Antibiotics, improper food, and stress have created a dysbiotic state in the gut and almost 81% of the world’s population has been affected due to the pandemic of COVID-19 and the prevalence of dengue virus in the past few years. The main intent of this study is to synthesize nanosynbiotics as nu traceuticals by combining probiotics, and prebiotics with nanoformulation. The effectiveness of the nanosynbiotics was evaluated using a variety of Nutra-pharmacogenetic assays leading to an AI-integrated formulation profiling was assessed by using machine learning methods. Consequently, Acetobacter oryzoeni as a probiotic and inulin as a prebiotic has been chosen and iron-mediated nanoformulation of symbiotic is achieved. Nanosynbiotics possessed 89.4, 96.7, 93.57, 83.53, 88.53% potential powers of Nutra-pharmacogenetic assays. Artificial intelligent solid dispersion formulation of nanosynbiotics has high dissolution, absorption, distribution, and synergism, in addition, they are non-tox, non-allergen and have a docking score of − 10.83 kcal/mol, implying the best interaction with Pregnane X receptor involved in dysbiosis. The potential of nanosynbiotics to revolutionize treatment strategies through precise targeting and modulation of the gut microbiome for improved health outcomes and disease management is promising. Their transformational influence is projected to be powered by integration with modern technology and customized formulas. Further in-vivo studies are required for the validation of nanosynbiotics as nutraceuticals.