Abstract
The bacterial composition of the gut lumen and mucosa is distinct and the mucosa-associated bacteria are thought to play a more critical role in interactions with the host immune system. However, limited studies of the gut mucosal microbiota in humans have been available due to methodological challenges. Here, we evaluated the potential use of colonic lavage samples for mucosal microbiota analysis in humans. Among the different types of colonic mucosal samples collected from healthy volunteers, the lavage samples contained a higher amount of bacterial DNA and were less contaminated with host DNA compared to mucosal brushing (brush) and biopsy. Although 16S gene amplicon sequencing showed that the bacterial composition of the lavage was intermediate between that of feces and biopsy, mucosal bacteria abundant in the biopsy were also enriched in lavage samples. Furthermore, differences in mucosal microbes between non-smokers and smokers were detectable in lavage samples. Our data emphasize that colonic lavage is suitable for analysis of the mucosal microbiota. Given its minimal invasiveness and high bacterial DNA content, the colonic lavage will promote research on the human mucosal microbiota, especially in gastrointestinal disorders.
Highlights
The bacterial composition of the gut lumen and mucosa is distinct and the mucosa-associated bacteria are thought to play a more critical role in interactions with the host immune system
Samples collected after bowel preparation seem to contain enriched mucosal bacteria and the aforementioned risks are reduced with these methods, especially colonic lavage, owing to their minimal invasiveness
We investigated the quality and quantity of bacterial DNA extracted from feces, colonic mucosal lavage, brush, and biopsy of healthy individuals and compared the bacterial composition of these samples to evaluate the suitability of lavage for mucosal microbiota analysis
Summary
The bacterial composition of the gut lumen and mucosa is distinct and the mucosa-associated bacteria are thought to play a more critical role in interactions with the host immune system. The invasive sampling method of a biopsy has a potential risk of unexpected bleeding and infection[20], which makes it difficult to apply to healthy individuals and patients with extra-intestinal diseases. Alternative sampling methods, such as endoscopic brush sample and colonic lavage, have been proposed for mucosal microbiota a nalysis[20,21,22]. We investigated the quality and quantity of bacterial DNA extracted from feces, colonic mucosal lavage, brush, and biopsy of healthy individuals and compared the bacterial composition of these samples to evaluate the suitability of lavage for mucosal microbiota analysis. We conducted a comparative analysis of microbiota between non-smokers and current smokers to ask whether the lavage samples are able to detect compositional changes in the mucosal microbiota between these groups
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