U.S. Environmental Protection Agency, Office of Research and Development, National Risk Management Research Laboratory, 26 West Martin Luther King Dr., Cincinnati, OH 45268, USA.
Appl Environ Microbiol. 2011 May;77(9):2992-3001. doi: 10.1128/AEM.02988-10. Epub 2011 Mar 4.
The fecal microbiome of cattle plays a critical role not only in animal health and productivity but also in food safety, pathogen shedding, and the performance of fecal pollution detection methods. Unfortunately, most published molecular surveys fail to provide adequate detail about variability in the community structures of fecal bacteria within and across cattle populations. Using massively parallel pyrosequencing of a hypervariable region of the rRNA coding region, we profiled the fecal microbial communities of cattle from six different feeding operations where cattle were subjected to consistent management practices for a minimum of 90 days. We obtained a total of 633,877 high-quality sequences from the fecal samples of 30 adult beef cattle (5 individuals per operation). Sequence-based clustering and taxonomic analyses indicate less variability within a population than between populations. Overall, bacterial community composition correlated significantly with fecal starch concentrations, largely reflected in changes in the Bacteroidetes, Proteobacteria, and Firmicutes populations. In addition, network analysis demonstrated that annotated sequences clustered by management practice and fecal starch concentration, suggesting that the structures of bovine fecal bacterial communities can be dramatically different in different animal feeding operations, even at the phylum and family taxonomic levels, and that the feeding operation is a more important determinant of the cattle microbiome than is the geographic location of the feedlot.
牛的粪便微生物组不仅在动物健康和生产力方面发挥着关键作用，而且在食品安全、病原体排放以及粪便污染检测方法的性能方面也起着关键作用。不幸的是，大多数已发表的分子调查未能充分详细地描述牛群内部和牛群之间粪便细菌群落结构的可变性。本研究使用 rRNA 编码区高变区的大规模平行焦磷酸测序技术，对来自六个不同饲养场的牛的粪便微生物群落进行了分析，这些牛在至少 90 天的时间内接受了一致的管理实践。我们从 30 头成年肉牛（每个饲养场 5 头）的粪便样本中总共获得了 633877 个高质量序列。基于序列的聚类和分类分析表明，群体内的变异性小于群体间的变异性。总的来说，细菌群落组成与粪便淀粉浓度显著相关，这主要反映在拟杆菌门、变形菌门和厚壁菌门种群的变化上。此外，网络分析表明，注释序列按管理实践和粪便淀粉浓度聚类，这表明牛粪便细菌群落的结构在不同的动物饲养场中可能有很大的不同，即使在门和科分类水平上也是如此，而且饲养场是牛微生物组的更重要决定因素，而不是饲料场的地理位置。
