Gene set enrichment analysis (GSEA) confirmed that the cells from the bacteria-dominant epithelial cell cluster 3 were indeed cancer cells, with gene-expression signatures characterized by an upregulation of signalling pathways involved in cancer progression, including EMT, PI3K–AKT–mTOR, hypoxia and the interferon (IFN) response, among others (Extended Data Fig. 6e–g). Here, MTOR is linked to cancer.