Thus, comparing the gene content of multiple gut microbiomes can help elucidate the ecological underpinnings of gut systems. Thus far, the functional genetic potential of the pig distal gut microbiota has not been studied using metagenomics, although it is CDK inhibitor reasonable to assume that the swine gut supports similar genetic complexity to the human gut system, as they both prefer omnivorous feeding behavior and harbor similar bacterial groups as determined
by several phylogenetic studies [13–15]. In this study we used metagenomic data analyses to characterize the swine selleck chemicals fecal microbiome with respect to species composition and functional content. In order to search for the potential presence of unique gene functions harbored by the swine gut microbiome, we performed a comparative metagenomic approach, in the context of phylogenetic and functional composition. Results Taxonomic distribution of swine fecal metagenomic sequences Approximately 130 Mb of swine fecal metagenome sequence data were retrieved using two different pyrosequencing platforms (454 GS20 and FLX), making this study the first metagenomic survey of the swine gut (Table 1). The average read length for the GS20 and FLX runs were 156 bp and 230 bp, respectively. Taxonomic distribution of 16S rRNA gene sequences from
the GS20 and FLX swine fecal metagenomes revealed similar taxonomic distributions (Figure 1). However, some differences in classification of 16S rRNA genes retrieved from the mafosfamide GS20 and FLX runs were noted. Most interestingly, fewer Firmicutes and more Bacteroidetes were classified using the FLX 16S rRNA genes (using both RDP Bucladesine purchase and Greengenes databases). This finding suggests shorter read lengths may lead to misclassification of these two divergent phyla. Additionally, more unclassified sequences were retrieved from
GS20 metagenomic reads with e-values less than 0.01. Table 1 Summary of pyrosequencing data from Yorkshire swine fecal samples Yorkshire Pig Fecal Metagenome GS20 Yorkshire Pig Fecal Metagenome FLX Total no. of sequences 157,221 462,501 Total sequence size (bp) 24,518,676 106,193,719 Average sequence length (bp) 155.95 229.61 Genes* 42677 124684 CDS* 42349 (99.23%) 124050 (99.49%) RNA* 328 (.77%) 634 (.51%) rRNA* 328 634 5S 25 46 16S 114 248 18S 1 2 23S 181 325 28S 1 3 Ribosomal Database Project 16S rDNA hits 328 (0.21%) 1100 (.24%) Greengenes 16S rDNA hits 295 (0.19%) 912 (0.20%) w/Func Prediction* 33249 (77.9%) 93804 (75.2%) COG* 33997 (79.7%) 97053 (77.8%) Pfam* 34589 (81.0%) 99027 (79.4%) TIGRfam* 16117 (37.8%) 44040 (35.3%) Genome Properties* 3881 (9.1%) 10599 (8.5%) Signalp* 11125 (26.1%) 35780 (28.7%) TransMb* 8863 (20.8%) 26949 (21.6%) MetaCyc* 3694 (8.7%) 10815 (8.7%) * Indicates that these summary statistics were generated using the IMG/M-ER annotation system offered through the Joint Genome Institute  using the proxygene method .