Distinct prophage infections in colorectal cancer-associated Bacteroides fragilis

Colorectal cancer (CRC) patients exhibit distinct gut microbiota disruption, known as dysbiosis, which is believed to play a causative role in CRC. One of the key bacterial species implicated in CRC dysbiosis is Bacteroides fragilis, which presents a paradox as it is also present in most healthy individuals. This discrepancy underscores the need for analysis beyond species-level associations and to investigate intraspecies variation within B. fragilis. From a highly specific collection of B. fragilis isolates from CRC patients and controls, a pangenome-wide association study was conducted, identifying intraspecies genetic variations associated with CRC. The CRC association of these genetic variations were then validated in a metagenome sequencing cohort of faecal samples from 877 individuals, with and without CRC. To test group differences a mixed effects logistic regression with cohort as a random effect was performed for each genetic variation. Here we show that CRC-associated B. fragilis isolates are infected with specific Caudoviricetes prophages, significantly more often than negative controls. The initial discovery was made in our highly specific isolate collection and then validated in an independent metagenome sequencing cohort, finding that CRC patients were twice as likely to have detectable levels of these phages (OR = 2.05, p = 2.522E-7, SE = 0.139). To our knowledge, these findings mark the first link between one of the most implicated driver bacteria and phages in CRC and suggest a more complex role of phages in CRC dysbiosis than current models suggest and highlights the potential of phages as CRC biomarkers. Colorectal cancer is linked to changes in human gut microbes, but how these changes are involved remain unclear. The common gut bacterium Bacteroides fragilis is often tied to colorectal cancer but is also present in healthy people. We investigated if there was something more to these bacteria that could explain how they were tied to colorectal cancer. Using genetic tests, we found that B. fragilis from colorectal cancer patients are infected with specific, and previously unknown, viruses. These findings suggest a partnership between bacteria and their viruses that may shape disease. If confirmed, these findings may support earlier detection of colorectal cancer and guide new ways to treat and prevent this disease. Damgaard et al. analyze Bacteroides fragilis genomes isolated from people with and without colorectal cancer, identifying prophages. Screening 877 faecal metagenomes, they find that these specific prophages are significantly enriched in colorectal cancer patients.