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Background <p>Inflammatory bowel disease (IBD), including Crohn’s disease (CD) and ulcerative colitis (UC), is characterized by chronic, relapsing inflammation of the gastrointestinal tract. Recent studies emphasize the importance of gut microbiome dysbiosis in IBD pathogenesis, where interactions among bacteria, fungi, protozoa, and viruses contribute to inflammation, immune modulation, and epithelial barrier disruption.</p> Methods <p>A comprehensive narrative literature review was conducted, focusing on human data and preclinical studies. Biomedical databases were searched for research related to microbial communities and their role in IBD development, specifically targeting microbial metabolites, gut fungi, protozoa, and viruses. Relevant studies were analyzed to assess their impact on immune pathways and microbial interactions.</p> Results <p>The review reveals how different microbial kingdoms collaborate through bacteria–fungi, bacteria–protozoa, and phage–bacteria interactions, influencing metabolite production and immune system function. Specific microbial metabolites like short-chain fatty acids (SCFAs), indoles, bile acids, and others play significant roles in regulating mucosal immunity and barrier function. Disruptions in these interactions lead to chronic inflammation and contribute to disease progression. Multi-kingdom therapies, including probiotics, yeast-based treatments, and fecal microbiota transplantation (FMT), show promise but face challenges due to clinical variability.</p> Conclusion <p>Understanding IBD as a disruption of microbial ecosystems enables the development of personalized treatment strategies. Multi-omics studies and microbiome-based interventions targeting specific microbial interactions hold potential for more effective, individualized therapies in IBD management. However, further research and larger clinical trials are necessary for translating these findings into routine clinical practice.</p> Graphical Abstract <p></p>

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Cross-kingdom microbial interactions in the gut during inflammatory bowel disease

  • 期刊论文

  • 出版模式：

    开放获取

  • 发表日期：

    2026年2月26日

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  • Liwei Li,
  • Fuqing Cai,
  • Zheng Liu,
  • Weijiu Mo,
  • Jinxiu Zhang,
  • Jiamin Qin,
  • Chenghai Liang,
  • Hengyuan Xu,
  • Shikai Liu,
  • Sufan Tang,
  • Peng Peng,
  • Jingrong Liang,
  • Huaqiang Ruan,
  • Rongbin Qin,
  • Feilong Luo,
  • Guang Xiong,
  • Chongze Yang,
  • Jun Zou,
  • Shiquan Liu,
  • Yan Geng,
  • Jiean Huang

摘要

Background

Inflammatory bowel disease (IBD), including Crohn’s disease (CD) and ulcerative colitis (UC), is characterized by chronic, relapsing inflammation of the gastrointestinal tract. Recent studies emphasize the importance of gut microbiome dysbiosis in IBD pathogenesis, where interactions among bacteria, fungi, protozoa, and viruses contribute to inflammation, immune modulation, and epithelial barrier disruption.

Methods

A comprehensive narrative literature review was conducted, focusing on human data and preclinical studies. Biomedical databases were searched for research related to microbial communities and their role in IBD development, specifically targeting microbial metabolites, gut fungi, protozoa, and viruses. Relevant studies were analyzed to assess their impact on immune pathways and microbial interactions.

Results

The review reveals how different microbial kingdoms collaborate through bacteria–fungi, bacteria–protozoa, and phage–bacteria interactions, influencing metabolite production and immune system function. Specific microbial metabolites like short-chain fatty acids (SCFAs), indoles, bile acids, and others play significant roles in regulating mucosal immunity and barrier function. Disruptions in these interactions lead to chronic inflammation and contribute to disease progression. Multi-kingdom therapies, including probiotics, yeast-based treatments, and fecal microbiota transplantation (FMT), show promise but face challenges due to clinical variability.

Conclusion

Understanding IBD as a disruption of microbial ecosystems enables the development of personalized treatment strategies. Multi-omics studies and microbiome-based interventions targeting specific microbial interactions hold potential for more effective, individualized therapies in IBD management. However, further research and larger clinical trials are necessary for translating these findings into routine clinical practice.

Graphical Abstract