摘要
In ruminants, evidence is accumulating regarding the associations between rumen microbial taxonomic features and feed efficiency. However, to date, how rumen microbial functional features contribute to the variations in feed efficiency of beef cattle has not been well understood. Moreover, whether the rumen microbiota could be selected and regulated by host genetics still needs to be answered. To fill the knowledge gap, four studies (Chapters 2 - 5) were designed and performed in this thesis. Chapter 2 aimed to develop a pipeline to identify and quantify the active rumen microbiota using total-RNA-based sequencing (metatranscriptomics), and to compare its outcomes with widely used 16S rRNA/rDNA amplicon sequencing. Taxonomic assessments of metatranscriptomics, 16S rRNA and 16S rDNA amplicon sequencing datasets were performed using a pipeline developed in house. Compared to 16S rRNA/rDNA amplicon sequencing, metatranscriptomics can identify more bacterial and archaeal taxa, and detect more interactions among microbial taxa. These findings validated the feasibility to conduct the taxonomic analysis for the active rumen microbiota using metatranscriptomics. In Chapter 3, metatranscriptomics was applied to characterize active rumen microbiomes of beef cattle with different feed efficiency (efficient: low residual feed intake [L-RFI]; inefficient: high residual feed intake [H-RFI]). Lachnospiraceae, Lactobacillaceae, and Veillonellaceae were more abundant in H-RFI cattle, and Methanomassiliicoccale were more abundant in L-RFI ones (P < 0.10). Meanwhile, 32 microbial metabolic pathways and 12 carbohydrate-active enzymes were differentially abundant (P < 0.05) between two groups, where most of them were more abundant in H-RFI cattle. These results suggest that rumen microbiomes of inefficient cattle may have higher and more diverse activities than those of efficient cattle. Chapter 4 was conducted to investigate the associations between the rumen microbiome and feed efficiency (RFI) in various beef cattle breeds. Rumen microbiomes from three breeds (Angus, Charolais, and Kinsella composite hybrid) were profiled using metagenomics and metatranscriptomics. There were distinguishable rumen microbiota and functional potentials among three breeds, but differences of functional activities caused by the breed effect were less apparent. Differential microbial taxonomic and functional features at both DNA and RNA levels were detected between H- and L-RFI cattle; nevertheless, most of them only showed differences between H- and L-RFI animals within a breed, suggesting that there are host genetics and rumen microbiome interactions contributing to the variations in feed efficiency. In Chapter 5, rumen microbiota from a cohort of 712 beef cattle were assessed using 16S rDNA amplicon sequencing, and results showed that breed, sex, and diet could influence rumen microbiota. Heritability estimation was conducted for microbial taxonomic features using the animal model based on the genomic relationship matrix. It revealed that host genetics affected the alpha- and beta-diversities of rumen microbiota, and the abundance of ~30% of rumen microbial taxa (heritability estimate ≥ 0.15). In addition, 19 SNPs located on 12 bovine chromosomes were found to be associated with 14 rumen microbial taxa. Our study revealed the host genetic effect on the rumen microbial colonization in cattle, highlighting the potential to manipulate the rumen microbiota through genetic selection and breeding. Overall, findings in this thesis enhanced our understanding on the associations between rumen microbial functional features (at both DNA and RNA levels) and feed efficiency in various beef cattle breeds. Moreover, it provides the evidence that the rumen microbiota is partially shaped by host genetics, which built a theoretical foundation for further manipulating the rumen microbiota using genetic approaches to improve feed efficiency in beef cattle.
摘要译文
在反刍动物中，有证据表明瘤胃微生物分类特征与饲料效率之间的关联。然而，迄今为止，尚未充分了解瘤胃微生物功能特征如何促进肉牛的饲料效率的变化。此外，仍然需要回答是否可以选择和受宿主遗传学调节瘤胃菌群。为了填补知识差距，在本文中设计和进行了四项研究（第2-5章）。第2章旨在开发一条管道，以使用总RNA的测序（metatranscriptomics）识别和量化活性瘤胃菌群，并将其结果与广泛使用的16S rRNA/rDNA扩增子测序进行比较。使用内部开发的管道对元转录组学，16S rRNA和16S rDNA扩增的分类数据集进行了分类学评估。与16S rRNA/rDNA扩增子测序相比，metatranscriptomics可以鉴定更多细菌和古细菌分类群，并检测微生物类群之间的更多相互作用。这些发现验证了使用metatranscriptomsics对主动瘤胃微生物群进行分类学分析的可行性。在第3章中，使用元文字组学来表征具有不同饲料效率的肉牛的活性瘤胃微生物组（有效：低残留饲料摄入量[L-RFI]；效率低下：高残余饲料摄入量[H-RFI]）。 Lachnospileaceae，乳杆菌科和Veillonellaceae在H-RFI牛中更丰富，而L-RFI的甲烷二甲虫更丰富（p <0.10）。同时，两组之间的32个微生物代谢途径和12种碳水化合物活性酶在差异上很丰富（p <0.05），其中大多数在H-RFI牛中更丰富。这些结果表明，低效率牛的瘤胃微生物组可能比有效的牛具有更高和更多样化的活动。进行第4章是为了调查各种肉牛品种中瘤胃微生物组和饲料效率（RFI）之间的关联。使用元基因组学和元文字组学分析了来自三个品种（Angus，Charolais和Kinsella复合杂种）的三种品种的瘤胃微生物组。三个品种之间存在明显的瘤胃微生物群和功能潜力，但是由于该品种效应引起的功能活动差异较小。在H-和L-RFI牛之间检测到DNA和RNA水平的差异微生物分类学和功能特征。然而，它们中的大多数仅显示出一种品种中的H-RFI动物之间的差异，这表明宿主遗传学和瘤胃微生物组相互作用有助于饲料效率的变化。在第5章中，使用16S rDNA扩增子测序评估了来自712个肉牛队列的瘤胃菌群，结果表明，品种，性别和饮食可能影响瘤胃微生物群。使用基于基因组关系矩阵的动物模型对微生物分类特征进行了遗传力估计。它表明，宿主遗传学影响了瘤胃微生物群的α和β多样性，并且瘤胃微生物分类群的大约30％（遗传力估计≥0.15）。此外，发现位于12个牛染色体上的19个SNP与14个瘤胃微生物类群有关。我们的研究表明，宿主遗传对牛瘤胃微生物定殖的影响，突出了通过遗传选择和育种来操纵瘤胃微生物群的潜力。总体而言，本文中的发现增强了我们对瘤胃微生物功能特征（DNA和RNA水平）与各种牛奶品种中的饲料效率之间关联的理解。此外，它提供了一个证据，表明瘤胃菌群是由宿主遗传学部分塑造的，宿主遗传学为进一步操纵瘤胃微生物群建立了一种理论基础，以提高肉牛的饲料效率。
Li, Fuyong. Rumen Microbiome Associated with Feed Efficiency and Host Genetics in Beef Cattle[D]. CA: University of Alberta, 2017