Diversity Indices Observed richness, Chao1 estimator, abundance-based coverage estimator check details (ACE), jackknife estimator, and bootstrap estimator were used to evaluate community richness. Community diversity was described using Shannon, non-parametric Shannon, and Simpson indices within Mothur v 1.5.0 . Sampling coverage was calculated
using Good’s coverage for the given operational taxonomic unit (OTU) definition, while the Boneh estimate was used to calculate the number of additional OTUs that would be observed for an additional 500 SSU reads. The aforementioned rRNA diversity indices and rarefaction curves were calculated using Mothur v 1.5.0 program with default parameters  and calculations for each index can found in the Mothur manual (http://www.mothur.org/wiki/Mothur_manual). Functional diversity was assessed using SEED Subsystems , COG, and Pfam abundances from all available gut metagenomes. Diversity estimators used included Shannon-Weiner, Simpson’s lambda, and Pielou’s evenness analyses for measuring species richness and evenness. Functional diversity estimates, K- dominance plots, Principal Components buy YH25448 Analysis, and clustering were performed using the PRIMER-E ecological software package . Acknowledgements The
U.S. Environmental Protection Agency, through its Office of Research and Development, funded and managed, selleck or partially funded and collaborated in, the research described herein. It has been subjected to the Agency’s administrative review and has been approved for external publication.
Any opinions expressed until in this paper are those of the author(s) and do not necessarily reflect the views of the Agency, therefore, no official endorsement should be inferred. Any mention of trade names or commercial products does not constitute endorsement or recommendation for use. This work was also partly funded by the United States Environmental Protection Agency Traineeship and National Science Foundation grant to DBO. Electronic supplementary material Additional file 1: Figures S1-S13. Fig. S1. Taxonomic distribution of viral sequences from swine feces. The percent of viral sequences retrieved from swine fecal GS20 (A) and FLX (B) metagenomes. Using the “”Phylogenetic Analysis”" tool within MG-RAST, the GS20 and FLX sequencing runs were searched against the SEED database using the BLASTx algorithm. The e-value cutoff for a hit to the database was 1×10-5 with a minimum alignment length of 30 bp. Fig. S2. Taxonomic distribution of bacterial orders 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.