Significance values of kernel regression tests, and McFadden’s R2 values, slope coefficients and significance values of logistic regression models show that magnitude of response for several IgG antibodies solicited by vaccines appear to relate to the structure of the microbiota.

In these tests, antibody levels were treated as binary, median split variables. Kernel regression asked whether participants that both have high or low concentrations of the antibody or T cell pool of interest have similar microbiota (as measured by weighted UniFrac) than participants with dissimilar concentrations of that variable of interest. Logistic regression GLMs ask whether the weighted UniFrac axis 1 (MDS1) scores (Fig 1) of the participants are statistically related the variables of interest. The logistic regression GLM coefficients tell us of the direction and strength of the association. R22 indicates Nagelkerke pseudo R2, p-values are calculated by permutation (Kernel regression) and directly (weighted Unifrac Regression), and Benjamini and Holchberg FDR values [27] are calculated using the bioconductor q-value package [29]. Bold text and yellow shading indicate statistically significant p (<0.05) and FDR (<0.20) values. Regression coefficients corresponding kernel p < 0.05 and FDR < 0.2, values are color-coded according to their sign; blue = positive, red = negative.