A prospective microbiome-wide association study of food sensitization and food allergy in early childhoodOriginal paper
Karen Pendergrass is a microbiome researcher specializing in microbiome-targeted interventions (MBTIs). She systematically analyzes scientific literature to identify microbial patterns, develop hypotheses, and validate interventions. As the founder of the Microbiome Signatures Database, she bridges microbiome research with clinical practice. In 2012, based on her own investigative research, she became the first documented case of FMT for Celiac Disease, four years before the first published case study.
Read MoreWhat was studied?
This prospective study asked whether the infant gut microbiome predicts later food sensitization and food allergy. Stool collected at ages 3 to 6 months was linked to allergy outcomes assessed at age 3. Researchers sequenced the 16S rRNA V3 to V5 regions on the Roche 454 platform and used closed-reference operational taxonomic unit classification. Differential abundance was tested with negative binomial models in Phyloseq and DESeq2. P-values were corrected for multiple comparisons using Benjamini-Hochberg.
Who was studied?
Subjects were infants in the Vitamin D Antenatal Asthma Reduction Trial, a United States birth cohort recruited in Boston, St. Louis, and San Diego. Complete data were available for 225 children, all with a family history of asthma or allergy. Stool was collected between ages 3 and 6 months, excluding infants on recent antibiotics. There were 87 cases of food sensitization and 14 cases of food allergy. Sensitization was defined by food-specific IgE, and allergy by provider diagnosis plus IgE evidence.
What were the most important findings?
Overall microbial diversity did not differ between cases and controls for either sensitization or allergy. Instead, specific genera were underrepresented in cases, all with lower read counts. For food sensitization, Haemophilus (logfold change -2.15, P = 0.003), Dialister (-2.22, P = 0.009), Dorea (-1.65, P = 0.02), and Clostridium (-1.47, P = 0.002) were reduced. For food allergy, Citrobacter (-3.41, P = 0.03), Oscillospira (-2.80, P = 0.03), Lactococcus (-3.19, P = 0.05), and Dorea (-3.00, P = 0.05) were reduced. Dorea was reduced in both outcomes.
What are the greatest implications of this study?
The temporal order, with microbial differences preceding disease, suggests the early gut microbiome may play a causal role in food allergy development. Reduced Dorea stood out across both sensitization and allergy. The authors note therapeutic potential for preventing or treating food allergy by shaping the infant microbiome. Limitations temper causal claims: only 14 allergy cases, genus-level analysis, and possible confounding by race and diet. Some resolved allergies may have been misclassified as controls.