Antibiotics have saved millions of lives. They’re one of the most important tools in modern medicine, and for many infections they’re absolutely necessary.

But scientists are learning something important: antibiotics don’t only affect the bacteria causing an infection. They also affect the trillions of beneficial microbes living in our gut — what we call the gut microbiome.

A new study published in Nature Medicine looked closely at this relationship by analyzing microbiome data and prescription records from nearly 15,000 individuals. What researchers found was striking: antibiotics can leave measurable changes in the gut microbiome years after they’re taken.¹

For parents thinking about infant gut health, this research helps explain why the early microbiome is so important — and why disruptions during infancy may have lasting effects.

The Gut Microbiome: Your Baby’s First Ecosystem

Your baby is born with the beginnings of a microbial community that will grow rapidly during the first months of life. These microbes do much more than help with digestion. In early life, the baby microbiome helps train the immune system, supports healthy metabolism, and protects against harmful bacteria.

One group of bacteria is especially important: Bifidobacterium. These beneficial microbes are uniquely adapted to digest the complex sugars in breast milk and help create a gut environment that supports healthy development.

But modern research shows something surprising:

About 90% of babies today are missing one or more key strains of Bifidobacterium.²

And when babies have low levels of beneficial gut bacteria, the risks for certain immune-related conditions rise. In fact, 3 in 4 babies with low levels of healthy gut bacteria are at higher risk of allergies, eczema, and asthma.

Understanding what shapes the infant microbiome — including antibiotics — is an important part of supporting long-term health.

What This New Study Discovered

The Nature Medicine study took a unique approach. Researchers combined two powerful datasets:

• Stool samples that revealed each person’s gut microbiome composition

• National pharmacy records showing exact antibiotic prescriptions

This allowed scientists to compare the microbiomes of people who had taken antibiotics with those who hadn’t — and to see how long those differences lasted.

The results were remarkable.

Even years after taking antibiotics, people still showed distinct differences in the types of bacteria living in their gut. In some cases, microbiome changes linked to antibiotic use were still detectable four to eight years later.

This suggests that when antibiotics disrupt the gut ecosystem, it may not always return to exactly the same balance it had before.

Not All Antibiotics Affect the Microbiome the Same Way

Another important finding was that different antibiotics affect the microbiome differently.

Some antibiotics were associated with long-term reductions in certain beneficial bacteria. Others were linked to increases in microbes that are more resistant to antibiotics.

In other words, antibiotics leave different microbial "footprints" depending on the type of medication and the person’s existing microbiome. This helps explain why microbiome recovery can vary from person to person.

Why This Matters for Infant Gut Health

While the adult microbiome is more resilient to disruptions, the infant gut is still developing. During the first months and years of life, a baby’s microbiome forms rapidly and plays a critical role in immune training, digestion, and protection against pathogens.

Antibiotics are often necessary and lifesaving, but they can disrupt this developing ecosystem. Because they kill bacteria broadly, antibiotics can reduce microbial diversity and beneficial bacteria that are important during early immune development.

One of the most important microbes in infancy is Bifidobacterium, particularly Bifidobacterium longum subsp. infantis (B. infantis). These bacteria are uniquely adapted to digest sugars in breast milk and help create a gut environment that supports healthy immune maturation.

Research has shown that B. infantis may also help buffer the microbiome against some downstream effects of antibiotics. In one large cohort study, children who received antibiotics but lacked protective microbiome signals had significantly higher odds of developing asthma, while those with microbiomes enriched in B. infantis showed a greatly reduced risk.³

None of this means antibiotics should be avoided when medically necessary. But it highlights why supporting beneficial microbes like Bifidobacterium during early life may be important for healthy immune development.

The Bigger Picture: Supporting the Modern Baby Microbiome

Research like this helps us understand a simple but important truth: The gut microbiome is an ecosystem, and once it’s disrupted, rebuilding it may take time.

For babies, supporting the development of a healthy microbiome early in life may help set the stage for stronger immune development and long-term health.

As scientists continue to study how antibiotics and other modern factors shape the microbiome, one thing is becoming clear: The microbes babies receive in early life matter — a lot.

Helping restore the beneficial bacteria that modern life sometimes disrupts may be one of the most powerful ways we can support the next generation’s health.

Check out the full publication here: https://www.nature.com/articles/s41591-026-04284-y.

*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:

1. Baldanzi, G., Wirbel, J., Zhernakova, A., Kurilshikov, A., Tigchelaar, E. F., Sinha, T., Mujagic, Z., Franke, L., Fu, J., Weersma, R. K., & Bork, P. (2026). Antibiotic use and gut microbiome composition links from individual-level prescription data of 14,979 individuals. Nature Medicine. https://doi.org/10.1038/s41591-026-04284-y. 

2. Jarman, J. B., Torres, P. J., Stromberg, S., Sato, H., Stack, C., Ladrillono, A., Pace, S., Jimenez, N. L., Haselbeck, R. J., Insel, R., Van Dien, S., & Culler, S. J. (2025). Bifidobacterium deficit in United States infants drives prevalent gut dysbiosis. Communications biology, 8(1), 867. https://doi.org/10.1038/s42003-025-08274-7.

3. Dai, D. L. Y., Petersen, C., Hoskinson, C., Del Bel, K. L., Becker, A. B., Moraes, T. J., Mandhane, P. J., Finlay, B. B., Simons, E., Kozyrskyj, A. L., Patrick, D. M., Subbarao, P., Bode, L., Azad, M. B., & Turvey, S. E. (2023). Breastfeeding enrichment of Bifidobacterium longum subsp. infantis mitigates the effect of antibiotics on the microbiota and childhood asthma risk. Med (New York), 4(2), 92–112. https://doi.org/10.1016/j.medj.2022.12.002.