor had a brand that had zero other ingredients and was not colored, so no bibs or staining practically and no ingredients I wouldn’t allow past his lips nutritionally.
  • I keep reading from reputable sources that breastmilk is not a good carrier of Vitamin D.
  • He was my first baby born in the winter, so his own chances of sun exposure were zilch.
  • My own Vitamin D was below the recommended level, even with fermented cod liver oil regularly in my diet. So if my levels were too low, even IF some got through in my breastmilk, it wasn’t going to cut it.

So we supplement with these drops (also available on Amazon).

And I’m dealing with it okay, a good reminder to be humble and not ride on the coattails of my own (old) research and past decisions, which are sometimes emotionally based and not always perfect (gasp!).

RELATED: Seed Synbiotic Probiotic Review & High Quality Fish Oil

This would be a good opportunity to remind you that I am neither a doctor nor medically trained, and any actions you might take after reading this post, which is full of opinions, some sources, and some personal experience, not advice – are your responsibility.

Baby’s Delicate Microbiome

The stage is set.

You know my first babies had nothing but breastmilk for the first six months, and after that they certainly didn’t have vitamins or supplements of any kind with their limited food intake, until I start a little FCLO intermittently around 18 mos. or older, depending on the kid.

You might also know that my whole family takes one supplement every single day, the only one we are 100% regular with (ok…we’re human…it’s probably about 95% of the time actually).

That’s probiotics.

I take them…but does the baby need them too?

With all the foods that my normal probiotic (or “probie” as our 3-year-old dubbed it when he learned to talk) includes, I haven’t given any to him because I still do adhere to the “introduce only one food at a time” philosophy to be able to watch for food sensitivities, and we haven’t yet started homemade yogurt (I typically wait for dairy until at least 8 months).

Plus, until recently I would have stubbornly said that OF COURSE breastmilk gives him every darn thing he needs! It’s nature’s perfect food!

But…when I read Lydia’s pointed article about the “5 Reasons American Kids Aren’t Healthy Today” I have to consider that I can’t do anything about the quality of the soil, the fact that I was formula-fed and grew up with margarine, white sugar, and some processed stuff in the midst of my mom’s amazing homemade food, and my general lack of sleep + baby’s terrible sleep habits.

We’re going to deal with those effects for a lifetime.

In spite of my efforts in the kitchen, in spite of the mostly excellent nutrition we provide here at the Kimball house…life ain’t perfect. I have to be open to the fact that even my kids might need some rebalancing. Can you hear the hubris just dripping?

And today we’re focusing on the very sensitive microbiome, of primary importance for our digestion, our immune system, and our overall health.

Could these tiny babes in arms actually be in need of probiotics as well, a little something to make sure their resident bacteria are setting up shop properly? And if so, what kind is safe for infants?

Here are five reasons you might want to consider a probiotic supplement for your little one:

Your Baby Might need Probiotics

1. Antibiotic Treatment

Antibiotics are very common in hospital births, both for moms who are Group B Strep positive as a preventative measure and for a variety of other reasons. Antibiotics during pregnancy are also of concern. Antibiotics even interfere with the effectiveness of probiotics, sadly (source).

This study discusses the massive importance of getting the microbiome right in the first few years and this one confirms that antibiotic use both in pregnancy or the child’s first year of life can alter the microbiome so much that the child has a far greater risk of obesity – 84% higher! Much research is now finding that the proper gut flora impacts weight gain, and it may be the cause of obesity in many people who just ‘can’t seem to lose the weight.’

It seems like a no-brainer to me that if baby or mother is given antibiotics during pregnancy, labor, or infancy/breastfeeding, that taking care of rebuilding the microbiome is of primary importance.

2. C-section births

The study mentioned above also found that C-sections resulted in a 46-percent higher risk of childhood obesity, controlled for maternal age, ethnicity, birth weight, sex, breastfeeding in the first year, and gestational antibiotics or delivery mode.

And this one found that “infants born through C-section had lower total microbiota diversity during the first 2 years of life,” as well as a less active immune response. The immune response may be related to an increased risk of autoimmune diseases such as Crohn’s Disease (source) and Celiac (source).

C-sections are likely to result in different flora vs. vaginal delivery in part because of the baby’s lack of exposure to mom’s flora in the birth canal (which calls into question the expedient births I have, to be honest!).

3. If mom has imbalanced flora at baby’s birth

This study demonstrates that probiotic supplementation in mothers during pregnancy can impact the baby as it grows, so it certainly makes sense that whatever gut imbalance mom might have would be passed on as well.

Another demonstration of the relationship between gut flora and the mother-fetal-infant relationship underlines the obesity link again, and although I haven’t read the full study, the references are many and fascinating.

How do we know if mom has balanced flora or not? Because of the relative insufficiency of the soil of our age and our culture’s lack of reliance on probiotic foods beyond the occasional yogurt, I’d gander that it’s more likely you’re unbalanced than not. If mom experiences any of the following, she (and baby) might benefit from probiotics:

Bristol stool chart
  • constipation (going less than once a day especially, but even “regular” once a day if the stools are a 1-3 on the Bristol stool chart above (more info here on that)
  • eczema or skin issues
  • IBS symptoms
  • type 6-7 stool from the chart indicates too-fast digestion too
  • candida symptoms or recurrent yeast infections
  • and I’m sure many more…

Can you just eat more fermented foods?

Sure. Catherine Clinton, ND, founder of WellFuture, shared this with me via email:

I still think that fermented foods, especially if made at home, are one of the cornerstones of health. I’ve been using our extra scobies in the compost and our garden is going crazy this year. I wish I could find some research about how that could transform our food and health…

And the food is good…but it may or may not be enough, depending on the other factors.

4. Formula Feeding

As much as formula makers have tried to mimic breastmilk, they haven’t gotten all the pieces yet, as demonstrated by this study which found that “breast-fed newborns have been demonstrated to carry a more stable and uniform population [of microbiota] when compared to the formula-fed ones.”

In fact, when breastfed infants are supplemented with just a small amount of formula and when they begin solid foods, their microbiome begins to shift more toward the (less desirable) formula-fed pattern. But luckily, supplementation with probiotics has also been shown in the same study to mitigate some of those negative effects.

5. Let’s talk Poop, Picky eating, Perfection, and Pain

Our Favorite Cloth Diaper for All Ages Gabe approved Softbums

Moms, sometimes you have to go with your gut.

If your gut says that something is not ideal with your baby’s digestion, either because of irregular or painful bowel movements, picky eating (for you or them), belly pain or perhaps colic symptoms, it’s not much of a leap to wonder if probiotics might help.

We live in an imperfect world, and I would guess that none of us eat a perfect diet across the board. (I don’t!!)

To make up for gaps in nutrition, genetics, soil health, the environment, and lifestyle, a supplemental probiotic is something that may help the body lay the foundation for good health throughout all of life. The early seeding of healthy bacteria is that important – not that we can’t make a good impact on our microbiome as adults, but the first five years are a window of opportunity that can’t quite be compensated for fully later on.

What probiotic to use for baby???

Because of the care taken in the formulation of WellBelly, a powdered probiotic especially for infants and young children, I don’t hesitate to recommend it.

Each ingredient is explained with peer-reviewed sources, and I really appreciate the focus on a young child’s digestive tract.

You can read more about the thought behind WellBelly in question 3 of this great interview with Catherine Clinton, founder of WellFuture. Every strain of probiotics has been carefully thought out for an infant (and what’s NOT in there is just as intentional).

UPDATE: I also have discovered a few more great infant/child probiotics from Buddies in my Belly powder and Mary Ruth’s liquid (use code KCRF15 for 15% off!), both easy to administer to infants.

And you, Katie?Well Belly probiotic

A reader asked me the other day on Facebook when I shared about WellBelly if I was giving it to our littlest one, Gabe. My response was that I wasn’t, only because he isn’t really eating food yet and we don’t use bottles at all, so I had no way of administering it to him.

I was a little startled by the question, and that plus writing this post has gotten me thinking.

Gabe has always had strange digestion. In fact, we were in the ER at four days of life with him because he hadn’t had a bowel movement in 48 hours.

He was fine, but he pretty much had only one or two poops a week for the next three or four months.

Then, rather suddenly, he switched to a morning BM quite consistently. One a day, within an hour of waking.

His first bite of food changed that!

Makes sense, now that I’ve read some of the research cited above, but even without the study to prove it I hypothesized that something about food had permanently altered his digestion (now I’d say gut flora) because his poo changed in smell and consistency for about two days after two bites of egg yolk.

He now goes days again without a BM.

And I saw too much of myself in the posts about adrenal fatigue that we’ve been sharing recently.


Perhaps I’m resting on my real food laurels a bit much again. Will I learn my lesson and get this kid on WellBelly soon?

Let’s cut the excuses – I’ve read a tip before that a little finger dipped in probiotic powder could easily get some into an infant, but I conveniently forgot that.

I don’t think it would be a difficult thing to add to our morning routine since we’re already giving the other kids probiotics anyway.

Why leave Gabe out?

UPDATE 2021: Which probiotics are the best?

Now that you’ve heard all about our family’s poop…how’s yours?

Do you take a daily probiotic supplement or regular fermented foods? Does baby?

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

About The Author

21 thoughts on “5 Reasons Your Baby Might Need Probiotics (& isn’t getting them from food)”

  1. I used WellBaby when ds5 was 10wk old because I had read about it on your blog! He had to be given antibiotics and so I pumped and then gave him the milk and the probiotics in a syringe while I nursed. I am about to order some more!

  2. As a mom who literally does not make enough milk to keep my babies alive due to IGT, please get over that one a half ounces of formula you gave your son. You could have written the article and gotten your point across without making such an issue of that. Any mom who has been forced to supplement is going to continue to feel the dagger of guilt and pain about having to supplement with comments like that. You are free to share your own experiences but you also have a wide audience and not every woman needs to know about your unneeded remorse over a little bit of formula, it’s really selfish of you

    1. Thanks for the important reminder, Liz – I know not everyone can breastfeed, and my mom is a good example. It’s a tricky balance between being real and writing about my own experience and giving advice that others can follow. I actually already edited the post to tone that down after someone reminded me of this point on Facebook. Hugs! Katie

  3. My pediatrician says that the baby will get some probiotics through breastmilk if I take them. So I would think that if mom is taking them then you wouldn’t have to give them to a baby that is exclusively breastfeeding.

  4. C section birth, formula supplementation for 24 hours, IV antibiotics for major infection for me, oral antibiotics ( several rounds) for me…. I made the choice to give probiotics from birth. Mt little one pooed several times a day on breast milk, and now poops two or three times on solids. His poop still smells like breast milk poop! I feel fairly sure his digestive system is healthy. I’m trying to avoid grains until one. We’ve done yoghurt most days though. He seems a healthy little babe.

  5. Our adopted baby get probiotics in his home made formula and some added ones each day. His reflux is almost gone and his eczema is almost gone too. He gets no wheat or dairy. Our bio daughter was nursed for 5 months or so then got commercial lactose free formula due to constipation with regular formula. We have started to give her the same probiotics as the baby and she is more pleasant. Who knows.

  6. I was just like you with baby #1 — breast milk should be enough! But the more we learn about food and nutrition, the more we realize that (as everywhere else) things are not always as they “should” be. (What do “organic,” “cage-free,” and “all natural” mean to you?) 🙂

    After baby #1, I was diagnosed with Hashimoto’s autoimmunity and then candidiasis within the first month of pregnancy with baby #2. I was already gluten-free for the Hashi’s and then had to remove all sugar and sweeteners, and I haven’t added them back yet. Now #2, almost 3 months old, is getting a vitamin D drop and 1/4 teaspoon of Baby Biotics powder almost daily. She has full-body eczema yet is full of smiles, but it makes me cry that I caused her dry, itchy skin. It’s my fault.

    I try to make things better for my daughters by feeding them real and fermented foods, but honestly, sometimes I wonder if it’s even possible to overcome a family history of formula feeding and gut dysbiosis. I’m going to try anyway, but it just breaks my heart thinking about what an uphill climb they may have fighting for their health in a country and culture that cares more about the lobbying dollar than it does about true public health.

    1. My eight month old baby had oozing, weeping, itchy, bad eczema until we had some allergy testing, and found that egg whites, wheat, peanuts, and dairy were possible problems for him. I had already been off wheat for months to try to help my hypothroid disease, but after the removal of each other food separately, my baby is now eczema-free, with beautiful, healthy skin. Our allergist was almost no help, she insisted it wasn’t a food allergy, and told us ways to cope with the eczema, it was my favorite osteopath, the one that treats me for the thyroid problem, that helped us with more testing. Also, those blood tests are tricky things, the allergist did some of the same ones as the osteopath, but the first ones showed up negative, and the second set showed the problem foods. With my first child, who also had bad weeping open sores of eczema, it was that same osteopath (doctors of osteopathy are Doctors with special training in certain areas, many have their own specialties, a good DO will be very helpful in diagnostics) who told me to go off of the Big Eight for a time, and helped us, along with the allergists tests, to figure out that our child had a tree nut allergy. Ninety-five percent of that child’s eczema disappeared with me going off of tree nuts.
      Have you tried going off of any of the other Big Eight (most common allergens), one of those might be the culprit!
      Honestly, I think that the 99 percent of mothers are trying to love and mother their children well, but get all the real and false guilt, while the 1 percent of mothers that are actually bad don’t get any of it? Totally unfair.

      I hope you find the culprit and that your child’s skin gets healthy. It was months before we figured it out, but we did, and what a profound change we got!

    2. Beth,
      That Mommy guilt is awful stuff! I’m so glad Parsley chimed in with her empathy and great advice; I’d second both. I’m guessing you’ll find a “trigger” food somehow, someday, hopefully sooner than later! Are you doing a full candida diet? You might be able to get past the bump of all this autoimmunity and mess in your history via a gut-healing diet like GAPS, tricky while BFing but not impossible. May God bless your detective work for baby 2 and your efforts keeping your Hashi’s and candida in check! Katie

      1. Thank you, ladies. No, I am not doing a full candida diet. I include fruit and dairy (raw milk/kefir + regular cheese, yogurt, etc.) and use xylitol and stevia extract for my treats. I always avoid soy, though I do occasionally use organic tamari because the soy has been fermented.

        Baby #2 did not have eczema until she was two months old, and I was thinking it was probably triggered by what was in the disposable diapers we bought at that time because the rash started in the diaper area and worked its way all over her trunk, limbs, and face. We quickly bought chlorine-free diapers instead and are using cloth as much as possible now, and the rash has dried up, though her skin still feels like sandpaper no matter how much coconut oil, shea butter, or argan oil I rub in. So I didn’t suspect a food allergy.

        I do see a D.O. for my thyroid, so I’ll talk to her about it at the end of July when I go. Baby #1 had an egg allergy at 1 that she was able to “outgrow” by taking NR Glow and lots of homemade broth. When we had #1 tested, the allergist was a complete jerk who told us we shouldn’t even be there, that kids get hives all the time and it’s no big deal. (My own mother agreed with him.) I came very close to losing my cool at that appointment!

        1. How old was your child when her egg allergy was calmed? How long was it from when you discovered that eggs were the problem was until she was healed? What was the thinking behind using the NR Glow?

          1. We discovered the egg allergy when she broke out in hives all over at her first birthday party. (I bawled.) We had been careful to order a wheat-free, food-coloring-free smash cake for her, but there were egg whites in the icing and she reacted. I think she was about 2 before I felt comfortable giving her cooked eggs, and she had no visible or behavioral reaction.

            The NR Glow is supposed to be an immune booster and can help with eczema. I have no idea if that was what actually helped. She would have small, bizarre reactions to other foods (red spots on her face), but I could never see a pattern. Now she’s 3 and has no food reactions at all — other than behavioral weirdness when someone gives her processed or super-sweet treats. We all get plenty of fermented foods for probiotics and focus on eating real food. Katie helps a lot with that! 🙂

            1. I’m really hoping that our baby’s egg, well that all of his food problems disappear when he’s a bit older too. I’m going to be fermenting more vegetables this summer, and learning to make water kefir, so hopefully that will help make our insides sturdier. Thanks for your reply. I’m always encouraged when I hear of other people’s little folks growing out of their food allergies/sensitivities.

              1. Oh Parsley, I hope your baby’s food problems disappear, too! We mamas work so hard in this generation to keep our babies healthy; I wonder how hard our babies will have to work should God bless them with children? It breaks my heart to think about it.

                I haven’t tried water kefir, but we do love kombucha and raw milk kefir. I’ve made kimchi, but overall I’m not so good at fermenting veggies — and actually eating them. Good for you!

                I’m praying that my 3yo’s issues actually did resolve and didn’t instead turn chronic. The baby, well, I just don’t know yet. The best plan I have right now is just to wait a few years until I’m not breastfeeding anymore and then put us all through GAPS. Right now doing GAPS is an overwhelming thought!!

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