TY - JOUR
T1 - MicroMap: a network visualisation resource for human microbiome metabolism
AU - Thinnes, C.C.
AU - Waschkowitz, R.
AU - Courtney, E.
AU - Culligan, E.
AU - Fahy, K.
AU - Ferrazza, R.A.M.
AU - Ferris, C.
AU - Lagali, A.
AU - Lane, R.
AU - Maye, C.
AU - Murphy, O.
AU - Noone, D.
AU - Ryan, S.
AU - Bet, M.
AU - Corr, M.C.
AU - Cummins, H.
AU - Hackett, D.
AU - Healy, E.
AU - Kulczycka, N.
AU - Lang, N.
AU - Madden, L.
AU - McHugh, L.
AU - Pyne, I.
AU - Varley, C.
AU - Harkin, N.
AU - Meade, R.
AU - O’Donnell, G.
AU - Nap, B.
AU - Martinelli, F.
AU - Heinken, A.
AU - Thiele, I.
N1 - © The Author(s) 2025. This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the
article’s Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/
PY - 2025
Y1 - 2025
N2 - 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.
AB - 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.
KW - r human microbiome metabolism
U2 - 10.1038/s41522-025-00853-0
DO - 10.1038/s41522-025-00853-0
M3 - Article
SN - 2055-5008
VL - 11
SP - 1
EP - 6
JO - npj Biofilms and Microbiomes
JF - npj Biofilms and Microbiomes
IS - 1
M1 - 222
ER -