药物干扰肠道微生物群落中多组学层的一致性。

IF 8.5 1区 生物学 Q1 BIOCHEMISTRY & MOLECULAR BIOLOGY Molecular Systems Biology Pub Date : 2023-09-12 Epub Date: 2023-07-24 DOI:10.15252/msb.202311525
Sander Wuyts, Renato Alves, Maria Zimmermann-Kogadeeva, Suguru Nishijima, Sonja Blasche, Marja Driessen, Philipp E Geyer, Rajna Hercog, Ece Kartal, Lisa Maier, Johannes B Müller, Sarela Garcia Santamarina, Thomas Sebastian B Schmidt, Daniel C Sevin, Anja Telzerow, Peter V Treit, Tobias Wenzel, Athanasios Typas, Kiran R Patil, Matthias Mann, Michael Kuhn, Peer Bork
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引用次数: 1

摘要

多组学分析用于微生物组研究,以了解暴露在不同条件下的微生物群落的分子变化。然而,并不总是清楚每种组学数据类型对我们的理解有多大贡献,以及它们是否相互一致。在这里,我们通过使用五个组学层(16S rRNA基因图谱、宏基因组学、宏转录组学、元蛋白质组学和代谢组学)绘制了由32种人类肠道细菌组成的合成群落对三种非抗生素药物的分子反应图。我们发现,所有具有物种分辨率的组学方法在估计相对物种丰度方面都是高度一致的。此外,不同的组学方法在捕捉功能变化方面是相辅相成的。例如,尽管几乎所有的组学数据类型都表明抗精神病药物氯丙嗪选择性地抑制了群落中的拟杆菌属代表,但元转录组和元蛋白质组表明,该药物诱导了与蛋白质质量控制相关的应激反应。代谢组学显示低聚糖摄取减少,可能是由拟杆菌门耗竭引起的。我们的研究强调了如何利用多组学数据集来揭示微生物群落对外部扰动的复杂分子反应。
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Consistency across multi-omics layers in a drug-perturbed gut microbial community.

Multi-omics analyses are used in microbiome studies to understand molecular changes in microbial communities exposed to different conditions. However, it is not always clear how much each omics data type contributes to our understanding and whether they are concordant with each other. Here, we map the molecular response of a synthetic community of 32 human gut bacteria to three non-antibiotic drugs by using five omics layers (16S rRNA gene profiling, metagenomics, metatranscriptomics, metaproteomics and metabolomics). We find that all the omics methods with species resolution are highly consistent in estimating relative species abundances. Furthermore, different omics methods complement each other for capturing functional changes. For example, while nearly all the omics data types captured that the antipsychotic drug chlorpromazine selectively inhibits Bacteroidota representatives in the community, the metatranscriptome and metaproteome suggested that the drug induces stress responses related to protein quality control. Metabolomics revealed a decrease in oligosaccharide uptake, likely caused by Bacteroidota depletion. Our study highlights how multi-omics datasets can be utilized to reveal complex molecular responses to external perturbations in microbial communities.

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来源期刊
Molecular Systems Biology
Molecular Systems Biology 生物-生化与分子生物学
CiteScore
18.50
自引率
1.00%
发文量
62
审稿时长
6-12 weeks
期刊介绍: Systems biology is a field that aims to understand complex biological systems by studying their components and how they interact. It is an integrative discipline that seeks to explain the properties and behavior of these systems. Molecular Systems Biology is a scholarly journal that publishes top-notch research in the areas of systems biology, synthetic biology, and systems medicine. It is an open access journal, meaning that its content is freely available to readers, and it is peer-reviewed to ensure the quality of the published work.
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