Microbiome signatures for detection of colorectal lesions in population-based FIT screening

Einar Birkeland, Ane Sørlie Kværner, Ekaterina Avershina, Cecilie Bucher-Johannessen, Vahid Bemanian, Hege Salvesen Blix, Anette Hjartåker, Willem M. de Vos, Giske Ursin, Geir Hoff, Kristin Ranheim Randel, Edoardo Botteri, Paula Berstad, Trine B. Rounge

The gut microbiome has been linked to colorectal cancer (CRC) development, with microbe-based classifiers distinguishing between CRC patients and healthy controls. However, there is a lack of studies addressing the utility of the microbiome in screening-relevant settings, including both precancers and CRC. In this Norwegian population-based study, we used fecal immunochemical test (FIT) leftovers from 1034 FIT-positive (i.e. positive for occult blood) screening participants for gut metagenome profiling using shotgun sequencing. Using comprehensive clinical, demographic, and lifestyle data, we modeled gut microbiome associations with CRC screening outcomes. Combining microbial profiles with quantitative FIT values improved detection of premalignant lesions beyond optimizing the FIT value alone, even after incorporating established CRC risk factors. Still, the FIT value maintained superior discriminative ability for CRC. We confirmed enrichment of bacteria such as Fusobacterium nucleatum and Peptostreptococcus stomatis in CRC. In contrast, other bacteria previously associated with the presence of CRC, including Hungatella hathewayi and Clostridium symbiosum, as well as pks-negative Escherichia coli, were enriched in those with no neoplastic findings, suggesting that in a FIT-positive population their presence may reflect other conditions causing intestinal bleeding rather than underlying neoplasia. Microbial profiles were predominantly associated with distal rather than proximal lesions. Together, our findings highlight the potential for microbial markers to improve FIT-based CRC screening, especially by differentiating those with premalignant lesions from those who test FIT-positive for other reasons. Here, the authors show that fecal immunochemical tests can be used as a proxy to profile the gut microbiome in a colorectal cancer screening cohort, identifying early detection signatures and improving discrimination of precancerous lesions among FIT-positive individuals.