Neighbor-joining phylogenetic tree of reads mapping to members of the Enterobacteriaceae family. Screening our dataset for putative E. coli/Shigella/Salmonella species we discovered most hits were from the fruit surface samples. We found that by including 16S rRNA reference sequences from members of other related genera including Citrobacter and Cronobacter, we could not confidently assign any sequences from our dataset to Salmonella due to poor phylogenetic resolution. However, we did determine that no reads mapping to the Enterobacteriaceae family were from E. coli/Shigella. The E. coli/Shigella monophyletic clade is colored in red, the Staphylococcus aureus outgroup is purple, and monophyletic clades of sequences from our dataset are colored in green.
Telias et al. BMC Microbiology 2011 11:81 doi:10.1186/1471-2180-11-81