Comparative gut metagenomics In this study, we examined the functional similarity of the Yorkshire pig fecal metagenome by comparing it to currently available metagenomic projects. Hierarchical clustering of functional profiles derived from gut metagenomes available in the MG-RAST database revealed that the GS20 and FLX swine fecal datasets shared approximately 70% similarity to other human metagenomes (Figure 4B). This analysis also showed the swine gut metagenome clustered more closely with chicken cecal and cow rumen metagenomes click here than to the human gut metagenomes (Figure 4B). We further investigated

subsystems associated with specialized cell wall and capsule enzymes, MS275 DNA recombination, and prophage genes since they were very abundant in the swine fecal metagenome (Additional File 1, Fig. S8). Within the DNA recombination and prophage subsystem, the

swine fecal metagenome was enriched for RstA phage-related replication proteins, terminases, and portal proteins. Additionally, more than 30 metagenomic contigs (i.e., > 500 bp) shared high homology to unknown phage proteins. For proteins involved in the cell wall and capsule subsystem, unknown glycosyl transferases, a phosphoglucosamine mutase, and a phosphotransferase were over abundant in the swine metagenome (Table 3). N-acetyl glucosamine-specific PTS system, proteins involved in mannose uptake, and novel capsular polysaccharide synthesis enzymes

were exclusively found within the swine fecal metagenome. Hierarchical clustering of all genes retrieved from the cell wall and capsule functional subsystem for each gut microbiome revealed that swine fecal cell wall/capsule profiles were greater than 60% similar to those of the cow rumen. Additionally, cell wall and capsule profiles in the swine samples were more similar to termite gut than the human gut (Additional File 1, Fig. S9). When carbohydrate subsystems were compared across gut microbiomes, maltose and maltodextrin utilization were the most abundant carbohydrate GPX6 subsystem in the swine, termite, and cow rumen. Analysis of carbohydrate metabolism using the SEED subsystem approach, revealed several proteins unique to the swine gut metagenome such as an outer surface protein part of the cellobiose operon, a beta-glucoside-specific IIA component and a cellobiose-specific IIC component of the PTS system, and a protein similar CDP-glucose 4,6-dehydratase. Table 3 List of cell wall and capsule SEED subsystem functions overabundant in swine fecal metagenome   Pig Feces Human Adult Human Infant Cow Rumen Termite Gut Mouse Cecum Fish gut putative glycosyltransferase – possibly involved in cell wall localization and side chain formation of rhamnose-glucose polysaccharide 112 9 10 10 0 1 0 Phosphoglucosamine mutase (EC 5.4.2.