Beyond abundances: exploring intra-species genetic diversity of the cancer gut microbiome

The human gastrointestinal harbours trillions of microorganisms (predominantly bacteria) with this collective “gut microbiome” now implicated in a variety of diseases, including cancer. While many studies have identified bacterial species enriched or depleted in patients with specific cancers, much less is known about whether intra-species genetic variation is associated with cancer or other clinical characteristics. To address this, this project will investigate the genomic and functional diversity of selected gut bacteria using the largest published clinically annotated gut shotgun metagenomic dataset to date- involving 1,364 cancer patients and 287 healthy controls (doi: 10.1016/j.cell.2026.09.009). Using a state-of-the-art bioinformatics pipeline, our laboratory has reconstructed over 42,000 medium- or high-quality prokaryote metagenome-assembled genomes (MAGs) from these data, creating the resource for investigating genetic and functional potential variation beyond standard abundance profiles. The student will perform quality-control, taxonomic & functional annotation of this large, clinically annotated MAG collection, and subsequently select 2-3 species of interest based on their literature review, genome recovery and sample representation. Their focused analysis will involve evaluating intra-species phylogeny, and comparisons of gene content / functional potential. The projects offers training in state-of-the-art genome-resolved metagenomics, comparative microbial genomics, statistical analysis and scientific visualisation. Candidates should have familiarity and experience with Shell scripting and analysis in the R programming environment; prior metagenomics experience is not required. The student will join the growing Gunjur laboratory and work closely with Dr Ashray Gunjur, consultant medical oncologist and computational microbiome scientist, as well as other researchers in the group.