LAUSR

OBJECTIVE The most used drug in rheumatoid arthritis (RA) remains methotrexate (MTX). Unfortunately, up to 50% of patients do not achieve a clinically adequate outcome. Here we study whether the gut microbiota patterns can aid in the prediction of MTX efficacy in RA. METHOD To dissect gut microbiome profiles of RA patients (n = 145), 16S rRNA gene sequencing was performed. Dirichlet multinomial mixture (DMM) clustering was used to identify enterotypes at genus level. The relationships between enterotypes and clinical measures (such as lymphocyte subsets and cytokines detected by flow cytometry) were explored. Then, enterotype stability was evaluated by the stratification of the RA patients cohort in Shanghai, China (n = 66) using the same method. Finally, the enterotype-based gut microbial human index (EGMI) classifier was applied to another independent RA patients cohort (n = 27) to identify the factors associated with MTX clinical response. RESULTS Our analysis revealed that the RA patients always displayed two different dysbiotic microbiota patterns: RA E1 comprised predominantly Prevotella and RA E2 comprised predominantly Bacteroides. Among all of the lymphocyte subsets and cytokines, only the number of CD8+ T cells showed a significant difference between RA E1 and RA E2. These results were validated in the RA patients cohort in Shanghai, China. Significant associations of RA E1 with clinical response to subsequent MTX treatment were confirmed by another independent RA patients cohort. CONCLUSION Together, EGMI classifier was useful to identify precisely and effectively enterotypes of individual RA patients, which could effectively evaluate MTX clinical responses.