Predicting colorectal cancer patient outcomes from tumor microbiomes
Most cancer-related deaths in colorectal cancer (CRC) patients are due to distant metastasis. Bacteria within the primary CRC tumor influence disease progression by stimulating metastasis-promoting signaling in cancer cells, modulating anti-tumor immunity, and altering the tumor microenvironment. We profiled primary CRC tumor microbiomes and identified beta diversity signatures that predict long-term metastasis-free survival (MFS). Notably, pathobionts including genotoxic colibactin-producing E. coli and enterotoxigenic Bacteroides fragilis were enriched in the tumors of patients with short MFS. Ongoing projects are investigating CRC tumor microbiome interactions with tumor immune microenvironment, tumor genetics, and clinical outcomes. We are developing tumor microbiome-based laboratory tests for clinical use in pathology laboratories.
Reference
Parajuli B, Midya V, Kiddle R, De Jager N, Eggers S, Spakowicz D, Hoyd R, Salhia B, Chan CHF, Churchman ML, Rounbehler RJ, Yao S, Rutkowski MR, Tarhini AA, Mudaranthakam DP, Masood A, Bocklage TJ, Lentz RW, Hatoum H, Ilozumba MN, Hardikar S, Ulrich CM, Round JL, Riedlinger G, Shriver CD, Bosch DE. Primary tumor microbiomes predict distant metastasis of colorectal cancer. NPJ Precis Oncol. 2025 Nov 24;9(1):405. doi: 10.1038/s41698-025-01188-x. PMID: 41286005; PMCID: PMC12748615.
Tumor microbiomes in IBD colitis-associated carcinoma
Dysbiosis and pathobionts contribute to inflammation and the risk of colitis-associated carcinoma (CAC) in animal models, but their roles in humans with this uncommon disease are unknown. We identified microbiome differences in human CAC compared with longstanding inflammatory bowel disease (IBD) and sporadic colorectal carcinoma (CRC). Twenty-four CAC resections were matched with CRC and IBD controls. Methods included histopathology, 16S rDNA metagenomics, and pathobiont-specific qPCR. Beta diversity differed by diagnosis (PERMANOVA p = 0.007). The distinguishing taxa included Akkermansia enriched in CRC, and Bacteroides spp. enriched in IBD. The non-neoplastic mucosae presented distinct beta diversity (p = 0.005), but the CAC/CRC tumor microbiomes were similar (p = 0.7). Within metastases and margins, Enterobacteriaceae were enriched in CAC, and Bacteroidales in CRC. Pathobiont-specific qPCR confirmed a greater frequency of pks+ E. coli and enterotoxigenic Bacteroides fragilis in CAC than IBD. High alpha diversity was associated with active inflammation, advanced cancer stage, and shorter overall survival (log-rank p = 0.008). Mucosal microbiomes distinguish CAC from longstanding IBD, implicating pathobionts as markers for disease progression. Integrating our findings with prior animal model research, pathobionts promote carcinogenesis in IBD patients through genotoxicity and host cell signaling.
Reference
Masaadeh AH, Eletrebi M, Parajuli B, De Jager N, Bosch DE. Human colitis-associated colorectal carcinoma progression is accompanied by dysbiosis with enriched pathobionts. Gut Microbes. 2025 Dec;17(1):2479774. doi: 10.1080/19490976.2025.2479774. Epub 2025 Mar 17. PMID: 40094201; PMCID: PMC11917176.
Secreted nuclease effector neutralization by active site mimicry
Intestinal bacteria secrete toxic DNAse effectors (Tde) for interbacterial competition. Immunity to Tde-mediated attack is conferred by immunity proteins (Tdi). When Tde interacts with Tdi through a polar amino acid-rich interface, it undergoes a large conformational change, disrupting the effector's fold and promoting proteolysis. Tdi immunity proteins have a highly conserved proline and dual glycine motif that structurally mimics the effector's active site motif. This mimetic motif displaces the active site loop, inactivating the effector enzyme. Tde/Tdi mediate antagonism among Bacteroidales through type VI secretion system, and among Bacillota through unknown secretion mechanisms. Ongoing projects are investigating Tde secretion mechanisms in Gram-positive intestinal bacteria.
References:
Abbasian R, Parajuli B, Yu L, Durocher B, Gardner E, Chodur E, Dwelley MK, Ellermeier CD, Ho TD, Bosch DE. Secreted nuclease effector neutralization by active site mimicry in Bacillota. mBio. 2026 Aug 17:e0151626. doi: 10.1128/mbio.01516-26. Epub ahead of print. PMID: 42606298.
Bosch DE, Abbasian R, Parajuli B, Peterson SB, Mougous JD. Structural disruption of Ntox15 nuclease effector domains by immunity proteins protects against type VI secretion system intoxication in Bacteroidales. mBio. 2023 Aug 31;14(4):e0103923. doi: 10.1128/mbio.01039-23. Epub 2023 Jun 22. PMID: 37345922; PMCID: PMC10470768.
Metagenomic polymorphic toxin effector and immunity profiling
Bacteria use antagonistic interbacterial weapons such as polymorphic toxin secretion systems (TSS) to compete for niches in the human gut microbiome. We developed a bioinformatic marker gene approach (PolyProf) to quantify TSS including ∼200 effector and immunity genes and applied it to ∼15,000 publicly available human metagenomes. PolyProf alpha and beta diversity readily distinguished 12 different human disease states. Decision tree machine learning models integrating bacterial taxonomy with PolyProf had near-perfect accuracy (ROC area 1.00) for all 12 disease states. During microbiome development in the first year of life, PolyProf alpha diversity increases, and beta diversity becomes increasingly like the maternal microbiome, influenced by vertical transfer, delivery mode, and breastfeeding. PolyProf is related to strain sharing among adults through social interactions. In summary, interbacterial antagonism with TSS shapes microbiome development and interpersonal strain sharing. Since PolyProf distinguishes diverse adult disease statuses, these dynamics may contribute to non-genetic inheritance.
Reference
Schroer HW, Beghini F, Raygoza Garay JA, Christakis NA, Bosch DE. Metagenomic polymorphic toxin effector and immunity profiling predicts microbiome development and disease-related dysbiosis. mSystems. 2026 Jun 23;11(6):e0030526. doi: 10.1128/msystems.00305-26. Epub 2026 May 22. PMID: 42171373; PMCID: PMC13288982.