Letter. investigating the intestinal mucosa-associated microbiota - relevance and potential pitfalls

SIRS, We read with great interest the paper from Shanahan et al.1 We completely agree with the authors about the relevant role of an accurate evaluation of the mucosal-associated microbiota, which represents the part of the intestinal flora directly interacting with the host. Most of the studies in the literature, to date, have evaluated the faecal microbiome, since faecal sample collection do not require invasive examination and could be easier to collect for both patients and researchers. Nonetheless, evidence is mounting about profound differences between faecal bacteria and the mucosal-associated microbiota.2, 3 Considering that molecular crosstalk between enteric bacteria and intestine takes place at the mucosal surface (i.e. pattern recognition receptors/ pathogen-associated molecular patterns interaction), and giving the spatially heterogeneous distribution of different bacterial species throughout the gut, the analysis of only the faecal microbiome could be misleading.