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Molecular Diversity Of Bacteroidales In Fecal And Environmental Samples And Swine-Associated Subpopulations, Regina Lamendella, Kent C. Li, Daniel B. Oerther, Jorge W. Santo Domingo
Molecular Diversity Of Bacteroidales In Fecal And Environmental Samples And Swine-Associated Subpopulations, Regina Lamendella, Kent C. Li, Daniel B. Oerther, Jorge W. Santo Domingo
Civil, Architectural and Environmental Engineering Faculty Research & Creative Works
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 …
Evaluation Of Swine-Specific Pcr Assays Used For Fecal Source Tracking And Analysis Of Molecular Diversity Of Swine-Specific "Bacteroidales" Populations, Regina Lamendella, Jorge W. Santo Domingo, Anthony C. Yannarell, Shreya Ghosh, Giovanni George Di, Roderick Ian Mackie, Daniel B. Oerther
Evaluation Of Swine-Specific Pcr Assays Used For Fecal Source Tracking And Analysis Of Molecular Diversity Of Swine-Specific "Bacteroidales" Populations, Regina Lamendella, Jorge W. Santo Domingo, Anthony C. Yannarell, Shreya Ghosh, Giovanni George Di, Roderick Ian Mackie, Daniel B. Oerther
Civil, Architectural and Environmental Engineering Faculty Research & Creative Works
In this study, we evaluated the specificity, distribution, and sensitivity of Prevotella strain-based (PF163 and PigBac1) and methanogen-based (P23-2) PCR assays proposed to detect swine fecal pollution in environmental waters. The assays were tested against 222 fecal DNA extracts derived from target and nontarget animal hosts and against 34 groundwater and 15 surface water samples from five different sites. We also investigated the phylogenetic diversity of 1,340 "Bacteroidales" 16S rRNA gene sequences derived from swine feces, swine waste lagoons, swine manure pits, and waters adjacent to swine operations. Most swine fecal samples were positive for the host-specific Prevotella-based PCR assays …
Reverse Transcription Of 16s Rrna To Monitor Ribosome-Synthesizing Bacterial Populations In The Environment, Ting Lu, Peter George Stroot, Daniel B. Oerther
Reverse Transcription Of 16s Rrna To Monitor Ribosome-Synthesizing Bacterial Populations In The Environment, Ting Lu, Peter George Stroot, Daniel B. Oerther
Civil, Architectural and Environmental Engineering Faculty Research & Creative Works
Identification and quantification of phylogenetically defined bacterial populations in the environment are often performed using molecular tools targeting 16S rRNA. Fluorescence in situ hybridization has been used to monitor the expression and processing of rRNA by targeting the 3' tail of precursor 16S rRNA. To expand this approach, we employed reverse transcription of total RNA using primer S-D-Bact-0338-a-A-18. Length heterogeneity detected by slab gel analysis, denaturing high-performance liquid chromatography (DHPLC) was used to differentiate the 5' tail of the precursor from mature 16S rRNA, and the relative abundance of the precursor compared to the abundance of mature 16S rRNA was …