Fig. 2

Principal Coordinates Analysis (PCoA) ordination plots of gut microbiome samples from patients with RA (n = 32). PERMANOVA analysis finds that the variance in gut microbial community composition can be explained by a MCII patient group, b age group, c use of csDMARDs, d sex, e smoking status, but not by f CDAI, g use of bDMARDs, nor h use of prednisone. All 64 gut microbiome samples (from 32 patients at both clinical visits) were analyzed simultaneously using PERMANOVA, while intra-subject longitudinal variation was accounted for by constraining permutations to within visits. R² and P values were derived from the adjusted PERMANOVA models. Each circle and triangle signifies baseline and follow-up, respectively. Lines connect time-points of the same patients. MCII, minimum clinically important improvement. MCII+, patients who showed MCII. MCII−, patients who did not show MCII. Non-integer “n” corresponds to cases wherein the patient reported differently at baseline than at follow-up