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IDENTIFICATION OF AVIAN-SPECIFIC FECAL METAGENOMIC SEQUENCES USING GENOME FRAGMENT ENRICHMENTS
Citation:
LU, J., J. W. SANTO-DOMINGO, AND O. C. SHANKS. IDENTIFICATION OF AVIAN-SPECIFIC FECAL METAGENOMIC SEQUENCES USING GENOME FRAGMENT ENRICHMENTS. Presented at 2006 American Society for Microbiology Annual Meeting, Orlando, FL, May 22 - 25, 2006.
Impact/Purpose:
To inform the public
Description:
Sequence analysis of microbial genomes has provided biologists the opportunity to compare genetic differences between closely related microorganisms. While random sequencing has also been used to study natural microbial communities, metagenomic comparisons via sequencing analysis remains a difficult task due to the genetic complexity of most microbial communities. In this study, we applied a genome fragment enrichment (GFE) method that selects for genomic regions that differ between different fecal metagenomes. Genomic hybridizations were performed between chicken fecal DNA and pig fecal DNA (C-P) and between chicken fecal DNA and an avian DNA composite consisting of turkey, goose and seagull metagenomic DNA fecal DNA (C-B) to enrich for chicken specific DNA fragments. Five hundred and forty two non-redundant unique chicken metagenomic sequences were retrieved and analyzed. Nearly all of the clone sequences (i.e., 96%) were homologous to prokaryotic genes, of which more than half could not be assigned to previously characterized functional roles. Approximately, 45% of the non-redundant sequences were related to genes present in intestinal bacteria belonging to Clostridia (19.2%), Bacteroidetes (13.7%) and Lactobacillales (12.2%). In general terms, sequences assigned characterized functional roles were associated with cellular processes (18.8%), metabolism (14.6%) and information storage and processing (10.5%). Several sequences from the C-P clone library were then used to develop chicken fecal specific PCR assays which were challenged against fecal DNA extracted from different animals, including mammals and birds. The results from the PCR studies showed that some of the assays were specific to chicken while others also tested positive for different avian species, suggesting a broad distribution of the latter genes among different avian fecal microbial communities. The results from this study suggest that GFE is a viable tool to identify differences between fecal metagenomes and to identify genetic markers that can potentially be used to discriminate between different fecal sources of pollution.