Prevotella stecorea-Mediated Protection Against Infection in Rural African Children: Evidence for Microbiome Immunity

Understanding how the gut microbiome confers immune protection in early life remains a fundamental challenge, particularly in high-infection-burden, underrepresented populations. We analysed longitudinal stool microbiome and illness data from 633 Gambian children aged 7–37 months enrolled in a randomized iron supplementation trial. Using 16S rRNA sequencing at three timepoints (Days 1, 15, and 85), we found that children who remained infection-free harboured a consistently higher relative abundance of Prevotella stercorea, a keystone taxon of non-industrialized gut ecologies. In contrast, Escherichia coli and other opportunistic pathogens were enriched in children who developed infections. These taxonomic signatures were temporally stable and embedded within distinct, co-occurring microbial networks. Strikingly, higher P. stercorea abundance was inversely associated with both infection frequency and duration. Our findings suggest the presence of a gut enterotype associated with reduced infection risk and introduce the concept of “microbiome immunity,” with implications for vaccine responsiveness, child survival, and microbiota-targeted interventions in global child health.