Early-Life Gut Bacteria Linked to Lower Food Allergy Risk, With Susanne Pedersen

Vaginal delivery, exclusive breastfeeding, and early exposure to siblings emerged as the strongest drivers of colonization with allergy-protective gut bacteria in infancy, offering clinicians a concrete context for how early-life exposures may shape long-term immune risk.

“What we see is that it seems to be very important for the early colonization with these aromatic lactate-producing bifidobacterial that that that you deliver naturally so by vaginal birth,” Susanne Brix Pedersen, a professor at Technical University of Denmark (DTU) Bioengineering, told HCPLive. “You can, of course, also introduce these bacteria to a cesarean section-born infant by giving a slurry of the fecal matter from the mother. [It] has been done in a few…studies conducted in the US.”

In a recent longitudinal study, investigators showed that infants colonized early with aromatic lactate–producing bifidobacteria were significantly less likely to develop food allergen–specific immunoglobulin E (IgE) and atopic dermatitis in childhood. The findings extend earlier work linking the infant gut microbiome to immune tolerance and help clarify which perinatal factors most strongly influence the acquisition of these beneficial microbes.

The study followed 147 children born in Sweden between 2003 and 2005, with fecal samples collected at 8 time points from birth through age 5 years, alongside maternal samples, blood draws, and clinical follow-up. Using genetic and metabolomic profiling, investigators identified a subset of bifidobacteria capable of converting aromatic amino acids into aromatic lactates. Infants with high abundance of these bacteria, particularly during the first 6 months of life, had elevated gut levels of aromatic lactates and a reduced risk of food allergen–specific IgE through 5 years old, as well as lower rates of atopic dermatitis at 2 years old.

Among early-life exposures, vaginal delivery had the most pronounced effect. Infants born vaginally were approximately 14 times more likely to be colonized with these bifidobacteria than those born by cesarean section.

Exclusive breastfeeding during the first 2 months of life also strongly promoted colonization, while early formula supplementation was associated with markedly lower bacterial abundance. Having older siblings further increased the likelihood of early colonization, suggesting a role for household microbial exposure.

Mechanistically, the protective association was mediated by 4-hydroxy-phenyllactate (4-OH-PLA), a bacterial metabolite that selectively inhibited IgE—but not IgG—production in ex vivo human immune cell cultures.

“It's quite important that you…don't see an inhibition of the IgG because the IgG is there to protect us against the different infections that we are acquiring during early life,” Pedersen said. “If we see an increase…or a decrease of that…that might have had some implications in terms of infection burden. Having a selective inhibition of the IgE, which is so IGE is connected to allergic diseases, but also, of course, to the ability of handling a parasite infection. In this case, we didn't see a total IGE inhibition, but an anti-allergen specific IGE inhibition.”

The findings point toward multiple potential prevention strategies, including supporting bifidobacterial growth through breastfeeding-associated substrates, targeted probiotic supplementation in infants with low colonization, or direct delivery of aromatic lactates. For clinicians, the results reinforce the importance of early-life counseling while underscoring that microbiome-based interventions are not yet ready for routine practice.

“[The next step] is actually to convene on these intervention studies to make sure that supplementation to, for instance, C-section born infants, would provide them with the right colonizing bifidobacteria in the early life,” Pedersen said.

Pedersen has no relevant disclosures.

References

1. Myers PN, Dehli RK, Mie A, et al. Early-life colonization by aromatic-lactate-producing bifidobacteria lowers the risk of allergic sensitization. Nat Microbiol. Published online January 12, 2026. doi:10.1038/s41564-025-02244-9

2. Pedersen S. Early-Life Bifidobacteria Linked to Lower Food Allergy Risk, With Susanne Brix Pedersen. Published on February 4, 2026. Accessed on February 5, 2026. https://www.hcplive.com/view/early-life-bifidobacteria-linked-lower-food-allergy-risk-susanne-brix-pedersen