Fig. 3

Differences in baseline gut microbiome features between MCII+ and MCII– patient groups. In regard to alpha-diversity, significantly higher species-level a Fisher’s Index (P = 0.004, MLRM) and b richness (P = 0.007, MLRM) were observed in the MCII+ group. c For beta-diversity, a higher distribution of Bray-Curtis distances between sample-pairs was found in the MCII+ group (P = 0.002, Mann-Whitney U test). d Among the seven microbial taxa found to have significantly different distributions between the two patient groups, six were of higher abundance in the MCII+ group. e A total of fifteen MetaCyc biochemical pathways were identified as differentially abundant between the MCII+ and MCII− groups. Except for beta-diversity, multiple linear regression models (MLRMs) were used to test for the statistical significance of the relationship between MCII patient group and microbiome features, while controlling for age group, sex, smoking status, and csDMARD use. P value corresponds to the regression model coefficient for the MCII patient group. ^*, 0.01 ≤ P < 0.05; ^**, 0.005 ≤ P < 0.01. MCII, minimum clinically important improvement. MCII+, patients who showed MCII. MCII−, patients who did not show MCII. Taxonomic ranks: c, class; o, order; f, family; g, genus; s, species. MetaCyc pathways: A, Superpathway of S-adenosyl-L-methionine Biosynthesis; B, L-homoserine and L-methionine Biosynthesis; C, Superpathway of L-methionine Biosynthesis; D, L-methionine Biosynthesis I; E, Superpathway of Tetrahydrofolate Biosynthesis and Salvage; F, Superpathway of Tetrahydrofolate Biosynthesis; G, L-ornithine de novo Biosynthesis; H, Superpathway of Pyridoxal 5′-phosphate Biosynthesis and Salvage; I, L-rhamnose Degradation I; J, CMP-3-deoxy-D-manno-octulosonate Biosynthesis I; K, L-arginine Biosynthesis IV; L, L-arginine Biosynthesis I; M, L-arginine Biosynthesis III; N, L-arginine Biosynthesis II; O, L-ornithine Biosynthesis