Integrated Online System for a Pyrosequencing-Based Microbial Source Tracking Method that Targets Bacteroidetes 16S rDNA
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)...
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| Veröffentlicht in: | Environmental science & technology 2012-01, Vol.46 (1), p.93-98 |
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| creator | Unno, Tatsuya Di, Doris Y. W Jang, Jeonghwan Suh, Yae Seul Sadowsky, Michael J Hur, Hor-Gil |
| description | 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. |
| doi_str_mv | 10.1021/es201380c |
| format | Article |
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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. 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| subjects | Animals Bacteriology Bacteroidetes - classification Bacteroidetes - genetics Base Sequence Batch Cell Culture Techniques Contamination Deoxyribonucleic acid DNA Environmental Microbiology Feces Feces - microbiology Genotype & phenotype Humans Molecular Sequence Data Online Systems Rheology RNA, Ribosomal, 16S - genetics Sequence Analysis, DNA - methods Taxonomy Temperature User-Computer Interface Waterways |
| title | Integrated Online System for a Pyrosequencing-Based Microbial Source Tracking Method that Targets Bacteroidetes 16S rDNA |
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