Metagenomic Analysis of Rat Gut Microbiome

Fresh fecal contents were directly collected from the rat's cecum at the end of the study and stored in Sample Protector (TaKaRa, Dalian, China) at −80°C. The MoBio Power Fecal DNA Isolation kit (Mo BioLaboratories, Carlsbad, CA, USA) was used for DNA extraction. The quality of the extracted DNA was examined by agarose gel electrophoresis, and the OD 260/280 was analyzed by spectrophotometry. DNA libraries were prepared from 2 μg of total DNA for each sample using TruSeq DNA LT Sample Prep Kit v2 (Illumina, San Diego, California). Metagenomic sequencing was performed on HiSeq 3000 platform (Illumina, San Diego, California). After removing adapters, the raw reads were filtered to remove low-quality reads and reads that belong to the host. These high-quality reads from the samples were then assembled to contigs using Meta-Velevt. MetaGeneMark was employed to predict open reading frames (ORFs). In addition, a metagenomic catalog was generated based on the samples obtained in this study. Furthermore, the high-quality clean paired-end reads from each sample were aligned by BWA version 0.5.7-6 to the reference genes. Then the relative abundance of genes was predicted as described previously [15 (link)].