A probiotic framework befitting the precision psychiatry healthcare model in MDD. This framework represents three main components of precision psychiatry: neurobiological bases, genetic bases, and environment and lifestyle elements of MDD that involve microbial intertwining. Modulation of gut microbiota is the rudimentary anti-depressive mechanism of probiotics. Some commonly explored probiotics of Lactobacillus spp. and Bifidobacterium spp., either as a single strain or multi-strain, exert anti-depressive mechanisms by acting on different pathophysiologic mechanisms implicated in depressive disorder. Stress and diet are mainly modifiable targets in the prevention of MDD. The microbial-based applications in the clinical management of MDD include some potential biomarkers obtainable through a patient’s blood analysis, assessment of vital frontolimbic regions in the brain using MRI, and integration of machine learning and development of depression-specific metabiotic as part of futuristic vision within this context.