High Microbiome Diversity Constricts the Prevalence of Human and Animal Pathogens in the Plant Rhizosphere Worldwide

Agricultural soils are often overlooked sources of human and animal pathogenic bacteria, which can cause a range of food-, air-, and waterborne diseases. The awareness of pathogens in soil is as old as that in modern microbiology, but we still know little about the factors driving their global distribution. Here, we compiled 342 pairs of bulk and rhizosphere soil microbiomes to identify 9,516 potential pathogenic amplicon sequence variants (ASVs), 75% of which were human-animal pathogens. The relative abundance and diversity of these pathogens in the rhizosphere were 81% and 11% higher, respectively, compared to bulk soils. Most of these pathogens are opportunistic, and 11 keystone species in the rhizosphere have been reported as human gut pathogens. Through different agricultural management practices, we revealed that increasing microbial diversity reduces pathogen prevalence. This study aligns the interest of sustainable food production and public health by providing incentives for the redesign of food production systems.