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Babies and Probiotics

Over recent years the connection between the gut microbiome (the bacteria in our gut, also know as our gut flora!) and chronic diseases has been stronger than ever.  There are a large number of publications linking less diverse flora to a myriad of conditions especially those in the asthma, allergy, and autoimmune realm.

The bacteria in our gut play several roles including:1

  • Critical role in regulation of the immune system
  • Provide protection against pathogen (bad bugs!) overgrowth
  • Influence host-cell growth and blood vessel growth
  • Regulate intestinal endocrine functions, neurologic signaling, and bone density
  • Provide a source of energy (5 to 10% of daily host energy requirements);
  • Biosynthesize vitamins, neurotransmitters, and multiple other compounds
  • Metabolize bile salts
  • React to or modify specific drugs
  • Eliminate exogenous toxins

Currently researchers are even studying how to implant drug peptides into the bacteria in our gut for certain conditions. One particularly interesting one is for the treatment of inflammatory Bowel disease, which often severe cases come with injectable agents that weaken the immune system all over. Wouldn’t it be great if we had targeted therapy just in the gut!

So the question is if our gut is so important, how do we help our children start out on the right track with solid gut flora.  The answer….you guessed it..probiotics!  Probiotics are “Live microbes that confer health benefits when administered in adequate amounts in the host.”1The key with infants though is to get them probiotics early in the first few days when their gut is designed to multiply those good bugs! The in utero environment was once considered sterile. However recently, DNA studies of the micro biome have found bacterial species in the placentas of healthy mothers, in amniotic fluid of preterm infants, and in meconium.1

Ideally babies born vaginally shouldn’t need this right, they swallow fluid during delivery through the vaginal canal that should seed their gut? While that is true, most of us Mommas have taken antibiotics in our lifetime, if not multiple courses, been under stress (which has been proven to change gut flora!)2, and often times are eating or have eaten a diet previously that was not friendly towards growing and multiplying good bacteria.  We also live in an environment where traces of antibiotics are in our water supply and food chain. So I recommend every baby whether born vaginally or c-section get probiotics during the first week of life. I also recommend Mommas take probiotics throughout their pregnancy.

Another way to help the flora grow is with breastmilk. Studies3,4 have shown that the guts of breast fed babies vs formula fed babies are different compositions of bacteria. Breastfed babies have more beneficial bifidobacteriam species.  Exclusive and partial formula-feeding have been shown to alter the gut bacteria toward adult patterns, increase pro-inflammatory bacterial species, increase gut permeability (leaky gut) and result in lower concentrations of fecal short-chain fatty acids compared with exclusive breastfeeding.4 While I realize this isn’t possible for every women, from my experience it’s hard, especially during those first few months.  Believe me lots of tears were shed in the process of making it work for us with my first child. Then of course pumping if you are working out of the home is hard too. But I promise it’s worth the attempt at least. The IGG in the breastmilk also helps seal the gut lining which makes your babies less susceptible to gut damage and autoimmune conditions such as type 1 diabetes5, and allergies, asthma, and airway disease.6

Studies have shown infant gut flora diversity and healthy guts have been linked to less risk of asthma/wheezing, food allergies, and many other autoimmune conditions.5-9 Some data is even suggesting good flora can modulate behavioral and neurodevelopmental disorders.10

Ther-Biotic Women’s Formula
Ther-Biotic for Infants

It’s pretty simple, babies don’t need a large amount of probiotics just a little bit to get their gut started and if you get it early, you don’t may not have to supplement daily later on. Most functional medicine providers and myself recommend either using a Women’s Formula like Ther-biotic® Women’s Formula  by Klaire Labs or their Ther-biotic® Infant Powder.  With the capsules, you can open the capsule and place a small amount of the powder on the breast or the tongue of the infant before feeding, then mom can close the capsule and swallow the rest.

After a few days of that you can also use the infant powder or continue to share yours. They are similar formulas.  The Women’s formula is designed to be the flora that are found in the vaginal canal so it’s just want baby should have swallowed in an ideal world. If baby becomes too gassy after a week or so of the powders, you can start to decrease the dose to 1-2 times per week.

OrthoMolecular Saccaromyces product

Metagenics also makes an infant drop called MetaKids® Baby Probiotic that has been easily to use with my son.  If gas becomes an issue with the baby again only give a few times a week after that initial week and consider using a strain called Saccaromyces Boulardii which is a healthy yeast that balances the gut flora and is well known for it’s beneficial effects in acute and chronic GI conditions.11  I is not a gas producing organism.I personally like the OrthoMolecular Saccaromyces product that doesn’t have to be stored in the fridge but Klaire Labs makes one too. There have been case reports of Saccharomyces Boulardii blood stream infections in immunocompromised patients, so I would not recommend use for those patients or premature infants.11

I wish I would have known to give probiotics earlier with my daughter, we started them at about 5 weeks after she was colicky and had reflux. Along with an elimination diet for me, she was lots better!  So it’s not too late even if you are reading this and your child is older they may benefit from replacing gut flora, depending on age, they may need a different formula. Our daughter was allergic to tree nuts, eggs, and a few other things early on, verified by skin prick testing, after a few years of vitamin D and probiotics and eating a gut friendly diet for the most part. The most recent skin test was negative for everything tested! Praise the Lord! She enjoyed splitting a Cashew LaraBar with mom today no problems! Feel free to reach out if you need specific recommendations on probiotics for you or your loved one!

More on gut healing in adults and kiddos to come! Also a post to come on metabolic disease and the gut, early life exposure to antibiotics can influence risk of diabetes and other metabolic conditions like obesity and allergies!12,13

*this post contains affiliate links to products I recommend, all the probiotics recommended in this post can be found in my FullScript Store You do have to set-up a quick account to use.


  1. Lynch S, Pederson O. The human intestinal microbiome in health and disease. N Engl J Med 2016;375:2369-79.DOI: 10.1056/NEJMra1600266.
  2. Konturek PC, Brzozowski T, Konturek SJ. Stress and the gut: pathophysiology, clinical consequences, diagnostic approach and treatment options. J Physiol Pharmacol. 2011 Dec;62(6):591-9.
  3. Madan JC, Hoen AG, Lundgren SN, Farzan SF, Cottingham KL, Morrison HG, Sogin ML, Li H, Moore JH, Karagas MR. Association of Cesarean Delivery and Formula Supplementation With the Intestinal Microbiome of 6-Week-Old Infants. JAMA Pediatr. 2016;170(3):212-219. doi:10.1001/jamapediatrics.2015.3732
  4. O’Sullivan A, Farver M, Smilowitz JT. The Influence of Early Infant-Feeding Practices on the Intestinal Microbiome and Body Composition in Infants. Nutrition and Metabolic Insights. 2015;8(Suppl 1):1-9. doi:10.4137/NMI.S29530.
  5. Endesfelder D, Engel M, Zu Castell W. Gut Immunity and Type 1 Diabetes: a Mélange of Microbes, Diet, and Host Interactions?. Current Diabetes Reports [serial online]. July 2016;16(7):60. Available from: MEDLINE with Full Text, Ipswich, MA. Accessed February 19, 2017 doi:10.1007/s11892-016-0753-3.
  6. Huang et al. Breastfeeding and timing of first dietary introduction in relation to childhood asthma, allergies, and airway diseases: A cross-sectional study. Journal of Asthma. 2016; Published on-line 07 Sept 2016. P 1-10.
  7. Uusitalo U, Liu X, Virtanen S, et al. Association of Early Exposure of Probiotics and Islet Autoimmunity in the TEDDY Study. JAMA Pediatrics [serial online]. January 2016;170(1):20-28. Available from: MEDLINE with Full Text, Ipswich, MA. Accessed February 19, 2017.
  8. Arrieta M, Stiemsma L, Finlay B, et al. Early infancy microbial and metabolic alterations affect risk of childhood asthma. Science Translational Medicine [serial online]. September 30, 2015;7(307):307ra152. Available from: MEDLINE with Full Text, Ipswich, MA. Accessed February 19, 2017.
  9. Fujimura K, Sitarik A, Lynch S, et al. Neonatal gut microbiota associates with childhood multisensitized atopy and T cell differentiation. Nature Medicine [serial online]. October 2016;22(10):1187-1191. Available from: MEDLINE with Full Text, Ipswich, MA. Accessed February 19, 2017.
  10. Hsiao E, McBride S, Mazmanian S, et al. Microbiota modulate behavioral and physiological abnormalities associated with neurodevelopmental disorders. Cell [serial online]. December 19, 2013;155(7):1451-1463. Available from: MEDLINE with Full Text, Ipswich, MA. Accessed February 19, 2017.
  11. Kelesidis T, Pothoulakis C. Efficacy and safety of the probiotic Saccharomyces boulardii for the prevention and therapy of gastrointestinal disorders. Therapeutic Advances in Gastroenterology. 2012;5(2):111-125. doi:10.1177/1756283X11428502
  12. Yallapragada S, Nash C, Robinson D. Early-Life Exposure to Antibiotics, Alterations in the Intestinal Microbiome, and Risk of Metabolic Disease in Children and Adults. Pediatric Annals [serial online]. November 2015;44(11):e265-e269. Available from: MEDLINE with Full Text, Ipswich, MA. Accessed February 19, 2017
  13. Johnson C, Ownby D, Joseph C, et al. Antibiotic exposure in early infancy and risk for childhood atopy. The Journal Of Allergy And Clinical Immunology [serial online]. June 2005;115(6):1218-1224. Available from: MEDLINE with Full Text, Ipswich, MA. Accessed February 19, 2017.

5 thoughts on “Babies and Probiotics

  1. Hey lady! Love that you are writing about what you have learned. We have fallen off the bandwagon of eating well and need to get back on! It’s encouraging to hear what other people are doing.
    Question for you- we use the same kind of probiotic that you have on here, but I’m not super familiar with the saccharomycees. What would make you choose to do that? Is that used alongside the probiotic or do you need to determine whether a yeast is necessary?
    I feel like I have read that many people with gut issues have a yeast overgrowth. Can this make it worse to add more even if it is a good yeast?

    1. Hi Christy! I understand falling off the bandwagon! It’s so hard sometimes, we’ve been there for sure. Right now it’s so hard for me because I’m constantly hungry from breastfeeding! I don’t think saccharomycees is necessarily for everyone along it is considered a non-pathogenic yeast in healthy individuals. It is in the OrthoMolecular Flora Boost Product for kids and their OrthoBiotic Product alongside the other probiotic strains. I don’t have that one picture above. The only reason I think I would try it in an infant or younger baby is if they were showing signs of food intolerance and couldn’t tolerate the other probiotics due to gas. My little guy is so gassy! There have been case reports of systemic fungal infections in immunocompromised patients, so I definitely would not use it in a premie or immunocompromised patient. I may edit the blog post to include that point! Here is a great article outlining all the efficacy and mechanisms for how it works! . For yeast overgrowth patients, some recommend using it because it helps to balance the flora and help heal the gut- Mark Hyman, MD recommends it while other functional medicine folks start with getting the yeast under control with prescription meds or botanicals first. The overgrowth of yeast that most have is Candida albicans not this type. It is commonly marketed as FloraStor and is available at most Pharmacies. One of it’s best uses is for diarrhea and antibiotic- associated diarrhea. Hope this helps.. let me know if you have other questions! That article above really is a great review on it!

  2. […] Stayed tuned for my next post which will discuss my favorite supplements (Quercetin, Stinging Nettles) and nutrients (Vitamin C, Bromelain, N-Acetyl-L-Cysteine) and their useful role in supporting allergic conditions. And if you need recommendations for probiotics for babies, head over to this post. […]

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