The gut microbiota is shaped by microbial interactions, environmental factors and continuous surveillance by the host immune system. Immunoglobulin A (IgA) recognizes selected microbial populations and contributes to the organization of gut microbial communities, but this immune dimension is rarely integrated into microbiome analyses. We developed quantitative approaches combining IgA engagement with the abundance and prevalence of microbial taxa. Across geographically distinct cohorts, these analyses identified conserved patterns of immune engagement involving both well-characterized commensals and poorly annotated taxa. In early multiple sclerosis, IgA-mediated microbial engagement was altered despite relatively preserved microbial diversity and composition. These changes were summarized at the community level using the Immunologically Engaged Gut Microbiota Index, which varied with disease activity and following fecal microbiota transplantation. In individuals with IgA deficiency, humoral immune impairment was associated with changes in both bacterial and viral communities, including increased phage richness and enrichment of phages predicted to infect Enterobacteriaceae, particularly Escherichia. These findings highlight antibody-mediated immune surveillance as an important component of gut microbiota organization.