The gastrointestinal tract is home to a multitude of commensal micro-organisms that co-develop with the host from birth to influence a wide range of physiological processes. These commensal organisms, collectively known as the gut-microbiota, are known to many control aspects of immune system development and function both directly and indirectly. This includes research from our laboratory showing that changes in the gut-microbiota and associated metabolites affects the balance between antibody-producing and regulatory B cell subsets in experimental models of autoimmunity. Further exploration of these signals in human arthritides across age (rheumatoid arthritis, juvenile idiopathic arthritis) could identify novel approaches to specifically target pathogenic B cell responses in both childhood and adult arthritis.