The human microbiome in rheumatic autoimmune diseases: A comprehensive review

• Dysbiosis occurs in patients with autoimmune and inflammatory rheumatic diseases.
• Genetic susceptibility and environmental factors interact with the host microbiota.
• Taxonomic and metagenomics sequencing reveal host-microbiota interactions.
• Work is needed to understand how the microbiome changes over time in autoimmunity.

The human microbiome consists of the total diversity of microbiota and their genes. High-throughput sequencing has allowed for inexpensive and rapid evaluation of taxonomic representation and functional capability of the microbiomes of human body sites. Autoimmune and inflammatory rheumatic diseases are characterized by dysbiosis of the microbiome. Microbiome dysbiosis can be influenced by host genetics and environmental factors. Dysbiosis is also associated with shifts in certain functional pathways. The goal of this article is to provide a current and comprehensive review of the unique characteristics of the microbiome of patients with autoimmune and inflammatory rheumatic diseases, measured using high-throughput sequencing. We also highlight the need for broader studies utilizing a longitudinal approach to better understand how the human microbiome contributes to disease susceptibility, and to characterize the role of the interaction between host genetics and microbial diversity in the pathogenesis of autoimmune diseases, disease manifestations, and progression.