Ablation of microbiota retards rotavirus (RV) infectivity. C57BL6 male mice aged 6–8 weeks were treated with ampicillin and neomycin 1 week before oral inoculation with 105 50% shedding doses (SD50) of mouse RV strain EC. A, Feces specimens were collected daily and assayed for RV antigens by enzyme-linked immunosorbent assay (ELISA). B, Male and female germ-free mice aged 6–8 weeks were infected with filter-sterilized RV. Feces specimens were collected daily and were assayed for RV antigen by ELISA. C, Total RNA from the duodenum was prepared, and a lysate of cells from antibiotic-treated mice was probed for NSP3 messenger RNA, representative of the RV genome, by quantitative reverse-transcription polymerase chain reaction (qRT-PCR). D, Duodenal cell lysate was prepared, and each sample was analyzed for ratios of positive-sense to negative-sense strands by single-stranded qRT-PCR. The ratio value positively correlates with RV replication. *P < .05.