Gut microbial dysbiosis with altered ecological processes characterizes pediatric cow’s milk protein allergy

Cow’s milk protein allergy (CMPA) is among those frequently seen food protein allergies during infancy and childhood. It ranks third among factors inducing allergic reactions, after peanut and nut allergies. The present work focused on investigating the impacts of gut microbial alterations within CMPA and exploring the associated microbial mechanisms. As indicated by our 16 S rRNA sequencing analysis, gut microbial richness and diversity in CMPA children apparently decreased relative to normal subjects. Bray-Curtis distance was adopted for assessing the microbial community structure, revealing significant inter-group differences. CMPA children also showed substantially depleted species in the phyla Bacillota and Bacteroidota. Furthermore, the gut microbiota assembly among CMPA children was mainly achieved by homogenization selection, with remarkably enhanced effect of homogenization selection and dispersal limitation. Multi-faceted profiling was conducted, identifying six key high-abundance and high-occupancy amplicon sequence variants (ASVs), which were taxonomically classified, at the 16 S rRNA amplicon sequencing level, into genera Escherichia-Shigella , Enterococcus , and Streptococcus . Of them, Escherichia-Shigella and Enterococcus were most closely related to CMPA. These key species were incorporated for constructing a random forest model, which performed well in differentiating between CMPA children healthy counterparts (area under the curve (AUC) > 85%). Based on co-occurrence network analysis, the CMPA gut microbiota network was densely connected and showed an intricate structure, and Escherichia-Shigella and Enterococcus were the dominant hub taxa. Upon functional predictions of gut microbiome, obvious changes in some pathways were detected, like bacterial epithelial invasion, ester metabolism, and immune-related processes. Key species were tightly related to some metabolic or disease-related pathways, like linoleic acid metabolism and bacterial dysentery. The above results indicate that the gut microbial composition and structure in CMPA children are tightly associated with CMPA phenotype. This work suggests that key intestinal taxa, especially Escherichia-Shigella and Enterococcus , are important for CMPA pathogenesis. The findings lay a basis for exploring these species as biomarkers or therapeutic targets for CMPA.