The aim of this study was to assess the roles of bacteria in degrading protein and carbohydrate during chicken and bovine manures composting. The results showed that protein and carbohydrate degraded greatly, especially during the thermophilic phase of composting. This was mainly caused by the abundant bacteria communities that related with protein and carbohydrate transformation in the thermophilic phase, which identified by the network analysis. Besides, the microbial degradation of nutrient substances performed specificity and universality. "Specificity" and "Universality" meant protein and carbohydrate degraded by certain bacteria and diverse groups of bacteria, respectively. "Specific" bacteria transformed protein and carbohydrate during chicken manure composting, whereas the transformation characteristic of bacteria to protein and carbohydrate in bovine manure was "universality". Structural equation models also verified these results, and they showed that more than 79% of protein and carbohydrate changes were transformed by bacteria.