Previous work by our group found that the rumen bacterial community is dynamic over the course of lactation and that high and low milk production efficiency (MPE) cows have different microbiota with specific taxa associated with either phenotype. However, this work did not consider the ruminal fungal and archaeal communities. To address this, we characterized the ruminal fungal and archaeal communities to determine if these microbial populations exhibit properties similar to that of the rumen bacteria with respect to MPE over time. Our results show a decrease in fungal diversity over the course of both lactation cycles with an increase during the transition period and the fungal community had only a few taxa associated with efficiency.
For the ruminal archaea, we found no change in diversity across both lactation cycles and only taxa in the genus Methanospera were found to be differentially abundant in high MPE cows. Additionally, given that our previous study used 454 pyrosequencing, we also sought to determine if a resequencing of the bacterial community using Illumina-based technology would alter our previous findings. We found that the ruminal bacterial community remained dynamic over the course of lactation, with some minor differences in taxa associated with efficiency. Overall, our results show that the rumen bacterial community is the primary microbial driver of host efficiency and that the rumen fungal and archaeal communities have little association with efficiency. Our resequencing analysis of the ruminal bacteria using Illumina-based technology demonstrates no significant deviations from our original broad conclusions with the exception of some specific taxonomic associations with efficiency.