Quyushengxin Formula Causes Differences in Bacterial and Phage Composition in Ulcerative Colitis Patients

Abstract

Background: Ulcerative colitis (UC) is a chronic inflammatory disease that affects the colon and the rectum. Recently, some studies have shown that microorganisms in the gut play important roles in many chronic diseases such as UC.

Methods: To study the candidate viruses and bacteria involved in UC and to investigate the therapeutic mechanism of Quyushengxin formula (QYSX) in UC patients, metagenomic sequencing was performed on the feces from healthy donors and UC patients before and after QYSX treatment.

Results: QYSX improved the symptoms of UC. In all participants, Caudovirales and Herpesvirales were the most dominant viruses. The abundance of Caudovirales in UC patients was significantly higher than that in the normal controls, while QYSX restored Caudovirales abundance. Furthermore, the abundance of crAssphage was enhanced in UC patients compared with the normal control, while the diversity was then decreased after QYSX treatment. However, there was no significant difference (P > 0.05). Additionally, other non-crAssphage bacteriophages including phiST, SP-10, and phi17:2 were higher in UC patients and QYSX decreased these viruses, while the trends of MED4-213, P-HM1, and P-HM2 were adverse. Interestingly, PhiDP23.1 was only found in UC patients before and after QYSX treatment. In addition, Bifidobacterium, Bacteroidetes, Prevotellaceae, Actinobacteria, and Corynebacteriales were the biomarkers in UC patients after QYSX treatment due to their high abundance. GO terms and KEGG analysis showed that the identified gut microbiome was involved in many biological processes and pathways.

Conclusions: QYSX could regulate disordered gut microbiome and phages, indicating that QYSX has great therapeutic potential for UC.

Figure 1

Effects of QYSX on fecal virome diversity. (a) Principal component analysis (PCA) of virome in healthy donors and ulcerative colitis (UC) patients before and after QYSX treatment. (b) Box plot analysis of the distance among all the samples. (c) Virome diversity analyzed by gene index. (d) Virome diversity analyzed by Shannon index analysis. (e) Virome diversity analyzed by Simpson index analysis. Normal: healthy donors; UC: UC patients; UC + QYSX: UC patients after QYSX treatment. QYSX alters virome composition in patients.

Figure 2

The effects of QYSX on fecal virome composition in UC patients. (a) Relative abundance of fecal virome at order level. (b) Venn diagram analysis of viral species in the three groups. (c) Relative abundance of virome at species level. (d) The diversity of crAssphage among the three groups. Note: a, healthy controls; b, UC patients before QYSX treatment; c, UC patients after QYSX treatment.

Figure 3

Different fecal virome enrichment in the three groups. (a) Linear discriminant analysis effect size (LEfSe) to identify virus that is differentially represented among healthy donors and UC patients before and after treatment. Note: a, healthy controls; b, UC patients before QYSX treatment; c, UC patients after QYSX treatment. (b) STAMP difference analysis used to compare the abundance of species between before and after treatment in UC patients. Note: b, UC patients before QYSX treatment; c, UC patients after QYSX treatment.

Figure 4

Effect of QYSX on bacterial composition. (a) Venn diagram analysis of the common and unique bacteria at phylum level. (b) Relative abundance of fecal bacteria at phylum level. Note: a, the healthy donors; b, UC patients; c, UC patients after QYSX treatment.

Figure 5

Linear discriminant analysis effect size (LEfSe) to identify differentially enriched bacteria. (a) The bar chart shows differentially enriched bacteria. (b) The circles radiating from the inside out represent the classification levels from the phylum to the genus (or species). Each of small circles at different classification levels represents a classification at that level, and the diameter of the small circle is proportional to the relative abundance. The species with no significant difference were uniformly colored yellow, and the biomarker of the different species followed the group for coloring. Red nodes represent the microbial groups that played an important role in the red group, while green nodes represent the microbial groups that played an important role in the green group, and the color meaning of other circles was similar. Note: blue (a), healthy donors; green (b), UC patients before QYSX treatment; red (c), UC patients after QYSX treatment.

Figure 6

Clustering analysis of Gene Ontology (GO) terms (a) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways (b) enriched in fecal microorganism. The red represents high abundance, and blue represents low abundance. Note: a, the healthy donors; b, UC patients; c, UC patients after QYSX treatment.