Hidden pathogen risk in mature compost: Low optimal growth temperature confers pathogen survival and activity during manure composting.

Livestock manure is a major reservoir for pathogens, posing significant environmental risks if used untreated. The efficacy of composting in fully inactivating pathogens remains controversial, particularly regarding the influence of their optimal growth temperature (OGT). This study investigated the composition and dynamic changes of pathogen communities and virulence factors (VFs) during the composting of chicken, bovine, ovine, and swine manure. We identified 134 pathogens across 16 composting piles, with ten pathogens exhibited increased abundance and transcriptional activity in curing phase. They included high-risk VFs-carrying pathogens, such as Mycolicibacterium thermoresistibile and Mycolicibacterium phlei, indicating the hidden pathogen risk in mature compost. Community-scale analyses revealed a linkage of these pathogens' survival with their low OGT and an increased number of heat shock proteins (HSPs), enabling them to tolerate high temperatures and regrow. Integrating our data with prior composting studies, we found that the surviving pathogens express 42 VFs and their persistence in mature compost was a widespread issue, highlighting a greater risk of pathogen spread than previously thought. Finally, we compiled the 134 pathogens and 1009 VFs into a comprehensive Environmental Risk of Compost Pathogens (ERCP) catalog, providing a valuable resource for routine pathogen surveillance.