Fig. 6

Relationship between gut genus abundance and calprotectin levels (changes per time interval). a Linear mixed effects models were used to test for an association between the taxon abundance change and calprotectin change accounting for ten time point pairs (P2–P3, P3–P4, etc.) from the same subject, adjusted for mode of delivery and breastfeeding time. Two models were considered: without interaction (w/o int.) and with interaction between time point pair and taxon change (w/ int.). If the interaction term was significant—Q (w/ int.) < 0.05, individual p values (FDR adjusted) were interpreted. If the common slope model was chosen—Q (w/o int.) < 0.05 and Q (w /int) > 0.05, the same common slope coefficient β (coef.) across all time points and one p-value (P2–P3) were shown. Coefficients and Q values were averaged over 128 Monte Carlo instances of the Dirichlet distribution, followed by center-log transform of each instance, b the common slope model (LRT, df = 1, P = 0.002, Q = 0.015) illustrating relationships between Ruminococcus (torques group) change (centered log-ratio transformed) and calprotectin change (rank transformed)—based on the first Monte Carlo instance