Dietary fibers boost gut microbiome-produced B vitamin pool and alter host immune landscape

This dataset contains fcs files of lymphocytes from the colonic lamina propria, lungs, and spleens of specific-pathogen-free (SPF), gnotobiotic (14-member synthetic microbiota, 14SM) or germ-free (GF) mice fed five distinct rodent diets (Standard chow 1, SC1; Standard chow 2, SC2; Fiber-supplemented diet, FS; Inulin-supplemented diet, IN; or Fiber-free diet, FF), analysed by mass cytometry. Three million cells per organ per animal were transferred into 15 mL conical tubes. For live/dead staining, cells were incubated with 5 μM cisplatin for 5 minutes. Cells were washed, and cell surface staining mix was added containing pre-conjugated antibodies for 30 minutes at room temperature. Samples were washed twice with FACS buffer, then fixed using the FoxP3 Fix/Perm kit (eBiosciences) for 45 minutes at 4°C, followed by permeabilization wash. Samples were then incubated with the intracellular staining mix for 30 minutes at room temperature. Cells were washed with FACS buffer twice, and pellets were resuspended in Cell-ID™ Intercalator-Ir (Fluidigm) in MaxPar fixation solution (Fluidigm, catalogue no. 201192B) and refrigerated overnight, or for up to five days. Prior to acquisition, samples were washed twice with 1X PBS, and then washed twice with deionized water. Cell pellets were further resuspended in deionized water at 0.5 × 10^6 cells/mL and topped up with 10% calibration beads (EQ Four Element Calibration Beads, Fluidigm). All samples were acquired on the Helios Mass Cytometer (Fluidigm). Effector immune populations and activated T cells in the gut accumulate in a microbiota-dependent manner. Shifts in the microbiome according to dietary fiber source and content result in altered concentrations of B vitamins available to the host, which is tied to distinct alterations in innate and adaptive immune populations.