AUTHOR=Lu Jiamin , Zhang Wen , He Yuzhou , Jiang Mei , Liu Zhankui , Zhang Jirong , Zheng Lanzhi , Zhou Bingzhi , Luo Jielian , He Chenming , Shan Yunan , Zhang Runze , Fan KaiLiang , Fang Bangjiang , Wan Chuanqi 

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

JOURNAL=Frontiers in Microbiology

VOLUME=Volume 16 - 2025

YEAR=2025

URL=https://www.frontiersin.org/journals/microbiology/articles/10.3389/fmicb.2025.1618177

DOI=10.3389/fmicb.2025.1618177

ISSN=1664-302X

ABSTRACT=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.