MicroMap: a network visualisation resource for human microbiome metabolism
The human microbiome critically influences metabolism and thereby our health. Constraint-based reconstruction and analysis (COBRA) is a proven framework for generating mechanism-derived hypotheses along the nutrition-host-microbiome-disease axis. However, no large-scale microbiome metabolism visualisation has been available. Therefore, we created the MicroMap, a manually curated network visualisation, which captures the metabolism of over a quarter million microbial genome-scale metabolic reconstructions. The MicroMap contains 5064 unique reactions and 3499 unique metabolites, including for 98 drugs. Users can intuitively explore microbiome metabolism, inspect metabolic capabilities, and visualise computational modelling results. Further, the MicroMap may serve as an educational tool to help diversify the computational modelling community. We generated 257,429 visualisations, covering all our current microbiome reconstructions, to visually compare metabolic capabilities between microbes. The MicroMap integrates with the Virtual Metabolic Human (VMH, www.vmh.life ), the COBRA Toolbox (https://opencobra.github.io ), and is freely accessible at the MicroMap dataverse ( https://dataverse.harvard.edu/dataverse/micromap ), along with all the generated reconstruction visualisations.
Authors
- C.D. Varley
- Rebecca Lane (ORCID: https://orcid.org/0000-0002-5233-5422)
- Grace O’Donnell
- C. Ferris (ORCID: https://orcid.org/0000-0003-4354-0093)
- Louise McHugh
- Eugene Healy (ORCID: https://orcid.org/0000-0001-5591-6970)
- Bram Nap (ORCID: https://orcid.org/0000-0003-2910-9109)
- David Noone
- Cyrille C. Thinnes (ORCID: https://orcid.org/0000-0002-8619-9537)
- NP Lang
- Roger Meade (ORCID: https://orcid.org/0000-0002-1223-2031)
- Maripat Corr
- Almut Heinken (ORCID: https://orcid.org/0000-0001-6938-8072)
- Ines Thiele (ORCID: https://orcid.org/0000-0002-8071-7110)
- L. V. Madden (ORCID: https://orcid.org/0000-0002-4743-3060)
- Filippo Martinelli (ORCID: https://orcid.org/0000-0002-6635-6793)
- H.T. Cummins
- David P. Hackett
- Scott Ryan
- Colm Maye
- Olivia Murphy
- Mihaela Bet
- Nina Kulczycka
- Renee Waschkowitz
- Ivana Pyne
- Niamh Harkin
- Eoghan Courtney
- Eoghan Culligan
- Katie Fahy
- Ruby A. M. Ferrazza
- Angeline Lagali
Institutions
- University College Dublin (IE)
- Inserm (FR)
- Ollscoil na Gaillimhe – University of Galway (IE)
- Trinity College Dublin (IE)
- University College Cork (IE)
- APC Microbiome Institute (IE)
- COPE Galway (IE)
- Nutrition-Génétique et Exposition aux Risques Environnementaux (FR)
- Université de Lorraine (FR)
Publication Details
- Journal
- npj Biofilms and Microbiomes
- Published
- 2025-11-28
- DOI
- https://doi.org/10.1038/s41522-025-00853-0
- Citations
- 1
- Primary Topic
- Microbial Metabolic Engineering and Bioproduction
- Type
- article
- Field-Weighted Citation Impact
- 0.81
Funders
- European Commission
- Science Foundation Ireland
- H2020 Marie Skłodowska-Curie Actions