pig gut Metagenome

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.