Metagenomic characterization of swine slurry in a North American swine farm operation.
Metagenomic characterization of swine slurry in a North American swine farm operation.
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北美养猪场操作中猪泥浆的宏基因组表征。
DOI：
10.1038/s41598-021-95804-y
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发表时间：
2021-08-20
影响因子：
4.6
通讯作者：
Gray GC
中科院分区：
文献类型：
--
作者：
Ramesh A;Bailey ES;Ahyong V;Langelier C;Phelps M;Neff N;Sit R;Tato C;DeRisi JL;Greer AG;Gray GC
现代大规模、高密度的农业环境天生易受病毒爆发的影响，无意中创造了有利于增加病原体传播和潜在的人畜共患病传播的条件。宏基因组测序已被证明是表征人、牲畜和环境样本中微生物负担的有用工具。在商业养殖环境，特别是养猪场的病原体特征方面，国际上的努力已经取得了成功，但是尚不清楚是否已经充分捕获了全部的微生物病原体，或者是否代表了其他地方的农场。为了加强国际合作，我们对来自美国农场的9个猪浆液和3个环境样本进行了新一代宏基因组测序，表征了浆液的微生物组成，并鉴定了新型病毒。我们总共组装了1792个病毒基因组，其中554个是新的/不同的。我们组装了1637个小核糖核酸病毒基因组片段，其中538个是新的。此外，我们还发现了10种新的病毒，它们属于一个新的分类群：猪Statoviruses；以前只在人类、猕猴、老鼠和牛身上报道过。我们组装了3种不同的posavirus和3种猪小核糖核酸病毒。除了所描述的病毒外，我们还在浆液中发现了其他真核生物属，如内阿米巴原虫和囊虫，以及细菌属，如李斯特菌、密螺旋体、胃梭菌和博德特拉菌。其中，发现了两种已知引起人类疾病的溶组织内阿米巴原虫和单核细胞增生李斯特菌。此外，还鉴定了四环素和MLS（大环内酯、利可沙胺、链状gramin）等抗菌素耐药基因。猪粪浆宏基因组监测对新型和耐药病原菌的检测具有很大的潜力。
Modern day large-scale, high-density farming environments are inherently susceptible to viral outbreaks, inadvertently creating conditions that favor increased pathogen transmission and potential zoonotic spread. Metagenomic sequencing has proven to be a useful tool for characterizing the microbial burden in both people, livestock, and environmental samples. International efforts have been successful at characterizing pathogens in commercial farming environments, especially swine farms, however it is unclear whether the full extent of microbial agents have been adequately captured or is representative of farms elsewhere. To augment international efforts we performed metagenomic next-generation sequencing on nine swine slurry and three environmental samples from a United States of America (U.S.A.) farm operation, characterized the microbial composition of slurry, and identified novel viruses. We assembled a remarkable total of 1792 viral genomes, of which 554 were novel/divergent. We assembled 1637 Picobirnavirus genome segments, of which 538 are novel. In addition, we discovered 10 new viruses belonging to a novel taxon: porcine Statoviruses; which have only been previously reported in human, macaques, mouse, and cows. We assembled 3 divergent Posaviruses and 3 swine Picornaviruses. In addition to viruses described, we found other eukaryotic genera such as Entamoeba and Blastocystis, and bacterial genera such as Listeria, Treponema, Peptoclostridium and Bordetella in the slurry. Of these, two species Entamoeba histolytica and Listeria monocytogenes known to cause human disease were detected. Further, antimicrobial resistance genes such as tetracycline and MLS (macrolide, lincosamide, streptogramin) were also identified. Metagenomic surveillance in swine fecal slurry has great potential for novel and antimicrobial resistant pathogen detection.
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影响因子：
0.9
作者：
Kashnikov AY;Epifanova NV;Novikova NA
通讯作者：
Novikova NA
影响因子：
11.8
作者：
Gray, Gregory C.;Mazet, Jonna A. K.
通讯作者：
Mazet, Jonna A. K.
小核糖核酸病毒的真正宿主。
影响因子：
3.2
作者：
Ghosh S;Malik YS
通讯作者：
Malik YS
影响因子：
3.2
作者：
Anderson BD;Lednicky JA;Torremorell M;Gray GC
通讯作者：
Gray GC
影响因子：
27.6
作者：
Handan-Nader, Cassandra;Ho, Daniel E.
通讯作者：
Ho, Daniel E.