Rumen fungal community response to whole rumen contents exhange in dairy cattle

This work seeks to expand on previous work which assessed the response of dairy cattle to a whole rumen contents exchange protocol. Three pairs of lactating dairy cows with disparate historic milk production efficiency were subjected to whole rumen contents exchange via the rumen cannula. Samples of rumen solids and liquids were collected before feeding at irregular intervals from 8 days prior to the exchange through 56 days following the exchange. Fungal amplicon libraries were generated using universal fungal primers flanking the ITS4 region and sequenced on the Illumina MiSeq, 2x300. This work seeks to elucidate the relationship between rumen fungal communities and animal productivity.