Systemic lupus erythematosus (SLE) and antiphospholipid syndrome are related, systemic autoimmune diseases of unclear etiology. Genetically predisposing factors are known; however, these alone cannot be decisive for the onset and severity of these diseases. This article explains the role of the bacterial microbiome in the origin and progression of these rheumatic diseases. The most recent knowledge in the field of microbiome research based on animal experimental approaches, patient cohorts and human samples is summarized. Various commensal bacteria that promote autoimmunity, so-called pathobionts, which originate from the gut, the skin and the oral cavity, are described. Additionally, their different mechanisms of action are described: Enterococcus gallinarum and Limosilactobacillus reuteri induce adaptive autoimmunity and innate type I interferon pathways via translocation from the small intestine to the liver and spleen; Bacteroides thetaiotaomicron, Actinomyces massiliensis, Pseudopropionibacterium propionicum, Corynebacterium amycolatum, Ruminococcus gnavus and Roseburia intestinalis lead to the formation of pathogenic T‑cell and autoantibody responses via the cross-reactivity with autoantigens (Ro60, dsDNA and ß2 glycoprotein I). Finally, potential future treatment approaches are also discussed, such as immunization against certain pathobionts or the targeted modulation of the microbiome via dietary approaches, which can successfully reduce autoimmune pathologies in animal models.