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bioRxiv · 10.1101/2025.03.14.643140

MICOMWeb: a website for microbial community metabolic modeling of the human gut

Fresno, C.·Oropeza-Valdez, J. J.·Alvarado-Luis, P. I.·Pena-Gonzalez, P.·Tovar, A. R.·Torres, N.·Diener, C.·Gibbons, S.·Resendis-Antonio, O.
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Abstract

SummaryMICOMWeb is a user-friendly website for easy microbial community metabolic modeling of the human gut. This website tackles three constraints when generating in silico metagenome-scale metabolic models: (i) the prior Python user knowledge for metabolic modeling using flux balance analysis with MICOM Python package, (ii) predefined and user-defined diets to generate ad hoc metabolic models, and (iii) the high- throughput computational infrastructure required to obtain the simulated growth and metabolic exchange fluxes, using real abundance from metagenomic shotgun or 16S amplicon sequencing; we present MICOMWebs features to easily run in silico experiments as a functional hypothesis generator for experimental validation on previously published data. Availability and ImplementationMICOMWeb is freely accessible for academic purposes at https://micomweb.c3.unam.mx.

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Fresno, C., Oropeza-Valdez, J. J., Alvarado-Luis, P. I., Pena-Gonzalez, P., Tovar, A. R., Torres, N., Diener, C., Gibbons, S., Resendis-Antonio, O.. 2025-03-17. MICOMWeb: a website for microbial community metabolic modeling of the human gut. https://doi.org/10.1101/2025.03.14.643140

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