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Consistency across multi-omics layers in a drug-perturbed gut microbial community.

Published version
Peer-reviewed

Repository DOI


Type

Article

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Authors

Wuyts, Sander 
Zimmermann-Kogadeeva, Maria  ORCID logo  https://orcid.org/0000-0001-6021-1246
Blasche, Sonja 

Abstract

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.

Description

Keywords

metabolomics, metagenomics, metaproteomics, metatranscriptomics, microbiology, Humans, Multiomics, RNA, Ribosomal, 16S, Microbiota, Metabolomics, Bacteria, Metagenomics

Journal Title

Mol Syst Biol

Conference Name

Journal ISSN

1744-4292
1744-4292

Volume Title

19

Publisher

Springer Science and Business Media LLC