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首页> 外文学位 >Microbial Source Tracking of Human and Animal Waste Pollution of Diverse Watersheds and of Urban Drainage Systems using Molecular Methods.
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Microbial Source Tracking of Human and Animal Waste Pollution of Diverse Watersheds and of Urban Drainage Systems using Molecular Methods.

机译：使用分子方法追踪各种流域和城市排水系统中人畜废弃物污染的微生物来源。

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摘要

The central hypothesis of microbial source tracking (MST) is that there exists a distinguishable relationship between microbes excreted in feces and their particular hosts. These associations could be due to adaptations of microbes to their host's gut environment and may involve coevolution between microbes and their hosts. In this study, we performed phylogenetic analyses on 16S rRNA gene sequences associated with different host groups to determine if Bacteroides dorei and Enterococcus faecium show co-evolutionary characteristics, thus, host specificity. Bioinformatic analyses were also conducted on E. faecium surface protein gene (espfm) for host specificity. The results of our analyses provide good support for B. dorei human host specificity, and very little support for such specificity in E. faecium. .;Given these findings, a redesigned primer and probe set was developed for a probe based qPCR assay that specifically targets bacterial sequences from a human-specific B. dorei lineage (HF68-HR183rc) and another targeting the E. faecium espfm gene. The results from comparative assays of HF68-HR183rc against a HF183 protocol obtained from the literature showed similar sensitivity, but an improvement in the specificity of our newly designed protocol. However, assays of rabbit samples showed a high number of positive assays with both the redesigned (58%) and the HF183 (67%) protocol. The newly designed HF68-HR183rc assay could be of considerable use to screen a watershed for human fecal sources of pollution if it is known not to be impacted by rabbits. Assays of the redesigned espfm protocol were not as successful as a quantitative assay, requiring an enrichment process.;The HF68-HR183rc qPCR MST protocol was used to help characterize the sources of pollution of sub-watersheds of the temperate environs of Philadelphia/Delaware watershed; watersheds of the tropical island of Puerto Rico; and different types of green infrastructures in Philadelphia and New York.;Keywords: microbial source tracking; Bacteroides dorei; Enterococcus faecium; qPCR; molecular (genetic) markers; 16S rRNA gene; bioinformatics; phylogenetic.
机译：微生物源跟踪（MST）的中心假设是，粪便中排泄的微生物与其特定宿主之间存在明显的关系。这些联系可能是由于微生物适应宿主的肠道环境而引起的，可能涉及微生物与其宿主之间的共同进化。在这项研究中，我们对与不同宿主群相关的16S rRNA基因序列进行了系统进化分析，以确定多歧杆菌和粪肠球菌是否显示出共同进化的特征，从而确定宿主特异性。还对屎肠球菌表面蛋白基因（espfm）进行了生物信息学分析，以确定宿主的特异性。我们的分析结果提供了对B. dorei人宿主特异性的良好支持，而对粪肠球菌中这种特异性的支持却很少。鉴于这些发现，针对基于探针的qPCR测定法开发了重新设计的引物和探针组，所述qPCR测定法特异性地靶向人特异性B. dorei谱系（HF68-HR183rc）的细菌序列和另一种靶向屎肠球菌espfm基因的细菌序列。从文献中获得的针对HF183方案的HF68-HR183rc的对比分析结果显示出相似的灵敏度，但改进了我们新设计方案的特异性。但是，兔样品的检测结果表明，采用重新设计的方案（58％）和HF183（67％）方案，都可以进行大量阳性检测。如果已知不受兔子的影响，新设计的HF68-HR183rc分析可用于筛查人类粪便污染源的分水岭。重新设计的espfm方案的分析不如定量分析成功，需要进行富集过程。HF68-HR183rc qPCR MST方案用于帮助表征费城/特拉华流域温带环境子流域的污染源;热带岛屿波多黎各的分水岭；费城和纽约的绿色基础设施类型不同。拟杆菌粪肠球菌;定量PCR;分子（遗传）标记； 16S rRNA基因;生物信息学系统发育的。

著录项

  • 作者

    Ryan, Michael O'Neil.;

  • 作者单位

    Drexel University.;

  • 授予单位 Drexel University.;
  • 学科 Engineering Environmental.
  • 学位 Ph.D.
  • 年度 2012
  • 页码 263 p.
  • 总页数 263
  • 原文格式 PDF
  • 正文语种 eng
  • 中图分类
  • 关键词

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