Identification of gut microbiome and transcriptome changes in ulcerative colitis and pouchitis

Abstract

Background

Pouchitis is the common postoperative complication of ulcerative colitis (UC) and is also considered as inflammatory bowel disease. The aim was to investigate the microbiological and transcriptional differences between the two illnesses.

Methods

Eighty-five participants were enrolled (37 UC, 15 healthy UC pouches, 15 pouchitis and 18 healthy volunteers) and stool samples were collected. Microbial populations were analyzed by pyrosequencing of 16S ribosomal DNA. Furthermore, transcriptome data of 119 UC and 28 pouch patients were obtained from two data sets for bioinformatics analysis.

Results

The results of gut microbiota community analysis showed that with aggravation of UC, intestinal microorganisms were characterized by a gradual decreased in diversity and numbers of butyrate-producing bacteria and Bacteroides. Besides, in addition to the decrease of probiotics, the proliferation of Escherichia–Shigella and Ruminococcus gnavus was observed in pouchitis which is related to multiple infection pathways. The function enrichment of differential expression genes and hub genes, as well as the immunological condition was shown to be distinct using transcriptome bioinformatics analysis between UC and pouchitis. A stronger immune response occurs in UC and may be associated with high expression of tumor necrosis factor and interleukin, while multiple hub genes such as CDK1 in pouchitis are associated with cell cycle regulation.

Conclusions

The characteristics of gut microbiota disturbance and transcriptome alteration in UC and pouchitis are different. Our findings suggested that pouchitis may have a unique pathogenesis which was separated from UC.

Keywords:

• Pouchitis
• ulcerative colitis
• gut microbiota
• bioinformatics analysis
• hub genes

Acknowledgements

We thank Liwen Bianji, Edanz Editing China (www.liwenbianji.cn/ac), for editing the English text of a draft of this manuscript.

Consent for publication

Not applicable.

Ethics approval and consent to participate

Our study was approved by the Ethics Committee of Tianjin Medical University General Hospital. All participants provided a written informed consent upon enrolment. The methods were carried out in accordance with the relevant guidelines.

Authors contributions

Li-Sheng Yang and Di Huang recruited patients for this study. Xin Gao and An-Qi He performed the bioinformatics analysis. Xin Gao and Li-Sheng Yang drafted the manuscript and all authors reviewed it. Xin Gao and Kai-Yu Li approved final version. Xin Gao and Tong Liu performed the statistical analysis.

Disclosure statement

The authors of this manuscript report no conflict of interest.

Data availability statement

The data and code that support the findings of this study are available from the corresponding author upon reasonable request.

Additional information

Funding

This study was supported by a grant from the Li Jie-shou Gut Barrier Foundation [Grant No. LJS_201008].