Several swine-specific microbial source tracking methods are based on PCR assays targeting Bacteroidales 16S rRNA gene sequences. The limited application of these assays can be explained by the poor understanding of their molecular diversity in fecal sources and environmental waters. In order to address this, we studied the diversity of 9,340 partial (>600bp in length) Bacteroidales 16S rRNA gene sequences from 13 fecal sources and nine feces-contaminated watersheds. The compositions of major Bacteroidales populations were analyzed to determine which host and environmental sequences were contributing to each group. This information allowed us to identify populations which were both exclusive to swine fecal sources and detected in swine-contaminated waters. Phylogenetic and diversity analyses revealed that some markers previously believed to be highly specific to swine populations are shared by multiple hosts, potentially explaining the cross-amplification signals obtained with nontargeted hosts. These data suggest that while many Bacteroidales populations are cosmopolitan, others exhibit a preferential host distribution and may be able to survive different environmental conditions. This study further demonstrates the importance of elucidating the diversity patterns of targeted bacterial groups to develop more inclusive fecal source tracking applications.


Civil, Architectural and Environmental Engineering


United States. Environmental Protection Agency

Keywords and Phrases

16S rRNA gene sequence; Diversity analysis; Environmental conditions; Environmental sample; Environmental water; Fecal sources; Microbial source tracking methods; Molecular diversity; Non-targeted; PCR assay; Polymerase chain reaction; RNA; Water pollution; Population statistics; bacterial DNA; ribosome DNA; RNA 16S; bioassay; biodiversity; biomarker; feces; gene expression; microbial activity; molecular analysis; phylogenetics; pig; population distribution; RNA; sampling; tracking; watershed; animal; article; Bacteroidetes; biodiversity; chemistry; classification; cluster analysis; DNA sequence; feces; genetic variability; genetics; isolation and purification; microbiology; molecular genetics; nucleotide sequence; phylogeny; swine; Animals; Bacteroidetes; Biodiversity; Cluster Analysis; DNA; Bacterial; DNA; Ribosomal; Environmental Microbiology; Feces; Genetic Variation; Molecular Sequence Data; Phylogeny; RNA; Ribosomal; 16S; Sequence Analysis; DNA; Swine

International Standard Serial Number (ISSN)


Electronic OCLC #


Print OCLC #


Document Type

Article - Journal

Document Version

Final Version

File Type





© 2013 American Society for Microbiology, All rights reserved.

Full Text Link