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Lupus and Taking Probiotics/Prebiotics: The truth [Updated JUL ’23]

Lupus and taking probiotics: Should you take probiotics if you have lupus, and what are the best probiotics for autoimmune disease?

Lupus and taking probiotics: My answer in short: “No” to pills; “Yes” to probiotic and prebiotic-rich foods! Lupus Question of the Day:
Probiotic supplements seem to be a real trend these days. Is gut bacteria linked to lupus? If so, is there value in taking probiotic supplements?

My answer:

There are good bacteria in the microbiome that improve our health and bad bacteria that harm us. The microbiome includes all the living organisms inside and on our body (but good ones and bad ones). Probiotics are made up of bacteria that when you consume them in food or supplements, you “hope” that they enter your gut and improve your gut microbiome.

Several bacteria in our microbiome have been shown to be bad for lupus and other autoimmune diseases. They have been linked with making the immune system more active and are associated with inducing the immune system to produce autoantibodies (like anti-SSA) that can attack our body. Others have been shown to protect us and decrease lupus disease activity. Most of these studies have been in lupus mice. However, there are also human studies as well.

I do not recommend taking a probiotic supplement if you have lupus and taking probiotics. Why? Animal studies show that some bacteria in these supplements actually make some autoimmune diseases worse, while improving others. I recommend the following (instead of taking probiotic pills or capsules). My recommendations regarding lupus and probiotics are below. I also recommend this regarding probiotics for autoimmune disorders such as Sjogren’s and rheumatoid arthritis:

– Eat foods rich in healthy probiotics regularly.

Examples include fermented sauerkraut, live-culture yogurt (I love Siggi’s), kimchee, miso, kombucha, and fermented pickles. Kombucha and lupus have not been studied together. However, I do not see any problems with it theoretically.

– Eat foods rich in prebiotics as well. Particularly “resistant starches” may be beneficial. A lupus mouse study showed decreased lupus disease activity in lupus mice fed a “resistant starch” diet. Examples of resistant starch foods = cooled potatoes that are cold, potatoes starch, cold oatmeal, beans, and legumes.

Sea moss and lupus: some of my patients ask me about sea moss. It may provide prebiotics and it appears to be healthy.

Make sure to avoid any supplement that touts it boosts the immune system. Lupus is a disease where the immune system is already over active. Effective treatments calm it down. Boosting the immune system further can worsen lupus. An example is Echinacea. Echinacea has caused severe lupus flares in some Johns Hopkins lupus patients.

Thank you to Kelli of “More than Lupus” for producing the “Ask Dr. T” series!
Go to her blog and Facebook page and join the lupus community!

For more in-depth information on diet lupus:

Read chapters 38, and 39 of The Lupus Encyclopedia, edition 2

Look up your symptoms, conditions, and medications in the Index of The Lupus Encyclopedia

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What are your comments and opinions?

If you have found a good diet with lupus, what has your experience been? What do you recommend for other patients?

Do you have any questions to ask Dr. Thomas?

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What are your favorite probiotic and prebiotic foods?
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Don Thomas, MD, author of “The Lupus Encyclopedia” and “The Lupus Secrets


  1. This was very informative. The one constant with my Lupus is that it has always attacked my lower digestive system. Probiotics seemed to make it worse. This is good to know.

  2. Do you recommend taking them along with antibiotics like Augmentin for sinus infection to reduce risk of GI upset from those?

    • Kelly: From infectious disease experts, I have heard to take probiotics especially after taking antibiotics to replenish beneficial bacteria that may have been depleted by the antibiotic

      Donald Thomas, MD

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