Autoimmune Research in Review: Microbiome, Microbiota, and Immune System Conditions

Microbiome and microbiota are attracting an increasing amount of attention in the world of medical research. Recently, we have reviewed some literature that link microbiome with allergy. However, microbiome is associated with autoimmune disorders just as often (Google scholar search results 14,000 for microbiome and allergy, 12,300 for microbiome and autoimmune). In this article, we will review some of the recent literature connecting microbiome and autoimmune conditions.

Environmental Exposure and Autoimmune Diseases

In early 2020, researchers Khan and Wang reviewed the influence of environmental factors on autoimmune diseases (ADs). They reviewed the subject from epidemiological and mechanistic approaches. Ultimately, Khan and Wang concluded that changes to the microbiome stemming from environmental exposures, and the chemicals related thereto, could contribute to the pathogenesis of ADs.

Microbiome and Connective Tissues

Connective tissues diseases (CTDs) have also been linked to microbiome. Research from Talotta et al looked at the pathogenesis of these issues as related to microbiome. They found that dysbiosis – an imbalance in microflora or microbiome – may have an impact on several CTDs, including Sjögren’s syndrome, systemic lupus erythematosus (SLE), and systemic sclerosis. They recommend additional research on the connection between CTDs and microbiota.

Microbiome and Inflammatory Bowel Diseases

Microbiome may have an impact on inflammatory bowel diseases (IBDs) as well. Researchers Salem et al looked at microbiome as it relates to IBDs and chronic rheumatic diseases (CRDs). Specifically, they looked at “whether specific gut dysbiosis may be the missing link between IBD and CRD in patients developing both diseases.”

The researchers conducted a systematic review of 80 studies which included roughly 5000 participants in total. They found that an increase in certain microbiota (including Bifidobacterium, Staphylococcus, and Lactobacillus) and a decrease in certain other phyla were common amongst both CRD and IBD patients.

Microbiome and Rheumatic Diseases

Autoimmune rheumatic diseases have also been linked to microbiome. In 2021, Researcher Konig published a review of rheumatic disease immunopathogenesis. He divided his research and findings by the specific rheumatic disease with the goal of analyzing and comparing a full spectrum of autoimmune rheumatic diseases. Konig found that there was “significant heterogeneity” in the microbiome characteristics reported in these studies and he advocated for a standardization in methodology to allow study findings to be more comparative.

Microbiome and Systemic Autoimmune Disease

Another group of researchers – Dehner et al – also compared recent studies, looking for insights into the microbiome mechanisms in systemic autoimmune diseases, with particular emphasis on cross-reactivity. Their research summarizing links between both mucosal and skin microbiota and autoimmune disorders was published in 2020. They concluded that microbiota-targeted treatments and other personalized approaches could be solutions.

The Connection Between Microbiome and Autoimmune Conditions

Microbiome and autoimmune conditions have a long history of association and research. However, scientific understanding of these mechanisms continues to evolve, and those developments encourage new approaches to interventions.


Dehner, C., Fine, R., & Kriegel, M. A. (2019). The microbiome in systemic autoimmune disease: mechanistic insights from recent studies. Current opinion in rheumatology, 31(2), 201–207.

Khan, M. F., & Wang, H. (2020). Environmental Exposures and Autoimmune Diseases: Contribution of Gut Microbiome. Frontiers in immunology, 10, 3094.

Konig M. F. (2020). The microbiome in autoimmune rheumatic disease. Best practice & research. Clinical rheumatology, 34(1), 101473.

Salem, F., Kindt, N., Marchesi, J. R., Netter, P., Lopez, A., Kokten, T., Danese, S., Jouzeau, J. Y., Peyrin-Biroulet, L., & Moulin, D. (2019). Gut microbiome in chronic rheumatic and inflammatory bowel diseases: Similarities and differences. United European gastroenterology journal, 7(8), 1008–1032.

Talotta, R., Atzeni, F., Ditto, M. C., Gerardi, M. C., & Sarzi-Puttini, P. (2017). The Microbiome in Connective Tissue Diseases and Vasculitides: An Updated Narrative Review. Journal of immunology research, 2017, 6836498.

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