Discussion
stoma
In this study, we present the longitudinal metataxonomic study of the small intestine microbiota, including diet intervention periods to assess the microbial impact of the consumption of bacteria-rich fermented dairy products. Although metataxonomic analysis was the focus of this study, we also determined whether the interventions affected small intestinal mucosal permeability or the SCFA composition of the stoma effluent, revealing that neither of these parameters was significantly affected during the dairy product interventions. Nevertheless, the SCFA measurements confirmed previous observations that substantial amounts of microbial fermentation end-products are already formed in the small intestine [Our metataxonomic results confirmed the previously reported high degree of difference of the small intestinal microbial composition between and within subjects [We expanded the metataxonomic analysis in this study with metatranscriptome analysis of the small intestine microbiota at the start and end of each of the intervention periods, using genome mapping and FMM analysis to determine the activity profile of the small intestine microbiome. Notably, comparative analysis of the metatranscriptome FMM patterns also showed that the individual from which the sample was taken was the co-variate that explained most of the observed variance in FMM (~ 25%). Nevertheless, the intervention period could explain approximately 5% of the total FMM variance, identifying the activation of the The striking variation in subject-specific relative abundance of the PDB allowed a stratified interpretation of the metataxonomic data, identifying the strong association of the abundance of the 