Department of Environmental Science and Engineering, Gwangju Institute of Science and Technology, Gwangju 500-712, Republic of Korea and.
Environ Sci Technol. 2012 Jan 3;46(1):93-8. doi: 10.1021/es201380c. Epub 2011 Aug 2.
Genotypic microbial source tracking (MST) methods are now routinely used to determine sources of fecal contamination impacting waterways. We previously reported the development of a pyrosequencing-based MST method that assigns contamination sources based on shared operational taxonomic units (OTUs) between fecal and environmental bacterial communities. Despite decreasing sequencing costs, pyrosequencing-based MST approaches are not used in routine water quality monitoring studies due in large part to difficulties in handling massive data sets and difficulties in determining sources of fecal contamination. In the studies presented here we describe the development of an online MST tool, PyroMiST ( http://env1.gist.ac.kr/∼aeml/MST.html) that uses total bacterial or Bacteroidetes 16S rDNA pyrosequencing reads to determine fecal contamination of waterways. The program cd-hit was used for OTU assignment and a Perl script was used to calculate the number of shared OTUs. The analyses require only a small number of pyrosequencing reads from environmental samples. Our results indicate that PyroMiST provides a user-friendly web interface for pyrosequence data that significantly reduces analysis time required to determine potential sources of fecal contamination in the environment.
基因型微生物源追踪（MST）方法现在常用于确定影响水道的粪便污染来源。我们之前报道了一种基于焦磷酸测序的 MST 方法的开发，该方法基于粪便和环境细菌群落之间共享的操作分类单元（OTUs）来分配污染来源。尽管测序成本降低，但基于焦磷酸测序的 MST 方法并未在常规水质监测研究中使用，主要原因是难以处理大量数据集以及难以确定粪便污染的来源。在本研究中，我们描述了一种在线 MST 工具 PyroMiST（http://env1.gist.ac.kr/∼aeml/MST.html）的开发，该工具使用总细菌或拟杆菌门 16S rDNA 焦磷酸测序读数来确定水道的粪便污染。程序 cd-hit 用于 OTU 分配，Perl 脚本用于计算共享 OTU 的数量。该分析仅需要从环境样本中获取少量的焦磷酸测序读数。我们的结果表明，PyroMiST 为焦序列数据提供了一个用户友好的网络界面，大大减少了确定环境中粪便污染潜在来源所需的分析时间。
