Best Probiotics for Babies and Infants

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Best probiotics for infants
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I’ve mentioned before how important gut health is for adults, kids, and babies. Much of our immune system resides in the gut, so making it as healthy as possible only makes sense. We try hard to optimize our guts by eating fermented foods, eliminating sugar, and taking a quality probiotic, but a baby’s sensitive gut needs a special approach.

I get so many questions about if babies should receive probiotics, what type and how much. Fortunately, there are several quality baby probiotics for infants on the market to help improve digestive health even when baby hasn’t had the best start. Please note that I am not a doctor and this is in no way medical advice. Especially if a baby has a specific digestive challenge, I recommend working with a qualified practitioner or expert.

How a Baby’s Gut Is Colonized

Where does the bacteria in our guts come from in the first place? There are a few determining factors:


Experts once believed that a baby was in a completely sterile environment in the amniotic sac. There is now some evidence to dispute this and it seems that baby may be exposed to beneficial bacteria even in utero. More research is needed here, but another great reason for moms to optimize their gut bacteria during pregnancy.

At Birth

Baby’s gut is colonized at birth via the amniotic fluid and the bacteria in the birth canal.

In a perfect world where women eat only nutrient-dense diets full of raw, cultured dairy, and fermented foods (and who had mothers and grandmothers who did the same), and who never took antibiotics or over-the-counter medicines, this is a very good thing.

Unfortunately, many of us have inherited our own mothers’ (poor) gut health and grew up during a time of nutrient-poor convenience foods. These convenience foods are high in sugars and starches which feed bad bacteria in the gut. These foods are also devoid of beneficial bacteria so we never get a chance to naturally replenish the gut.

It makes sense then that our babies may not be getting the best microbiome from the start.

To make matters more difficult, babies who are born via cesarean like my baby #3 don’t get access to the good bacteria in mom’s vagina (if she has them in the first place). Those babies are colonized by mom’s skin or other bacteria in the sterile operating room.

From Breastmilk

Babies’ gut microbiomes are further colonized by breastmilk. Breastmilk contains all of the nutrients babies need for optimal health, and it also contains live enzymes and beneficial bacteria (plus antibodies and many other beneficial compounds).

What mom eats (as well as other environmental factors) change the microbiota makeup of breastmilk. So if mom isn’t eating a healthy diet rich in probiotics, her milk may not be as good as it could be (though it’s still amazing and the best choice for babies when possible).

Additionally, if babies are given formula or solid food before about 6 months of age, it can negatively affect the gut microbiome.

(Just a note here: I do realize that in some instances formula is the only option and I’m not trying to shame anyone. I barely squeaked by without needing to supplement with formula with #3. I just want to point out that there are many factors that impact the microbiome of the gut, and this is definitely one of them in today’s society.)

How Gut Bacteria Affects Baby

If you ask any random group of moms and grandmas, you’ll probably hear plenty about allergies, eczema, colic, and gas in infants. These health issues are common today because of our collective bad gut health, but that doesn’t mean they are normal. Babies shouldn’t have these issues.

Why is it happening? I have some guesses:

  • Beneficial bacteria is important for proper digestion of food (especially starches) and to absorb nutrients. Without this balance in the gut, babies can have digestive issues like colic, acid reflux, and gas.
  • Gut health also plays a big role in overall immunity. As Hippocrates said, “All disease begins in the gut.” Studies back this up. Interestingly, when mice with poor gut bacteria were given a fecal transplant from a healthy mouse their health improved.
  • As far back as the 1930s researchers have noticed a connection between the gut and skin. Studies show that many people with gut health issues also have skin issues. Other studies found that probiotic supplementation decreased skin symptoms. Anecdotally, I know many families who have seen marked reduction in skin issues like eczema when they began addressing gut health.

Though gut health is incredibly important for optimal health, and many of us don’t have very good gut health, there’s still hope. Whether baby was born via cesarean birth, fed formula, given solids too early, or simply inherited mom’s poor gut health, there are easy things we can do to improve gut health naturally.

Natural Ways to Improve Baby’s Gut Health

If you suspect your infant’s gut health isn’t what it should be, here are some proactive steps any mom can take:

If Breastfeeding, Improve Mom’s Diet

The first step to improving a breastfed baby’s gut health is for mom to improve her diet. Mom continues to inoculate baby with her breastmilk and the healthier she is, the healthier her milk is.

Foods to eat to improve gut health include:

  • Bone broth – The gelatin and collagen in bone broth help to seal the gut lining and glutamine helps to strengthen it. Here’s why and how to make it.
  • Fermented foods – An excellent way to get probiotics is unpasteurized fermented foods like yogurt, sauerkraut, and kimchi. These foods are naturally rich in beneficial bacteria. You can make them at home or there are now several quality brands in stores, too.
  • Pastured meats and wild-caught fish – These sources are higher in omega-3 fatty acids that help reduce inflammation. We use this source for meats and this one for fish and other seafood.
  • Cooked vegetables – Vegetables are important for their nutrient profile but can be rough on a healing digestive tract. Cooking vegetables makes them easier to digest.
  • Omega-3s from fish oil – We get ours from quality seafood and our favorite fish oil supplement.
  • Vitamin D – Vitamin D deficiency is widespread in our indoors, workaholic culture and has been linked to leaky gut. To combat this our family spends time in the sun (with these precautions) and takes a quality vitamin D supplement when we’re not getting as much sunlight.

Of course nutrient-dense foods are especially important during pregnancy and nursing but avoiding nutrient-poor (high-starch) foods or other foods that can cause more gut dysbiosis is just as important.

Avoid Foods That Harm the Gut

In addition to adding in nutrient-dense foods like the ones above, it’s important to avoid consuming foods that undermine gut health:

  • GlutenThis one is controversial, but gluten can cause the gut cells to release zonulin, a protein that can break apart the tight junctions holding your intestines together (resulting in leaky gut).
  • Grains – Even gluten-free ones. Most grains contain anti-nutrients (like phytic acid) that are difficult to digest. Soaking and sprouting grains can help make them easier to digest, but grains are also high in sugars/starches which can feed bad bacteria. It’s best to avoid them for baby’s sensitive gut, at least at first.
  • Refined sugar and artificial sweetenersSugar can feed bad bacteria and cause more inflammation. Artificial sweeteners have also been connected to depleted beneficial bacteria. Instead of refined and artificial sweeteners I choose to use natural sweeteners (like maple syrup and honey) in moderation, or even stevia.
  • Vegetable oils – These oils contain a high percentage of omega-6 fatty acids and are highly inflammatory. My family never eats these and only sticks with healthy fats like coconut oil, lard, butter, and tallow.

A probiotic supplement for Mom can be helpful too especially when the gut bacteria are seriously depleted.

Give Baby Nutrient-Dense, Easy-to-Digest Foods

Once baby is ready for solids after six months of age, I follow the same real-food principles above for his/her foods. Here is what I fed my babies and in what order when first introducing solid foods.

Give a Probiotic Supplement to Baby Directly

Breastfeeding is the best way to give baby probiotics, but if breastfeeding isn’t possible there’s still hope. Probiotic supplements can be given to baby as early as a few days old. Also, even if baby is breastfed, it can’t hurt to add a bit more probiotics to baby’s diet (especially if mom’s gut health isn’t optimal).

If you’re bottle feeding you can add probiotics to the bottle (or homemade formula recipe).

Best Baby Probiotics for Infants

In nature we’re not likely to find sources of just one or two strains of probiotics by themselves. It’s much more likely that there will be many strains present (some of which we may not even know about yet). The best probiotics for infants will include a wide variety of strains, similar to those found in fermented foods (or the dirt).

Option 1: Fermented Foods

If baby is eating solid foods, fermented foods are one of the best ways to get probiotics into him. Fermented foods have many more strains of bacteria than supplements and also are more likely to make it into the colon. Here is a great source for anyone trying to get started with ferments.

Option 2: Quality Baby Probiotics Supplement

Though any good quality probiotic will do, I like to stick with a children’s probiotic (or one that has the same strains). The reason is that there are a few strains that are especially beneficial to babies and children.

  • B. BifidumThis is one of the first strains to colonize baby’s intestines. It’s found in breastmilk and in the vagina.
  • B. InfantisThis is the strain that is most commonly found in infants and one of the first the mother passes to the infant after birth. This strain is known to acidify the gut to make it inhospitable to foreign invaders.
  • L. Rheuteri – This is a strain that is most commonly found in children’s probiotics. Studies show it is beneficial in treating colic among other common health issues.

Probiotics for infants and children typically come in two forms:

  • Liquid probiotics – This is probably the best form of probiotics for infants as they are easy to use. Liquid drops can be put directly into baby’s mouth or dripped onto the nipple or a pacifier.
  • Powdered probiotics – Powdered probiotics can be used in a similar way. Sprinkle some powdered probiotics on the nipple or a pacifier. Or just sprinkle it on their tongue. I would avoid mixing it with water as the added water can mess with baby’s electrolyte balance.

While there’s no perfect probiotic out there (why I like to stick with food-based probiotics), the above are good options that I would use if I had another baby.

How to Introduce Baby to Ferments

Lacto-fermented foods can be an acquired taste, so it makes sense to offer them as early as possible so baby gets used to them. As soon as baby is eating solids, he can try ferments. Eating ferments during pregnancy is the best way to give baby an early taste. But if it’s too late for that, start out slow at about 6 months.

  • Start by giving him a little taste of sauerkraut brine on a spoon. He may make a sour face or he may lunge forward for more.
  • If he doesn’t like it offer again in a week. Keep trying until he begins to enjoy it.
  • After trying the brine you can offer sauerkraut or other fermented vegetables.
  • Yogurt is a ferment that most babies will like but some moms prefer to wait on dairy until closer to the first birthday. Dairy can also be tough to digest for anyone with suboptimal gut health.

Best Probiotics for Infants: Bottom Line

Breastfeeding is the best way to give baby probiotics (and heal their gut), but I realize it’s not always possible. Luckily, giving baby probiotics in other ways can help repopulate the gut and reduce health issues associated with bad gut health.

Have you dealt with gut health issues? How did you introduce more probiotics?

Katie Wells Avatar

About Katie Wells

Katie Wells, CTNC, MCHC, Founder of Wellness Mama and Co-founder of Wellnesse, has a background in research, journalism, and nutrition. As a mom of six, she turned to research and took health into her own hands to find answers to her health problems. is the culmination of her thousands of hours of research and all posts are medically reviewed and verified by the Wellness Mama research team. Katie is also the author of the bestselling books The Wellness Mama Cookbook and The Wellness Mama 5-Step Lifestyle Detox.


15 responses to “Best Probiotics for Babies and Infants”

  1. Brittany Robinson Avatar
    Brittany Robinson

    Katie, the powdered probiotics by Klaire Labs, says for infants starting at 6 months old. Would it be okay to give to infants 2 months old?

  2. Ally Avatar

    What a great article! I unfortunately have to have a cesarean section and I have been googling relentlessly (with little success until now) how to mitigate the side effects thereof. This gives such a well rounded view of all the things I still have within my power. Thank you!

  3. Stephanie Cole Avatar
    Stephanie Cole

    Hi there! I’m using Qiara Probiotics for about….hmmm..almost 2 years now! I find it really good as my kids grew finely with it and I guess it became a hobby that we take it regularly. I hope you’ll find a suitable probiotic for you! 🙂

  4. daniela keating Avatar
    daniela keating

    Hi! What is your favorite brand for probiotics? There are so many out there and I can’t seem to decide witch one. I am considering Mommy’s Bliss to be the one to get but I wanted to hear your opinion.


  5. Rosie Avatar

    I listened to your recent podcast with Kiran about probiotics. Given this new information, are you still comfortable recommending eating fermented foods as a source of probiotics? Or even other probiotics that are not JustThrive brand?

    I’ve used Bio Kult a lot for me and my kids and they say that they are resistant to the harsh stomach acid environment, but after listening to your podcast I’m really not sure. How we are supposed to know if any of the probiotics we purchase in the stores are effective at all?
    I like how you point out other ways to improve gut health and diversity aside from relying on a pill.
    But for those who need extra help with a supplement it would be great if we had a resource to know if the brand we choose is effective at all.

  6. Christina Avatar

    I purchased the Bio Kult probiotics and they look like they have light brownish red specs in the white powder , is this normal? I contacted amazon for a replacement because I have purchased them in the past and do not remember this color variation. Could you enlighten me to whether those specs are normal? Thanks much!

  7. Maria Avatar

    Hi Katie! I have two questions. First, with the liquid drops, the link is to a women’s probiotic supplement. If you were to use this with your infant, what dosage would you give him/her? Second, I recently listened to your podcast with Kiran Krishnan, talking about spore-based probiotics being significantly more effective than other probiotics. Would you recommend this (Just Thrive probiotics) for use infants? If so, what dosing would you suggest?

    Thank you!

    1. Katie Wells Avatar

      I give my kids Just Thrive and would have been comfortable giving it to my babies as well. They’re nice because they survive at high heat or cold temps so they can be added to pureed foods, smoothies or even hot food recipes.

      1. Christianna Avatar

        Can I give the JustThrive probiotics to my 13 month old?
        If so, could I open the pill to get the probiotics out?

        1. SJ Winter Avatar

          Always double-check with your pediatrician but that’s what we did. Yes, you can open it and sprinkle it into their mouth or if you are still breastfeeding, you can put some around the nipple.

  8. Rebecca Avatar

    The liquid probiotic you recommended has stevia and monk fruit as other ingredients. Should newborns consume stevia and monk fruit? I am guessing not… but know it’s probably a very small amount. Still… I am hesitant

  9. Ninon Avatar

    My babygirl (almost 2) has been drinking kefir everyday since about 8 months old… is this a good thing to do? 🙂 I use raw organic milk to make it.

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