The microbiome compositional and functional differences between rectum mucosa and faeces

In recent years, most studies on the gut microbiome have primarily focused on fecal samples, leaving the microbial communities in the rectal mucosa relatively unexplored. Recognizing this gap, our study employed metagenomic sequencing technology to delve into the microbial communities in both normal rectal mucosal tissues and fecal samples from patients at risk for early-stage colorectal cancer. We selected 20 patients with colonic polyps and utilized shotgun metagenomics to analyze the microbial composition in both sample types. Our findings revealed a pronounced distinction between the microbial communities in the intestinal mucosa and feces, primarily attributed to the higher microbial diversity in feces. As the biodiversity in feces is higher and many microbes found in the mucosa can also be detected in feces, fecal sampling can to some extent reflect the situation of the intestinal mucosal microbiota. However, due to the significant differences between fecal and intestinal mucosal microbiota, and the fact that most studies primarily use sequencing techniques to study the fecal microbiota, our comprehensive understanding of the microbial community in the rectal mucosa remains limited. Our research attempts to bridge this knowledge gap, reveals the differences in microbial communities between feces and rectal mucosa in the Chinese population, and performs functional analysis of KEGG Orthology (KO). Additionally, we also conducted an in-depth analysis of differential markers and KO pathway functions in intestinal mucosal tissue based on different clinical phenotypes. Overall, this study presents a system-level map of the differences between fecal and rectal mucosal microbial communities in potential colorectal cancer samples, providing critical insights into the role of gut microbiome in the pathogenesis of colorectal cancer and paving the way for the development of new prevention and treatment strategies.