A method of determining tolerance to an agent in a healthy subject is disclosed. The method comprises: (a) determining a signature of a microbiome in a sample of the healthy subject who has been subjected to the agent or condition and (b) comparing the signature of the microbiome of the healthy subject to at least one reference signature of a pathological microbiome, wherein when the signature of the microbiome of the healthy subject is statistically significantly similar to the reference signature of the pathological microbiome, it is indicative that the healthy subject is intolerant to the agent.
