Abstract
<title>Abstract</title> <p> Using a longitudinal cohort of 633 Gambian children (IHAT-GUT, NCT02941081), we resolve two mechanistically distinct ecological pathways linking <italic>Prevotella stercorea</italic> to infection risk. Its abundance positively predicts gut microbiome richness, consistent with community-level colonisation resistance for enteric outcomes. However, its association with reduced acute respiratory infection (ARI) persists unchanged after richness adjustment, identifying a species-autonomous pathway independent of community diversity. Weight-for-age z-score (WAZ) is uncorrelated with microbiome richness within strata, supporting WAZ as a proxy for host immune-metabolic reserve rather than a determinant of microbiome composition. In Low-WAZ children, <italic>P. stercorea</italic> at Day 1 associates with suppressed CRP, whereas in higher-WAZ children, elevated Day 1 inflammation predicts subsequent <italic>P. stercorea</italic> colonisation at Day 85, consistent with host-context-dependent immune selection. ARI and fever protection is richness-independent and concentrated in Low-WAZ children. <italic>P. copri</italic> does not retain an independent protective association when modelled jointly. These findings have direct implications for microbiome-directed interventions. </p>