Skip to main content
Comparative Fecal Metagenomics Unveils Unique Functional Capacity of the Swine Gut
BMC Microbiology
  • Regina Lamendella
  • Jorge W. Santo Domingo
  • Shreya Ghosh
  • John Martinson
  • Daniel B. Oerther, Missouri University of Science and Technology

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.

Civil, Architectural and Environmental Engineering
Keywords and Phrases
  • RNA 16S,
  • virulence factor,
  • archaeal RNA,
  • bacterial RNA,
  • animal experiment,
  • animal tissue,
  • bacterial cell wall,
  • bacterial gene,
  • bacterial virulence,
  • Bacteroidetes,
  • carbohydrate metabolism,
  • Clostridia,
  • DNA extraction,
  • experimental pig,
  • feces,
  • Firmicutes,
  • intestine function,
  • metagenomics,
  • Methanosarcina,
  • microbial diversity,
  • microbiome,
  • nonhuman,
  • nucleotide sequence,
  • phylogeny,
  • Prevotella,
  • pyrosequencing,
  • review,
  • sequence homology,
  • stress,
  • Treponema,
  • animal,
  • archaebacterium,
  • bacterium,
  • biodiversity,
  • classification,
  • comparative study,
  • DNA sequence,
  • gastrointestinal tract,
  • genetics,
  • metagenome,
  • microbiology,
  • RNA gene,
  • swine,
  • Animalia,
  • Bacteroidetes phylum,
  • Suidae,
  • Animals,
  • Archaea,
  • Bacteria,
  • Genes,
  • rRNA,
  • RNA,
  • Archaeal,
  • Bacterial,
  • Ribosomal,
  • 16S,
  • Sequence Analysis,
  • DNA
Document Type
Article - Journal
Document Version
Final Version
File Type
© 2011 BioMed Central, All rights reserved.
Publication Date
Citation Information
Regina Lamendella, Jorge W. Santo Domingo, Shreya Ghosh, John Martinson, et al.. "Comparative Fecal Metagenomics Unveils Unique Functional Capacity of the Swine Gut" BMC Microbiology Vol. 11 (2011) ISSN: 1471-2180
Available at: