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The MicroMap is a network visualisation resource for microbiome metabolism.

Cyrille C Thinnes1,2,3,4, Renee Waschkowitz1,2,3,4, Eoghan Courtney5

  • 1Digital Metabolic Twin Centre, University of Galway, Ireland.

Biorxiv : the Preprint Server for Biology
|February 24, 2025
PubMed
Summary
This summary is machine-generated.

We developed MicroMap, a visualization tool for microbiome metabolism. It helps researchers explore microbial metabolic capabilities and understand their role in health and disease.

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Area of Science:

  • Computational systems biology
  • Microbiome research
  • Metabolic network analysis

Background:

  • The human microbiome is vital for metabolism, influencing health and disease.
  • Constraint-based reconstruction and analysis (COBRA) is used for microbiome research, but lacks large-scale visualization resources.
  • Existing tools do not comprehensively capture microbiome metabolic networks.

Purpose of the Study:

  • To create a manually curated visualization resource for microbiome metabolism.
  • To address the gap in large-scale visualization tools for microbiome metabolic networks.
  • To make microbiome metabolism accessible to a broader audience.

Main Methods:

  • Developed MicroMap, a manually curated microbiome metabolic network visualization.
  • Integrated over a quarter million microbial genome-scale metabolic reconstructions.
  • Captured 5,064 unique reactions and 3,499 unique metabolites, including 98 drugs.
  • Generated 257,429 visualizations for comparative analysis of microbial metabolic capabilities.

Main Results:

  • MicroMap provides intuitive exploration of microbiome metabolism.
  • Users can inspect microbial metabolic capabilities and visualize computational modeling results.
  • Facilitates comparison of metabolic capabilities across different microbes.
  • MicroMap integrates with the Virtual Metabolic Human (VMH) and COBRA Toolbox.

Conclusions:

  • MicroMap is a valuable resource for understanding microbiome metabolism.
  • It enhances accessibility of microbiome metabolism for researchers and educators.
  • Facilitates hypothesis generation in the nutrition-host-microbiome-disease axis.
  • The resource is freely accessible and supports comparative analysis.