Lupus and Taking Probiotics/Prebiotics: The truth [Updated JUN ’26]

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?”

When discussing lupus and taking probiotics, my answer in short is: “No” to pills, but “Yes” to probiotic and prebiotic-rich foods!

To begin with, here is a deeper look at why I recommend this dietary approach for lupus. Similarly, this advice applies to other autoimmune disorders like Sjögren’s and rheumatoid arthritis.

The Link Between Gut Bacteria and Lupus

Fundamentally, good bacteria in your microbiome improve your health, alongside bad bacteria that harm you. Specifically, the microbiome includes all the living organisms inside and on your body. As a result, probiotics consist of bacteria that you consume in food or supplements. You “hope” they will enter your gut and subsequently improve your gut microbiome.

Unfortunately, research shows that several bacteria in our microbiome are bad for lupus and other autoimmune diseases. Furthermore, scientists link these bad bacteria to making the immune system more active. They also induce the immune system to produce autoantibodies (like anti-SSA) that attack the body.

Conversely, other bacteria protect us and decrease lupus disease activity. Admittedly, researchers have conducted most of these studies on lupus mice. Nevertheless, human studies are emerging as well.

Lupus and Taking Probiotics: Why I Don’t Recommend Pills

Therefore, if you ask about lupus and taking probiotics in pill form, I do not recommend it.

Why? Specifically, animal studies show that some bacteria in these supplements actually make certain autoimmune diseases worse, even while improving others. Consequently, these pills have an unpredictable effect on an already overactive immune system. For this reason, I strongly advise against taking probiotic pills or capsules.

Dietary Recommendations: Real Foods First

Alternatively, instead of supplements, I recommend getting your gut-supporting nutrients directly from your diet:

• First, eat foods rich in healthy probiotics regularly: For instance, great examples include fermented sauerkraut, live-culture yogurt (I love Siggi’s), kimchi, miso, kombucha, and fermented pickles. Admittedly, researchers have not studied kombucha and lupus together. Still, I do not see any theoretical problems with it.

• Secondly, eat foods rich in prebiotics: Essentially, prebiotics feed the good bacteria in your gut. In particular, “resistant starches” offer high benefits. In fact, a study showed decreased lupus disease activity in lupus mice eating a “resistant starch” diet. For example, resistant starch foods include cold potatoes, potato starch, cold oatmeal, beans, and legumes.

• Additionally, consider sea moss: Recently, some patients have asked me about sea moss. Ultimately, it may provide prebiotics, and it appears to be very healthy.

A Warning on “Immune-Boosting” Supplements

Finally, make sure to avoid any supplement that claims it boosts the immune system. After all, lupus is a disease where the immune system is already overactive. As a result, effective treatments aim to calm it down.

Therefore, boosting the immune system further can actually worsen lupus. For example, Echinacea is a well-known immune booster. Unfortunately, this specific supplement has caused severe lupus flares in some Johns Hopkins lupus patients.

Join the Lupus Community

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 and 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.

If you enjoy the information from The Lupus Encyclopedia, please click the “SUPPORT” button at the top of the page to learn how you can help. 

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!