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REVIEW article

Front. Microbiol.

Sec. Infectious Agents and Disease

Volume 16 - 2025 | doi: 10.3389/fmicb.2025.1618177

This article is part of the Research TopicMulti-Omics Approaches in Disease Microbiology: From Biomarkers to Therapeutic InterventionsView all 6 articles

Multi-omics decodes host-specific and environmental microbiome interactions in sepsis

Provisionally accepted
Jiamin LuJiamin Lu1,2Wen ZhangWen Zhang1,2Yuzhou HeYuzhou He3Mei JiangMei Jiang4Zhankui LiuZhankui Liu1,2Jirong ZhangJirong Zhang1,2Lanzhi ZhengLanzhi Zheng5Bingzhi ZhouBingzhi Zhou3Jielian LuoJielian Luo1,2Chenming HeChenming He1,2Yunan ShanYunan Shan6Runze ZhangRunze Zhang1,2KaiLiang FanKaiLiang Fan7*Bangjiang FangBangjiang Fang1,2*Chuanqi WanChuanqi Wan1,2*
  • 1Longhua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China
  • 2Institute of acute and critical care, Shanghai University of Traditional Chinese Medicine, Xuhui, Shanghai, China, Shanghai, China
  • 3The Second Affiliated Hospital of Zhejiang Chinese Medical University, Hangzhou, Zhejiang, China;, Hangzhou, China
  • 4Tianjin University of Traditional Chinese Medicine, Tianjin, China
  • 5First Affiliated Hospital, Zhejiang Chinese Medical University, Hangzhou, Zhejiang Province, China
  • 6School of Traditional Chinese Medicine, Hubei University of Chinese Medicine, Wuhan, Hubei, China, Shangdong, China
  • 7The Affiliated Hospital of Shandong University of Traditional Chinese Medicine, Jinan, Shandong, China., Shandong, China

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Sepsis is a life-threatening organ dysfunction caused by a dysregulated host response to infection, and its pathogenesis involves complex interactions between the host and the microbiome. The integration of multi-omics has important value in revealing the mechanism of host-microbiome interaction. It is a key tool for promoting accurate diagnosis and guiding dynamic treatment strategies in sepsis. However, multi-omics data integration faces technical challenges, such as data heterogeneity and platform variability, as well as analytical hurdles, such as the "curse of dimensionality." Fortunately, researchers have developed two integration strategies: data-driven and knowledge-guided approaches, which employ various dimensionality reduction techniques and integration methods to handle multi-omics datasets.This review discusses the applications of multi-omics technologies in host-microbiome interactions in sepsis, highlighting their potential in identifying novel diagnostic biomarkers and developing personalized and dynamic treatment strategies. It also summarizes commonly used systems biology resources and computational tools for data integration; the review outlines the challenges in this field and proposes potential directions for future studies.

Keywords: Bioinformatics tools, comparative genome analysis, microbiome, multi-omics, Sepsis

Received: 25 Apr 2025; Accepted: 10 Jun 2025.

Copyright: © 2025 Lu, Zhang, He, Jiang, Liu, Zhang, Zheng, Zhou, Luo, He, Shan, Zhang, Fan, Fang and Wan. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

* Correspondence:
KaiLiang Fan, The Affiliated Hospital of Shandong University of Traditional Chinese Medicine, Jinan, Shandong, China., Shandong, China
Bangjiang Fang, Institute of acute and critical care, Shanghai University of Traditional Chinese Medicine, Xuhui, Shanghai, China, Shanghai, China
Chuanqi Wan, Longhua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China

Disclaimer: All claims expressed in this article are solely those of the authors and do not necessarily represent those of their affiliated organizations, or those of the publisher, the editors and the reviewers. Any product that may be evaluated in this article or claim that may be made by its manufacturer is not guaranteed or endorsed by the publisher.

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