Gut Microbiota and Metabolite Changes in Patients With Ulcerative Colitis and Clostridioides difficile Infection

Abstract

Background: Patients with ulcerative colitis (UC) are at an increased risk of developing Clostridioides difficile infection (CDI), which in turn leads to poor outcomes. The gut microbial structure and metabolites in patients with UC and CDI have been scarcely studied. We hypothesized that CDI changes the gut microbiota and metabolites of patients with UC.

Materials and methods: This study included 89 patients: 30 healthy controls (HC group), 29 with UC alone (UCN group), and 30 with UC and CDI (UCP group). None of the participants has been exposed to antibiotic treatments during the 3 months before stool collection. Stool samples were analyzed using 16S rRNA gene sequencing of the V3-V4 region and gas chromatography tandem time-of-flight mass spectrometry.

Results: The UCN group displayed lower diversity and richness in gut microbiota and a higher relative abundance of the phylum Proteobacteria than the HC group. There were no significant differences between the UCN and UCP groups in the α-diversity indices. The UCP group contained a higher relative abundance of the genera Clostridium sensu stricto, Clostridium XI, Aggregatibacter, and Haemophilus, and a lower relative abundance of genera Clostridium XIVb and Citrobacter than the UCN group. In the UCP group, the increased metabolites included putrescine, maltose, 4-hydroxybenzoic acid, 4-hydroxybutyrate, and aminomalonic acid. Spearman's correlation analysis revealed that these increased metabolites negatively correlated with Clostridium XlVb and positively correlated with the four enriched genera. However, the correlations between hemoglobin and metabolites were contrary to the correlations between erythrocyte sedimentation rate and high-sensitivity C-reactive protein and metabolites.

Conclusion: Our study identified 11 differential genera and 16 perturbed metabolites in patients with UC and CDI compared to those with UC alone. These findings may guide the design of research on potential mechanisms and specific treatments for CDI in patients with UC.

Keywords: 16S rRNA; Clostridioides difficile infection; gut microbiota; metabolites; ulcerative colitis.

FIGURE 1

Comparison of gut microbial structure among the HC, UCN, and UCP groups. (A) The Venn diagram shows the overlapping OTUs from the gut microbiomes of the three groups. (B–E) Alpha-diversity indices (the box plots of observed OTUs, Chao1, and the Shannon and the Simpson indices) among the three groups. *P < 0.05, ^**P < 0.01. (F) Beta-diversity index (plots of NMDS) among the three groups. HC, healthy control group; OTUs, operational taxonomic units; UCN, ulcerative colitis with negative Clostridioides difficile test results; UCP, ulcerative colitis with positive Clostridioides difficile infection.

FIGURE 2

(A) The structure of the gut microbiota at the phylum level among the three groups. (B) The significantly different taxa at the phylum level among the three groups. *P < 0.05, ^**P < 0.01, ^***P < 0.001. (C) The significantly different taxa at the genus level between the HC and UCN groups. (D) The significantly different taxa at the genus level between the UCN and UCP groups. HC, healthy control group; UCN, ulcerative colitis without negative Clostridioides difficile test results; UCP, ulcerative colitis with positive Clostridioides difficile infection.

FIGURE 3

Differential relative abundance of bacterial taxa among the three groups. (A) A cladogram made by LEfSe demonstrates different bacterial taxa between the HC and UCN groups. (B) LDA score of enriched bacterial taxa between the HC and UCN groups. Only taxa meeting an LDA > 3 are shown. (C) A cladogram made by LEfSe demonstrates different bacterial taxa between the UCN and UCP groups. (D) LDA score of enriched bacterial taxa between the UCN and UCP groups. Only taxa meeting an LDA > 3 are shown. HC, healthy control group; UCN, ulcerative colitis with negative Clostridioides difficile test results; UCP, ulcerative colitis with positive Clostridioides difficile infection.

FIGURE 4

(A) PCA score plot of metabolite profile among the three groups. (B) OPLS-DA score plots of samples from the HC and UCN groups. (C) OPLS-DA score plots of samples from the UCN and UCP groups. (D) Volcano plots of differential metabolites between the UCN and HC groups, where red dots represent increased metabolites and blue dots represent decreased metabolites. (E) Volcano plots of differential metabolites between the UCP and UCN groups, where red dots represent increased metabolites and blue dots represent decreased metabolites. HC, healthy control group; UCN, ulcerative colitis with negative Clostridioides difficile test results; UCP, ulcerative colitis with positive Clostridioides difficile infection.

FIGURE 5

Correlation analysis of differential gut microbiota genera (relative abundance > 0.2%) and differential metabolites between the HC and UCN groups (A), and between the UCN and UCP groups (B). (C) Correlation analysis of differential metabolites and laboratory tests between the UCN and UCP groups. *p < 0.05; **p < 0.01; HC, healthy control group; UCN, ulcerative colitis with negative Clostridioides difficile test results; UCP, ulcerative colitis with positive Clostridioides difficile infection.