Increasing evidence suggests that perturbations in the intestinal microbiota in early infancy are implicated in the pathogenesis of food allergy (FA); existing evidence on the structure and composition of the intestinal microbiota in human beings with FA is limited and conflicting. The main object of the study was to compare the faecal microbiota between healthy and cow's milk allergy (CMA) infants at the baseline immediately after the diagnosis, and to evaluate the changes in the faecal microbiota after 6 months of treatment of CMA infants with hypoallergenic formula (HF), compared with healthy children fed on standard milk formulae. Sixty infants younger than 4 months of age with challenge-proven CMA and 60 healthy age-matched children were investigated in this prospective case - control follow-up study. Faecal samples were collected at baseline and at 6 months of follow-up, microbial diversity and composition were characterized by high-throughput 16S rRNA sequencing. The average age (±SD) of the infants at inclusion was 2.9 ± 1.0 months. Children with CMA have lower gut microbiota diversity and an elevated Enterobacteriaceae to Bacteroidaceae (E/B ratio) in early infancy compared with healthy children (115.8 vs. 0.8, P = 0.0002). After 6 months of treatment with HF, CMA infants had a higher Lactobacillaceae (6.3% vs. 0.5%, P = 0.04) and lower Bifidobacteriaceae (0.3% vs. 8.2%, P = 0.03) and Ruminococcaceae (1.5% vs. 10.5%, P = 0.03) abundance compared with control children. Conclusion: Low gut microbiota diversity and an elevated E/B ratio in early infancy may contribute to the development of FA, including CMA. A strict elimination diet may weaken FA by reducing E/B ratio and promoting a gut microbiota that would benefit the acquisition of oral tolerance.
Keywords: 16S rRNA sequencing; Cow’s milk allergy; Diversity; Gut microbiota; Infants.