title: Integrated online system for a pyrosequencing-based microbial source tracking method that targets Bacteroidetes 16S rDNA.
abstract: 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.
authors.affiliation: Department of Environmental Science and Engineering, Gwangju Institute of Science and Technology, Gwangju 500-712, Republic of Korea and.
authors.forename: Tatsuya
authors.initials: T
authors.lastname: Unno
authors.forename: Doris Y W
authors.initials: DY
authors.lastname: Di
authors.forename: Jeonghwan
authors.initials: J
authors.lastname: Jang
authors.forename: Yae Seul
authors.initials: YS
authors.lastname: Suh
authors.forename: Michael J
authors.initials: MJ
authors.lastname: Sadowsky
authors.forename: Hor-Gil
authors.initials: HG
authors.lastname: Hur
mesh_terms: D000818:Animals; D041963:Bacteroidetes / Q000145:classification / Q000235:genetics*; D001483:Base Sequence; D061249:Batch Cell Culture Techniques; D004783:Environmental Microbiology; D005243:Feces / Q000382:microbiology; D006801:Humans; D008969:Molecular Sequence Data; D009862:Online Systems; D012336:RNA, Ribosomal, 16S / Q000235:genetics*; D012212:Rheology; D017422:Sequence Analysis, DNA / Q000379:methods*; D013696:Temperature; D014584:User-Computer Interface
chemical_list: D012336:RNA, Ribosomal, 16S