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M2R: a Python add-on to cobrapy for modifying human genome-scale metabolic reconstruction using the gut microbiota
Ewelina Weglarz-Tomczak1, Jakub M Tomczak2, Stanley Brul1
1Swammerdam Institute for Life Sciences, Faculty of Science, University of Amsterdam, Amsterdam, The Netherlands.
Bioinformatics (Oxford, England)
|February 1, 2021
Summary
M2R is a new Python tool that integrates gut microbiota metabolism into human metabolic models. This software aids in analyzing the complex metabolic interactions between gut microbes and human cells.
Area of Science:
- Computational Biology
- Metabolic Modeling
- Microbiome Research
Background:
- The human gut microbiota comprises trillions of microorganisms crucial for nutrient processing and impacting host physiology, immunity, and metabolism.
- Understanding the interplay between gut microbes and human cells is vital for deciphering gastrointestinal health and disease.
Purpose of the Study:
- To introduce M2R, a novel Python add-on for integrating gut microbiota metabolic models with human genome-scale metabolic models (GEMs).
- To facilitate the analysis of host-microbe metabolic interactions and their dysregulation.
Main Methods:
- M2R modifies the lower bounds of exchange reactions in human GEMs (e.g., RECON3D) using aggregated microbial in- and out-fluxes.
- The software allows users to easily adjust metabolite pools entering and leaving the GEM.
Main Results:
- M2R enables the incorporation of gut microbiota metabolic information into human GEMs.
- The tool simplifies the process of analyzing metabolic exchanges between host and microbes.
Conclusions:
- M2R provides a valuable resource for researchers studying gut microbiota-human cell metabolic interactions.
- This integration is essential for understanding metabolic dysregulation in the gut.
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