Shotgun Metagenomics of Dietary Fiber Modulation

Digesta of the large intestine of both dietary fiber deprivation and xylan supplementation were subjected to shotgun metagenomics sequencing. Briefly, total genomic DNA was extracted using the E.Z.N.A Soil DNA Kit (Omega Bio-tek, Norcross, GA, U.S.). Concentration and purity were determined with TBS-380 and NanoDrop2000, respectively. The quality of extracted DNA was checked on 1% agarose gel. Then, DNA was fragmented to approximately 400 bp using Covaris M220 (Gene Company Limited, China). Adapter ligation, cleanup, and enrichment were performed using NEXTFLEX Rapid DNA-Seq (Bioo Scientific, USA). Shotgun metagenomic sequencing was performed on Illumina NovaSeq/Hiseq Xten at Majorbio Bio-Pharm Technology Co., Ltd. (Shanghai, China). Quality control was performed using fastp (version 0.19.4) to trim adapters and filter low-quality reads with the parameter “--cut_by_quality3 -W 4 -M 20 -n 5 -c -l 50 -w 3” [27 (link)]. Bowtie2 (version 2.4.1) was used to remove reads aligned to the swine genome [28 (link)].