Crohn's Disease Differentially Affects Region-Specific Composition and Aerotolerance Profiles of Mucosally Adherent Bacteria

Abstract

Background: The intestinal microbiota play a key role in the onset, progression, and recurrence of Crohn disease (CD). Most microbiome studies assay fecal material, which does not provide region-specific information on mucosally adherent bacteria that directly interact with host systems. Changes in luminal oxygen have been proposed as a contributor to CD dybiosis.

Methods: The authors generated 16S rRNA data using colonic and ileal mucosal bacteria from patients with CD and without inflammatory bowel disease. We developed profiles reflecting bacterial abundance within defined aerotolerance categories. Bacterial diversity, composition, and aerotolerance profiles were compared across intestinal regions and disease phenotypes.

Results: Bacterial diversity decreased in CD in both the ileum and the colon. Aerotolerance profiles significantly differed between intestinal segments in patients without inflammatory bowel disease, although both were dominated by obligate anaerobes, as expected. In CD, high relative levels of obligate anaerobes were maintained in the colon and increased in the ileum. Relative abundances of similar and distinct taxa were altered in colon and ileum. Notably, several obligate anaerobes, such as Bacteroides fragilis, dramatically increased in CD in one or both intestinal segments, although specific increasing taxa varied across patients. Increased abundance of taxa from the Proteobacteria phylum was found only in the ileum. Bacterial diversity was significantly reduced in resected tissues of patients who developed postoperative disease recurrence across 2 independent cohorts, with common lower abundance of bacteria from the Bacteroides, Streptococcus, and Blautia genera.

Conclusions: Mucosally adherent bacteria in the colon and ileum show distinct alterations in CD that provide additional insights not revealed in fecal material.

Keywords: Crohn disease; IBD; microbiome; mucosally adherent microbiota; postoperative CD.

FIGURE 1.

Ileal mucosa adopts a more colon-like aerotolerance profile in CD. Boxplots of the relative abundance of taxa assigned to 1 of 5 aerotolerance categories (obligate anaerobes, anaerobes, facultative anaerobes and microaerophiles, aerobes, obligate aerobes) in non-IBD colon (yellow), CD colon (orange), non-IBD ileum (light blue), and CD ileum (dark blue) mucosa. P values calculated based on Wilcoxon rank-sum test.

FIGURE 2.

Obligate anaerobic taxa are predominantly differentially abundant between mucosal region and disease. Volcano plots of differential abundance meta-analysis data exhibiting that the presence of CD leads to the alterations in Bacteroidetes and Firmicutes taxa that are classified as obligate anaerobes in the colonic mucosa (A), with the relative of abundance of obligate anaerobic taxa increased in the presence of CD reflecting the aerotolerance analysis seen in the ileum (B). Within-disease non-IBD mucosa shows that the colonic mucosa is a signficantly more anaerobic environment compared to the ileal mucosa (C); this difference is greatly reduced in the presence of disease. Differential taxa abundance meta-analysis conducted using DESeq2 and LEfSe on all phylogenetic levels. Global P values from combined DESeq2 and LEfSe analyses constructed using Fisher method (FDR ≤ 0.05). Taxa with sp labels indicate that an exact species could not be ascertained.

FIGURE 3.

Similar and divergent alterations seen between cohorts in postoperative recurrence of CD. Volcano plots of differential abundance meta-analysis of alterations between patients with and without postoperative recurrence at UNC (A) and WashU (B) show little overlap between the 2 locations. Differential taxa abundance meta-analysis was conducted using DESeq2 and LEfSe on all phylogenetic levels. Global P values from combined DESeq2 and LEfSe analyses constructed using Fisher method (FDR ≤ 0.05). Taxa with sp labels indicate that an exact species could not be ascertained.