Fig. 3

16S rRNA Linear Mixed Model Analysis for 11 organisms. Linear mixed model analysis (multivariate ANOVA with repeated measures) for Diet*StudyDay*Fermentation Time Points interaction. Linear graphs representing the 11 organisms out of 127 that have significant 3-way interaction for the different fermentation time points and Diet/Date groups in function of their relative abundance: Dorea (A), Lachnospira (B), Bacteroides fragilis (C), Akkermansia muciniphila (D), Bifidobacterium adolescentis (E), Betaproteobacteria (F), Enterobacteriaceae (G), Bacteroides egerthii (H), Ruminococcus bromii (I), Prevotella (J), and Slackia (K). Exact p-values from the test are also reported in Table S1. Pairwise multiple comparison (Tukeys HSD Analysis) for the 11 organisms obtained after the Linear mixed model analysis within each time-point, is represented by symbols: a (*) symbol indicates a difference between study days 0 and 21 for the same diet, and a (^) symbol indicates a difference between MRE and habitual (HAB) diets for the same study day. One symbol indicates p ≤ 0.05, two symbols indicates p ≤ 0.01, and three symbols indicates p ≤ 0.001. Exact p-values from the test are also reported in Table S2