Disentangling Gut Microbiome Alterations in Children with Cow’s Milk Allergy: Impact of Sex, Milk Elimination, and Family History of Allergies

<b>Background</b>: Children with cow's milk allergy (CMA) present alterations in their gut microbiome, but any potential sex-dependency of these has not been addressed. Further, whether eliminating milk from children's diet has similar effects on the gut microbiomes of boys and girls is also not known. Here, our main objective is to analyze how CMA and development of oral tolerance (DOT) to milk proteins affect the gut microbiota in female and male children. We also perform exploratory analyses to investigate whether milk elimination and/or a family history of allergies underlie sex-associated differences. <b>Methods</b>: We obtained 16S rRNA gene sequences of the intestinal microbiota of 32 children aged 5-12 years with CMA, of which 14 had active CMA and 18 had developed oral tolerance, along with 36 age-matched healthy controls (51.5% male). PERMANOVA and differential abundance analyses were employed to evaluate overall compositional differences and to identify bacteria varying between the groups. <b>Results</b>: The effects of CMA on the gut microbiome are more pronounced in girls, including female-specific decreases in bacteria potentially related to protection from allergy, such as <i>Monoglobus</i> and <i>Anaerostipes</i>. The girls' microbiomes were also found to be more influenced by a family history of allergy, remaining farther from the healthy state upon DOT. In contrast, milk elimination affects more taxa in boys in the control group than in girls in the control group, although it alters global microbiome composition in both. In all, milk elimination and family history fail to explain most microbiome alterations observed in CMA, indicating that the latter are specifically linked to disease development. <b>Conclusions</b>: Gut microbiome alterations associated with CMA are sex-dependent, suggesting that sex-specific strategies, dietary and otherwise, may be more effective at modulating them toward healthier states.