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MICOM is a Python package for metabolic modeling of microbial communities developed in the Gibbons Lab at the Institute for Systems Biology and the Human Systems Biology Group of Prof. Osbaldo Resendis Antonio at the National Institute of Genomic Medicine Mexico.

MICOM allows you to construct a community model from a list on input COBRA models and manages exchange fluxes between individuals and individuals with the environment. It explicitly accounts for different abundances of individuals in the community and can thus incorporate data from 16S amplicon sequencing or metagenomic experiments. It allows optimization with a variety of algorithms modeling the trade-off between egoistic growth rate maximization and cooperative objectives.


MICOM is published at https://msystems.asm.org/content/5/1/e00606-19. Please cite this article when referencing MICOM.

To get an idea which assumptions and strategies MICOM uses we recommend to start with some background on the methods. The easiest way to use MICOM is using the workflow API.


Getting help#

General questions on usage can be asked in Github Discussions


We are also available on the cobrapy Gitter channel


Questions specific to the MICOM Qiime2 plugin (q2-micom) can also be asked on the Qiime2 forum


Indices and tables#