Jingwan Zhang, Joyce Wing Yan Mak, Siew C. Ng
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.