There is now strong evidence that microbiomes play an important role in human health, as there are clear linkages to many of the major non-communicable diseases. This report assesses the key policy challenges for innovation in the microbiome. Evidence is accumulating that through diet, the gut microbiome can be altered to generate greater well-being, to offer better protection against non-communicable diseases, and even to cure such conditions. The report argues that if such a promising scientific field is to lead to innovative applications, policies on science and innovation must be improved in five areas: 1) science policy; 2) enabling translational science; 3) public-private collaboration; 4) regulatory frameworks; and 5) skills, communication and the public.