Kaitlyn E. Barrack, Sarvesh Surve, Antonia Karine Silva Bezerra, Caitlin E. Murphy, Shannon M. Soucy, Miguel A. Aguilar Ramos, Rebecca Valls, Rebekah D. Ruff, Emily P. Balskus, Julie Sanville, Juliette C. Madan, George A. O’Toole
ABSTRACT Cystic fibrosis (CF) alters the gastrointestinal microbiome from an early age, leading to significant changes in microbial composition and functionality. This study explores the physiological and microbiological factors contributing to dysbiosis in children with cystic fibrosis (cwCF), characterized by an increase in potentially pathogenic Escherichia coli and a decrease in beneficial anaerobes, such as Bacteroides . We employed an in vitro medium representative of the nutritional environment of the CF colon to test the role of factors, including mucin, fat, bile, pH, antibiotics, and features associated with inflammation (e.g., nitrate, sulfate, formate, and reactive oxygen species), on the growth of clinical isolates of E. coli and Bacteroides spp., with a focus on Bacteroides vulgatus . We further examined interactions between these two microbes under CF-like conditions and identified glycerol, a surrogate of increased fat, as a significant driver of altered microbial competition. Finally, we investigated genetic determinants influencing these microbial interactions by performing a transposon mutagenesis screen in E. coli . The results pointed to the role of colibactin, a DNA-damaging genotoxin associated with an increased risk of colorectal cancer (CRC), in mediating this microbial competition. This work enhances our understanding of the mechanisms of microbial competition in the CF gut and potential CRC risk in persons with CF through the identification of early-life microbial biomarkers. IMPORTANCE The risk of CRC development in CF populations is significantly increased. This in vitro study examines the interplay of altered intestinal physiology in the microbial dysbiosis common in the CF gut, implicating the high-fat/glycerol environment in a competition-mediated depletion of immune-modulating Bacteroides vulgatus . This work identifies candidate features of the young CF intestine and gut microbiome that may contribute to dysbiosis, development of inflammation, and CRC in these populations, informing potential prognostic and therapeutic approaches.