A raw dataset of colonic contents microbiota analysis of betaine supplementation in Bama-mini pigs

Total genomic DNA was extracted from 300 mg colonic luminal contents using Mag-Bind® Stool DNA Kit (Omega, Guangzhou, China) following the manufacturer’s instructions. The DNA concentration and purity were confirmed by agarose gel electrophoresis. The V3‒V4 region of the 16S rRNA gene was amplified with the forward primer 338F (5′-GCACCTAAYTGGGYDTAAAGNG-3′) and reverse primer 806R (5′-TACNVGGGTATCTAATCC-3′). The amplicon libraries were sequenced on the Illumina MiSeq platform (Illumina, San Diego, USA) with the MiSeq Reagent Kit v3 600 cycles according to the standard protocols by Shanghai Personal Biotechnology Co. Ltd. (Shanghai, China).Alpha diversity (including Chao1, Simpson, and Shannon) of the operational taxonomic unit (OTU) level was measured using the OTU table using the QIIME2 (2019.4) software. The beta diversity analysis was performed to evaluate the structural variation of colonic microbiota communities. Partial least squares discriminant analysis (PLS-DA) was also performed to determine the microbial variation among the three groups. The differences in the relative abundances of colonic microbiota at the phylum and genus levels were analyzed by the Kruskal-Wallis rank-sum test. Linear discriminant analysis (LDA) effect size (LEfSe) was conducted to identify biomarkers of the microbial taxa among the three groups using the default parameters of 2.00 for LDA.