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  • Writer's pictureMed Insider

The Dynamic between the Microbiome and Autoimmune Diseases

By Aleena Kuriakose


  • Disrupting the wellbeing of microbiomes can lead to autoimmune disease.

  • Germ-free models help reveal the microbiota’s significance in influencing our immunity.

  • Researchers are currently investigating potential cures to autoimmune disease based on the characteristics of gut microbiomes.


When we think of bacteria, pathogens are often the first ones to cross our mind. However, in reality, only about 5% of bacteria are pathogenic. Our skin houses more than 1,000 species of non-pathogenic bacteria. The digestive system within our stomach teems with millions of these bacteria. The wellbeing of these microbiomes, the communities of bacteria and archaea that live in and on our bodies, are essential to our health. Studies have suggested that the disruption of these microbiomes are associated with complex health disorders. Indeed, we depend largely on the health of the microbiomes that thrive on and within us. Therefore, any amendment to the microbiome composition can result in abnormal functions within our body. Scientists suspect that one such consequence is autoimmune disease, when the body mistakenly attacks its own cells.

Gut Microbiota: Germ Free Models

The microbiome in the gastrointestinal (GI) tract has been shown to be involved in immune system homeostasis, thus providing significant health benefits to the host. To establish this link, many experiments have been conducted, such as germ-free (GF) models where animals are initially situated in a sterile location: they have never been exposed to any microorganisms. The GF models are an effective technique that reveal the significance of the microbiota’s role in molding both innate and adaptive immunity, specifically their role in regulating the development of antigen presenting cells (APCs). APCs have co-evolved with microbiota and are responsible for protecting the body against infection and controlling immune tolerance to the regular gut microbiome.

One study showed that there is a cause-effect relationship between the gut microbiome and the endocannabinoidome (eCBome) — a complex signaling system that regulates GI tract function and cell-microbe interactions through observing GF mice. In other words, the gut microbiome directly impacts the presence or lack of intestinal microbes and eCBome signaling.

Gut Microbiota Alterations and its Impact on the Immune System

Altering the gut microbiome has demonstrated inducing inflammation and resulting in loss of immune tolerance. Since the microbiome is directly involved in immune homeostasis, it is not surprising that alterations to the microorganism community would result in abnormal functions, such as autoimmune disease. Case in point, scientists have indicated the gut microbiome in autoimmune conditions such as lupus, type 1 diabetes, rheumatoid arthritis, and multiple sclerosis.

Autoimmune Disease: Could there be a Cure?

However, researchers are currently investigating potential cures to autoimmune disease based on the characteristic of gut microbiomes’ ability to trigger autoimmune conditions. For example, scientists have discovered evidence of Prevotella (Gram-negative bacteria) DNA in the joints of individuals with rheumatoid arthritis, suggesting that bacteria or its remnants transported by immune cells, can get into joints. Based on this finding and others, researchers envision a possible future therapy by targeting these microorganisms that cross the GI tract and in other affected organs.


Life: The Science of Biology, 12th edition


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