Gut microbiota refers to the collective assembly of micro-organisms in a given host ‎environment. It includes, in addition to the well characterized bacterial communities, different ‎life forms of viruses and fungi. Knowledge of these life forms and their functions is currently ‎expanding paralleling with advances in microbiological next generation methodologies which ‎enabled to recognize even unculturable organisms. In the normal health state, these life forms ‎are in a symbiotic relationship with the host where they can provide some biological functions ‎not executed by the host. Vitamin K biosynthesis is a well-known example of this. On the other ‎hand, in disease state, these microbiota communities become disturbed where beneficial ‎members are lost in favour of some pathological forms which may increase the pathological ‎process. In this regard, the gastrointestinal tract is the best model to study these interactions ‎given the direct contact of these microbiota communities with the host mucosal surfaces. In this ‎review, we would revise some of these microbiota changes in different gastrointestinal diseases. ‎
Gut microbiota changes in different gastrointestinal diseases provides an insight into the ‎possible role of gut microbiota in the development of different GI diseases. However, the main ‎question is “are these changes a cause or a result of a disease process". Moreover, trying to alter ‎gut microbiota with a therapeutic intent is the best way to prove such a causal relationship ‎where improvement of the disease process, after gut microbiota modulation, is a strong ‎indicator of gut microbiota role in the pathogenesis of this disease‎‎‎.