Davis researchers characterize gut consortia in young pigs with support from GC sequencing core

Recent advances in sequencing technology have enabled the identification of microbial species in the gut with great accuracy. Many of these studies have been conducted in mouse, but now researchers from the Department of Animal Science and the Department of Food Science and Technology have cast their analytic gaze into the intestines of young pigs, an animal whose alimentary system is more similar to our own. The shift from mother’s milk to solid food is a digestive milestone in the life history of any young mammal, and as the authors note, the 'abrupt weaning methods used in pig rearing allow for an excellent experimental design to compare the effects of diet.' After collecting DNA every few days for the first seven weeks of their subjects’ lives, the UC Davis researchers delivered their samples, consisting of 16s rRNA PCR products as well as total genomic DNA, to the Genome Center DNA Technologies core, where manager Lutz Froenicke and staff assessed the diversity found therein. The sequencing was performed on an Illumina MiSeq, a $99,000 machine that is available for use by academic and industrial customers at reasonable rates. The results, which include the make-up of the initial establishment of the new microbiome as well as the dramatic change in species balance when milk is withdrawn, can be used to improve animal husbandry and to inform pediatric nutrition as well. The open access report was published in the journal Microbiome: Diet shapes the gut microbiome of pigs during nursing and weaning.