Researchers must be able to generate experimentally testable hypotheses from sequencing-based observational microbiome experiments to discover the mechanisms underlying the influence of gut microbes on human health. We describe geneshot, a novel bioinformatics tool for identifying testable hypotheses based on gene-level metagenomic analysis of WGS microbiome data. By applying geneshot to two independent previously published cohorts, we identify microbial genomic islands consistently associated with response to immune checkpoint inhibitor (ICI)-based cancer treatment in culturable type strains. The identified genomic islands are within operons involved in type II secretion, TonB-dependent transport, and bacteriophage growth.
CITATION STYLE
Minot, S. S., Barry, K. C., Kasman, C., Golob, J. L., & Willis, A. D. (2021). geneshot: gene-level metagenomics identifies genome islands associated with immunotherapy response. Genome Biology, 22(1). https://doi.org/10.1186/s13059-021-02355-6
Mendeley helps you to discover research relevant for your work.