SRA

Human rotavirus (RV) infection is a leading cause of dehydrating diarrhea in infants and young children worldwide. We evaluated the role of microbiota in RV infected mice, and the effect of probiotics. For DNA sequencing, DNA extraction from mixture of cecum and colonic contents from suckling mice on 2-5 days old was performed by bead beating and lysozyme digestion. 16S rDNA analysis of the microbial community structure in intestinal contents was performed using a MiSeq platform. The amplicon of V3-V4 region in 16S rDNA was purified using AMPure XP magnetic beads. The Illumina Nextera XT Index kit with dual 8-base indices was used to allow for multiplexing. PCR reactions were performed to incorporate two unique indices to the 16S amplicons. After purification with AMPure XP beads, the purified barcoded library was fluorometrically quantified using a QuantIT PicoGreen ds DNA Assay Kit. Libraries were then diluted to 4 nM using 10 mM Tris-HCl (pH 8.0), followed by pooling the same volume for multiplex sequencing. The multiplexed library pool (10 pM) was spiked with 35% PhiX control DNA (10 pM) to improve base calling during sequencing. Sequencing was conducted using a 2 x? 250-bp paired-end run with MiSeq Reagent Kit v2.