Immunology and the Microbiome

Fermented sauerkraut, pickled carrots, pickled cucumbers, pickled celery in glass jars on a white wooden kitchen table. Fermented foods have probiotics that may help replenish gut microbiome.
Read time: 4 minutes

The human body, inside and out, is covered in microbes, with the bulk of them lining the intestinal walls. Recent research is examining the relationship between microbes and the body and the ways in which this relationship impacts the immune system. Although this research is still in the early stages, some researchers and clinicians believe that the microbiome could become a cornerstone of autoimmune disease treatment.1,2

Gut Microbes and Autoimmune Disease

Gut microbiota are implicated in almost every chronic condition. An imbalanced intestinal microbiome may drive inflammatory conditions such as obesity, diabetes, inflammatory bowel disease, colorectal cancer, and immunosenescence in the elderly,3-5 as well as endocrine diseases6 and autoimmune conditions.7 The accumulation of microbes that are perceived as pathogens in the microbiome likely contributes to the inflammatory cascade that impacts immune function and tolerance.8

Sensitive periods for the microbiome include childhood and pregnancy, during which the microbiome may undergo profound changes.9 Differences have been suggested to exist in pregnant women between their first and third trimesters; in the last months of pregnancy, researchers noticed an abundance of Proteobacteria and Actinobacteria and a depletion of Faecalibacterium (a butyrate producer with anti-inflammatory effects).9 These types of alterations in the microbiome may trigger both local and systemic inflammation.9 In addition, during childhood, the gut microbiome is influenced by environmental factors such as geographic area, breastfeeding, exposure to antibiotics, and method of delivery. Vaginally delivered infants acquire bacterial communities resembling their own mother’s vaginal microbiota (Lactobacillus, Prevotella, Sneathis sppwhile Cesarean section–delivered infants harbor bacterial communities similar to those found on the skin surface (Staphylococcus, Corynebacterium, and Propionibacterium).9

This line of research points to the potential for treatment and prevention of autoimmune conditions using therapies directed at the microbiome. Several exciting new studies have focused on the microbiome, therapeutic probiotics, and autoimmune conditions.10-12 Clinical trials suggest that even central nervous system autoimmune conditions may benefit from treatments that target the microbiome and its activity.13

“How are microbes in our gut acting as potential triggers for autoimmune diseases like rheumatoid arthritis?” asks IFM educator Robert Rountree, MD . In the following video, he talks about emerging research connecting the microbiome and its genetic expressions to human health and wellness.

(Video Time: 3 minutes) IFM educator Robert Rountree, MD, has provided his unique combination of traditional family medicine, nutrition, herbology, and mind-body therapy in Boulder, CO, since 1983. He is a diplomate of the American Board of Holistic Medicine.

The gut microbiota and their metabolites exert immunomodulatory effects,14 particularly through antigen-specific T cells and their related anti and pro-inflammatory cytokines, as well as several other mediators of inflammation.14 Dysbiosis can affect immunologic tolerance in autoimmunity via mechanisms including bystander activation, molecular mimicry, auto-inflammatory activation of the innate immune system, and polyclonal activation of B cells and T cells.15

Nutritional Support

Recent research suggests that probiotic treatments may impact the immune system by influencing the activity of cells in the gut.10,16,17 One study found that a four-strain probiotic is capable of modifying the immune response in vitro by enhancing colonic butyrate production in cells from healthy humans:18 the production of anti-inflammatory cytokines (IL-6 and IL-10) was increased and the production of inflammatory chemokines (MCP-1, CXCL 10, and IL-8) was reduced. While this research was conducted in vitro, the results suggest that probiotic species acting alone may not result in a clinical effect; rather, bacteria interact with and alter metabolic and immune byproducts.18 A 2021 meta-analysis that included 18 randomized controlled trials found that the consumption of Lactobacillus (L.) plantarum strains promoted host immunity by significantly increasing levels of the anti-inflammatory cytokine IL-10 while significantly reducing levels of IL-4 and pro-inflammatory cytokines IFN-γ and TNF-α.19

Recent studies also highlight that a breach of the intestinal barrier through dysbiosis and translocation of commensal bacteria to other organs may trigger several autoimmune pathways10 and that dysbiosis may be associated with the consumption of Western-style diets, which are rich in fats and high in sugar.20 A 2019 clinical study found that high-fat diets decreased the concentration of beneficial short-chain fatty acids and increased measurements of plasma proinflammatory factors,21 while a 2021 cross-over clinical trial of patients with ulcerative colitis in remission found that a low-fat, high-fiber diet decreased markers of inflammation and reduced measures of intestinal dysbiosis.22

A better understanding of the interactions between the microbiome and the immune system may lead to new ways of treating and preventing autoimmune dysfunction. Innate and adaptive immunity play an important role in the containment and clearance of microbial pathogens, and it has been hypothesized that the increasing incidence of autoimmune diseases could be due to considerable shifts in the gut microbiota.23 To learn more about both the genetic and environmental factors that contribute to autoimmune diseases and ways to rebalance the microbiome to enhance health and well-being, please follow the links below:

Learn More About Immune Imbalance

Related Articles and Podcasts

Innate Immunity: Diet and Lifestyle Support

The Role of the Microbiome in Immune-Related Diseases

The Pediatric Microbiome and Building Healthy Adults With Liz Mumper, MD, FAAP


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  12.  de Groot P, Nikolic T, Pellegrini S, et al. Faecal microbiota transplantation halts progression of human new-onset type 1 diabetes in a randomised controlled trial. Gut. 2021;70(1):92-105. doi:1136/gutjnl-2020-322630
  13.  Jiang J, Chu C, Wu C, et al. Efficacy of probiotics in multiple sclerosis: a systematic review of preclinical trials and meta-analysis of randomized controlled trials. Food Funct. 2021;12(6):2354-2377. doi:1039/d0fo03203d
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