Obesity is an emerging global epidemic with profound challenges to world healthcare economies and societies. Traditional approaches to fight obesity have not shown promise in promoting a decline in obesity prevalence. The gut microbiota are becoming widely appreciated for its role in regulating metabolism and thus represents a target for new therapies to combat obesity and associated co-morbidities. In this review, we provide an overview of altered microbial community structure in obesity, dietary impact on the gut microbiota, host-microbe interactions contributing to the disease, and lastly improvements in microbial assemblage after bariatric surgery and with therapies targeting the gut microbiome.