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Comparative Study
, 71 (10), 5999-6007

Comparison of Bacteroides-Prevotella 16S rRNA Genetic Markers for Fecal Samples From Different Animal Species

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Comparative Study

Comparison of Bacteroides-Prevotella 16S rRNA Genetic Markers for Fecal Samples From Different Animal Species

Lisa R Fogarty et al. Appl Environ Microbiol.

Abstract

To effectively manage surface and ground waters it is necessary to improve our ability to detect and identify sources of fecal contamination. We evaluated the use of the anaerobic bacterial group Bacteroides-Prevotella as a potential fecal indicator. Terminal restriction length polymorphism (T-RFLP) of the 16S rRNA genes from this group was used to determine differences in populations and to identify any unique populations in chickens, cows, deer, dogs, geese, horses, humans, pigs, and seagulls. The group appears to be a good potential fecal indicator in all groups tested except for avians. Cluster analysis of Bacteroides-Prevotella community T-RFLP profiles indicates that Bacteroides-Prevotella populations from samples of the same host species are much more similar to each other than to samples from different source species. We were unable to identify unique peaks that were exclusive to any source species; however, for most host species, at least one T-RFLP peak was identified to be more commonly found in that species, and a combination of peaks could be used to identify the source. T-RFLP profiles obtained from water spiked with known-source feces contained the expected diagnostic peaks from the source. These results indicate that the approach of identifying Bacteroides-Prevotella molecular markers associated with host species might be useful in identifying sources of fecal contamination in the environment.

Figures

FIG. 1.
FIG. 1.
Examples of T-RFLP peaks resulting from cow and human fecal samples cut with AciI, MspI, and HaeIII.
FIG. 2.
FIG. 2.
UPGMA cluster analysis based on Jaccard similarity coefficients of all samples with a combination of all three enzymes (AciI, MspI, and HaeIII).
FIG. 3.
FIG. 3.
UPGMA cluster analysis based on Jaccard similarity coefficients of cow samples with a combination of all three enzymes (AciI, MspI, and HaeIII). Samples were collected from farms in three locations: WV, West Virginia; VA, Virginia (two farms, A and C); and IN, Indiana (three farms, A, B, and C).
FIG. 4.
FIG. 4.
Discriminant analysis displayed in three dimensions of all samples and a combination of all three T-RFLP enzymes (AciI, MspI, and HaeIII). Selected T-RFLP peaks associated with the discriminant axis that defines each source group.

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