This study explored the use of a biosecure, static composting structure to inactivate MAP. In Experiment #1, it was concluded that composting is unlikely to achieve temperatures necessary to inactivate MAP associated with cattle mortalities and that M. smegamatis is an unlikely surrogate for MAP. This study also used the same system to explore changes in the microbial community in mortality compost after exposure to thermophilic temperatures. As high-throughput sequencing technologies advance, it is possible to characterize microbial communities in environments with a high degree of resolution. In Experiment #2, as members of Clostridia were present at temperatures > 55°C, it appears that anaerobic conditions existed within regions of the compost. Extreme temperatures and non-homogeneous high moisture conditions resulted in spatial distribution of temperature in a biosecure, static composting system, which failed to meet conditions necessary for complete composting and pathogen reduction.