Comparison of metagenomic analysis of fecal and gastrointestinal tract samples for identifying beneficial gut microorganisms

Abstract

Introduction: Previous research on the gut microbiome has primarily focused on fecal microbiota, raising concerns about whether fecal samples accurately represent the entire intestinal microbiota. Studies have shown that microbial communities across the gastrointestinal (GI) tract are more diverse than those in feces, suggesting that microbial composition may vary depending on the sampling method. Additionally, analyzing the broader diversity of microbial communities in the GI tract may enhance the identification of potentially beneficial microbiota. Methods: In this study, we compare gut microbiome datasets obtained from fecal samples and GI samples (collected by pooling luminal contents and mucosal scrapings from the stomach to the end of the colon) of 6-month-old mice using 16S rRNA sequencing. We further investigate the associations between gut microbiota and motor, cognitive, and emotional functions in mice, examining differences between the two sample types. To assess these variations, we apply DESeq2 analysis to identify microbial species enriched in high-functioning groups and evaluate how their selection may differ depending on the sampling approach. Results: Our findings reveal notable differences in microbial composition between fecal and GI samples, suggesting that sampling methods may influence the identification of beneficial bacteria. Discussion: These results highlight the importance of selecting an appropriate sampling approach in microbiome research to ensure a comprehensive understanding of gut microbiota-host interactions.