Diversity of the autochthonous colonic microbiota

A longstanding hypothesis in intestinal microbial ecology is that autochthonous microbes (resident) play a role that is distinct from allochthonous microbes (transient microbes in the fecal stream). A challenge has been to identify this pool of microbes. We used laser capture microdissection to collect microbes from the mouse ascending colon. This area contains transverse folds that mimic human intestinal folds and contains a distinct population of intestinal microbes that is associated with the mucosa. Our analysis of bacterial 16S rRNA genes showed that this area was enriched for Lachnospiraceae and Ruminococcaceae. In this addendum, we further compare this community to studies of mucosa-associated microbes in humans. This analysis reveals common phylogenetic groups of bacteria that are present in both mouse and human. However, we found microorganisms at the genus and species levels including Faecalibacterium prausnitzii which appears to be specific for humans. We propose that that examination of the mucosa-associated microbes in wild type and genetically modified mice will be a valuable component to define host microbial interactions that are essential for homeostasis.