The Microbiome Modeling Toolbox: from microbial interactions to personalized microbial communities

Federico Baldini; Almut Heinken; Laurent Heirendt; Stefania Magnusdottir; Ronan M T Fleming; Ines Thiele

doi:10.1093/bioinformatics/bty941

The Microbiome Modeling Toolbox: from microbial interactions to personalized microbial communities

Bioinformatics. 2019 Jul 1;35(13):2332-2334. doi: 10.1093/bioinformatics/bty941.

Authors

Federico Baldini¹, Almut Heinken¹, Laurent Heirendt¹, Stefania Magnusdottir¹, Ronan M T Fleming^{1

2}, Ines Thiele¹

Affiliations

¹ Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette L-4362, Luxembourg.
² Division of Systems Biomedicine and Pharmacology, Leiden Academic Centre for Drug Research, Faculty of Science, Leiden University, CC Leiden, The Netherlands.

Abstract

Motivation: The application of constraint-based modeling to functionally analyze metagenomic data has been limited so far, partially due to the absence of suitable toolboxes.

Results: To address this gap, we created a comprehensive toolbox to model (i) microbe-microbe and host-microbe metabolic interactions, and (ii) microbial communities using microbial genome-scale metabolic reconstructions and metagenomic data. The Microbiome Modeling Toolbox extends the functionality of the constraint-based reconstruction and analysis toolbox.

Availability and implementation: The Microbiome Modeling Toolbox and the tutorials at https://git.io/microbiomeModelingToolbox.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Microbial Interactions
Microbiota*