Pediatric food allergies are becoming increasingly common, likely because of complex interactions between the gut microbiome and immune cells during infancy. Food protein-induced allergic proctocolitis (FPIAP), a common food allergy that causes passing of bloody stools and mucus, occurs in up to 17% of infants. However, no studies have consistently tracked the microbiomes of children who develop FPIAP to learn more about why it occurs. To fill this gap, researchers recently examined nearly 1,000 fecal samples collected from infants throughout their first year of life. Compared to the controls, the 81 infants who developed FPIAP had different microbial community structures. Most notably, the infants who developed FPIAP had greater Enterobacteriaceae abundance and lower Clostridiales abundance than the controls, both before symptom onset and during the symptomatic period, suggesting that these two bacterial groups may play roles in FPIAP development. Although the mechanisms remain to be determined, this study lays a foundation for further research on the microbiome’s contribution to FPIAP and may aid in the development of strategies to prevent food allergies in infants.