Comparison of microbiota of recycled manure solids and straw bedding used in dairy farms in eastern Canada

Abstract

Recycled manure solids (RMS) bedding is an alterna-tive bedding option that is growing in popularity on Canadian dairy farms. However, the microbiological characteristics and production of RMS bedding are poorly documented under on-farm conditions in eastern Canada. This bedding could support the presence of pathogens and could have an effect 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 generally con-tained 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. mono-cytogenes: 11%). Finally, 2 RMS production systems (extraction of the liquid fraction followed by matura-tion in an opened or enclosed container vs. in a heap) did not influence the microbiota richness and bacteria distribution (alpha-diversity), but did influence the micro-biota structure (beta-diversity). In conclusion, animal and human pathogens were found in greater numbers and more frequently in unused RMS than unused straw, and this could eventually affect dairy cow or human health.