Gut microbiome in IBD: past, present and the future

IBD has become a global disease in the 21st century that shifts through four epidemiological stages. Alterations in the gut microbiome consisting of a complex multikingdom community of bacteria, fungi and viruses are strongly linked to disease pathogenesis. Advances in sequencing technologies, multiomics integration and experimental approaches have shed new insights into host–microbiota interactions in IBD and characterised mechanisms through which the microbiota and its metabolites contribute to disease. We review the evolution of microbiome-based research, with a focus on genetic and environmental factors affecting the gut microbiota, the role of cross-kingdom microbiome and their bioproducts in disease development and new strategies by which microbiome-based approaches can be used to diagnose, monitor, prevent and treat IBD.