Harnessing agricultural microbiomes for human pathogen control

Plant microbial communities comprise a complex network ofmicroorganisms present on surface and internal tissues, whichinteract with the host plant and the environment. Each plantcompartment represents a microhabitat characterised by specificconditions that support distinct microbial communities. Whilst theplant microbiota is predominately beneficial or benign in nature,plant pathogens and, to a lesser extent, human pathogens, can benaturally present in the microbiome or become incorporated intothe community. For edible crops, human pathogens represent ahealth risk and are increasingly responsible for foodborne disease,with fresh produce accounting for over 1/3 of all foodborneoutbreaks in some countries. Growing evidence that certainhuman pathogens are well adapted to occupying plant nichesnecessitates a shift in thinking regarding their ecological rangeand should be incorporated within control strategies. In this articlewe argue that it is possible, through agricultural managementpractices, to enhance suppression of human pathogens bymicrobiota associated with horticultural crops. We examine theenvironmental fitness of these pathogens and the ecology ofsuppressive interactions, explore the knowledge gaps andapproaches needed to fill these, and provide our perspectiveson the potential to harness agricultural microbiomes to reduce therisk of disease transmission into the food-chain.