Comparative gut metagenomics using 16S rRNA gene sequences We performed comparative metagenomics on 16S rRNA gene sequences derived

from publicly available gut metagenomic datasets to reveal phylotype differences between mammalian, avian, and invertebrate distal gut microbiomes. The distribution of bacterial phyla from swine feces appeared closest to that of the cow rumen and chicken cecum, sharing more similar proportions of Bacteroidetes, Firmicutes, Proteobacteria, and Actinobacteria (Figure 2). A statistical analysis comparing bacterial distribution between hosts revealed several significantly different bacterial groups. (Additional File 2, Table S1 and S2). Human adult and infant distal gut microbiomes had significantly higher abundances of Actinobacteria (p < 0.05) than did the swine microbiome (Additional File 2, Table S2). The selleck kinase inhibitor fish gut microbiome was comprised mostly of Proteobacteria and Firmicutes, while the termite gut was dominated by Spirochetes. Interestingly, the swine fecal metagenome also harbored significantly more Spirochetes than many other hosts. (Additional File 2, Selleck AZD9668 Table S3). Figure 2 Taxonomic distribution of bacterial phyla from swine and other currently available gut microbiomes within MG-RAST.

The percent of sequences assigned to each bacterial order from swine and other gut metagenomes is shown. Using the “”Phylogenetic Analysis”" tool within MG-RAST, each gut metagenome was searched against the RDP and greengenes databases using the BLASTn algorithm. The percentage of each bacterial phlya from swine, human infant, and human adult metagenomes were each averaged since there was more than one metagenome for each of these hosts within the MG-RAST database. The e-value cutoff for 16S rRNA gene hits to the RDP and greengenes databases was 1×10-5 with a minimum alignment length of 50 bp. Among the Bacteroidetes, Prevotella were significantly more abundant in the swine fecal metagenome when compared to all other gut metagenomes (p < 0.05), with the exception of the cow rumen, while Bacteroides species were more abundant in chicken and human distal gut microbiomes (Figure

3). Additionally, Anaerovibrio and Treponema genera were exclusively found within the pig fecal metagenomes. Hierarchical clustering of phylotype distribution ADP ribosylation factor (genus-level) from each gut microbiome revealed that community structure of the swine fecal microbiome was significantly different (p < 0.05) from the other gut microbiomes (Figure 4A). Of all the microbiomes used in the comparative analysis, the swine metagenomes exhibited the highest resemblance to the cow rumen, displaying 59% similarity at the genus level. Surprisingly, swine fecal community structure (genus-level) was less than 40% similar to any of the human fecal microbiomes used in this study. Figure 3 Taxonomic distribution of bacterial genera from swine and other currently available gut microbiomes within MG-RAST.