The present disclosure is related to a method and system for stratification of subjects as one of responders or non-responders to a therapy. It is imperative to critically evaluate the baseline/initial microbiome structure and composition of individuals and stratifying them before prescribing any microbiome-based drug/dietary interventions. The method identifies a panel of biological features/indicators/markers/signatures that can accurately stratify/classify/group individuals into responders and non-responders (for a given microbiome-based drug/therapy) based upon the differences in the metabolic functions of the gut microbial communities between the baseline gut microbiome profile (i.e. before the administration of an intervention) and after treatment gut microbiome profile (i.e. after the administration of the intervention). Individuals with samples showing an improvement in gut-health status after the administration of the pre-biotic intervention were tagged as responders and the rest were tagged as non-responders.