An atlas of the tissue and blood metagenome in cancer reveals novel links between bacteria, viruses and cancer

ABSTRACT Host tissue infections by bacteria and viruses can cause cancer. Massively parallel sequencing now routinely generates datasets large enough to contain detectable traces of bacterial and viral nucleic acids of taxa that colonize the examined tissue or are integrated into the host genome. However, this hidden resource has not been comprehensively studied in large patient cohorts. In the present study, 3000 whole genome sequencing datasets are leveraged to gain insight into novel links between viruses, bacteria and cancer. The resulting map confirms known links and expands current knowledge by identifying novel associations. Moreover, the detection of certain bacteria or viruses is associated with profound differences in patient and tumor phenotypes, such as patient age, tumor stage, survival, somatic mutations in cancer genes or gene expression profiles. Overall, these results provide a detailed, unprecedented map of links between viruses, bacteria and cancer that can serve as a reference for future studies.