肠道菌群
生物
失调
疾病
分类单元
相对物种丰度
丰度(生态学)
微生物群
计算生物学
生态学
免疫学
生物信息学
医学
病理
作者
Ran Wang,Xubin Zheng,Fangda Song,Man Hon Wong,Kwong Sak Leung,Lixin Cheng
出处
期刊:Bioinformatics
[Oxford University Press]
日期:2023-04-21
卷期号:39 (5)
被引量:1
标识
DOI:10.1093/bioinformatics/btad213
摘要
Abstract Motivation Human gut microbiota plays a vital role in maintaining body health. The dysbiosis of gut microbiota is associated with a variety of diseases. It is critical to uncover the associations between gut microbiota and disease states as well as other intrinsic or environmental factors. However, inferring alterations of individual microbial taxa based on relative abundance data likely leads to false associations and conflicting discoveries in different studies. Moreover, the effects of underlying factors and microbe–microbe interactions could lead to the alteration of larger sets of taxa. It might be more robust to investigate gut microbiota using groups of related taxa instead of the composition of individual taxa. Results We proposed a novel method to identify underlying microbial modules, i.e. groups of taxa with similar abundance patterns affected by a common latent factor, from longitudinal gut microbiota and applied it to inflammatory bowel disease (IBD). The identified modules demonstrated closer intragroup relationships, indicating potential microbe–microbe interactions and influences of underlying factors. Associations between the modules and several clinical factors were investigated, especially disease states. The IBD-associated modules performed better in stratifying the subjects compared with the relative abundance of individual taxa. The modules were further validated in external cohorts, demonstrating the efficacy of the proposed method in identifying general and robust microbial modules. The study reveals the benefit of considering the ecological effects in gut microbiota analysis and the great promise of linking clinical factors with underlying microbial modules. Availability and implementation https://github.com/rwang-z/microbial_module.git.
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