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

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

University of Luxembourg
Leiden Academic Centre for Drug Research

Research output: Contribution to a Journal (Peer & Non Peer) › Article › peer-review

110 Citations (Scopus)

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.

Original language	English
Pages (from-to)	2332-2334
Number of pages	3
Journal	Bioinformatics
Volume	35
Issue number	13
DOIs	https://doi.org/10.1093/bioinformatics/bty941
Publication status	Published - 1 Jul 2019
Externally published	Yes

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10.1093/bioinformatics/bty941

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author = "Federico Baldini and Almut Heinken and Laurent Heirendt and Stefania Magnusdottir and Fleming, \{Ronan M.T.\} and Ines Thiele",

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AU - Baldini, Federico

AU - Heinken, Almut

AU - Heirendt, Laurent

AU - Magnusdottir, Stefania

AU - Fleming, Ronan M.T.

AU - Thiele, Ines

PY - 2019/7/1

Y1 - 2019/7/1

N2 - 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.

AB - 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.

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U2 - 10.1093/bioinformatics/bty941

DO - 10.1093/bioinformatics/bty941

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The microbiome modeling toolbox: From microbial interactions to personalized microbial communities

Abstract

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