Early childhood represents a critical window for immune and gut microbiota development, with lasting implications for disease susceptibility. Altered microbial exposures during infancy have been strongly associated to the rising prevalence of allergic diseases and asthma, yet the underlying mechanisms and early predictive biomarkers remain poorly defined. Here, we did a longitudinal profiling of the gut microbiome of 500 infants followed from birth to 3 years (n=2000). Leveraging the NorthPop birth cohort, a deeply phenotyped, population-based longitudinal resource integrating shotgun fecal metagenomics, plasma metabolomics, immune profiling, lifestyle data, and register-based clinical outcomes, we will quantify differences in the gut microbiome composition and function between pre- and pandemic-born children and identify microbial features associated with altered exposures. Secondly, we will also apply causal mediation and trajectory analyses to assess whether microbiome alterations predict and mediate respiratory and allergic disease outcomes and to develop predictive models of disease trajectories.