Gut microbiota in mucosa and feces of newly diagnosed, treatment-naïve adult inflammatory bowel disease and irritable bowel syndrome patients

Abstract

The knowledge on how gut microbes contribute to the inflammatory bowel disease (IBD) at the onset of disease is still scarce. We compared gut microbiota in newly diagnosed, treatment-naïve adult IBD (Crohn's disease (CD) and ulcerative colitis (UC)) to irritable bowel syndrome (IBS) patients and healthy group. Mucosal and fecal microbiota of 49 patients (13 UC, 10 CD, and 26 IBS) before treatment initiation, and fecal microbiota of 12 healthy subjects was characterized by 16S rRNA gene sequencing. Mucosa was sampled at six positions, from terminal ileum to rectum. We demonstrate that mucosal microbiota is spatially homogeneous, cannot be differentiated based on the local inflammation status and yet provides bacterial footprints superior to fecal in discriminating disease phenotypes. IBD groups showed decreased bacterial diversity in mucosa at all taxonomic levels compared to IBS. In CD and UC, Dialister was significantly increased, and expansion of Haemophilus and Propionibacterium characterized UC. Compared to healthy individuals, fecal microbiota of IBD and IBS patients had increased abundance of Proteobacteria, Enterobacteriaceae, in particular. Shift toward reduction of Adlercreutzia and butyrate-producing taxa was found in feces of IBD patients. Microbiota alterations detected in newly diagnosed treatment-naïve adult patients indicate that the microbiota changes are set and detectable at the disease onset and likely have a discerning role in IBD pathophysiology. Our results justify further investigation of the taxa discriminating between disease groups, such as H. parainfluenzae, R. gnavus, Turicibacteriaceae, Dialister, and Adlercreutzia as potential biomarkers of the disease.

Keywords: Crohn’s disease; Gut microbiota; fecal microbiota; gut mucosa; inflammatory bowel disease; irritable bowel syndrome; treatment-naïve patients; ulcerative colitis.

Figure 1.

Spearman correlation of bacterial abundances (family level) among positions along the gut within each patient: terminal ileum (TI), ascending colon (CA), transverse colon (CT), descending colon (CD), sigmoid colon (CS), and rectum (R). Inflamed positions are labeled in red. For patients A and B, relative abundance profiles are presented in Supplementary Figure S3. CD – Crohn’s disease, UC – ulcerative colitis, IBS – irritable bowel syndrome.

Figure 2.

Microbial diversity of intestinal mucosa at six locations along the gut, colored by position (a, b) and inflammation status (c, d). Terminal ileum (TI), ascending colon (CA), transverse colon (CT), descending colon (CD), sigmoid colon (CS), and rectum (R). (a, c) Alpha diversity measured by phylogenetic diversity PD. B.-H. corrected Wilcoxon test between categories showed no significance. (b, d) The first three principal coordinates of weighted UniFrac (percentage of the variation explained in brackets) are shown for beta diversity. Bonferroni-corrected t-test between categories showed no significance.

Figure 3.

Microbial diversity of intestinal mucosa at six positions along the gut (a-c), and after merging sequences for all positions in the patient-specific profiles (d-f). Alpha diversity measured by phylogenetic diversity PD, with B.-H. corrected Wilcoxon test between categories. (a, e). The first three principal coordinates of weighted UniFrac (percentage of the variation explained in brackets) are shown for beta diversity (b, f), with Bonferroni-corrected t-test between categories. First two principal components in PCA and loadings for top ten families are shown before (c) and after position merging (d). CD – Crohn’s disease, UC – ulcerative colitis, IBS – irritable bowel syndrome. *p < .05, **p < .01, ***p < .001, ****p < .0001.

Figure 4.

Heatmap of family level effect sizes in pairwise comparisons of mucosal profiles. K-means clustering of families with six clusters. Dendrogram on top shows clustering based on distance of effect size profiles, for each pairwise comparison. CD – Crohn’s disease, UC – ulcerative colitis, IBS – irritable bowel syndrome, ENT – Bacteroides versus Prevotella dominated enterotype.

Figure 5.

Heatmap of clustered family level effect sizes in pairwise comparisons of fecal profiles, based on k-means clustering of families with seven clusters. Dendrogram on top shows clustering based on distance of effect size profiles, for each pairwise comparison. CD – Crohn’s disease, UC – ulcerative colitis, IBS – irritable bowel syndrome, H – healthy, ENT – Bacteroides versus Prevotella dominated enterotype.

Figure 6.

Microbial diversity indices per sample type. (a) Alpha diversity indices – PD, Chao1 and Shannon, with B.-H. corrected Wilcoxon test between categories. (b) and (c) beta diversity PCoA in weighted UniFrac per sample type (feces or mucosa) with Bonferroni-corrected t-test between categories, and separated by disease (CD, UC, IBS) for each specimen type, respectively. The number in brackets represents percentage of total variance explained by the given PCoA. *p < .05, **p < .01, ***p < .001, ****p < .0001.