Diversity of the autochthonous colonic microbiota

Abstract

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.

Figure 1

Model of the interaction of host and microbiota in the intestine. The epithelial monolayer produces mucus as well as antimicrobial peptides and proteins that form electrostatic interactions in the intestinal lumen. This forms a specialized niche where autochthonous (resident) microbes appear to reside. Autochthonous microbes (1) are comprised of compact interlacing layers of predominately large, fusiform-shaped bacteria that appeared in close apposition to the apical surface of the colonic epithelium. These microbial communities are distinct, both morphologically and phylogenetically, as compared to allochthonous (transient) microbes (2) that are located in the central lumen (digesta) as part the fecal stream. Allochthonous communities include rod- and coccoid-shaped bacteria associated with undigested food particles.

Figure 2

Mucosa-associated autochthonous microbes in the human and mouse colon are enriched for Lachnospiraceae and Ruminococcaceae families. We compared diversity at the family level. Each chart represents the taxonomic composition. Sequences were previously obtained in another study from the ascending-, transverse-, descending-colon and rectum biopsies of healthy humans. This data was extracted from a comprehensive molecular analysis of almost full-length 16S rRNA gene sequences. Pyrosequencing analysis was used to examine microbial diversity between interfold (29,560 reads) and digesta (38,120 reads) regions from the colon of wild-type mice. Lachnospiraceae and Ruminococcaceae are indicated by arrows and outlined with a dotted line to highlight these families. Noteworthy, the enrichment of both Lachnospiraceae and Ruminococcaceae families was also observed in mucosal biopsies obtained from healthy humans who had undergone bowel preparation. These data indicate that detection of these bacterial families can be accomplished regardless the methodology for sample acquisition. Unclassified Bacteroidetes and Firmicutes correspond to sequences not classifiable at family level (as of December 2010). Both data sets were classified using the Classifier version 2.2 at the Ribosomal Database Project.

Figure 3

Common and specific phylogenetic genera of autochthonous bacteria associated to the colonic mucosa of both mouse and human. We compared diversity at the genus level. Each heat-map represents the relative abundance of each genus from Lachnospiraceae, Ruminococcaceae and Incertae Sedis XIV families (all members of the Clostridium cluster XIV). Sequences were obtained from the ascending-, transverse-, descending-colon and rectum biopsies of healthy humans, and interfold and digesta regions from the colon of wild-type mice. Unclassified (Unclass) Ruminococcaceae and Lachnospiraceae correspond to sequences not classifiable at genus level (for details see legend in Fig. 2).