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Phylogenetic Analysis of Bacteroidales 16S rRNA Genes Unveils Sequences Specific to Diverse Swine Fecal Sources
Citation:
Lamendella, R., B. Iker, J. W. SANTO-DOMINGO, AND D. Oether. Phylogenetic Analysis of Bacteroidales 16S rRNA Genes Unveils Sequences Specific to Diverse Swine Fecal Sources. Presented at American Society for Microbiology 109th General Meeting, Philadelphia, PA, May 17 - 21, 2009.
Impact/Purpose:
To inform the public.
Description:
Two of the currently available methods to assess swine fecal pollution (Bac1 and PF163) target Bacteroidales 16S rRNA genes. However, these assays have been shown to exhibit poor host-specificity and low detection limits in environmental waters, in part due to the limited number of sequences used during method development. In order to identify environmentally relevant, swine specific populations, we evaluated the molecular diversity and phylogeny of Bacteroidales 16S rRNA gene sequences from different fecal and environmental sources. A total of 8,250 sequences were used in this study, including sequences from nine different animal types, human septic tanks, swine manure pits, swine lagoons, waters adjacent to swine operations, and Bacteroidales sequences curated in the ARB/Silva database. Phlylogenetic analysis revealed nine swine-specific, Prevotella-related clusters containing both swine source and swine polluted water clones. These clades contained between 27 and 279 pig-related sequences from swine feces, lagoon, and manure pits, and waters adjacent to swine operations. In silico analysis showed that the PF163 and Bac1 sequences matches less than 5% of the sequences in the nine swine clades. More importantly, PF163 and Bac1 targeted less than 3% of the sequences generated from swine polluted waters. These data suggest that the currently available pig-specific assays may underestimate swine pollution in the environment. In contrast, sequence comparison of the swine clades unveiled several host-specific sequences that matched 16 to 51% of sequences derived from waters impacted by swine fecal pollution. These sequences represent novel targets for pig-specific fecal source tracking method development. In summary, this study suggests that the development of host-specific assays benefits significantly from probing the diversity of source tracking targeted populations in both fecal and environmental matrices.
