Susanne Brix Pedersen, professor at DTU Bioengineering

Susanne Brix Pedersen

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 

“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.

Myers PN, Dehli RK, Mie A, et al. Early-life colonization by aromatic-lactate-producing bifidobacteria lowers the risk of allergic sensitization. 

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

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Vaginal delivery, exclusive breastfeeding, and early sibling exposure strongly predicted colonization with bifidobacteria that suppress IgE responses in a recent study.


 Inside the Study Linking Infant Gut Bacteria to Lower Allergy Risk

Infants colonized early with specific bifidobacteria that produce aromatic lactate metabolites were significantly less likely to develop 

 and atopic dermatitis in childhood, according to new longitudinal data published in 

The findings add mechanistic clarity to the long-standing hypothesis that the infant gut microbiome helps shape immune tolerance during a narrow developmental window. In a prospective cohort of 147 children followed from birth to age 5, investigators identified a distinct microbiota–metabolite–immune axis associated with reduced food allergen–specific immunoglobulin E (IgE) and lower rates of eczema

The study, led by investigators at the Technical University of Denmark (DTU), tracked infants born between 2003 and 2005 in Sweden, with serial fecal sampling at 8 time points from birth through 5 years of age, alongside maternal samples, blood draws, and clinical data. Using genetic and metabolomic analyses, the team focused on a subset of bifidobacteria capable of converting aromatic amino acids into aromatic lactates. They wanted to see whether specific diseases could be prevented by having a certain microbiota early in life.

Infants with a high abundance of these bacteria, particularly in the first 6 months of life, had elevated gut levels of aromatic lactates and a markedly lower risk of food allergen–specific IgE through age 5. Infants with high levels of bifidobacteria that produced aromatic lactate metabolites had reduced atopic dermatitis at 2 years old. The protective association was mediated by 4-hydroxy-phenyllactate (4-OH-PLA), a bacterial metabolite that selectively inhibited IgE production in ex vivo human immune cell cultures without affecting IgG.

“Even though that we see that [4-hydroxy-phenyllactate] can reduce IGE production…in human immune cell populations, we don't know exactly why,” said investigator Susanne Brix Pedersen, professor at DTU Bioengineering, in an interview with 

. “We know that humans, but not other animals except chimpanzees…have a specific receptor that can bind to these aromatic lactates, but we haven't been able to see that it's mediated via these receptors ye, so it might be other routes for interaction with the immune cells that has just not been discovered yet, but we do see this reduction.”

Early-life exposures strongly influenced whether infants acquired these bacteria. Vaginal delivery, exclusive breastfeeding during the first two months, and exposure to older siblings were all associated with higher colonization, with vaginally delivered infants up to 14 times more likely to acquire the strains from their mothers.

If confirmed, the findings could inform new preventive strategies—ranging from targeted probiotics to metabolite-enriched formulas—aimed at reducing the growing global burden of childhood allergies and asthma. Pedersen emphasized that this current data does not yet establish causality.

“There's no causal link at this moment,” Pederson said. “As I see it, we have this prospective study where we see associations, but we don't have any studies that have been designed to actually look at the causal interaction at this moment, but we are undertaking a bigger study in 1000 Danish infants, where we are trying to…investigate this in detail.”

Longitudinal data identify aromatic lactate–producing bifidobacteria and the metabolite 4-hydroxy-phenyllactate as key factors in early immune tolerance.

Susanne Brix Pedersen

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