16S rRNA gene amplicon sequencing of stool sample from participant 9 treated with inulin for 6 hours
Our study was performed with state-of-the-art Raman microspectroscopy, Raman-activated cell-sorting (RACS) and fluorescence-activated cell-sorting (FACS) in order to evaluate which microorganisms are stimulated by the widely-used prebiotic inulin. We performed anaerobic incubations of human fecal microbiota amended with inulin and in the presence of two cellular activity markers (heavy water [D2O] and L-Azidohomoalanine [AHA]) to detect inulin-stimulated cells. Incubations were also conducted in the presence of mesoporous silica nanoparticles (MSNs) functionalized with inulin and with the fluorescence dye rhodamine to evaluate the spatial interaction between gut bacteria and MSNs grafted with inulin. Using these approaches, we recovered a different species belonging to the major phyla of the gut microbiota, including Firmicutes, Bacteroidetes, and Actinobacteria. The capability of the sorted strains to use inulin was assessed by enzymatic assay, cultivation in inulin-supplemented media, and by incubation with stable isotope-labeled inulin.