Gut microbiota altered in infants with FPIES

Alterations in gut microbiota composition were observed in infants diagnosed with food protein–induced enterocolitis syndrome (FPIES), with reduced Bifidobacterium and increased Bacteroides compared with healthy controls, according to findings from a prospective observational study conducted in Sweden. The results, published in The Journal of Allergy and Clinical Immunology, add to emerging evidence that microbial dysbiosis may play a role in non–immunoglobulin E (IgE)–mediated food allergy.¹

FPIES is a delayed, cell-mediated food allergy that typically presents in infancy with repetitive vomiting, pallor, and lethargy within hours of ingestion. Although prior research has linked gut microbiota to IgE-mediated food allergy, data on non–IgE-mediated conditions such as FPIES remain limited.

“Our results reveal clear differences in the gut bacterial composition of children with FPIES, an area where knowledge has so far been limited,” said Kotryna Simonyte Sjödin, PhD, a molecular biologist and associate professor at Umeå University.²

Prospective cohort compares microbiota at diagnosis

Investigators analyzed fecal microbiota from 56 infants diagnosed with FPIES and 43 age-matched healthy controls from the same geographic region in northern Sweden.¹ The mean age at diagnosis was 8.5 months, and most children reacted to a single food trigger, most commonly cow’s milk, oat, or hen’s egg.

FPIES diagnoses were established using international criteria, with oral food challenges performed when clinical history alone was insufficient. Fecal samples were collected at the time of diagnosis and analyzed using 16S ribosomal RNA gene sequencing. Controls were derived from a previously established cohort of healthy infants with longitudinal microbiota data.

The primary objective was to assess differences in microbial diversity and composition between groups. Secondary analyses evaluated associations between microbiota and clinical or environmental factors, including delivery mode, breastfeeding duration, antibiotic exposure, and household pet exposure.

Distinct microbial composition despite similar diversity

Alpha diversity, measured by the Shannon index, did not differ significantly between infants with FPIES and controls at any age. However, beta diversity analysis demonstrated significant differences in overall microbial composition between groups (P < .01), indicating distinct microbial community structures.

At the taxonomic level, infants with FPIES had significantly lower relative abundance of Bifidobacterium and higher abundance of Bacteroides when data were pooled across age groups (linear discriminant analysis score ≥3.0; P < .05). Additional increases in Haemophilus and Veillonella were also observed.

Age-related trends were consistent across both groups, with increasing microbial diversity over time. However, differences in specific taxa persisted. Infants with FPIES also demonstrated reduced abundance of other beneficial taxa, including members of the Lachnospiraceae family, in regression analyses.

Importantly, these associations remained after restricting analyses to vaginally delivered infants, suggesting that delivery mode alone did not account for the observed differences.

Clinical context and interpretation

The findings support a growing body of literature linking early-life gut microbiota to immune development and food allergy risk. Reduced Bifidobacterium, which is commonly associated with breastfeeding and immune regulation, may reflect impaired microbial maturation in infants with FPIES.

In contrast, increased Bacteroides and other taxa may indicate a shift toward a microbial profile associated with altered immune signaling. While causal relationships cannot be established, the results suggest that microbial composition at the time of diagnosis differs in infants with FPIES compared with healthy peers.

Clinically, FPIES remains a diagnosis based on history and, when necessary, oral food challenge. There are no established biomarkers or microbiota-based diagnostics. However, these findings raise the possibility that microbial signatures could eventually contribute to earlier identification or risk stratification.

“Longitudinal studies incorporating metagenomic approaches are warranted to clarify the role of specific microbial taxa in FPIES pathophysiology and tolerance acquisition,” wrote investigators.

References

1. Winberg A, Simonyté Sjödin K, Öhlund M, West CE. Loss of symbiotic gut bacteria in children at diagnosis of food protein–induced enterocolitis syndrome. J Allergy Clinl Immunol. Published online March 11, 2026. doi:10.1016/j.jaci.2026.02.043
2. Gut microbiota differs in children with rare food allergy. News release. Umea University. April 2, 2026. Accessed April 6, 2026. https://www.eurekalert.org/news-releases/1122564