Scientific advances occurring at a dizzying pace around the world continue to reveal the vital roles of the microbiota in the organism. Scientific evidence revealed in recent years about the content and functions of the microbiota shows that it is of great importance for the health of the organism. The relationship of microbiota with many systems and organs is revealed every day. A small change in the content and function of the microbiota affects many organs and systems. Therefore, in this study, we aimed to provide a transdisciplinary updated look at the content and functions of microbiota, including many disciplines. Our current study also provides a transdisciplinary look at both the structure and functions of the microbiota at the macro and molecular levels in terms of systems. We hope it serves as an example for future studies to reveal the unknowns of every aspect of the microbiota.