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.本团队此前的研究发现，瘤胃细菌群落（rumen bacterial community）在泌乳期进程中呈现动态变化特征，且高产奶效率（Milk Production Efficiency, MPE）与低产奶效率奶牛的微生物群存在显著差异，其特定类群分别与对应表型相关联。但该研究未涉及瘤胃真菌与古菌群落。 为弥补这一研究局限，本研究对瘤胃真菌及古菌群落开展了结构表征，旨在明确这些微生物类群在泌乳期进程中，是否在产奶效率层面呈现出与瘤胃细菌相似的特性。 研究结果显示，在两次泌乳周期中，真菌多样性均呈下降趋势，仅在过渡期出现升高；且仅存在少量与产奶效率相关的真菌类群。 针对瘤胃古菌，本研究未观察到其在两次泌乳周期中发生多样性变化，仅甲烷囊菌属（Methanospera）的类群在高产奶效率奶牛中呈现出丰度差异。 此外，鉴于此前的研究采用了454焦磷酸测序（454 pyrosequencing）技术，本研究同时尝试探究：使用基于Illumina的测序技术（Illumina-based technology）对细菌群落进行重测序，是否会改变此前的研究结论。结果表明，瘤胃细菌群落仍在泌乳期进程中保持动态变化，仅在与产奶效率相关的类群上存在些许细微差异。 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素，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类群关联存在差异外，整体结论与最初的核心发现并无显著偏差。