Combined Signature of the Fecal Microbiome and Plasma Metabolome in Patients with Ulcerative Colitis

Abstract

BACKGROUND Ulcerative colitis is a chronic, idiopathic inflammatory disease that destroys the colon structure. Nevertheless, the exact pathogenesis is not clear and needs to be fully elucidated. MATERIAL AND METHODS Stool and plasma samples were used for 16S ribosomal RNA sequencing and liquid chromatography mass spectrometry, respectively. In addition, we detected the level of trimethylamine N-oxide. Finally, we performed Pearson correlation analysis between the microbiome and the metabolome. RESULTS Twenty-three active ulcerative colitis, 25 inactive ulcerative colitis, and 30 control cases were included. Thirty-four significantly different metabolites were found between the active ulcerative colitis and control groups, 38 were found between the inactive ulcerative colitis and control groups, and only 1 was found between the active ulcerative colitis and inactive ulcerative colitis groups. The plasma trimethylamine N-oxide level of the inactive ulcerative colitis and active ulcerative colitis groups was significantly higher than that of the control group. Moreover, we identified significant changes in 24, 18, and 12 bacterial genera for active ulcerative colitis-control, inactive ulcerative colitis-control, and active ulcerative colitis-inactive ulcerative colitis, respectively. Cross-correlation indicated an association between sphingosine 1-phosphate and Roseburia, Klebsiella, and Escherichia-Shigella. Through the pathway analysis, we found sphingolipid metabolism was one of the most significantly increased pathways. CONCLUSIONS Although levels of trimethylamine N-oxide were higher in ulcerative colitis patients, they did not achieve statistical significance in active ulcerative colitis and inactive ulcerative colitis groups. Sphingosine 1-phosphate was increased in ulcerative colitis patients and there were several microbiota associated with it. Although further study is still needed, sphingosine 1-phosphate will probably become a new target for treatment of ulcerative colitis.

Figure 1

aUC, iUC, and Control patients harbor distinct microbial populations. (A) The number of OTUs present in aUC patients only (green), iUC patients only (red), Control patients only (blue), or shared among the 3 groups in a scaled Venn diagram. (B) Relative abundance at the phylum level. (C) Relative abundance at the genus level. Different phyla and genera are color-coded. aUC – active ulcerative colitis; iUC – inactive ulcerative colitis.

Figure 2

(A) Relative abundance at the class level. (B) Relative abundance at the order level. (C) Relative abundance at the family level. (D) Relative abundance at the species level. Different class, order, family, and species are color-coded. aUC – active ulcerative colitis; iUC – inactive ulcerative colitis.

Figure 3

(A) Alpha diversity was shown analyzed by the Chao1 index. Minimum values (the lowest of the line), median values (thick horizontal line), 25^th and 75^th percentile values (box outline), and maximum values (the highest of the line). (B) PLS-DA and (C) OPLS-DA scores plots based on the metabolite profiling data obtained from Control, iUC and aUC patients, the green, red and blue circles indicate Control, iUC and aUC patients respectively. (D) TMAO levels of the Control, iUC and aUC patients. * Indicates p<0.05.

Figure 4

Inter-omic Pearson’s correlation between significant different metabolites and bacterial genera for UC and Control patients. The correlation was considered statistically significant with p<0.05+|r| coefficient >0.22.

Figure 5

Inter-omic Pearson’s correlation between significant different metabolites and all bacterial genera for UC and Control patients. * Indicates levels of significance with p<0.05.

Figure 6

Summary of pathway analysis with MetPA in aUC-Control patients (A). a – Sphingolipid metabolism; b – Phenylalanine metabolism; c – Arginine and proline metabolism; d – Tyrosine metabolism. Another summary of pathway analysis with MetPA in iUC-Control patients (B). a – Phenylalanine metabolism; b – Tyrosine metabolism; c – Sphingolipid metabolism.