In the human gut resides a complex microbial community whose size is equal to that of the human body eucaryotic cells, but with a functional capacity which outnumbers that of the host by a number of 100. Recent evidence suggests that this microbial community, often named as the gut microbiome, is important not only for the onset of infectious disease but also for the development also of non-communicable conditions, like Crohn’s disease and diabetes. Diet is a major regulator of the human gut microbiome composition and function. Early in life differences occur in the gut microbiome of breastfed compared with bottle-fed children, and it is notion that early gut colonization may influence long-term health. However, the role of diet in the causal pathway between the gut microbiome and disease can be very complex. Differences in the gut microbiome of obese people have been observed, but it is unclear if these are primary obesity initiators or simply the secondary effects of hyperphagia. Likewise in patients with coeliac disease, it is unclear in the gut microbiome pays a role in the disease underlying pathogenesis or any changes observed are the effect of treatment with gluten free diet. An exciting area of future research is whether we can use microbial signatures as prognostic markers of adverse disease outcomes in condition, like intestinal failure,and alsoif dietary manipulation of the gut microbiome can control disease activity outcomes in patients with Crohn’s disease and ulcerative colitis.