We are interested in the relationship of microbes in cancer, both those in the microbiota of the gut, skin, and other sites, and those which have infiltrated tumors. Microbes can have a positive or negative affect on tumor growth and overall patient survival. We rely upon several methods to explore this: traditional amplicon (16S rRNA and ITS) sequencing, whole genome shotgun sequencing, and immunological methods such as IgA and IgG seq.

We are developing new computational tools to interpret this data. We are working in collaboration with John McCulloch to develop JAMS (https://github.com/johnmcculloch/JAMS_BW) , a system which automates much of the work involved in whole shotgun analysis and which produces numerous figures such as PCA plots, heatmaps, and box plots in order to look at differential abundance of microbes according to supplied metadata (such as disease state, genotype, and age). JAMS also works on the functional level to look at differential abundance of gene functions, which may be of more importance than taxonomic differences.