Open Access Highly Accessed Research article

Comparative fecal metagenomics unveils unique functional capacity of the swine gut

Regina Lamendella14, Jorge W Santo Domingo2*, Shreya Ghosh1, John Martinson3 and Daniel B Oerther15

Author Affiliations

1 University of Cincinnati, Department of Civil and Environmental Engineering, Cincinnati, OH 45220, USA

2 National Risk Management Research Laboratory, U. S. Environmental Protection Agency, Cincinnati, OH 45268, USA

3 National Exposure Research Laboratory, U. S. Environmental Protection Agency, Cincinnati, OH 45268, USA

4 Lawrence Berkeley National Laboratory, Earth Sciences Division, Berkeley, CA 94720, USA

5 Department of Civil and Environmental Engineering, Missouri University of Science and Technology, Rolla, MO 65409, USA

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BMC Microbiology 2011, 11:103  doi:10.1186/1471-2180-11-103

Published: 15 May 2011

Abstract

Background

Uncovering the taxonomic composition and functional capacity within the swine gut microbial consortia is of great importance to animal physiology and health as well as to food and water safety due to the presence of human pathogens in pig feces. Nonetheless, limited information on the functional diversity of the swine gut microbiome is available.

Results

Analysis of 637, 722 pyrosequencing reads (130 megabases) generated from Yorkshire pig fecal DNA extracts was performed to help better understand the microbial diversity and largely unknown functional capacity of the swine gut microbiome. Swine fecal metagenomic sequences were annotated using both MG-RAST and JGI IMG/M-ER pipelines. Taxonomic analysis of metagenomic reads indicated that swine fecal microbiomes were dominated by Firmicutes and Bacteroidetes phyla. At a finer phylogenetic resolution, Prevotella spp. dominated the swine fecal metagenome, while some genes associated with Treponema and Anareovibrio species were found to be exclusively within the pig fecal metagenomic sequences analyzed. Functional analysis revealed that carbohydrate metabolism was the most abundant SEED subsystem, representing 13% of the swine metagenome. Genes associated with stress, virulence, cell wall and cell capsule were also abundant. Virulence factors associated with antibiotic resistance genes with highest sequence homology to genes in Bacteroidetes, Clostridia, and Methanosarcina were numerous within the gene families unique to the swine fecal metagenomes. Other abundant proteins unique to the distal swine gut shared high sequence homology to putative carbohydrate membrane transporters.

Conclusions

The results from this metagenomic survey demonstrated the presence of genes associated with resistance to antibiotics and carbohydrate metabolism suggesting that the swine gut microbiome may be shaped by husbandry practices.