Gut microbial dysbiosis associated to diarrheic irritable bowel syndrome can be efficiently simulated in the Mucosal ARtificial COLon (M-ARCOL)

Abstract

Irritable bowel syndrome (IBS) is a common chronic gastrointestinal disorder, with diarrhea-predominant IBS (IBS-D) as the most frequent subtype. The implication of gut microbiota in the disease's etiology is not fully understood. In vitro gut systems can offer a great alternative to in vivo assays in preclinical studies, but no model reproducing IBS-related dysbiotic microbiota has been developed. Thanks to a large literature review, a new Mucosal ARtifical COLon (M-ARCOL) adapted to IBS-D physicochemical and nutritional conditions was set-up. To validate the model and further exploit its potential in a mechanistic study, in vitro fermentations were performed using bioreactors inoculated with stools from healthy individuals (n = 4) or IBS-D patients (n = 4), when the M-ARCOL was set-up under healthy or IBS-D conditions. Setting IBS-D parameters in M-ARCOL inoculated with IBS-D stools maintained the key microbial features associated to the disease in vivo, validating the new system. In particular, compared to the healthy control, the IBS-D model was characterized by a decreased bacterial diversity, together with a lower abundance of Rikenellaceae and Prevotellaceae, but a higher level of Proteobacteria and Akkermansiaceae. Of interest, applying IBS-D parameters to healthy stools was not sufficient to trigger IBS-D dysbiosis and applying healthy parameters to IBS-D stools was not enough to restore microbial balance. This validated IBS-D colonic model can be used as a robust in vitro platform for studies focusing on gut microbes in the absence of the host, as well as for testing food and microbiota-related interventions aimed at personalized restoration of gut microbiota eubiosis.

Keywords: IBS-D; M-ARCOL; SCFA; bile acids; gut microbiota; in vitro gut model; mucus.

Figure 1.

Experimental design in the M-ARCOL.

Figure 2.

Fecal sample characterization.

Figure 3.

Alpha and beta-diversity of bacterial communities during M-ARCOL experiments.

Figure 4.

Cross-compared effect of IBS-D versus healthy stools and colonic parameters on bacterial and archaeal populations in the luminal environment of the M-ARCOL. M-ARCOL was inoculated with stools collected from four healthy volunteers (HS1, HS2, HS3, and HS4) and four IBS-D patients (IS1, IS2, IS3, and IS4) and set-up to reproduce either healthy (HP) or IBS-D (IP) parameters. Graphs focus on the last 4 days of fermentation experiments (D08 to D11). Luminal bacterial composition determined by 16S metabarcoding in bioreactors inoculated with healthy (a) or IBS-D (b) stools. (c) qPCR quantification of selected bacterial populations in the luminal medium. Results are expressed as mean 16S rRNA copies/g ± standard error of the mean (SEM, n = 4). Statistical differences between all conditions for each population as tested by two-ways ANOVA are indicated by different letters (p < 0.05) (d) Differential analysis performed at the family level, showing significant differences with at least one of three tested methods (DeSeq2, Metacoder, and MetagenomeSeq R-analysis). (e) Archaea abundances determined by metabarcoding analysis. HS: healthy stool; IS: IBS-D stool; HP: healthy parameters; IP: IBS-D parameters.

Figure 5.

Cross-compared effect of IBS-D versus healthy stools and colonic parameters on bacterial and archaeal populations in the mucosal environment of the M-ARCOL.

Figure 6.

Cross-compared effect of IBS-D versus healthy stools and colonic parameters on gut microbiota activities in the M-ARCOL.