Comparison of Bacterial Community Profiles From the Large Intestine, Rectal Swabs, and Stool Samples

Abstract

Background: The human gastrointestinal tract contains a complex and dynamic population of microorganisms, known as the gut microbiota. Critically, although interest in the role that the gut microbiota plays in human health has increased in recent years, there remains no standard sampling protocol for analyzing these organisms. Here, we aimed to characterize the microbial composition of distinct segments of the large intestine and to determine whether rectal swabs are suitable for identifying the colon microbiota. Methods: A total of 100 participants who underwent screening colonoscopy from October 2019 to October 2020 were included in this study. Large intestinal samples (ascending colon, descending colon, sigmoid colon, and rectum) were aspirated by colonoscopy. Rectal swabs were collected before colonoscopy, and stool samples were collected before patients began colonoscopy preparation. All samples were subjected to 16S ribosomal RNA gene sequencing. Findings: We identified differences in the number of phylum-level operational taxonomic units in large intestinal samples, rectal swabs, and stool. Five major phyla were detected in all samples (Firmicutes, Bacteroides, Proteobacteria, Actinobacteria, Fusobacteria), although their relative abundances varied. Notably, we found that the microbial composition of rectal swabs is most similar to those of the sigmoid colon and rectum, whereas the microbiota in stool are relatively different than those from the large intestine and rectal swabs. Interpretation: Our results reveal the existence of microbial heterogeneity within different large intestinal compartments and further suggest that rectal swabs are an acceptable and practical tool for gut microbiota analysis. Funding Information: This study was supported by MediCloud. Declaration of Interests: The authors declare no competing interests. Ethics Approval Statement: This study was approved by Yongin Severance Institutional Review Board (IRB No 9-2019-0014) and was performed in compliance with the Declaration of Helsinki. Written consent was obtained from all patients prior to participation.