16S sequencing of murine microbiota following administration of Enterococcus faecium or control
To identify the shifts of murine microbiota caused by E. faecium (Efm) colonization, we prepared Efm drinking water by harvesting and resuspending the overnight culture of Efm in filter-sterilized drinking water to 10^9 CFU/ml. We administered this drinking water to mice for 14 days and then the fecal samples were collected. DNA from mouse fecal samples was extracted with DNeasy PowerSoil Pro kit (Qiagen) accroding to the manufacturer's instruction. Bacterial 16S rRNA gene was amplified at the V4 region using primer pairs and paired-end amplicon sequencing was perfromed on the Illumina MiSeq system at NYU Genome Technology Core.