You are here:
Swine Fecal Metagenomics
Citation:
Lamendella, R., S. Gosh, D. B. Oether, J. Martinson, AND J. W. SANTO-DOMINGO. Swine Fecal Metagenomics. Presented at American Society for Microbiology 2008 General Meeting, Boston, MA, June 01 - 05, 2008.
Impact/Purpose:
Poster Presentation
Description:
Metagenomic approaches are providing rapid and more robust means to investigate the composition and functional genetic potential of complex microbial communities. In this study, we utilized a metagenomic approach to further understand the functional diversity of the swine gut. Total DNA extracts from eight Yorkshire pig fecal samples were pooled and used as a template for pyrosequencing. Quantitative species composition of swine fecal metagenomic fragments (i.e. approximately 150,000 reads or 25 Mbp) was performed using the Metagenome Analyzer (MEGAN), while functional composition was annotated by employing comparisons against COG, STRING, and KEGG databases. Comparative metagenomics were also performed between the pig- and human-fecal metagenomes by comparing BLAST-X homology and COG comparisons for each dataset and by using two-way clustering of metagenomic fragments based on relative enrichment of COG and KEGG functional processes. Nearly half of the pig metagenomic sequence data had no significant matches with currently available databases. The rest of the sequences were assigned to Bacteria (42%), Eukaryota (5%), and Archaea (2%), while less than one percent of the reads were of viral origin. Bacteroidetes (44%), Firmicutes (42%), and Proteobacteria (8%) were the dominant bacterial groups. The majority (60%) of the sequences were associated with cellular functions including, cell wall/cell membrane biogenesis, translation/ribosomal structure and biogenesis, amino acid transport and metabolism, energy production and conversion, DNA replication/recombination/repair, and carbohydrate transport and metabolism. When the swine fecal metagenome was compared to the previously annotated human metagenome, functional genes encoding for outer membrane proteins involved in nutrient binding as well as hypothetical proteins involved in carbohydrate metabolism were more abundant in the swine metagenome.. The results from this study suggest that the pig gastrointestinal tract harbors a diverse microbial community with novel functional attributes, some of which might be involved in relevant host-microbial interactions.