Metronidazole-Treated Mouse Gut Microbiome

Bacterial genomic DNA extraction, amplification, and 16S rRNA gene sequencing of the metronidazole-treated SPF WT mice was carried out using a FastDNA^TM SPIN kit according to the manufacturer’s protocol (MP Biomedical, Aurora, CT, USA) by Chunlab Inc., Seoul, South Korea [44 (link)]. Briefly, the DNA was first amplified using barcoded primers specific to the V1 and V3 regions of the bacterial 16S rRNA genes. Sequences were then sorted out by their respective unique barcodes, and low-quality reads were removed. Bacterial 16S rRNA gene sequencing of 1 μg of PCR amplified product of each sample was done using the 454 GS FLX Titanium Sequencing System (Roche, Branford, FL, USA). Sequence reads were identified using the EZBioCloud Genome Database. Fecal microbial composition, diversity, and clustering were analyzed using the CLcommunity bioinformatics software provided by Chunlab Inc., Seoul, Korea.