Metagenomic analysis of intestinal mucosa revealed a specific eukaryotic gut virome signature in early-diagnosed inflammatory bowel disease

Abstract

Intestinal dysbiosis is one of the causes underlying the pathogenesis of inflammatory bowel disease (IBD), encompassing ulcerative colitis (UC) and Crohn's disease (CD). Besides bacteria, microbiota comprises both prokaryotic and eukaryotic viruses, that together compose the gut virome. Few works have defined the viral composition of stools, while the virome populating intestinal mucosae from early-diagnosed IBD patients has never been studied. Here we show that, by in-depth metagenomic analysis of RNA-Seq data obtained from gut mucosae of young treatment-naïve patients, early-diagnosed for CD and UC, and from healthy subjects (Ctrl), UC patients display significantly higher levels of eukaryotic Hepadnaviridae transcripts by comparison with both Ctrl and CD patients, whereas CD patients show increased abundance of Hepeviridae versus Ctrl. Moreover, we found that UC gut mucosa is characterized by lower levels of Polydnaviridae and Tymoviridae, whereas the mucosa of patients with CD showed a reduced abundance of Virgaviridae. Our findings support the idea that certain eukaryotic viruses might trigger intestinal inflammation and contribute to IBD pathogenesis and pave the way not only for the discovery of novel diagnostic biomarkers but also for the development of anti-viral drugs for the treatment of IBD.

Keywords: Inflammatory bowel disease; eukaryotic gut virome; inflammation; metagenomics.

Figure 1.

RNA-Seq analysis reveals an IBD-specific virome signature. A. Table showing the characteristics of patients included in GSE57945 study. B. GSEA functional enrichment of viral response GO categories in the indicated groups. The horizontal line represents statistical significance. C. Bioinformatics pipeline. D. Relative abundance of viral orders in Ctrl, UC, cCD, and iCD. E-F. Principal component analysis (PCA) of viral order (C) and viral family (D) relative abundance in Ctrl, UC, cCD, and iCD. Data are mean± s.e.m.

Figure 2.

Early-diagnosed IBD patients showed increased abundance of specific eukaryotic viruses. A. Viral family relative abundance in Ctrl, UC, cCD, and iCD. B-E. Dot-plot (B) and MA-plots (C-E) showing Hepadnaviridae differential abundance for the indicated comparisons. F. Dot-plot showing HBx transcript differential enrichment in UC vs Ctrl, iCD, and cCD. G-K. Dot-plots for Hepeviridae (G) and Baculoviridae (J) and MA-plots (H, I, K) showing the differential abundance of the indicated comparisons. Red dots in MA-plot represent statistically enriched viral families (P ≤ 0.05). Data are represented as mean ± s.e.m. *P < 0.05; ***P < 0.005.

Figure 3.

Defined viral entities prevail over others in the IBD-specific eukaryotic gut virome. Dot plots displaying statistical significant Pearson R² correlation coefficients for the following comparisons: Hepadnaviridae vs Polydnaviridae (A), Hepadnaviridae vs Tymoviridae (B), Hepeviridae vs Virgaviridae (F), Baculoviridae vs Partitiviridae (I), Baculoviridae vs Bromoviridae (J), and histogram showing relative sequence abundance for the Polydnaviridae (C), Tymoviridae (D), Virgaviridae (E), Partitiviridae (H), and Bromoviridae (I) viral families. Data are represented as mean ± s.e.m. *P < 0.05; ** P < 0.01; ***P < 0.005.