Correlating feed efficiency with ruminal bacterial, fungal and archaeal community composition in dairy cows over two lactations

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.本团队此前的研究表明，瘤胃细菌群落会在泌乳周期中呈现动态变化，且高产奶效率（milk production efficiency, MPE）与低产奶效率奶牛的瘤胃微生物群存在差异，其特定类群分别与对应表型相关。但该研究未涉及瘤胃真菌与古菌群落。为弥补这一研究空白，我们对瘤胃真菌和古菌群落开展了表征分析，旨在明确这些微生物种群在泌乳周期中与MPE相关的特性是否与瘤胃细菌相似。研究结果显示，在两个泌乳周期中，真菌多样性均呈下降趋势，但在泌乳过渡期多样性有所升高；且仅存在少量真菌类群与产奶效率相关。 针对瘤胃古菌，我们发现两个泌乳周期内其多样性无显著变化，仅甲烷微菌属（Methanospera）的类群在高MPE奶牛中呈现丰度差异。此外，鉴于本团队此前的研究采用454焦磷酸测序技术，我们还尝试通过基于Illumina的测序技术对细菌群落进行重测序，以验证此前的研究结论是否会发生改变。结果表明，瘤胃细菌群落仍在泌乳周期中呈现动态变化，仅在与产奶效率相关的类群上存在少量差异。综上，本研究结果证实，瘤胃细菌群落是调控宿主产奶效率的核心微生物驱动因子，而瘤胃真菌与古菌群落与产奶效率的关联性较弱。基于Illumina技术的瘤胃细菌重测序分析显示，除部分与产奶效率相关的特定分类学关联存在差异外，本研究的核心结论与最初的整体结论无显著偏差。