FIG 3.

(a) Taxonomic classification (normalized) of “all_ scaffolds” into phyla based on plasmidome (MG-RAST) and 16S rRNA (QIIME) sequences. The MG-RAST analysis was based on the lowest common ancestor. (b) Functional classification (normalized) of “all_ scaffolds” into SEED subsystem categories using MG-RAST (parameters: 1e−5 maximum E value cutoff, 60% maximum identity cutoff, 15-bp minimum alignment length cutoff). It is important to note that the phylogenetic assignment provides the taxonomic classification of the closest known gene homolog and is not indicative of the microbe that originally contained the plasmid at the ORFRC.