Microbiota Signatures in Early Life and Their Association With Food Allergy: A Systematic Review.

Food allergy (FA) is increasing worldwide, and early life may be a critical window for immune training. We systematically reviewed observational human studies linking early-life microbiota (infant, maternal, environmental, or extraintestinal) profiled using culture-based and/or culture-independent methods (including sequencing-based approaches) to subsequent FA or food sensitization outcomes in infants, children, and adolescents up to 18 years of age. PubMed, Web of Science Core Collection, Embase, Scopus, and LILACS were searched from database inception to March 2026. Inclusion required microbiota sampling during pregnancy or childhood and clinically ascertained FA/sensitization; non-human studies and studies without sequencing or clinical outcomes were excluded. Risk of bias was assessed using QUIPS. Owing to heterogeneity, we performed narrative synthesis. Forty studies were included (n = 6530 participants; 2077 cases). Across cohorts, cases were associated with lower diversity, early beta-divergence (1-6 months), neonatal enrichment of Proteobacteria (Pseudomonadota)/Enterobacteriaceae and selected taxa (Clostridium, Streptococcus, Sutterella), and depletion within the first year of Bifidobacterium, Blautia, and butyrate producers (Roseburia, Faecalibacterium). Functional profiles often suggested delayed maturation and reduced short-chain fatty acid capacity. Evidence was limited by moderate risk of bias, residual confounding, and heterogeneous outcome definitions. These findings support distinct early-life microbial configurations associated with FA susceptibility versus tolerance, informing mechanism-based prevention. Trial Registration: PROSPERO CRD420251234739.