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In the era of high throughput DNA sequencing technologies, there has been an explosion in the last 10 years of our knowledge of human microbiomes, especially the gut microbiome and its contribution to health and disease. This understanding has confirmed that the gut is an incredible complex ecosystem with critical health implications. Inflammatory bowel diseases, primarily Crohn's disease and ulcerative colitis, are diseases where a direct link to the gut microbiome is best understood. These pathologies are difficult to treat and dramatically on the rise globally, possibly linked to lifestyle changes, like diet, urbanisation, and antibiotics exposure. Here we canvas our current knowledge of the link between the gut microbiome and these diseases. Large-scale and longitudinal population-wide studies of gut microbiomes in combination with appropriate animal models will be instrumental to propel the field from cataloguing correlations to understanding causation. [ABSTRACT FROM AUTHOR]