Alterations in the mucosa-associated fungal microbiota in patients with ulcerative colitis

Abstract

Background: Fungi colonize the human gut and might play a key role in the pathogenesis of ulcerative colitis (UC). However, studies on the fungal composition in the gut (especially adhering to the intestinal mucosa) of UC patients is limited.

Results: The number of fungi decreased significantly in inflamed mucosa compared with that in HS mucosa. Fifteen major genera were examined, among which Wickerhamomyces, unidentified genus of Saccharomycetales, Aspergillus, Sterigmatomyces, and Candida showed increasing trends, whereas Exophiala, Alternaria, Emericella, Epicoccum, Acremonium, Trametes, and Penicillium showed decreasing trends in UC patients compared to the HS. The pro-inflammatory cytokines (IL-Iβ, TNF-α, INF-γ, IL-6, IL-17A, and IL-23) were up-regulated in the UC group. The genera Wickerhamomyces, Nigrospora, and Penicillium were positively correlated, while Sporobolomyces and Trametes were negatively correlated with the expression of several colonic pro-inflammatory cytokines and the Baron and/or Mayo score.

Conclusions: Our study confirms the alteration of the colonic fungal microbiota in the UC patients, which might be associated with mucosal inflammation and pathogenesis of UC. Further studies need to identify the roles of different intestinal fungi in detail, and to determine the mechanism of the host-fungal interaction underlying the development of UC.

Methods: Mucosal samples of inflamed descending colon from 14 active UC patients and 15 healthy subjects (HS) were analyzed by high-throughput sequencing to compare the fungal microbiota. The expressions of pro-inflammatory cytokines (IL-Iβ, TNF-α, INF-γ, IL-6, IL-17A, and IL-23) in intestinal mucosal tissues were examined. The Baron and Mayo scores of UC patients were evaluated, and the correlation between intestinal fungal composition and intestinal inflammatory status was analyzed.

Keywords: high-throughput sequencing; intestinal fungi; mucosal inflammation; mucosal-associated microbiota; ulcerative colitis.

Figure 1

(A) qRT-PCR of 18S rDNA was performed on per ng total DNA isolated from the mucosal specimens of HS and UC patients. (B) Relative expression of 18S rDNA level in mucosal specimens of HS and UC patients measured by qRT-PCR and normalized to RPLPO. (C) The Shannon-Weiner biodiversity index (Shannon index) was measured to represent the diversity of fungi in the gut.

Figure 2. Fungal compositions vary in colonic mucosa between healthy subjects (HS) and UC patients

(A) Fungal operational taxonomic units (OTUs) (97% similarity level) number in colonic mucosa of HS and UC patients. (B) Partial least-squares discriminant analysis (PLS-DA) scores plot based on the relative abundance of fungal OTUs in colonic mucosa of HS and UC patients. (C) Heat maps showing the 19 core OTUs of fungal communities inferred from colonic mucosa, with each subject shown individually. Each vertical lane corresponds to a subject, and the colored squares in each row indicate the relative abundance of the core OTU among the 29 subjects.

Figure 3

Distribution of fungi in colonic mucosal samples at the phylum level, exhibited integrally (A) and individually (B). And the Basidiomycota/Ascomycota relative abundance ratio in HS and UC groups were studied (C).

Figure 4. Distribution of fungi in colonic mucosal samples of HS and UC patients at the genus level

Figure 5. Comparison of 15 main fungal genera (relative abundance ≥ 0.01 on average) in the colonic mucosa of HS and UC patients

^*P < 0.05.

Figure 6

Relative expression of pro-inflammatory cytokine (IL-1β (A), TNF-α (B), IFN-γ (C), IL-6 (D), IL-17A (E), and IL-23 (F)) levels in the colonic mucosa of HS and UC patients. ^*P < 0.05.

Figure 7. Correlation between intestinal fungal composition and intestinal inflammatory status

Red box indicate positive correlation, green box indicate negative correlation. The darker color indicates stronger correlation. ^*P < 0.05, ^**P < 0.01.