Cystic Fibrosis (CF) is the most common autosomal recessive genetic disease in Caucasians. It is caused by mutations in the CFTR gene, leading to poor hydration of mucus and impairment of the respiratory, digestive, and reproductive organ functions.Advancements in medical care have lead to markedly increased longevity of patients with CF, but new complications have emerged, such as early onset of colorectal cancer (CRC). Although the pathogenesis of CRC in CF remains unclear, altered host-microbe interactions might play a critical role. Here, we characterize the changes in the gut microbiome and host gene expression in colonic mucosa of CF patients relative to healthy controls. We find that CF patients show decreased microbial diversity, decreased abundance of taxa such as Butyricimonas, Sutterella, and Ruminococcaceae, and increased abundance of other taxa, such as Actinobacteria and Firmicutes. We find that 1543 genes, including CFTR, show differential expression in 2 the colon of CF patients compared to healthy controls. Interestingly, we find that these genes are enriched with functions related to gastrointestinal and colorectal cancer, such as metastasis of CRC, tumor suppression, cellular dysfunction, p53 and mTOR signaling pathways. Lastly, we modeled associations between relative abundances of specific bacterial taxa in the gut mucosa and host gene expression, and identified CRCrelated genes, including LCN2 and DUOX2, for which gene expression is correlated with the abundance of CRC-associated bacteria, such as Ruminococcaceae and Veillonella. Our results provide new insight into the role of host-microbe interactions in the etiology of CRC in CF. colorectal cancer.progress faster to more advanced neoplasms [4]. In fact, loss of CFTR expression in tumors of non-CF patients has been associated with a worse prognosis in early stage CRC [5]. Recently, specific recommendations for CRC screening were introduced in standard care of adult CF patients, which include earlier initiation of screening and shorter intervals for surveillance [6].Although previous studies have identified CFTR as a tumor suppressor gene that may play a role in early onset of colon cancer [5,7], the pathogenesis of CRC in CF remains unclear. A number of factors can be considered. Thus, stagnant mucus in CF is associated with bacterial overgrowth at the mucosal surface [8,9], which might result in greater levels of tonic microbial stimulation of the epithelia and account for their increased rate of their turnover [10]. It is likely that the altered microbiota composition and microbiota-mucosal interface are also the reasons for a chronic state of low-grade mucosal inflammation in CF [11,12]. Notably, in the colon CFTR is hyper-expressed in the stem cell compartment of the intestinal crypt [13,14], which is the site of CRC origination [15].Than and colleagues have shown altered expression of genes involved in immune cell homeostasis and inflammation, mucins, cell signaling and growth regulation, detoxification and stress response, lipid meta...