Short description 

Many microbiome researchers seek to investigate the functional potential of microbial ecosystems with a holistic, multi-omics approach. Currently, interoperability between genomic, transcriptomic, and proteomic data for instance is a bottleneck. The workflow of this analysis that is being established by MULTI tackles such issues to facilitate future work for members of the community.

The first application and basis for the establishment of the workflow is the investigation of antimicrobial resistance in different Listeria monocytogenes strains by applying multi-omics data analysis. Three different L. monocytogenes strains were cultured on sub-lethal concentrations of biocides, their genomes sequenced, and transcriptomics and proteomics data collected. These data will provide insights into the functional responses of the bacteria to the biocide by analyzing pathways that differ in their gene expression or protein translation. Genome-scale metabolic reconstructions can be integrated with both transcriptomics and proteomics data, resulting in multi-omics data integration, which can provide insights into the different functional responses of microbial cells to an antimicrobial substance.

Graphical abstract

Graphical abstract “Use Case MULTI” by Stefania Magnusdottir and Ulisses Nunes da Rocha with visual adaptation by Katharina M.E. Grünwald and Maja Magel is licensed under a Creative Commons Attribution 4.0 International License (CC BY 4.0).

How you can contribute 

You are a … 

• microbiologist with short and long read genomic sequences of bacterial isolates:
  Use the workflow to assemble circular genomes of your isolates, annotate genes and proteins, and create genome-scale metabolic reconstructions.
• microbiologist with isolate genome sequences and transcriptomics and/or proteomics data:
  Use the workflow to analyze differential gene expression (transcriptomics), protein translation (proteomics), and integrate these data sets with the genomes using genome-scale metabolic reconstructions.
• microbiologist with experience in transcriptomics or proteomics analyses:
  Check out the preliminary guidelines on data processing, analysis, and integration of genomics, transcriptomics, and proteomics data.
  Give suggestions and feedback on the workflow and useful additional features that could be implemented.

Output 

Below, you will find the output provided by the Use Case. If you are interested in the development stages of the project, these are indicated by the following tenses and suffixes.
The output for the research community is already established (-ed for past tense), is currently being (-ing for present progressive) in progress, or will be soon set-up (present tense) for future endeavors.

Modular analysis pipeline output

• Creating a modular pipeline on multi-omics analyses on closely-related bacterial strains or species by November 2023

• Selected state-of-the-art tools and scripts for genome circularization and annotation, differential expression RNA seq analysis (transcriptomics), automatic genome-scale metabolic reconstruction, and context-specific metabolic models from transcriptomics data
  
  

• Create a modular pipeline on multi-omics analyses on non-closely-related bacterial strains or species by June 2024 based on the previous pipeline
  
  

• Create a modular pipeline on multi-omics analyses of microbial communities by November 2025

• Selected state-of-the-art tools and scripts for MAG assembly from metagenomic data, taxonomic lineage assignment, MAG quality control
  
  

• Selected a state-of-the-art tool for hybrid genome assembly using short and long genomic sequences.
• Select a state-of-the-art tool for proteomics analysis.

Infrastructure output

• Create a workflow that can facilitate the integration and analysis of multi-omics data by ensuring that the inputs and outputs of each tool are compatible with each other.
• Create written and video tutorials to train researchers to use the workflow and the individual tools therein for summer 2023, 2024 and 2025