pig gut Metagenome. pig gut

In this study, we evaluated age- and gut-site specific alterations in microbiota, metabolites, structure and gene expression for microbial signalling, immune and barrier function along the gut of suckling and newly weaned piglets receiving sow milk or additionally creep feed from day of life (DoL) 10. In order to do so, gastric and caecal digesta and jejunal and caecal tissue were collected at DoL7, 14, 21, 28, 31 and 35 (n=5/diet/sex/day) for microbial and metabolite composition, histomorphology and gene expression. The DNA was extracted from gastric and caecal digesta which was followed by 16S rRNA gene and ITS gene amplicon sequencing using Illumina chemistry and platform and a paired end approach. Specifically, the V3-V4 hypervariable regions of bacterial 16S rRNA gene and the ITS2 region for the fungal communities were amplified using a 250 bp read length paired-end protocol (Microsynth, Balgach, Switzerland) on an Illumina MiSeq sequencing v2 platform, including the 16S rRNAand ITS PCRs, library preparation and sequencing.

本研究针对自出生日（Day of Life, DoL）10日起接受母猪乳汁或额外补充教槽料的哺乳仔猪与刚断奶仔猪，评估了其肠道内随年龄和肠道部位特异性变化的微生物群、代谢物、肠道结构，以及参与微生物信号传导、免疫与肠道屏障功能的基因表达情况。
为开展此项研究，本研究在DoL7、14、21、28、31及35日时采集胃与盲肠食糜、空肠及盲肠组织（每组饮食/性别/时间点的样本量n=5），用于后续微生物与代谢物组成分析、组织形态学检测及基因表达分析。
研究人员从胃和盲肠食糜中提取脱氧核糖核酸（DNA），随后采用Illumina技术与测序平台，通过双端测序方法开展16S核糖体RNA（16S rRNA）基因与转录间隔区（ITS）基因的扩增子测序。
具体而言，本研究在Illumina MiSeq测序v2平台上采用250bp读长双端测序方案，扩增细菌16S rRNA基因的V3-V4高变区与真菌群落对应的ITS2区域；该实验流程由瑞士巴尔加赫的Microsynth公司完成16S rRNA与ITS的聚合酶链式反应（PCR）、文库制备及全部测序工作。