Distinct patterns of gut microbiome dysbiosis correlated with disease activity in a study of 61 female patients with systemic lupus erythematosus (SLE). The results of faecal 16S rRNA analysis were confirmed in two independent SLE cohorts and revealed a fivefold increase in the amount of Ruminococcus gnavus in patients with SLE compared with healthy individuals. Expanded populations of R. gnavus were particularly prevalent in patients with lupus nephritis; individuals with active nephritis also had high serum concentrations of antibodies against cell wall lipoglycans from certain strains of R. gnavus.