Differential clustering of fecal and mucosa-associated microbiota in ‘healthy’ individuals

Objective: Fecal samples are often used to characterize gut microbiota. However, whether or not fecal microbiota differs from mucosa-associated microbiota remains largely unknown. This may be specifically relevant in conditions that are characterized by complex mucosal microbe–host interactions, such as Crohn’s disease. We aimed to determine the degree of agreement between fecal and mucosal microbiota profiles in ‘healthy’ individuals, using two commonly used collection procedures. Methods: The gut microbiota composition of fecal samples (sent at ambient temperature before storage at −70°C) and of colonic biopsies (obtained at endoscopy and immediately stored at −70°C) was determined by sequencing the 16S rRNA gene. Altogether 31 randomly selected ‘healthy’ individuals from the population-based colonoscopy (Popcol) study were included. Results: The fecal samples were characterized by a reduced degree of richness (P < 0.0001) and diversity (P = 0.016), and also differences in several phyla, including a lower relative abundance of Proteobacteria (P < 0.0001) and Verrucomicrobia (P = 0.008) than in biopsies. Only three of 30 individuals had a similar fecal and mucosal microbiota profile, based on weighted UniFrac analysis. A difference in Crohn’s disease dysbiosis-associated bacteria was observed, including a lower relative abundance of Faecalibacterium (P = 0.004) and a higher relative abundance of Ruminococcus (P = 0.001) in feces than in biopsies. Conclusions: The observed differences between fecal samples, transported at ambient temperature, and the colonic mucosa-associated microbiota have implications for the interpretation of the previous literature, and may be specifically relevant to studies on Crohn’s disease.