Zhou Mi, O'Hara Eóin, Tang Shaoxun, Chen Yanhong, Walpole Matthew E, Górka Paweł, Penner Gregory B, Guan Le Luo
Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB T6G 2P5 Canada.
Key Laboratory for Agro-Ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, The Chinese Academy of Sciences, Changsha 410125, China.
Vet Sci. 2021 Jul 19;8(7):138. doi: 10.3390/vetsci8070138.
The current study employed both amplicon and shotgun sequencing to examine and compare the rumen microbiome in Angus bulls fed with either a backgrounding diet (BCK) or finishing diet (HG), to assess if both methods produce comparable results. Rumen digesta samples from 16 bulls were subjected for microbial profiling. Distinctive microbial profiles were revealed by the two methods, indicating that choice of sequencing approach may be a critical facet in studies of the rumen microbiome. Shotgun-sequencing identified the presence of 303 bacterial genera and 171 archaeal species, several of which exhibited differential abundance. Amplicon-sequencing identified 48 bacterial genera, 4 archaeal species, and 9 protozoal species. Among them, 20 bacterial genera and 5 protozoal species were differentially abundant between the two diets. Overall, amplicon-sequencing showed a more drastic diet-derived effect on the ruminal microbial profile compared to shotgun-sequencing. While both methods detected dietary differences at various taxonomic levels, few consistent patterns were evident. Opposite results were seen for the phyla Firmicutes and Bacteroidetes, and the genus . This study showcases the importance of sequencing platform choice and suggests a need for integrative methods that allow robust comparisons of microbial data drawn from various omic approaches, allowing for comprehensive comparisons across studies.
本研究采用扩增子测序和鸟枪法测序来检测和比较以育成期日粮（BCK）或育肥期日粮（HG）喂养的安格斯公牛瘤胃微生物群，以评估这两种方法是否能产生可比的结果。对16头公牛的瘤胃消化物样本进行微生物分析。两种方法揭示了不同的微生物特征，表明测序方法的选择可能是瘤胃微生物群研究中的一个关键方面。鸟枪法测序鉴定出303个细菌属和171个古菌物种的存在，其中一些呈现出丰度差异。扩增子测序鉴定出48个细菌属、4个古菌物种和9个原生动物物种。其中，两种日粮之间有20个细菌属和5个原生动物物种的丰度存在差异。总体而言，与鸟枪法测序相比，扩增子测序显示日粮对瘤胃微生物特征的影响更为显著。虽然两种方法在不同分类水平上都检测到了日粮差异，但几乎没有明显的一致模式。厚壁菌门和拟杆菌门以及属出现了相反的结果。本研究展示了测序平台选择的重要性，并表明需要采用综合方法，以便对来自各种组学方法的微生物数据进行可靠比较，从而实现跨研究的全面比较。
