Cancer Microbiome

Cancers are found in a complex environment that includes immune cells as well as the microbiome, which may promote or fight against cancer. We are using innovative approaches to understand the role of the microbiome in cancer.

Our group developed a method to find pathogens that cause human disease by high-throughput sequencing and subtraction/comparison to the cancer genome (Weber et al., 2002), with updated versions for next-generation sequencing (Kostic et al., 2011) culminating most recently in GATK-PathSeq (Walker et al., 2018). Through this approach, we were able to identify Fusobacterium nucleatum association with human colorectal cancer (Kostic et al., 2011).  We went on to show that Fusobacterium can potentiate tumorigenesis in mouse models of colorectal cancer (Kostic et al., 2013).  More recently, we showed that Fusobacterium persists in colorectal cancer metastases to the liver and in mouse xenografts of human colorectal cancer (Bullman et al., Science, 2017).  Furthermore, treatment of these xenografts with the Fusobacterium-killing antibiotic, metronidazole, appeared to slow the growth of the xenografts (Bullman et al., 2017).  

With the support of the Cancer Research UK Grand Challenge program, we are embarked on a systematic approach to understanding the role of Fusobacterium in colorectal carcinoma pathogenesis.

More recently, we have built and benchmarked a host-subtraction and classification pipeline entitled PathSeq-T2T to isolate microbial reads from bulk tumor sequencing data (Dohlman et al., 2026). Following decontamination, most non-orodigestive cancer types lacked distinguishable microbial signals. However, we identified a diverse array of microbial communities within orodigestive cancer types, including the protozoan parasite Trichomonas. 

​Our current focus is on comprehensively characterizing tumor-resident microbes across diverse cancer types. Ongoing projects include profiling the microbial communities in small intestine neuroendocrine tumors, gastric cancers - in collaboration with the Clinical Proteomics Tumor Analysis Consortium (CPTAC), and colorectal cancers.