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There is an extensive and diverse microbial community residing within the human body, the microbiota. Evidence that this community plays an important role in health and disease is ever increasing, although our understanding of the mechanisms behind this link remains limited. Studies have demonstrated that the microbiota present in various regions, including the gut, skin and the mouth, in individuals with rheumatic diseases differs from that of healthy controls. The nature of these differences is slowly becoming clearer, and studies are now beginning to reveal functional differences associated with these compositional differences. Further clarification of the differences in microbiota in various human diseases may lead to novel diagnostic, preventive and treatment approaches. This role of the microbiome in rheumatic disease is the focus of this themed collection, which comprises a selection of recent full-text articles and chapters from the Springer Nature portfolio.