Do Babies Really Need a Probiotic?

Key Takeaways

• Chronic inflammatory conditions are on the rise in the pediatric population - today’s children are 15-20% more likely to have a chronic condition compared to children 20 years ago.

• Nearly every baby has microbiome disruption, notably missing the most important microbes for early immune training: Bifidobacterium.

• Microbiome restoration, and Bifidobacterium probiotics specifically, can improve pediatric health outcomes.

Do babies really need a probiotic? It’s a question we get asked a lot. For good reason, too. We’re not fans of oversupplementation at Persephone - food and a healthy lifestyle get you really far when it comes to gut health. But when it comes to babies, the answer to this question is a firm, unwavering YES. 

Unfortunately, gut microbiome disruption, or dysbiosis, is overwhelmingly common in pediatrics. Babies just aren’t born with the critical microbes they need for healthy development. While cesarean delivery, antibiotic use, and formula are a part of this, microbiome dysbiosis is a problem in nearly every single infant, no matter how they are born, fed or the medicines they’ve received. 

Persephone Biosciences conducted the largest, most diverse study of US infants, analyzing the microbiomes of over 400 babies from nearly every US state. The findings were clear: over 90% are missing the most important species of Bifidobacterium for infants, B. infantis.¹ While Persephone published the largest study, this is not an isolated finding. Other studies have also reported this disappearance, noting that the gut pH has risen over the last century², leaving the gut environment less protected from pathogens.^3,4

It's no coincidence that this is mirrored by the drastic increase in chronic inflammatory health conditions in our society, especially in the youngest among us. A shocking 40% of children have a chronic disease.⁵ And that number is growing. Today’s children are 15-20% more likely to have a chronic condition compared to children 20 years ago.⁶ If you are a healthcare practitioner, you are seeing this in real time - eczema, allergies, and asthma are commonplace. 

Early-life microbiome disruption is a likely major contributor to this rise in chronic conditions because of its role in immune education. The gut is the interface of the ‘outside’ and ‘inside’ worlds - where the immune system is exposed to pathogens as well as commensal, beneficial gut microbes. In the first few years of life, the immune cells in the gut lining must learn which exposures to respond to and which not to - friend v foe. When this goes well, the immune system is able to accurately and quickly respond to and eliminate pathogens and infectious microbes. When this process is disrupted, the immune system misinterprets everyday exposures as foreign - food, environment and even ourselves, known as auto-immune conditions. This creates a state of chronic inflammation, which even beyond immediate symptoms can influence other systems like metabolic and brain health - contributing to conditions like obesity and neurodevelopmental conditions later in life. These immune training processes begin almost immediately after birth, with some immune pathways beginning to solidify as early as 3 months old.⁷

One of the most important players in this process are Bifidobacterium species. There are many different species of Bifidobacterium, and they have a range of jobs throughout the lifespan. In early life, they are the primary educators for the immune system. Here are two of the important roles they play:

• Promote regulatory T cell maturation, a critical component of the immune system for immune tolerance - or preventing reaction to non-threatening antigens like food. 

• Digest human milk oligosaccharides (HMOs) found in breastmilk into metabolites critical for maintaining the acidic environment that keeps pathogens at bay, have anti-inflammatory properties, and promote a strong gut barrier. Bifidobacterium infantis is the most effective HMO digester of all the Bifidobacterium species.⁸

Without adequate Bifidobacterium, especially Bifidobacterium infantis, the early microbiome cannot properly educate the immune system, which can lead to lifelong chronic inflammation. 

This is where the answer to our question, “Do babies really need a probiotic?” becomes clear - yes. Sufficient Bifidobacterium is a critical component of early immune development, and with so many babies lacking these key microbes, probiotics become an essential tool. 

And research shows that restoring the microbiome community early has real-life benefits. Early results from Persephone’s own clinical studies, looking at the impact of The Daily Synbiotic shows colonization of the Bifidobacterium, improved HMO digestion by the microbiome, and improvement in sleep for toddlers. And these are just the initial results from a longitudinal study. Others have also demonstrated early microbiome interventions work - a recent study found that a microbiome testing and education program for infants under 6 months old led to a 51% increase in Bifidobacterium levels and 83% lower odds of developing eczema.⁹ Another study found that babies whose microbiome ‘c-section signature’ (a microbiome that looks like those born by c-section) is resolved in the first year of life, the risk of asthma declines to that of vaginally born babies. ¹⁰ A recent meta-analysis of 25 clinical studies found a significant reduction in eczema development with early use of infant-specific Bifidobacterium probiotics. ¹¹

Given the current state of the infant microbiome, early support with modern ¹², high-quality Bifidobacterium probiotics is an important tool for establishing lifelong health for all babies.

*Medical Disclaimer
The information provided on this blog is for educational purposes only and is not intended as medical advice, diagnosis, or treatment. Every baby is unique, and health decisions should always be made in partnership with a qualified healthcare professional. If you have questions or concerns about your child’s health, diet, or development, please consult your pediatrician or another trusted healthcare provider before making changes.

References:

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2. Henrick, B. M., Hutton, A. A., Palumbo, M. C., Casaburi, G., Mitchell, R. D., Underwood, M. A., Smilowitz, J. T., & Frese, S. A. (2018). Elevated Fecal pH Indicates a Profound Change in the Breastfed Infant Gut Microbiome Due to Reduction of Bifidobacterium over the Past Century. mSphere, 3(2), e00041-18. https://doi.org/10.1128/mSphere.00041-18.

3. Casaburi, G., Duar, R. M., Brown, H., Mitchell, R. D., Kazi, S., Chew, S., Cagney, O., Flannery, R. L., Sylvester, K. G., Frese, S. A., Henrick, B. M., & Freeman, S. L. (2021). Metagenomic insights of the infant microbiome community structure and function across multiple sites in the United States. Scientific reports, 11(1), 1472. https://doi.org/10.1038/s41598-020-80583-9

4. Insel, R. A., Jarman, J. B., Torres, P. J., Van Dien, S., Culler, S. J., & de Vos, W. M. (2025). Restoring a gut Bifidobacterium community in early infancy. Cell host & microbe, 33(12), 2012–2016. https://doi.org/10.1016/j.chom.2025.10.017

5. Van Dyck PC, et al. "A National and State Profile of Leading Health Problems and Health Care Quality for US Children." Academic Pediatrics. 2011;11(3 Suppl):S22-33.

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7. Henrick BM, Rodriguez L, Lakshmikanth T, et al. "Bifidobacteria-mediated immune system imprinting early in life." Cell. 2021;184(15):3884–3898.e11.

8. Sela, D. A., Chapman, J., Adeuya, A., Kim, J. H., Chen, F., Whitehead, T. R., Lapidus, A., Rokhsar, D. S., Lebrilla, C. B., German, J. B., Price, N. P., Richardson, P. M., & Mills, D. A. (2008). The genome sequence of Bifidobacterium longum subsp. infantis reveals adaptations for milk utilization within the infant microbiome. Proceedings of the National Academy of Sciences of the United States of America, 105(48), 18964–18969. https://doi.org/10.1073/pnas.0809584105.

9. P. A. Nieto et al., “Improving immune-related health outcomes post-cesarean birth with a gut microbiome-based program: A randomized controlled trial,” Pediatric Allergy and Immunology, vol. 36, no. 9, p. e70182, 2025, doi: 10.1111/pai.70182.

10. Stokholm, J., Thorsen, J., Blaser, M. J., Rasmussen, M. A., Hjelmsø, M., Shah, S., Christensen, E. D., Chawes, B. L., Bønnelykke, K., Brix, S., Mortensen, M. S., Brejnrod, A., Vestergaard, G., Trivedi, U., Sørensen, S. J., & Bisgaard, H. (2020). Delivery mode and gut microbial changes correlate with an increased risk of childhood asthma. Science translational medicine, 12(569), eaax9929. https://doi.org/10.1126/scitranslmed.aax9929

11. Sjælland, M. A., Philipsen, M. T., Henriksen, T. B., Skipper, J., & Rubak, S. (2025). Probiotics in Term Infants: Clinical Impact of Infant-Type Bifidobacteria: A Systematic Review and Meta-analyses. The Journal of Nutrition, 155(12), 4075-4086. https://doi.org/10.1016/j.tjnut.2025.10.006.