Background and Aims: Inflammatory bowel diseases (IBD) are typified by episodic recurrence of overt inflammation of the gut mucosa. There is currently no cure for IBD, and treatments principally target suppression of host immune response. Gut microbial “dysbiosis” is now widely believed to be a hallmark of new onset and recurrent disease, but the functional bases of “dysbiosis” remains ill-defined, particularly with respect to the involvement of the mucosa-associated microbiota (MAM) in the trigger(s) and natural history of IBD. Here, we aim to evaluate use a novel ex vivo combination of microbe culture with metagenomic sequencing (MC-MGS) to longitudinally characterize changes in the MAM of a murine model of IBD.
Methods and Results: Eight rag−/− mice received i.p. either anti-CD40+ IgG monoclonal antibodies to induce colitis, or an IgG isotype control. Colonic biopsies and faecal pellets from the mice were collected at baseline and at day-9. The MAM were cultured from tissue using habitat-simulating medium prepared to contain either plant/host-based carbohydrates. Total DNA was extracted from tissue directly, faecal pellets, and microbial cultures and here, compared by 16S rRNA gene amplicon sequencing. The microbiota profiles of all mice were similar at baseline but separated into two distinct clusters by day-9 according to treatment. The MAM communities of the colitic and non-colitic mice predicted from tissue DNA extracts could be differentiated by a greater relative abundance of taxa affiliated with Lachnospiraceae and Muribaculum, respectively. The alpha-diversity metrics suggest that the MAM recovered with host-derived carbohydrates are more diverse than cultures recovered using plant-based carbohydrates.
Conclusions: The consortia recovered by MC-MGS provide a good representation of the microbial diversity associated with murine colonic tissue. While further improvements in approach are expected, MC-MGS advances the recovery of the MAM and facilitates a biologically enhanced characterization of host-microbe interactions in animal models of IBD.