Queensland Alliance for Agriculture and Food Innovation, Centre for Animal Science, The University of Queensland, Brisbane, QLD, 4072, Australia.
Faculty of Science, School of Veterinary Science, The University of Queensland, Brisbane, QLD, 4072, Australia.
Sci Rep. 2022 Sep 5;12(1):15075. doi: 10.1038/s41598-022-19022-w.
Cattle enterprises are one of the major livestock production systems globally and are forecasted to have stable growth in the next decade. To facilitate sustainable live weight production, optimal reproductive performance is essential. Microbial colonisation in the reproductive tract has been demonstrated as one of the factors contributing to bovine reproductive performance. Studies also implied that reproductive metagenomes are different at each stage of the estrous cycle. This study applied Oxford Nanopore Technologies' adaptive long-read sequencing to profile the bovine reproductive microbiome collected from tropical cattle in northern Queensland, Australia. The microbiome samples were collected from cattle of different sexes, reproductive status and locations to provide a comprehensive view of the bovine reproductive microbiome in northern Australian cattle. Ascomycota, Firmicutes and Proteobacteria were abundant phyla identified in the bovine reproductive metagenomes of Australian cattle regardless of sexes, reproductive status and location. The species level taxonomical investigation suggested that gastrointestinal metagenome and the surrounding environment were potentially the origins of the bovine reproductive metagenome. Functional profiles further affirmed this implication, revealing that the reproductive metagenomes of the prepubertal and postpartum animals were dominated by microorganisms that catabolise dietary polysaccharides as an energy substrate while that of the pregnant animals had the function of harvesting energy from aromatic compounds. Bovine reproductive metagenome investigations can be employed to trace the origins of abnormal metagenomes, which is beneficial for disease prevention and control. Additionally, our results demonstrated different reproductive metagenome diversities between cattle from two different locations. The variation in diversity within one location can serve as the indicator of abnormal reproductive metagenome, but between locations inferences cannot be made. We suggest establishing localised metagenomic indices that can be used to infer abnormal reproductive metagenomes which contribute to abortion or sub-fertility.
牛场是全球主要的畜牧业生产系统之一，预计在未来十年将稳定增长。为了实现可持续的活体重生产，最佳的繁殖性能是必不可少的。生殖道中的微生物定植已被证明是影响牛繁殖性能的因素之一。研究还表明，繁殖宏基因组在发情周期的每个阶段都不同。本研究应用 Oxford Nanopore Technologies 的自适应长读测序技术，对来自澳大利亚昆士兰州北部热带牛的牛繁殖微生物组进行了分析。这些微生物组样本来自不同性别、繁殖状态和地点的牛，以提供澳大利亚北部牛的牛繁殖微生物组的综合视图。牛繁殖宏基因组中无论牛的性别、繁殖状态和地点如何，都富含子囊菌门、厚壁菌门和变形菌门。物种水平的分类学调查表明，胃肠道宏基因组和周围环境可能是牛繁殖宏基因组的起源。功能谱进一步证实了这一推测，揭示了未成熟和产后动物的繁殖宏基因组主要由能够分解膳食多糖作为能量底物的微生物主导，而怀孕动物的繁殖宏基因组则具有从芳香化合物中获取能量的功能。牛繁殖宏基因组的研究可以用于追踪异常宏基因组的起源，这有助于疾病的预防和控制。此外，我们的结果表明，来自两个不同地点的牛的繁殖宏基因组多样性不同。一个地点内的多样性变化可以作为异常繁殖宏基因组的指标，但不能对不同地点之间进行推断。我们建议建立本地化的宏基因组指数，可以用来推断导致流产或低生育率的异常繁殖宏基因组。
