Oral Microbiome in Systemic Autoimmune Diseases: A Systematic Review

The oral cavity represents a key but underexplored interface between host immunity and microbial communities. The aim of this systematic review was to synthesize current literature on oral microbiota alterations in systemic autoimmune diseases.

PubMed and Web of Science databases were searched for human studies published between January 2000 and April 2025. Eligible observational studies compared adults with diagnoses of systemic autoimmune diseases to controls and characterized oral microbiota diversity and/or composition using sequencing-based methods. Different oral habitats were analyzed (saliva, dental plaque, oral mucosa, gingival crevicular fluid).

42 studies met inclusion criteria: 19 on rheumatoid arthritis, 18 on primary Sjögren's syndrome, 5 on systemic lupus erythematosus, and 1 on anti-neutrophil cytoplasmic autoantibody-associated vasculitis. 16S rRNA gene sequencing predominated and only 3 studies used shotgun metagenomics, among which one also profiled the oral virome. Across systemic autoimmune diseases, dysbiosis was characterized by enrichment of anaerobic genera (Prevotella, Veillonella) and depletion of commensals (Neisseria, Haemophilus), with distinct β-diversity separation from controls. Periodontal disease and reduced salivary secretion significantly modulated microbial communities but did not fully explain disease-associated alterations.

The oral microbiome exhibited shared dysbiotic signatures. However, methodological and clinical heterogeneity limited direct comparison between studies.