In patients with systemic lupus erythematosus (SLE), fecal microbiota transplantation (FMT) significantly decreased disease activity scores with no serious adverse events, according to study results published in Journal of Autoimmunity.

Researchers conducted 12-week single-arm pilot clinical trial included patients aged 18 to 65 years with a SLE diagnosis and a systemic lupus erythematosus disease activity index 2000 (SLEDAI-2K) score of at least 6. Capsules of FMT were prepared using fecal samples from healthy donors. Patients received 30 capsules once a week at weeks 0, 1, and 2. The primary endpoint was the SLE responder index-4 (SRI-4) at week 12. Secondary endpoints included changes in SLEDAI-2K scores, microbiome composition, intestinal levels of short chain fatty acids (SCFA), serum cytokines, and lymphocyte phenotyping. Patients were monitored for adverse events throughout the trial.

In total, 20 participants were enrolled and 18 completed the trial. No serious adverse events or deaths were observed. During the 12 weeks of the study, the proportion of participants achieving SRI-4 response was 42.12% (95% CI, 63.72%-23.14%). The mean SLEDAI-2K scores decreased significantly from 9.45±3.97 at baseline to 6.61±4.43 at week 12. A significant decrease in anti-dsDNA antibody levels was also observed (P =.045).

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Treatment with FMT resulted in changes in gut microbiota richness and composition, with increased SCFA-producing genera and reduced inflammation-related genera. An increase in SCFA levels in the gut corresponded with this shift. Immunological effects of FMT included reduced interleukin-6 levels and CD4+ memory/naive ratios in the peripheral blood, which may be associated with changes in SCFAs in the gut.

Limitations of the study included the single-arm design, small sample size, observed short-term effects of FMT, and variability in participants’ baseline medications.

The study authors concluded, “[T]he first FMT clinical trial in active SLE patients indicated that FMT was a short-term feasible, safe, and effective therapy for patients with SLE. It alters effectively the gut microbial community from a pro-inflammatory style to an anti-inflammatory style. This pilot trial provides sufficient evidence for a randomized, double-blind, placebo-controlled, multicenter clinical study to evaluate the long-term safety and effectiveness of FMT in SLE patients.”


Huang C, Yi P, Zhu M, et al. Safety and efficacy of fecal microbiota transplantation for treatment of systemic lupus erythematosus: An EXPLORER trial. J Autoimmun. Published online June 8, 2022. doi:10.1016/j.jaut.2022.102844