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MicroMap: a network visualisation resource for human microbiome metabolism.

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

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

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Summary
This summary is machine-generated.

We developed MicroMap, a novel network visualization tool, to explore the metabolism of over a quarter million microbial genome-scale metabolic reconstructions. This resource aids in understanding the microbiome

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Area of Science:

  • Microbiome research
  • Metabolic network analysis
  • Computational biology

Background:

  • The human microbiome significantly impacts host metabolism and health.
  • Constraint-based reconstruction and analysis (COBRA) is vital for microbiome research.
  • A lack of large-scale visualization tools hinders microbiome metabolism exploration.

Purpose of the Study:

  • To create a comprehensive network visualization for microbiome metabolism.
  • To enable intuitive exploration and comparison of microbial metabolic capabilities.
  • To support the computational modeling community and education.

Main Methods:

  • Developed MicroMap, a manually curated network visualization.
  • Integrated over a quarter million microbial genome-scale metabolic reconstructions.
  • Included 5064 reactions, 3499 metabolites, and 98 drugs.

Main Results:

  • MicroMap visualizes the metabolism of 257,429 microbial reconstructions.
  • Facilitates intuitive exploration of microbiome metabolic capabilities.
  • Provides comparative analysis of metabolic functions across microbes.

Conclusions:

  • MicroMap offers a scalable solution for microbiome metabolism visualization.
  • Enhances understanding of the nutrition-host-microbiome-disease axis.
  • Serves as an educational resource and integrates with existing tools like VMH and COBRA Toolbox.