DRP005269
Fecal microbiota of mice administrated with fecal sample of an UC patient with or without 13 strains of Treg-inducing bacteria, followed by dietary perturbation with low fiber diet from day 35 to 48.
Eight germ-free IQI mice were purchased from Sankyo Laboratories, Japan and maintained in the animal facility of RIKEN. Each of these mice was administered an equal amount of resuspended fecal material obtained from an Ulcerative Colitis Japanese patient (UC5 stool sample, see Atarashi et al., 2015). Mice were allowed to equilibrate for 14 days, time at which half of them was inoculated with the 13-strain consortium as in Bucci et al. (2016). All the mice were fed with a gamma ray-sterilized high-fiber diet (CMF chow, Oriental Yeast Japan) for 34 days, then switched to a low-fiber diet (AIN93G-formula diet, Oriental Yeast Japan) for 14 days, and returned to and maintained on the CMF high-fiber diet the remaining 14 days. Stool samples were collected every 1-3 days. Bacterial genomic DNA was extracted from 1-2 fecal pellets using lysozyme, achromopeptidase followed by proteinase K and phenol/chloroform extraction (Atarashi et al., 2015) and quantified using a Qubit dsDNA HS assay kit and Qubit fluorometer (Invitrogen). The 16S rRNA gene hypervariable V1-V2 regions were PCR-amplified using universal primers (a barcoded 27Fmod and 338R) and, multiplexed amplicon 454-pyrosequencing was carried out.