Integrative meta-omics in Galaxy and beyond.

Area of Science:

• Microbiology
• Bioinformatics
• Systems Biology

Background:

• Omics technologies enable large-scale microbial community analysis.
• Integrating metagenomics, metatranscriptomics, and metaproteomics (meta-omics) provides deeper insights into microbial interactions and nutrient utilization.
• Galaxy platform offers tools for complex biological data analysis.

Purpose of the Study:

• To present three integrative meta-omics workflows for enhanced analysis and integration of multi-omics data.
• To introduce ViMO (Visualizer for Meta-Omics), a web application for visualizing microbial community metabolism.
• To improve the reconstruction and analysis of microbial community structures and functions.

Main Methods:

• Development of three integrative meta-omics workflows within the Galaxy platform.
• Application of workflows to a cellulose-degrading microbial consortium from a biogas reactor.
• Utilizing metagenomics for reconstructing high-quality metagenome-assembled genomes (MAGs).
• Integration of metatranscriptomics and metaproteomics data mapped onto MAGs.
• Visualization of MAGs, active pathways, and functional information using the ViMO web application.

Main Results:

• Successful application of workflows to a complex microbial consortium, enabling the recovery of several MAGs.
• An optimized metagenomics workflow improved MAG quality through single- and co-assembly and post-binning dereplication.
• ViMO effectively visualized MAG taxonomy, quality, CAZymes, KEGG pathways, and expression levels (mRNA and protein).
• Analysis revealed key roles of uncultured microorganisms in biomass degradation.

Conclusions:

• The developed meta-omics workflows and ViMO represent a significant advancement in analyzing omics data, particularly within Galaxy.
• The optimized metagenomics workflow facilitates high-quality microbial community reconstruction.
• This integrated approach enhances the analysis of microbiome metabolism by combining multi-omics data.