The central role of gut microbiota in the regulation of health and disease has been convincingly demonstrated. Polymicrobial inter-kingdom interactions between bacteria (the bacteriome) and fungal (the mycobiome) communities of the gut have become a prominent focus for development of potential therapeutic approaches. In addition to polymicrobial interactions, the complex gut ecosystem also mediates interactions between host and the microbiota. These interactions are complex and bidirectional, microbiota composition can be influenced by host immune response, disease-specific therapeutics, antimicrobial drugs, and overall ecosystems.