Living Well & Understanding the Body:

Probiotics, Prebiotics, and Autoimmune Disease

Anna Drangowska-Way, PhD October 6, 2022

What are Prebiotics and Probiotics?

The idea of probiotics and prebiotics as part of a wellness routine has recently increased in popularity. The internet and social media platforms share a plethora of claims on the benefits of their consumption; however, many claims require a discerning eye in regard to scientific evidence. In fact, a study published in the Frontiers in Medicine analyzed 150 Google-populated web pages for the keyword search term “probiotics,” and concluded that only 35% cited scientific literature.

Probiotics have a long history; even people in ancient times consumed fermented milk for its health benefits. The WHO defines probiotics as “live microorganisms which, when administered in adequate amounts, confer a health benefit to the host.” On the other hand, prebiotics are compounds in food whose function is to help with the growth and activity of the gut microbiota. 


The state of our gut microbiome (the community of microorganisms living in our digestive tracts) plays a large role in influencing the state of our immune system [1] [2]. There are also differences in the microbiome composition of those living with autoimmunity.

Is it possible for probiotics and prebiotics to alter the microbiome’s composition to benefit those living with autoimmunity?

Dietary supplementation with prebiotics and probiotics has been documented to exhibit a therapeutic effect. Beneficial microbes in our intestines can inhibit pathogenic microbes, modify intestinal permeability, as well as impede or boost an immune response. Microbes can also ferment prebiotics – such as fiber – and produce molecules that have anti-inflammatory properties or can inhibit pathogen growth [3]. While scientists have gained insight into many molecular pathways involved in these processes, they are still working to define strains that exhibit the most therapeutic potential.


The therapeutic value of probiotics and prebiotics have been studied in several autoimmune diseases, with varying results.

Rheumatoid arthritis (RA)

While some earlier studies have shown no significant improvement in disease activity from probiotic treatment in RA patients, others suggest the beneficial effect of probiotic supplementation in patients consuming either Lactobacillus casei – a mix of three bacteria, Lactobacillus acidophilus, Lactobacillus casei, and Bifidobacterium bifidum or Bacillus coagulans GBI-30, 6086 – alongside anti-arthritic medications.

In another study, researchers performed a meta-analysis of studies investigating the influence of microbiota treatment in RA patients. The authors found that some disease markers were lower in patients taking probiotics compared to the placebo group. However, the difference in disease activity scores was not significant between the two groups. Another researcher investigated the effect of prebiotics in patients with RA. The authors used high-fiber supplementation and observed improvement in disease markers after one month of the treatment.

Inflammatory Bowel Disease: Ulcerative colitis (UC) and Crohn’s disease (CD)

Research on those with Ulcerative colitis shows promise in using probiotics as a treatment option. While there are studies that show no beneficial effect of Escherichia coli Nissle 1917 on patients with active UC, E. coli Nissle was shown to be effective in maintaining remission at the same level as the gold standard treatment (mesalazine) in another study. 

Multiple studies reinforce the positive effects of probiotics on patients with UC. In one study, researchers found that VSL#3 (an eight-strain probiotic including lactobacilli, bifidobacilli, and Streptococcus thermophilus) significantly increased remission and positively impacted patients with UC [4] [5] [6]. This effect was not observed in Crohn’s disease.

Patients living with Ulcerative colitis were also given oligofructose-enriched inulin as a prebiotic, which significantly reduced colitis when taken in high doses. In the study, this led to an increased production of colonic butyrate, a bacterial product with anti-inflammatory properties and decreasing fecal inflammatory marker calprotectin [7]. Similarly, Ulcerative colitis patients taking Germinated Barley Foodstuff combined with routine pharmaceutical medication showed a significant reduction in inflammation markers, abdominal pain, and cramping. 

Multiple sclerosis (MS)

There is evidence from both rodent and human studies suggesting that intestinal microbiota play an important role in MS. A study using MS mouse models showed that introducing probiotics allowed for the modulation of immune responses resulting in decreased disease severity. Research has also supported that altering the gut microbiome can suppress the development of MS by modifying immune system components. Additionally, a clinical trial in patients with MS showed a positive impact on symptoms and quality of life in MS patients who were regularly taking probiotic capsules.

Systemic lupus erythematosus (SLE)

In one experiment, the immune system markers of rodents with SLE given Lactobacillus paracasei or Lactobacillus reuteri were observed to have notable improvements. While the mice model showed promising results, further studies are necessary to define whether this kind of treatment will be successful in patients with SLE. 


Probiotics and prebiotics are common buzzwords in the media, oftentimes with unverified claims promoting health. While generally regarded as safe, there are several points to remember when considering probiotics and prebiotics: 

  • Probiotics and prebiotics are umbrella terms for many microorganisms and compounds. Findings from scientific studies are relevant only to the specific microorganisms or compounds that are studied and do not mean all probiotics and prebiotics can produce the same effect.
  • Many of the claims, correlations, and information presented on the internet regarding probiotics and prebiotics, especially in regard to symptom management, are not supported by scientific evidence.
  • Probiotics and prebiotics are sold as supplements and often do not undergo the rigorous tests or studies that are required for medications.
  • Probiotics are considered safe for the general population. However, since people with autoimmune diseases are often on immunosuppressive medications, some question whether it is safe to give those patients probiotics.
  • While evidence suggests using certain probiotics or prebiotics in treating diseases, research often includes small group sizes. More extensive clinical trials are needed to gain more robust data. 
  • A consensus has not been made on the use of probiotics and prebiotics by the scientific or medical community at large. So far, there has not been an FDA-approved therapy that uses probiotics and guidelines on the use of probiotics and prebiotics have not been published by recognized medical institutions or professional societies.

Science seems to be scratching the surface of which probiotics and prebiotics can potentially help patients with autoimmune diseases and which supplements can harm or exacerbate autoimmune disease symptoms. Before probiotics or prebiotics are used as a treatment, it is essential to take safety measures and select optimal strains and protocols, by consulting a medical professional. 

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The information in this article is for educational purposes only and should not be taken as medical advice. Please seek professional medical counsel for best practices in addressing your health plan.


  1. Article Sources
    1. Round, J. L., & Mazmanian, S. K. (2009). The gut microbiota shapes intestinal immune responses during health and disease. Nature reviews. Immunology, 9(5), 313–323.

    2. Ivanov, I. I., Frutos, R. de, Manel, N., Yoshinaga, K., Rifkin, D. B., Sartor, R. B., Finlay, B. B., & Littman, D. R. (2008). Specific microbiota direct the differentiation of IL-17-producing t-helper cells in the mucosa of the small intestine. Cell Host & Microbe, 4(4), 337–349.

    3. Jadhav, P., Jiang, Y., Jarr, K., Layton, C., Ashouri, J. F., & Sinha, S. R. (2020). Efficacy of Dietary Supplements in Inflammatory Bowel Disease and Related Autoimmune Diseases. Nutrients, 12(7), 2156.

    4. Shen, J., Zuo, Z. X., & Mao, A. P. (2014). Effect of probiotics on inducing remission and maintaining therapy in ulcerative colitis, Crohn’s disease, and pouchitis: meta-analysis of randomized controlled trials. Inflammatory bowel diseases, 20(1), 21–35.

    5. Derwa, Y., Gracie, D. J., Hamlin, P. J., & Ford, A. C. (2017). Systematic review with meta-analysis: the efficacy of probiotics in inflammatory bowel disease. Alimentary pharmacology & therapeutics, 46(4), 389–400.

    6. Ganji-Arjenaki, M., & Rafieian-Kopaei, M. (2018). Probiotics are a good choice in remission of inflammatory bowel diseases: A meta analysis and systematic review. Journal of cellular physiology, 233(3), 2091–2103.

    7. Casellas, F., Borruel, N., Torrejón, A., Varela, E., Antolin, M., Guarner, F. & Malagelada, J.R. (2007). Oral oligofructose-enriched inulin supplementation in acute ulcerative colitis is well tolerated and associated with lowered faecal calprotectin. Alimentary Pharmacology & Therapeutics, 25(9), 1061–1067.

About the Author

Anna Drangowska-Way, PhD attended the University of Wrocław in Poland, where she obtained a Bachelor’s and Master’s in Biotechnology, followed by a PhD in Biology from the University of Virginia. During her doctoral studies, she joined the Genetics Society of America’s Early Career Scientist Leadership Program and is a member of the Communication and Outreach Subcommittee. Currently, she works with ASAPbio as a Communications Assistant and is a Freelance Science Writer.