The uncomposted faeces of dairy cow are usually stacked on cow breeding farms, dried under natural conditions and then used as cow bedding material or they may be continuously piled up. However, no information is available to evaluate variations in the human and animal pathogen genes and antibiotic resistance during the accumulation of fresh faeces of dairy cow to manure. Here, we present the metagenomic analysis of fresh faeces and manure from a dairy farm in Ning Xia, showing a unique enrichment of human and animal pathogen genes and antibiotic resistance genes (ARGs) in manure. We found that manure accumulation could significantly increase the diversity and abundance of the pathogenic constituents. Furthermore, pathogens from manure could spread to the plant environment and enphytotic pathogens could affect the yield and quality of crops during the use of manure as a fertilizer. Levels of virulence genes and ARGs increased with the enrichment of microbes and pathogens when faeces accumulated to manure. Accumulated manure was also the transfer station of ARGs to enrich the ARGs in the environment, indicating the ubiquitous presence of environmental antibiotic resistance genes. Our results demonstrate that manure accumulation and usage without effective manure management is an unreasonable approach that could enrich pathogenic microorganisms and ARGs in the environment. The manure metagenome structure allows us to appreciate the overall influence and interaction of animal waste on water, soil and other areas impacted by faecal accumulation and the factors that influence pathogen occurrence in products from dairy cows.

中文翻译：

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奶牛粪便堆积过程中微生物群落，致病性相关基因和抗生素抗性基因的变化。

未堆肥的奶牛粪便通常堆放在奶牛养殖场，在自然条件下干燥，然后用作奶牛的垫料，也可以将它们连续堆放。但是，尚无信息可评估奶牛新鲜粪便到粪便积累过程中人和动物病原体基因的变异以及抗生素抗性。在这里，我们介绍了来自宁夏一家奶牛场的新鲜粪便和粪便的宏基因组学分析，显示了粪便中人类和动物病原体基因和抗生素抗性基因（ARG）的独特富集。我们发现粪便积累可以显着增加病原体成分​​的多样性和丰度。此外，粪便中的病原体可能会传播到植物环境中，而粪便中的病原体可能会影响农作物的产量和品质。当粪便积累到粪便时，随着微生物和病原体的富集，毒力基因和ARGs的水平增加。积累的粪肥也是ARGs的转运站，以丰富环境中的ARGs，这表明环境抗生素抗性基因无处不在。我们的结果表明，没有有效粪便管理的粪便积累和使用是一种不合理的方法，可能会使环境中的病原微生物和ARGs富集。粪便的基因组结构使我们能够欣赏动物粪便对水的整体影响和相互作用，