Probiotics for Infants: Everything You Need to Know

You probably know that what you feed your baby is important. From breastfeeding to starting solids, to getting them to eat vegetables, you’re making sure baby is healthy from day one. But in some cases, we may need to do more. Probiotics for infants, whether in food or supplement form, just might be one of the best things you can give baby to support his health.

How baby’s gut is colonized

It was once thought that amniotic fluid was sterile, but we now know that it’s not, and it’s your baby’s first introduction to bacterial colonization. The kind of bacteria in the amniotic fluid depends on the kind of bacteria in mom’s gut flora. During a vaginal birth baby is further colonized by bacteria in mom’s birth canal (during a cesarean birth baby is often colonized by mom’s skin).

In a perfect world, mom would have great flora to pass onto her baby and we wouldn’t have to mess with the baby’s virgin gut. In reality, many women don’t have optimal microbiomes, and this affects their children. Our gut flora was colonized by our mother’s and her’s by her mother’s and so on. Over the last century we have been subjected to antibiotics, high sugar/starch diets, and lots of processed foods which all degrade our gut flora. For many of us, we have a long line of bad gut health.

So if you or your mom (or even your grandmother) have ever taken antibiotics, eaten store bought bread or pasta everyday, or eaten fermented foods fewer than once a day, your baby may need probiotics. That’s why probiotics for infants are so important.

How does gut bacteria affect health?

As Hippocrates says, “All disease begins in the gut”.  An imbalanced gut microbiome can cause:

✔ Digestive issues

Without the proper balance of gut bacteria, baby may have colic, acid reflux, constipation, diarrhea, or develop more serious digestive issues like Irritable Bowel Syndrome (IBS) or Crohn’s Disease. A study found that fecal transplant in adults (placing a bit of “healthy” poo into the colon of an unhealthy person) cured 91-93% of patients with digestive issues. This supports the idea that good gut flora can treat and prevent many digestive issues; and why we may want to use probiotics for infants.

✔ Immune system issues

Eighty percent of our immune system resides in our gut, so it makes sense that sub-optimal gut flora would cause an ill functioning immune system. When gut bacteria isn’t optimal, baby’s immune system is not going to be optimal. That means baby will be more likely to catch colds, flus, and other illnesses. We can ward off some of these issues with the use of probiotics for infants.

✔ Mood

There is a large pool of data supporting the brain-gut connection. Gut bacteria has been shown to directly affect mood, from depression and anxiety to shyness. One study found that feeding mice Lactobacillus probiotics helped reduce anxiety. Another study found that different gut bacteria can actually change a mouse from timid to bold and vice versa. Further, researchers found that if corrected early enough, good bacteria could help reverse the mouse pup’s anxiety, but if they were weaned by the time they got the good bacteria they continued to have high levels of anxiety. Of course, mouse trials don’t directly correlate to humans but the results are interesting and support what we do know about baby’s gut flora needs.

✔ Weight problems

Probiotics for infants may even impact your baby’s weight. (Strange as it sounds!) One study found that mice with a TLR5 deficiency (a protein that keeps gut flora balanced) had excessive weight gain, insulin resistance, diabetes, and fatty liver disease. What was really interesting is that the researchers transplanted some fecal matter from the overweight mice to skinny mice and the skinny mice started eating more, gaining weight, and eventually developed the metabolic issues of the TLR5 deficient mice. Long story short, the weight and metabolic issues of these mice were a direct result of bad gut bacteria.

Another study transplanted feces from overweight humans to mice and the same reaction happened, the mice became overweight. Interestingly, the mice who were given human feces from a thin human (who was the overweight human’s twin!) did not become overweight. In this study the mice ate the same diet in the same amounts.

✔ Skin issues

I know many moms who used probiotics for infants to help alleviate many skin conditions. Countless studies have proven a correlation between acne and other conditions like depression, anxiety, and digestive issues. Acne patients have been shown to have considerably more leaky gut issues and inflammation than those without acne. Another study found that suboptimal gut flora also contributed to the skin being less efficient as a protective organ and more susceptible to inflammation and infection. Babies skin is particularly sensitive to rashes, eczema, etc. and some sources say that baby skin issues like eczema, cradle cap, and baby acne are caused by imbalanced gut flora.

How to give probiotics to infants

We now know how important gut health is for overall health for baby (and adults), but how do we make sure baby has healthy gut flora? There are a few ways you can provide probiotics for infants:

Probiotics for infants: Breastfeed

Breastfeeding is the best way to keep baby’s gut lining intact and healthy. Your milk will supply baby with probiotics and immunoglobin A (IgA) which helps seal the gut lining. You want to be sure that you’re also consuming probiotic rich foods like kefir, raw sauerkraut and pickles, yogurt, miso, etc. This will help enrich your own bacterial balance, which will help your milk and baby.

If you can’t or don’t want to breastfeed, there are formula options that can still help keep baby’s gut healthy.

Probiotics for infants: Fermented foods

I always believe food is the best route to go, especially with young children with delicate systems.

Obviously, we can’t give babies true solids until around 6 months old, but we can give them one food at a very young age. Breast milk yogurt. (I know; it sounds weird but stick with me…)

I discovered this accidentally. Because Paloma had a case of silent reflux at just 6 weeks old, I fed her probiotics each day. I would pump an ounce or so of breast milk, mix it with 1/8 tsp. of infant probiotics and feed it to her with a syringe. One time, I forgot to feed it to her (hello, mama brain!) and the mixture sat overnight on my counter.

The next day, the milk had magically transformed into yogurt! Woah! I talked with my healthcare provider and she said it would be a safe to feed to my baby. It was also much easier to give to Paloma than a liquid with a syringe. I believe the probiotics are more “activated” in this yogurt form and more predigested for baby to absorb better. Of course, always check with your child’s pediatrician before giving to your child.

That aside, when baby is old enough for solids, you can add naturally fermented foods to his diet. I would start with just the juice of these probiotic powerhouses. For example, you could feed them a teaspoon or so of sauerkraut or pickle juice with a spoon. You can then start adding in small amounts of kefir or yogurt and go from there. Feeding them early will help baby develop a taste for sour and fermented foods.

Probiotic supplements

Finally, probiotic supplements are a great addition to be sure baby is getting adequate probiotics. Also, if you’re breastfeeding, take probiotics yourself to boost the bacterial flora in your colostrum and breastmilk.

Best probiotics for infants

Researchers of an Australian study found that the best probiotics for infants were ones that included 2-3 strains or species of probiotics (instead of just one) but were cautious about adding any more. They point out that using just a few strains per dose is better than using many strains (at lower concentrations). Many holistic doctors suggest adding as many different strains as you can, as long as you aren’t going over the recommended dose of probiotics in whole. Fermented foods contain many different strains and species of probiotics, so it makes sense that a supplement should include many as well. The reason is that different strains hang out in different parts of the digestive tract and perform different functions.

Each strand of probiotics can be beneficial to your infant but here are the top three to look out for.

1. B. Bifidum is one of the first strains to colonize baby’s intestines and adheres to the intestinal wall better than other strains. It continues to be an important bacteria for digestion and nutrient absorption. It may help with infant skin conditions like eczema and yeast infections. It may also help with infant digestive issues such as necrotizing enterocolitis (NEC), IBS, constipation, diarrhea, and even lung infections.

2. B. Infantis is the strain that is most prevalent in infants and declines as we age. It helps with overall health and digestion. One review found that it can reduce inflammation and support immune function.

3. L. Rheuteri is a strain that has been found to have many benefits to young children and infants. One study found that children, ages 6 months to 3 years, who took supplemental L. Rheuteri had nearly one third less cases of diarrhea and half as many respiratory infections. Another study found that L. Rheuteri helped was an excellent treatment for colic. It was also found to reduce tooth decay! Read more about the benefits of L. Reuteri here.

In addition to these 3 super strains, its important to get a variety of other strains as well to round out the microbiome. In our research there were only a few brands that made the cut for quality and variety of strains (more below).

How to give probiotics to infants

The best probiotics for your baby are liquid or powdered probiotics for the first year or two of life.

Liquid probiotics

Liquid probiotics can be given to baby in a little breast milk or formula or directly into her mouth. This way baby is not getting any additional water (which can cause imbalance in her electrolytes). Always, always, always talk to your pediatrician before giving baby any supplement. Also, always start slow with probiotics and watch for any bowel or behavior changes.

While there are some other ingredients in this formulation, it has a nice blend of native probiotic strains specific to infants (including the 3 super strains). Moms have really sang this probiotics praises on Amazon too 🙂

You can purchase here.

Powder probiotics

These powdered probiotics can be mixed into a little breastmilk or formula as well, or you can put onto your breasts directly as I talk about here. When baby is eating solids, these probiotics for infants can be mixed into baby’s water cup or into her food. You can also continue giving liquid probiotics if you prefer.

I like this probiotic powder because there are no additional ingredients, which is very hard to find on the marketplace! It also includes a nice spectrum of infant native bacteria (including our top 3) that you can’t find in most other brands. You can buy these here. A comparable brand (in quality, price, and strains) can be found here.

Here is another option that is less expensive and comes from a a trusted brand. They don’t have as many strains but are a good start. I used these to make Paloma’s breast milk yogurt. If you add this one every 3rd day it makes a good cumulative variety of strains.

Bottom line on probiotics for infants

Unbalanced gut flora can be inherited and may cause serious health issues in the future. Adding probiotics for infants to baby’s diet, either through food or supplementation, can help her have the best possible start.



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  1. Hi my infant aged 1yr 9mths is suffering from eczema, would you think is a good idea if I start giving her probiotics and if you can please send me a few brands which I can go for.

  2. Thank you so much for this write up and recommendations! Probiotics at the age of 25 completely changed my life-as it turned out wheat completely ruined my gut biome and I never felt good after eating.
    Now I’m doing as much research as possible for my babies I’m expecting soon!

  3. Hi, what dosage of the Klaire Labs Infant Probiotics would you recommend for a 3 month old? I’m starting him on this probiotic since he has silent reflux and I’m hoping it will help him. I’ve read that it is a concentrated probiotic so I’m thinking it should be less than 1/4 tsp which is the recommended dosage. Also, should this be given all in at one time or should the dosage be split throughout the day? He is unfortunately taking formula so I’m thinking of putting the powder in his milk. Thanks

  4. I give my son probiotics every morning, is it then okay for him to eat and oatmeal cereal with probiotics in it?

  5. I’ve just recently found out my daughter can not tolerate milk. Advice from health food shop I bought bio kult (advanced multi-strain formula for infants with omega 3 and vitD. I’ve not started her on this yet. But was wondering should I use this an a multivitamin are is there need for both? She is 1 an has a very balanced diet although I don’t want her missing out on anything due to not having her milk intake. Thank you

  6. Serious question here, why do children need a specific probiotic? I’ve always just opened the capsule of the probiotic I take and mix it into my son’s food. ?

  7. Haven’t seen any quantity recommendations for infants ? What quantity of powdered pro-biotic should we give our 16 month old boy ?


  8. Hi, I’m starting my baby on solids soon and would really like to know how you make breastmilk yogurt! When you said sitting over the counter, how long was that and at what temperature? 🙂

    • Hi, I am very interested in making breast milk yogurt too. Please share.
      Thank you.

  9. Hello there,
    I just discovered your website. Really enjoying so far there are a lot of nice topics and articles. I do have a question for you mama natural. Can I start giving my 9months old probiotics?

  10. Do you recommend one for EBF moms to take so the baby gets it in breast milk?

    • “Natren” is an excellent brand available at Whole Foods. They have adult and children’s formuals. I take the Holy Trinity version personally.

  11. I would like to start introducing probiotics to my 8 month old daughter. I eat them daily through homemade fermented foods and kombucha. I have found a powdered one I would consider giving to her, but I would honestly rather just give her something I’ve made myself at home, in food form (and also save some money). She is primarily breastfed, but is also eating fruits and veggies now. Do you think it’s ok to start giving her sauerkraut juice? What about a little kombucha? Would fermented foods be just as good as a powdered/liquid form?

  12. are powdered probiotics safe for newborns? have 2 week old. thank you for all info and knowledge sharing always!

  13. How long not do you give probiotics for? Do you give them ongoing continuously or do you give your children a course 3 times a year for instance? I can’t seem to find any advice on this and nothing on the packets/labels. Thank you in advance.

    • Every day continuously. We all have them daily in my house, not just kids. If that’s too much for you give as often as possible, but I find it’s easier to have the daily habit.

    • Also especially if there’s ever a true need for antibiotics. For that I always keep a bottle of Saccharomyces Boulardii (also by Klaire Labs) which is one of the few strains that survive antibiotics. It’s cheaper than buying Florastor at the drugstore (which is what I’ve done in the past when I had an unexpected need for antibiotics). Fortunately we haven’t had to use any antibiotics since we’ve boosted our probiotic and vitamin routine. We also use a chewable ENT/ Dental brand recommended by Mommypotamus, won’t link to it here.

  14. I don’t seem to find L. rheuteri listed in either of the powdered probiotics recommended?

    • It’s the last one they talk about, looks like she recommends it every three days.

  15. Do you recommend any specific probiotics for breastfeeding moms, would those probiotics pass on to the baby through breast feeding though?

  16. How early should you give baby probiotics….I have a 3 week old.

    • Once a day or whatever the bottle says 🙂

  17. I’ll be starting baby on Klaire’s infant probiotics soon and myself on their adult formula (package arrives today!). I’m hoping to undo the damage caused to my gut flora by a round of antibiotics a week before birth and a calcium-channel blocker (nifedipine) prescribed to treat my gestational hypertension that caused total constipation and likely annihilated my previously great gut health.

    In the meantime, my pediatrician suggested holding baby upright in a seated position for five minutes after the morning feed to stimulate the gastrocolic reflex. This practice has really helped jump-start daily pooping for my exclusively breastfed infant who previously went a week or even ten days without pooping. Try it!

  18. Have you ever used the Garden of Life Raw probiotics for kids? That’s what I’m currently using, just because I use some of their other products.

  19. Do you have a brand that you would recommend for a toddler? My son is 3 and we desperately need some.

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