Abstract: A computer-implemented method for stratifying a patient with irritable bowel syndrome (IBS). The method comprises detecting the presence, absence, or abundance of multiple bacteria in a biological sample obtained from the patient to generate a patient microbiome profile; and operating a trained classifier on the patient microbiome profile to output a signal stratifying the patient with irritable bowel syndrome (IBS) into a first group or a second group. Stratification of the patient into the first group is indicative that the patient has a not significantly altered microbiome in comparison to the average microbiome not indicative of IBS. Stratification of the patient into the second group is indicative that the patient has an altered microbiome in comparison to the average microbiome not indicative of IBS.