A method of determining the therapeutic effect of an agent, such as a metabolite, comprising:(a) exposing a pathological microbiome to the agent； and(b) comparing the signature of the pathological microbiome following the exposing with a reference signature of a healthy microbiome, wherein when the signature of the microbiome is statistically significantly similar to the healthy microbiome reference signature, it is indicative that the agent has a therapeutic effect on the microbiome. The agent may be provided to a subject having a pathological microbiome once it has been classified as therapeutic.
