Gut microbiome and mycobiome in inflammatory bowel disease patients with Clostridioides difficile infection

Si Yu; Xiaomeng Ge; Hui Xu; Bei Tan; Bowen Tian; Yujie Shi; Yimin Dai; Yue Li; Songnian Hu; Jiaming Qian

doi:10.3389/fcimb.2023.1129043

Gut microbiome and mycobiome in inflammatory bowel disease patients with Clostridioides difficile infection

Front Cell Infect Microbiol. 2023 Feb 6:13:1129043. doi: 10.3389/fcimb.2023.1129043. eCollection 2023.

Authors

Si Yu¹, Xiaomeng Ge², Hui Xu¹, Bei Tan¹, Bowen Tian¹, Yujie Shi¹, Yimin Dai¹, Yue Li¹, Songnian Hu^{3

4}, Jiaming Qian¹

Affiliations

¹ Department of Gastroenterology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China.
² Microbial Resource and Big Data Center, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.
³ State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.
⁴ University of Chinese Academy of Sciences, Beijing, China.

Abstract

Background: Clostridium difficile infection (CDI) is common in patients with inflammatory bowel disease (IBD) and has been reported as a risk factor for poor outcome. However, gut microbiome and mycobiome of IBD patients with CDI have been barely investigated. This study aimed to assess the gut microbiome and mycobiome in IBD patients with CDI.

Methods: We collected fecal samples from patients with active IBD and concomitant CDI (IBD-CDI group, n=25), patients with active IBD and no CDI (IBD-only group, n=51), and healthy subjects (HC, n=40). Patients' characteristics including demographic data, disease severity, and medication history were collected. Metagenomic sequencing, taxonomic and functional analysis were carried out in the samples.

Results: We found that the bacterial alpha diversity of the IBD-CDI group was decreased. The bacterial and fungal beta diversity variations between IBD patients and HC were significant, regardless of CDI status. But the IBD-CDI group did not significantly cluster separately from the IBD-only group. Several bacterial taxa, including Enterococcus faecium, Ruminococcus gnavus, and Clostridium innocuum were overrepresented in the IBD-CDI group. Furthermore, IBD patients with CDI were distinguished by several fungal taxa, including overrepresentation of Saccharomyces cerevisiae. We also identified functional differences in IBD patients with CDI include enrichment of peptidoglycan biosynthesis. The network analysis indicated specific interactions between microbial markers in IBD-CDI patients.

Conclusion: IBD patients with CDI had pronounced microbial dysbiosis. Gut micro-ecological changes in IBD patients with CDI might provide insight into the pathological process and potential strategies for diagnosis and treatment in this subset of patients.

Keywords: Clostridioides difficile infection; gut microbiome; inflammatory bowel disease; metagenomics; mycobiome.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Bacteria
Clostridioides difficile*
Clostridium Infections* / microbiology
Gastrointestinal Microbiome*
Humans
Inflammatory Bowel Diseases* / microbiology
Mycobiome*

Grants and funding

This work was supported by CAMS Innovation Fund for Medical Sciences (CIFMS) from Chinese Academy of Medical Sciences 2021-I2M-1-062; Beijing Municipal Natural Science Foundation (7212078); and National key clinical specialty construction project ZK108000.