Mediation analysis
We conducted mediation analyses only on significantly changed features in each group using pingouin (parameters: seed=42, covar=[baseline age, sex and BMI]). The diet (separately for PPT and MED) was the predictor, the oral and gut microbiome (species or pathways) were the mediators and glycemic measurements, or metabolites and cytokines were the outcomes. The change in predictor, mediator and outcome values were used. P-values were obtained using two-sided bootstrap, and a significant mediating effect was determined if the predictor had a significant effect on the mediator (In the strain mediation analyses the diets (PPT and MED) were combined and the environments (oral and gut) were separated since no significant differences were found between the diet groups in terms of genetic dissimilarity. The diet (together for PPT and MED) was the predictor, the microbial strains (in the oral or gut environment) were the mediators and glycemic measurements, or metabolites and cytokines were the outcomes. Since the genetic dissimilarity measurement lacks direction (negative or positive), the absolute change in predictor, mediator and outcome values were used. Out of the species that exist in over 50 participants, the top ten most strain-replaced species were tested in the analysis.