摘要
In this study, we investigated the degree to which host genetics shape the rumen microbiome. Complex and diverse microbial communities can alter the nutrient profile available to the animal and subsequent performance. Studies of the gut microbiome have demonstrated that host genotype influences gut microbial species composition. Therefore, microbial species composition in the rumen may be a complex trait that manifests through the convergence of host-genetics and environmental factors. To test this hypothesis, we collected rumen contents and blood samples from 586 beef cattle on different diets from two locations. The rumen samples were used to sequence the V4 region of the 16S rDNA on an Illumina MiSeq platform. Animals were genotyped with various platforms and a common set of 61,974 SNP were used to conduct a genome-wide association study (GWAS) using the microbiome (OTUs, families and phyla) as response variables. The GWAS was performed using Bayesian GBLUP fitting fixed effects of cohort (location and date), and the first 2 principle components to account for population stratification. Median posterior genomic heritability estimates were 0.110, 0.124, and 0.141 at the OTU, family and phylum taxonomic level, respectively. The top 8 1-Mb windows for OTUs, families and phyla were located on 7 different chromosomes. These regions affect the rumen microbiota in multiple ways; some (chromosome 19; position 3.0–4.0 Mb) are associated with closely related taxa (Prevotellaceae, Paraprevotellaceae, and RF16), some (chromosome 27; position 3.0–4.0 Mb) are associated with distantly related taxa (Prevotellaceae, Fibrobacteraceae, RF16, RFP12, S24-7, Lentisphaerae, and Tenericutes) and others (chromosome 23; position 0.0–1.0) controlling both related and unrelated taxa. Overall, the 8 regions identified control 11 different families and 6 different phyla. This study shows that host genetics can affect rumen bacterial community members and points towards the possibility that genomics can be used to manipulate the rumen microbiome.
摘要译文
在这项研究中，我们调查了宿主遗传学影响瘤胃微生物组的程度。复杂多样的微生物群落可以改变动物可获得的营养状况和随后的生产性能。肠道微生物组的研究表明，宿主基因型会影响肠道微生物的组成。因此，瘤胃中微生物种类的组成可能是一个复杂的特征，可以通过宿主，遗传和环境因素的融合来体现。为了验证这一假设，我们从两个地方的不同饮食中收集了586头肉牛的瘤胃含量和血样。瘤胃样品用于在Illumina MiSeq平台上对16S rDNA的V4区进行测序。用各种平台对动物进行基因分型，并使用微生物组（OTU，家族和门）作为反应变量，使用一套通用的61,974个SNP进行基因组范围的关联研究（GWAS）。 GWAS是使用贝叶斯GBLUP拟合队列（位置和日期）的固定效应以及前两个主要成分来解决人口分层的方法来执行的。在OTU，家庭和门类分类学水平上，后基因组遗传力中位数估计分别为0.110、0.124和0.141。 OTU，科和门的前8个1 MB窗口位于7个不同的染色体上。这些区域以多种方式影响瘤胃微生物群。一些（染色体19；位置3.0–4.0 Mb）与密切相关的类群（前vo科，副前tell科和RF16）相关联，其中一些（染色体27；位置3.0–4.0 Mb）与远缘相关的类群（原核科，纤维杆菌科，RF16，RFP12，S24-7，扁豆菌和Tenericutes）以及其他（染色体23；位置0.0–1.0）控制相关和不相关的分类单元。总体而言，这8个地区确定了11个不同的科和6个不同的门。这项研究表明宿主遗传学可以影响瘤胃细菌群落成员，并指出基因组学可以用于操纵瘤胃微生物组的可能性。
Waseem Abbas[1];Jeremy T Howard[2];Henry A Paz[3];Kristin E Hales[3];James E Wells[3];Larry A Kuehn[3];Matthew L Spangler[1];Galen E Erickson[1];Samodha C Fernando[1]. 93 Host genetics help shape the rumen microbiome in beef cattle[J]. Journal of Animal Science, 2019,97(Sup2): 51-52