Comparative fecal metagenomics unveils unique functional capacity of the swine gut

Lamendella, Regina; Santo Domingo, Jorge W.; Ghosh, Shreya; Martinson, John; Oerther, Daniel B.

doi:10.1186/1471-2180-11-103

Title: Comparative fecal metagenomics unveils unique functional capacity of the swine gut

Journal Article · Sun May 15 00:00:00 EDT 2011 · BMC Microbiology

DOI:https://doi.org/10.1186/1471-2180-11-103· OSTI ID:1626477

Lamendella, Regina ^[1]; Santo Domingo, Jorge W. ^[2]; Ghosh, Shreya ^[3]; Martinson, John ^[4]; Oerther, Daniel B. ^[5]

Univ. of Cincinnati, OH (United States). Dept. of Civil and Environmental Engineering; Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
US Environmental Protection Agency (EPA), Cincinnati, OH (United States). National Risk Management Research Lab.
Univ. of Cincinnati, OH (United States). Dept. of Civil and Environmental Engineering
US Environmental Protection Agency (EPA), Cincinnati, OH (United States). National Exposure Research Lab.
Univ. of Cincinnati, OH (United States). Dept. of Civil and Environmental Engineering; Missouri Univ. of Science and Technology, Rolla, MO (United States). Dept. of Civil and Environmental Engineering

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.

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Research Organization:: Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States). National Energy Research Scientific Computing Center (NERSC)

Sponsoring Organization:: USDOE Office of Science (SC), Biological and Environmental Research (BER). Earth and Environmental Systems Science Division

Grant/Contract Number:: AC02-05CH11231

OSTI ID:: 1626477

Journal Information:: BMC Microbiology, Vol. 11, Issue 1; ISSN 1471-2180

Publisher:: BioMed CentralCopyright Statement

Country of Publication:: United States

Language:: English

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