Method and System for Microbiome-Derived Companion Diagnostics

A method of treating a DNA alkylation-associated condition, the method comprising:

• obtaining a microbiome sample from an individual;
• detecting a DNA alkylation-associated condition based on presence and/or amount of one of colibactin or colibactin-like compound in the microbiome sample;
• and
• administering a colibactin-inhibiting treatment to the individual for treating the DNA alkylation-associated condition.

A method for characterizing compatibility of a drug for a user, the method comprising:

• collecting a set of microbiome samples from a set of individuals comprising a set of first individuals who respond to a therapy for a microbiome-related condition and a set of second individuals who do not respond to the therapy for the microbiome-related condition;
• determining one or more microbiome datasets based on the set of microbiome samples;
• extracting a set of microbiome features from the one or more microbiome datasets, the microbiome features facilitating differentiation between individuals who respond and individuals who do not respond to the therapy;
• determining a companion diagnostics model based on the set of microbiome features;
• and
• determining the compatibility of the drug for the user using the companion diagnostics model.