Methods: Food-allergic (history of immediate hypersensitivity to food with positive food-specific skin and/or serum IgE) and healthy control infants <= 12 months of age were enrolled. Stools samples were collected and detailed health, environmental and dietary questionnaires were completed serially every 4 months. Bacterial DNA was extracted and the V4 region of the bacterial 16S rRNA gene was sequenced using the Illumina MiSeq instrument.
Results: 137 infants (52 food-allergic and 85 controls) were enrolled. There were significant differences in fecal microbiota between the 2 groups. At the phyla level, there was decreased relative abundance of Firmicutes and Proteobacteria, and increased relative abundance of Bacteroidetes in food-allergic babies. These differences could be traced down to altered abundance of taxa at the genus level. Differences for food-allergic babies 1-6 months of age included decreased abundances of genera in Bacteroidetes (Parabacteroides and Alistipes) and Firmicutes (Blautia, Clostridium, Subdoligranulum, Veillonella, Staphylococcus and Enterococcus) and increases in other Firmicutes (Sarcina and Cellulosilyticum). Differences for food-allergic babies 7-12 months of age included decreased abundances of genera in Bacteroidetes (Parabacteroides, Alistipes, and Prevotella), Firmicutes (Eubacterium, Clostridium and Ruminococcus), and Proteobacteria (Campylobacter), and increases in other Firmicutes (Dorea) and Proteobacteria (Parasutterella).
Conclusions: Our data supports the presence of a gut microbial signature in food allergy. Evaluation of a larger group (500 subjects) and longitudinal follow-up for 3 years with fecal microbiota analysis and questionnaires every 4 months is in progress.