A field study of clinically sick pigs on commercial farms shows that matching molecular pathogen detection with microbial community profiling changes how a herd is read. The work points to oral fluid as a practical, high-diversity sample for routine monitoring. Quick answer Molecular diagnostics and microbiome profiling from the same sick pigs give a clearer picture than either method alone. In 164 field samples, lung tissue showed the lowest microbial diversity while oral fluid carried the richest, most monitorable community. Pairing a positive pathogen result with its microbial context supports faster, more targeted treatment decisions on commercial swine farms. Why pathogen detection in swine needs more than a single test…