Autoimmune Disease and the Gut
An autoimmune disease is the immune system attacking the body it's supposed to defend. Research keeps circling back to the gut as part of the story — carefully, and with more questions than answers so far.
Before anything else, if you're on an immunosuppressant
Speak to your clinician before taking any probiotic, including ours.
Probiotics are very safe for healthy people. In people who are severely immunocompromised or critically ill, there are documented cases of the organisms themselves causing bloodstream infection — rare, and serious.1 Many people managing autoimmune disease are on medication that suppresses immune function, which puts this page's readers squarely in the group that should ask first.
That's the whole warning, and it's at the top rather than the bottom because it matters more than the rest of the article.
What is an autoimmune disease?
The immune system is built to recognize what belongs to you and what doesn't. In autoimmune disease that recognition fails, and the body's own cells get flagged as foreign.
What follows is an immune response aimed inward. Sometimes that's autoantibodies; sometimes it's T cells attacking directly; often it's both.2 Which one dominates varies by condition, and it's part of why these diseases look so different from one another.
Organ-specific
The attack is narrow. Hashimoto's thyroiditis targets the thyroid. Type 1 diabetes targets the insulin-producing cells of the pancreas and essentially nothing else. Remarkably precise, which is its own kind of unsettling.
Systemic
The attack is broad. Lupus and rheumatoid arthritis can involve joints, skin, kidneys, blood vessels and more at once, which is why they're so much harder to pin down and to treat.
Commonly affected: glands including the thyroid, pancreas and adrenals; nerves; joints; muscles; connective tissue; the GI tract; and sometimes the heart or brain.3
Who's more likely to develop one?
Anyone can. Some groups carry more risk than others.3
Women, often in their childbearing years
More women than men develop autoimmune disease, and onset frequently falls during those years. Why remains an open question — hormones are the usual suspect, and it isn't settled. We look at the broader sex differences in Women as Bacterial Hosts.
People with a family history
Certain genes raise the likelihood. Genes rarely act alone, though — most cases seem to need a genetic predisposition and something that sets it off.
People with certain environmental exposures
Sunlight, solvents, and some viral and bacterial infections have all been implicated as triggers. This is the "something that sets it off" half of the pairing above.
Some racial and ethnic groups
Lupus tends to be more severe among African-American and Hispanic people; type 1 diabetes is more common among white people.3
Worth naming what sits alongside genetics there: access to care, time to diagnosis and social determinants all shape how severe a condition becomes. Disparity in outcomes is not purely a matter of biology.
So where does the gut come into it?
Through a proposed route called translocation — bacteria, or fragments of them, crossing the intestinal barrier and reaching places they shouldn't.
The gut lining is selectively permeable by design, and that permeability can increase. Reviewers have examined it specifically as a possible danger signal in autoimmune disease: material crossing a compromised barrier could plausibly provoke an immune response that ends up aimed at the host.4
The study everyone cites
In 2018, researchers found that a gut bacterium called Enterococcus gallinarum could travel from the intestine to the liver and lymph nodes in mice bred to be susceptible to autoimmunity. Once there, it triggered autoantibodies and T-cell responses. Antibiotics suppressed it and prevented deaths; so did a vaccine targeting the organism.5
Then they looked in people. E. gallinarum DNA turned up in liver biopsies from patients with autoimmune disease, and cocultures with human liver cells reproduced what the mice had shown.5
Worth holding two things at once. The causal work was done in genetically predisposed mice. The human findings were correlative — the bacterium was present, which is not the same as it having caused anything. The authors say as much. It's a genuinely striking result and it isn't a demonstration that gut bacteria cause autoimmune disease in people.
More on how permeability is measured, and what "leaky gut" does and doesn't mean, in Leaky Gut and Immune System + Microbiome.
What's actually useful to do?
Stay with your medical team, and take what they've prescribed exactly as prescribed. Autoimmune disease is managed, sometimes very well, and none of that management happens through a supplement aisle.
Beyond that, the general gut advice is the same as it is for everyone — varied diet, fiber, sleep, movement — and it's worth doing on its own merits rather than as a treatment.
Be wary of anything online promising to reverse an autoimmune condition through diet or supplements. That market is large, the claims are confident, and the evidence behind them generally isn't.
Where does Flourish fit?
Honestly: this is a conversation for your clinician before it's a conversation with us.
Flourish Original and Flourish Junior are living liquid probiotics — eleven strains, small-batch fermented in Iowa — taken daily to support digestive and microbiome health. That's the claim, and it doesn't extend to autoimmune disease.
Flourish is a dietary supplement made to support digestive and microbiome health. It is not a treatment for, and will not prevent or reverse, any autoimmune condition. If you take immunosuppressants, are receiving chemotherapy, or are otherwise immunocompromised, speak to your clinician before taking any probiotic. Never stop or change prescribed medication on the basis of an article.
Ready to try a living probiotic?
Eleven living strains. One daily shot. For the whole family — after a word with your doctor, if you're managing a diagnosed condition.
Shop Flourish Original · Shop Flourish Junior · Probiotics & Medication
A few questions we hear a lot
Can I take a probiotic if I have an autoimmune disease?
Ask your clinician first, particularly if you're on an immunosuppressant. Probiotic organisms have caused bloodstream infections in severely immunocompromised patients — rare, but documented, and a good reason to have the conversation before the first dose.1
Do gut bacteria cause autoimmune disease?
Not established. The strongest evidence is a 2018 study where a gut bacterium translocated to the liver and drove autoimmunity in genetically susceptible mice, with the same organism found in liver biopsies of patients.5,6 Causal in mice, correlative in humans.
Is it antibodies or T cells doing the damage?
Depends on the condition, and often both. Some autoimmune diseases are antibody-driven; others, including type 1 diabetes and multiple sclerosis, are primarily T-cell mediated.2
Why do more women get autoimmune diseases?
Nobody has a settled answer. More women than men are affected and onset often falls in the childbearing years,3 with hormones the most-discussed explanation — discussed rather than demonstrated.
Can diet reverse an autoimmune condition?
There's no good evidence for that, and plenty of confident marketing suggesting otherwise. Eating well is worth doing regardless; it isn't a replacement for treatment.
What does "translocation" mean?
Bacteria or their fragments crossing the intestinal barrier into tissue where they don't belong. It's the mechanism the 2018 study demonstrated,5 and the reason intestinal permeability keeps coming up in autoimmune research.4
About this article
Written by: Lorilyn Van Dyke, Entegro Health | Originally published: January 2022
Important information
This article is for general education and isn't a substitute for professional medical advice, diagnosis, or treatment. Autoimmune conditions require medical management — please work with your physician or specialist and never stop, start or change a prescribed medication on the basis of something you read here. If you are immunocompromised, speak to a clinician before taking any probiotic. These statements have not been evaluated by the Food and Drug Administration. This product is not intended to diagnose, treat, cure, or prevent any disease.
Sources
- Doron, S., & Snydman, D. R. (2015). Risk and safety of probiotics. Clinical Infectious Diseases, 60(Suppl 2), S129–S134. Source
- Wang, L., Wang, F.-S., & Gershwin, M. E. (2015). Human autoimmune diseases: a comprehensive update. Journal of Internal Medicine, 278(4), 369–395 — on the roles of autoantibodies and T cells across autoimmune conditions. Source
- U.S. Department of Health and Human Services, Office on Women's Health. Autoimmune diseases — who is affected, risk factors and commonly involved systems. Source
- Mu, Q., Kirby, J., Reilly, C. M., & Luo, X. M. (2017). Leaky Gut As a Danger Signal for Autoimmune Diseases. Frontiers in Immunology, 8, 598. Source
- Manfredo Vieira, S., Hiltensperger, M., Kumar, V., et al. (2018). Translocation of a gut pathobiont drives autoimmunity in mice and humans. Science, 359(6380), 1156–1161. Source
- National Institutes of Health. Gut microbe drives autoimmunity — NIH Research Matters summary of the study above. Source
