Aspects describe capturing various bacteria levels within a process affected by microbial agents. A model of the process and a model of expected bacteria growth are analyzed and, based on the analysis, at least one process parameter is automatically modified to improve or optimize the product or process or other business or operational objectives. Also provided are at least two autonomous agents within the process. The at least two autonomous agents communicate and autonomously implement an action in an upstream stage and/or downstream stage within the process, wherein the at least two autonomous agents access the representation of the process and the biological representation and/or bio-chemical representation to implement the action.