With recent advances in gene sequencing and gnotobiotic model, interest in the field of gut microbiota has taken a leap. It is found that a dysbiotic state of gut microbiome is playing a pivotal role in pathological conditions and metabolic disorders such as Inflammatory bowel disorder, Diabetes mellitus and Obesity. Faecal microbiota transplant is found useful for treatment of recurrent Clostridium difficile infections. Human gut microbiome is a vital organ by itself and not many studies have able to show complex functional properties. This review aims to provide an insight on how gut microbiome dysbiosis has been linked to conditions like inflammatory disease, diabetes mellitus and obesity and various recent methods for characterization of gut microbiota.