The effect of vancomycin on the gut microbiota of pregnant sows

16S rRNA gene sequencing and data analysis of the intestinal microbiomeThe faeces bacteria were extracted by the commercial assay kits. After DNA extraction, a portion of the 16S rRNA gene was amplified using the 515F/806R primers which were designed to amplify the V4 region of the 16S rRNA gene. The PCR products were subjected to electrophoretic detection, and run on a 2% agarose gel. Library construction was used by TruSeq DNA PCR-Free Sample Preparation Kit (Illumina, Santiago, USA). After quantitative analysis by Qubit and Q-PCR and passing the library test, high-throughput Illumina HiSeq (HiSeq 2500, Santiago, America) sequencing platform 16S rRNA was used for sequencing. With respect to intestinal microbiota analysis, quality filtering on raw sequences was performed according to the QIIME (Version 1.7.0) quality-controlled process. Then the chimera sequence was removed by using UCHIM algorithm. Sequences were assigned to the same operational taxonomic units (OTUs) at a 97% identity using Uclust. For each representative sequences from individual OTUs, the GreenGene Database was used based on RDP classifier algorithmto annotate taxonomic information. Use the QIIME software to calculate the Unifrac distance and draw the PCA using a set of R software (Version 2.15.3).