Comparison of Microbiota of Recycled Manure Solids and Straw Bedding used in Dairy Farms in Eastern Canada

Recycled manure solids (RMS) bedding is an alternative bedding option growing in popularity in Canadian dairy farms. The microbiological characteristics and production of RMS bedding, however, are poorly documented under on-farm conditions in eastern Canada. This bedding could support the presence of pathogens and could have an impact on cow and human health. The aim of this study was to describe the RMS microbiota when used under dairy cows and compare it with straw bedding. Unused and used bedding from 27 RMS and 61 straw-bedded dairy farms were collected and compared using 16S amplicon sequencing, bacterial counts, and Salmonella spp. and Listeria monocytogenes detection. Microbiota composition of unused RMS and unused straw were different. After use, both bedding microbiota were similar in their bacterial composition, structure, and diversity. Unused RMS in general contained higher bacterial counts than did unused straw, except for Klebsiella spp. counts. Salmonella spp. and L. monocytogenes were more frequently detected in unused RMS (Salmonella spp.: 11%; L. monocytogenes: 30%), than in unused straw (Salmonella spp.: 0%; L. monocytogenes: 11%). Finally, the different RMS production systems (mainly extraction of the liquid fraction followed by maturation in a box vs. in a heap) did not influence the microbiota richness and bacteria distribution (alpha diversity) but did influence the microbiota structure (beta diversity). In conclusion, animal and human pathogens were found in greater numbers and more frequently in unused RMS, and this could eventually impact dairy cow or human health.Key Words: dairy cow, bedding, recycled manure solids, straw, microbiota