Extensive analysis of the complexity and diversity of microbiota using metagenomics in the
gut and other body sites has provided evidence that dysbiosis occurs in many disease states. With the
application of next generation sequencing technology this research is starting to uncover the impact of
microbiota on metabolic, physiological and immunological pathways and elucidate the cellular and
molecular mechanisms involved. To highlight these advances we have focused on autoimmunity and gut and liver related
diseases and discuss the opportunities and challenges of translating microbiome research towards its application in
humans. Towards this goal we discuss the application of fecal microbiome transplantation (FMT) for the treatment of
multiple chronic gut associated inflammatory diseases such as Clostridium difficile infection (CDI) and inflammatory
bowel disease (IBD). The potential role of human migration across continents and cultures leading to alteration in their
microbiome and its implication in health and disease is also discussed.
Keywords: Autoimmune diseases, fecal microbiota transplantation, gut microbiota, human migration and microbiome,
inflammatory gut diseases, immune system, liver diseases, microbiome, next generation sequencing.
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