摘要
BackgroundMicroorganisms are responsible for fermentation within the rumen and have been reported to contribute to the variation in feed efficiency of cattle. However, to what extent the breed affects the rumen microbiome and its association with host feed efficiency is unknown. Here, rumen microbiomes of beef cattle (n = 48) from three breeds (Angus, Charolais, Kinsella composite hybrid) with high and low feed efficiency were explored using metagenomics and metatranscriptomics, aiming to identify differences between functional potentials and activities of same rumen microbiomes and to evaluate the effects of host breed and feed efficiency on the rumen microbiome.ResultsRumen metagenomes were more closely clustered together and thus more conserved among individuals than metatranscriptomes, suggesting that inter-individual functional variations at the RNA level were higher than those at the DNA level. However, while mRNA enrichment significantly increased the sequencing depth of mRNA and generated similar functional profiles to total RNA-based metatranscriptomics, it led to biased abundance estimation of several transcripts. We observed divergent rumen microbial composition (metatranscriptomic level) and functional potentials (metagenomic level) among three breeds, but differences in functional activity (metatranscriptomic level) were less apparent. Differential rumen microbial features (e.g., taxa, diversity indices, functional categories, and genes) were detected between cattle with high and low feed efficiency, and most of them were breed-specific.ConclusionsMetatranscriptomes represent real-time functional activities of microbiomes and have the potential to better associate rumen microorganisms with host performances compared to metagenomics. As total RNA-based metatranscriptomics seem to avoid potential biases caused by mRNA enrichment and allow simultaneous use of rRNA for generation of compositional profiles, we suggest their use for linking the rumen microbiome with host phenotypes in future studies. However, if exploration of specific lowly expressed genes is desired, mRNA enrichment is recommended as it will enhance the resolution of mRNA. Finally, the differential microbial features observed between efficient and inefficient steers tended to be specific to breeds, suggesting that interactions between host breed genotype and the rumen microbiome contribute to the variations in feed efficiency observed. These breed-associated differences represent an opportunity to engineer specific rumen microbiomes through selective breeding of the hosts.
摘要译文
背景微生物负责瘤胃内的发酵，并且据报道有助于牛饲料效率的变化。然而，该品种对瘤胃微生物组的影响程度及其与寄主饲料效率的关系尚不清楚。在此基础上，利用宏基因组学和元转录组学研究了来自三个品种（安格斯，夏洛来牛，金缕兰复合杂种）的肉牛（n = 48）的瘤胃微生物组，其目的是鉴定功能电位和相同瘤胃微生物组活性之间的差异。并且评估宿主品种和饲料效率对瘤胃微生物组的影响。结果人类宏基因组更紧密地聚集在一起，因此在个体中比元转录组更加保守，这表明RNA水平上的个体间功能变异高于DNA上的个体间功能变异。水平。然而，尽管mRNA富集显着增加了mRNA的测序深度并且产生了与基于总RNA的转录组学相似的功能特征，但是它导致了对几种转录物的有偏差的丰度估计。我们在三个品种中观察到不同的瘤胃微生物组成（元转录水平）和功能电位（宏基因组水平），但功能活性（元转录水平）的差异不太明显。在具有高和低饲料效率的牛之间检测到差异瘤胃微生物特征（例如，分类群，多样性指数，功能类别和基因），并且它们中的大多数是品种特异性的。结论：细胞转录组代表微生物组的实时功能活动并具有与宏基因组学相比，将瘤胃微生物与宿主表现更好地联系起来的潜力。由于基于总RNA的元转录组学似乎避免了由mRNA富集引起的潜在偏差并且允许同时使用rRNA来产生组成谱，我们建议将它们用于在未来研究中将瘤胃微生物组与宿主表型连接。然而，如果需要探索特定的低表达基因，推荐mRNA富集，因为它将增强mRNA的分辨率。最后，在有效和低效转向之间观察到的差异微生物特征倾向于特异于品种，表明宿主品种基因型和瘤胃微生物组之间的相互作用有助于观察到的饲料效率的变化。这些与品种相关的差异代表了通过选择性繁殖宿主来设计特定瘤胃微生物组的机会。
Fuyong Li[1][2]]Thomas C. A. Hitch[3]]Yanhong Chen[1]]Christopher J. Creevey[3]]Le Luo Guan[1]]. Comparative metagenomic and metatranscriptomic analyses reveal the breed effect on the rumen microbiome and its associations with feed efficiency in beef cattle[J]. Microbiome, 2019,7(1)