Alterations in diversity of the oral microbiome in pediatric inflammatory bowel disease

Abstract

Background: Oral pathology is a commonly reported extraintestinal manifestation of Crohn's disease (CD). The host-microbe interaction has been implicated in the pathogenesis of inflammatory bowel disease (IBD) in genetically susceptible hosts, yet limited information exists about oral microbes in IBD. We hypothesize that the microbiology of the oral cavity may differ in patients with IBD. Our laboratory has developed a 16S rRNA-based technique known as the Human Oral Microbe Identification Microarray (HOMIM) to study the oral microbiome of children and young adults with IBD.

Methods: Tongue and buccal mucosal brushings from healthy controls, CD, and ulcerative colitis (UC) patients were analyzed using HOMIM. Shannon Diversity Index (SDI) and Principal Component Analysis (PCA) were employed to compare population and phylum-level changes among our study groups.

Results: In all, 114 unique subjects from the Children's Hospital Boston were enrolled. Tongue samples from patients with CD showed a significant decrease in overall microbial diversity as compared with the same location in healthy controls (P = 0.015) with significant changes seen in Fusobacteria (P < 0.0002) and Firmicutes (P = 0.022). Tongue samples from patients with UC did not show a significant change in overall microbial diversity as compared with healthy controls (P = 0.418).

Conclusions: As detected by HOMIM, we found a significant decrease in overall diversity in the oral microbiome of pediatric CD. Considering the proposed microbe-host interaction in IBD, the ease of visualization and direct oral mucosal sampling of the oral cavity, further study of the oral microbiome in IBD is of potential diagnostic and prognostic value.

FIGURE 1

(a) SDI of tongue and buccal mucosal samples from control population demonstrating a trend toward overall decreased diversity in control buccal samples as compared with control tongue samples (ΔSDI = −0.122, P = 0.067). Significant differences at the phylum level were seen within this comparison. Fusobacteria (ΔSDI = −0.157, P < 0.0002) and Firmicutes (ΔSDI = −0.038, P = 0.037) were less abundant in buccal samples, whereas Bacteroidetes were more abundant (ΔSDI = 0.033, P = 0.030). (b) PCA of tongue and buccal mucosal samples from control population. Tongue samples are represented by blue triangles, buccal samples by red circles. This type of data compression analysis demonstrates the clustering of samples based on their location and similar microbial profiles.

FIGURE 2

(a) SDI analysis of tongue samples across cohorts. Overall diversity of CD was significantly reduced as compared with control samples (ΔSDI = −0.143, P = 0.015). In comparison, overall diversity of tongue samples in UC is not significantly different from control samples (ΔSDI = 0.012, P = 0.418). (b) SDI analysis of buccal mucosa samples across cohorts. Overall diversity of CD was reduced as compared with control samples (ΔSDI = −0.125, P = 0.091). Overall diversity of buccal samples in UC is similar to control samples (ΔSDI = 0.073, P = 0.254).

FIGURE 3

(a) ΔSDI of tongue samples from CD and UC patients using control tongue samples as the reference value. Significant phyla are denoted with the asterisk. CD Samples were significantly reduced in Firmicutes (ΔSDI = −0.033, P = 0.022), Fusobacteria (ΔSDI = −0.128, P < 0.0001) and overall diversity (ΔSDI = −0.143, P = 0.015). Tongue samples from UC patients were overall not significantly different from control tongue samples (ΔSDI = 0.012, P = 0.418). Losses, however were noted in Fusobacteria (ΔSDI = −0.086, P = 0.006), whereas Spirochaetes (ΔSDI = 0.007, P = 0.006), Synergistetes (ΔSDI = 0.058, P = 0.009), and Bacteroidetes (ΔSDI = 0.028, P = 0.030) were all enriched. (b) ΔSDI of buccal mucosa samples from CD and UC patients using control buccal samples as the reference value. No individual phyla were significantly different. Overall diversity in buccal samples across cohorts was not statistically significant; however, CD trended toward decreased overall diversity.