Inferring composition and function of the human gut microbiome in time and space: A review of genome-scale metabolic modelling tools
The human gut hosts a complex community of microorganisms that directly influences gastrointestinal physiology, playing a central role in human health. Because of its importance, the metabolic interplay between the gut microbiome and host metabolism has gained special interest. While there has been...
Main Authors: | , , |
---|---|
Format: | Article |
Language: | English |
Published: |
Elsevier
2020-01-01
|
Series: | Computational and Structural Biotechnology Journal |
Online Access: | http://www.sciencedirect.com/science/article/pii/S200103702030502X |
id |
doaj-a141971353524b40a22eba7be607a7f3 |
---|---|
record_format |
Article |
spelling |
doaj-a141971353524b40a22eba7be607a7f32021-01-02T05:09:24ZengElsevierComputational and Structural Biotechnology Journal2001-03702020-01-011838973904Inferring composition and function of the human gut microbiome in time and space: A review of genome-scale metabolic modelling toolsÁlvaro Altamirano0Pedro A. Saa1Daniel Garrido2Department of Chemical and Bioprocess Engineering, School of Engineering, Pontificia Universidad Católica de Chile, Vicuña Mackenna, 4860 Santiago, ChileDepartment of Chemical and Bioprocess Engineering, School of Engineering, Pontificia Universidad Católica de Chile, Vicuña Mackenna, 4860 Santiago, ChileCorresponding author.; Department of Chemical and Bioprocess Engineering, School of Engineering, Pontificia Universidad Católica de Chile, Vicuña Mackenna, 4860 Santiago, ChileThe human gut hosts a complex community of microorganisms that directly influences gastrointestinal physiology, playing a central role in human health. Because of its importance, the metabolic interplay between the gut microbiome and host metabolism has gained special interest. While there has been great progress in the field driven by metagenomics and experimental studies, the mechanisms underpinning microbial composition and interactions in the microbiome remain poorly understood. Genome-scale metabolic models are mathematical structures capable of describing the metabolic potential of microbial cells. They are thus suitable tools for probing the metabolic properties of microbial communities. In this review, we discuss the most recent and relevant genome-scale metabolic modelling tools for inferring the composition, interactions, and ultimately, biological function of the constituent species of a microbial community with special emphasis in the gut microbiota. Particular attention is given to constraint-based metabolic modelling methods as well as hybrid agent-based methods for capturing the interactions and behavior of the community in time and space. Finally, we discuss the challenges hindering comprehensive modelling of complex microbial communities and its application for the in-silico design of microbial consortia with therapeutic functions.http://www.sciencedirect.com/science/article/pii/S200103702030502X |
collection |
DOAJ |
language |
English |
format |
Article |
sources |
DOAJ |
author |
Álvaro Altamirano Pedro A. Saa Daniel Garrido |
spellingShingle |
Álvaro Altamirano Pedro A. Saa Daniel Garrido Inferring composition and function of the human gut microbiome in time and space: A review of genome-scale metabolic modelling tools Computational and Structural Biotechnology Journal |
author_facet |
Álvaro Altamirano Pedro A. Saa Daniel Garrido |
author_sort |
Álvaro Altamirano |
title |
Inferring composition and function of the human gut microbiome in time and space: A review of genome-scale metabolic modelling tools |
title_short |
Inferring composition and function of the human gut microbiome in time and space: A review of genome-scale metabolic modelling tools |
title_full |
Inferring composition and function of the human gut microbiome in time and space: A review of genome-scale metabolic modelling tools |
title_fullStr |
Inferring composition and function of the human gut microbiome in time and space: A review of genome-scale metabolic modelling tools |
title_full_unstemmed |
Inferring composition and function of the human gut microbiome in time and space: A review of genome-scale metabolic modelling tools |
title_sort |
inferring composition and function of the human gut microbiome in time and space: a review of genome-scale metabolic modelling tools |
publisher |
Elsevier |
series |
Computational and Structural Biotechnology Journal |
issn |
2001-0370 |
publishDate |
2020-01-01 |
description |
The human gut hosts a complex community of microorganisms that directly influences gastrointestinal physiology, playing a central role in human health. Because of its importance, the metabolic interplay between the gut microbiome and host metabolism has gained special interest. While there has been great progress in the field driven by metagenomics and experimental studies, the mechanisms underpinning microbial composition and interactions in the microbiome remain poorly understood. Genome-scale metabolic models are mathematical structures capable of describing the metabolic potential of microbial cells. They are thus suitable tools for probing the metabolic properties of microbial communities. In this review, we discuss the most recent and relevant genome-scale metabolic modelling tools for inferring the composition, interactions, and ultimately, biological function of the constituent species of a microbial community with special emphasis in the gut microbiota. Particular attention is given to constraint-based metabolic modelling methods as well as hybrid agent-based methods for capturing the interactions and behavior of the community in time and space. Finally, we discuss the challenges hindering comprehensive modelling of complex microbial communities and its application for the in-silico design of microbial consortia with therapeutic functions. |
url |
http://www.sciencedirect.com/science/article/pii/S200103702030502X |
work_keys_str_mv |
AT alvaroaltamirano inferringcompositionandfunctionofthehumangutmicrobiomeintimeandspaceareviewofgenomescalemetabolicmodellingtools AT pedroasaa inferringcompositionandfunctionofthehumangutmicrobiomeintimeandspaceareviewofgenomescalemetabolicmodellingtools AT danielgarrido inferringcompositionandfunctionofthehumangutmicrobiomeintimeandspaceareviewofgenomescalemetabolicmodellingtools |
_version_ |
1724359581785653248 |