The human gut contains numerous organisms including bacteria, viruses and fungi. These gut microbes have co-evolved with host through for a very long time and at baseline, provide a beneficial relationship with the host. This paper will focus on bacteria, which are multiple factors more than human cells in number. These bacteria have a significant effect on humans and play a significant role in maintaining one’s health. Despite the countless research projects that target these bacteria, their composition, behavior and pathology continues to challenge scientists and clinicians. Each microbial composition is unique to its host. However, there are major phyla under which the majority of beneficial bacteria fall in a healthy individual. Besides its biodiversity, the major characteristics of gut microbiota are their stability over time and resilience after perturbation. In pathological situations, dysbiosis is observed with a loss in overall diversity – an occurrence, which leads to such conditions as inflammation and identification of these bacteria by the immune system. This in turn mounts an immune response to the gut bacteria, which were originally not recognized by the immune system. Metagenomics are utilized by scientists to not only figure out the composition of the different gut bacteria, but also to give information about their genome and therefore more insight into their possible functions. Clinical data, treatment and all the factors able to influence microbiome should be studied extensively and incorporated together to shed light on the interplay between these organisms and the host.
