Metabolic diseases, especially type 2 diabetes and obesity, are growing global health-care concerns. New therapeutic approaches are urgently needed to address the emerging epidemic of obesity and diabetes. Recent studies have highlighted the role of gastrointestinal microbial communities in metabolic health and disease. The microbiome, the collective genomic and metabolic potential of the gut microbiota, may have a key role in many chronic diseases through its mitigation of immune-inflammatory responses. Here we provide an overview of present knowledge about the gut microbiome, its putative role in metabolic diseases and the potential for microbiome focused treatments involving either modulation of the microbial ecosystem or influencing microbiota–human host cross-talk pathways.