Bacterial species identified in this study that have been reported elsewhere as pathogenic in various hosts.

*Many of these species have been isolated from environmental samples (eg. aquatic or terrestrial), this does not however imply that they are actively dividing outside of a host.**These species were also found using full-length 16S rRNA gene Sanger sequencing (see methods).++Although these species were not found in either pyrosequencing run, the Aeromonas genus was found at high levels. The greater resolution of the longer Sanger reads likely allowed for species level classification with Sanger reads, but not pyrotag reads.