Background: Colorectal cancer (CRC) develops primarily from precursor polyps through the conventional adenoma and serrated pathways. The gut microbiome contributes to CRC pathogenesis, yet microbial alterations preceding neoplasia diagnosis remain undefined. We characterized pre-diagnostic microbial signatures and compared them to those observed across stages of colorectal neoplasia.
Methods: Among ~20,000 Nurses’ Health Study II (NHSII) women who provided a stool sample in 2019-2023, we profiled stool metagenomes from 421 participants with incident polyps diagnosed on average 2.5±1 years post-collection and 408 polyp-free controls. Histological data were available for 210 cases (103 adenomas, 74 serrated, 33 with both). For cross-stage comparison, we analyzed metagenomes from 1,297 CRC cases, 569 prevalent adenomas, and 1,351 healthy individuals from the NHSII and 15 published studies. Microbial species associations with disease status and histological subtype were assessed using MaAsLin3, controlling for age, body mass index, sex, and read number.
Results: We identified 26 species associated with incident polyps (q<0.25), including enrichment of Bacteroides fragilis and depletion of Roseburia faecis, consistent with established CRC signatures. Subtype-specific analysis revealed 37 and 24 species associated with adenomas and serrated polyps, respectively. Several species exhibited opposing associations between subtypes (e.g., Ruminococcus gnavus enriched in adenomas but depleted in serrated polyps). Cross-stage comparison showed that ~60% of prevalent adenoma- and CRC-associated species presented concordant directionality in the incident adenoma dataset, including consistent significant depletion of Blautia obeum across the disease continuum.  In contrast, 69% of the CRC-associated species had opposite directionality in the incident serrated polyp dataset, exemplified by Clostridium sp. AF20-17LB, enriched in serrated polyps but depleted in prevalent adenoma and CRC.
Conclusions: Gut microbial alterations are detectable years before polyp diagnosis. Incident adenomas share directional microbial signatures with later-stage neoplasia, suggesting that some CRC-associated shifts are established early in conventional carcinogenesis. The divergent microbial profile of serrated polyps points to a biologically distinct, pathway-specific microbial involvement, consistent with the distinct molecular underpinnings of the serrated pathway.