The human gut harbours a complex, diverse, and dynamic microbial community containing nearly 40 trillion bacteria. These microorganisms occupy a nutrient-rich environment and in return, make essential contributions to many aspects of human health, including immune function, metabolism, and neurobehaviours. Microbial diversity, and specific communities and strains, have been associated with risk of obesity, diabetes, and inflammatory bowel disease. Evidence from animal studies and small human trials suggests that faecal transplantation of lean phenotype-associated microbiota can prevent weight gain and improve glycaemic traits. The question then arises: will there be a safe and non-invasive strategy in humans that can reshape an impaired gut microbiota into a healthier status and thereby improve metabolic health of individuals with obesity?