Fig. 3

Changes in the gut microbiota composition during first two years of life. a linear mixed effects analysis followed by pairwise comparison of time- points (adjusted for mode of delivery and breastfeeding time), a Genera (present in at least 20% samples) significantly associated with time, b Longitudinal abundance of the Staphylococcus and Ruminococcus (torques group). The overall p-value—a likelihood ratio test (LRT) of nested models (FDR adjusted across genera); PXPY—contrast p values between the two time points (PX and PY), FDR adjusted for all possible contrasts, t.ratio—t statistics for the contrasts estimates (a positive value, colored blue, indicates a decrease in abundance, a negative value, colored red, indicates an increase in abundance). Red arrows indicate time intervals with a significant increase of zonulin, blue arrows indicate time intervals with a significant decrease of calprotectin (see also Fig. 1). Taxa abundances (unrarefied) were transformed by generating 128 Monte Carlo instances of the Dirichlet distribution for each gut sample, followed by center-log transform of each instance. A linear mixed effects analysis was performed for each instance separately and the results were averaged over 128 instances. P2-7th day, P3-1st month, P4-6th month, P5-12th month, P6-24th month