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Figure 4 | BMC Microbiology

Figure 4

From: Comparative fecal metagenomics unveils unique functional capacity of the swine gut

Figure 4

Hierarchical clustering of gut metagenomes available within MG-RAST based on the taxonomic (A) and functional (B) composition. A matrix consisting of the number of reads assigned to the RDP database was generated using the "Phylogenetic Analysis" tool within MG-RAST, using the BLASTn algorithm. The e-value cutoff for 16S rRNA gene hits to the RDP database was 1×10-5 with a minimum alignment length of 50 bp. A matrix consisting of the number of reads assigned to SEED Subsytems from each gut metagenome was generated using the "Metabolic Analysis" tool within MG-RAST. The e-value cutoff for metagenomic sequence matches to this SEED Subsystem was 1×10-5 with a minimum alignment length of 30 bp. Resemblance matrices were calculated using Bray-Curtis dissimilarities within PRIMER v6 software [38]. Clustering was performed using the complete linkage algorithm. Dotted branches denote that no statistical difference in similarity profiles could be identified for these respective nodes, using the SIMPROF test within PRMERv6 software.

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