The Microbiome of Esophageal Cancer

In anticipation of the International Human Microbiome Congress, our group has diligently worked to generate data to present for our HMP demo project studying the microbiome of patients who have developed esophageal cancer, gastrointestinal reflux disease, and barrett’s esophagus.  We received a large number of samples in December of 2010 which surveyed four body sites (esophagus, fecal, oral and stomach) of twelve patients.  Upon isolation of DNA, we amplified a variable region of the 16S gene for each sample using barcoded PCR primers.  Incorporation of the 454 A and B adaptors to our primers also provided minimal loss of sequence data when compared to previous methods that would ligate the adaptors to amplicons after PCR.  This method also allowed us to generate sequence reads which are all in the same 5’-3’ orientation.  A large dataset with high quality sequence reads was generated and is currently going thru phylogenetic analysis.  Metagenomic data is also currently being generated from DNA extracted from esophageal brushings taken from a healthy individual as well as a patient who has developed esophageal cancer.  This comparative analysis will be scientifically beneficial in identifying key structural and functional elements that are known to increase pathogenesis of a complex disease such as cancer.  We are anxiously awaiting results from the analysis of these sequences and expect to present a thorough investigation on the esophagus microbiome.