From Network Analysis to Functional Metabolic Modeling of the Human Gut Microbiota

ABSTRACT An important hallmark of the human gut microbiota is its species diversity and complexity. Various diseases have been associated with a decreased diversity leading to reduced metabolic functionalities. Common approaches to investigate the human microbiota include high-throughput sequencing...

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Autores principales:	Eugen Bauer, Ines Thiele
Formato:	article
Lenguaje:	EN
Publicado:	American Society for Microbiology 2018
Materias:	computational modeling constraint-based modeling gut microbiome metabolic modeling network approaches Microbiology QR1-502
Acceso en línea:	https://doaj.org/article/eeb96a5e15e741c3bd2adc3ae90f35a6
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spelling	oai:doaj.org-article:eeb96a5e15e741c3bd2adc3ae90f35a62021-12-02T18:39:16ZFrom Network Analysis to Functional Metabolic Modeling of the Human Gut Microbiota10.1128/mSystems.00209-172379-5077https://doaj.org/article/eeb96a5e15e741c3bd2adc3ae90f35a62018-06-01T00:00:00Zhttps://journals.asm.org/doi/10.1128/mSystems.00209-17https://doaj.org/toc/2379-5077ABSTRACT An important hallmark of the human gut microbiota is its species diversity and complexity. Various diseases have been associated with a decreased diversity leading to reduced metabolic functionalities. Common approaches to investigate the human microbiota include high-throughput sequencing with subsequent correlative analyses. However, to understand the ecology of the human gut microbiota and consequently design novel treatments for diseases, it is important to represent the different interactions between microbes with their associated metabolites. Computational systems biology approaches can give further mechanistic insights by constructing data- or knowledge-driven networks that represent microbe interactions. In this minireview, we will discuss current approaches in systems biology to analyze the human gut microbiota, with a particular focus on constraint-based modeling. We will discuss various community modeling techniques with their advantages and differences, as well as their application to predict the metabolic mechanisms of intestinal microbial communities. Finally, we will discuss future perspectives and current challenges of simulating realistic and comprehensive models of the human gut microbiota.Eugen BauerInes ThieleAmerican Society for Microbiologyarticlecomputational modelingconstraint-based modelinggut microbiomemetabolic modelingnetwork approachesMicrobiologyQR1-502ENmSystems, Vol 3, Iss 3 (2018)
institution	DOAJ
collection	DOAJ
language	EN
topic	computational modeling constraint-based modeling gut microbiome metabolic modeling network approaches Microbiology QR1-502
spellingShingle	computational modeling constraint-based modeling gut microbiome metabolic modeling network approaches Microbiology QR1-502 Eugen Bauer Ines Thiele From Network Analysis to Functional Metabolic Modeling of the Human Gut Microbiota
description	ABSTRACT An important hallmark of the human gut microbiota is its species diversity and complexity. Various diseases have been associated with a decreased diversity leading to reduced metabolic functionalities. Common approaches to investigate the human microbiota include high-throughput sequencing with subsequent correlative analyses. However, to understand the ecology of the human gut microbiota and consequently design novel treatments for diseases, it is important to represent the different interactions between microbes with their associated metabolites. Computational systems biology approaches can give further mechanistic insights by constructing data- or knowledge-driven networks that represent microbe interactions. In this minireview, we will discuss current approaches in systems biology to analyze the human gut microbiota, with a particular focus on constraint-based modeling. We will discuss various community modeling techniques with their advantages and differences, as well as their application to predict the metabolic mechanisms of intestinal microbial communities. Finally, we will discuss future perspectives and current challenges of simulating realistic and comprehensive models of the human gut microbiota.
format	article
author	Eugen Bauer Ines Thiele
author_facet	Eugen Bauer Ines Thiele
author_sort	Eugen Bauer
title	From Network Analysis to Functional Metabolic Modeling of the Human Gut Microbiota
title_short	From Network Analysis to Functional Metabolic Modeling of the Human Gut Microbiota
title_full	From Network Analysis to Functional Metabolic Modeling of the Human Gut Microbiota
title_fullStr	From Network Analysis to Functional Metabolic Modeling of the Human Gut Microbiota
title_full_unstemmed	From Network Analysis to Functional Metabolic Modeling of the Human Gut Microbiota
title_sort	from network analysis to functional metabolic modeling of the human gut microbiota
publisher	American Society for Microbiology
publishDate	2018
url	https://doaj.org/article/eeb96a5e15e741c3bd2adc3ae90f35a6
work_keys_str_mv	AT eugenbauer fromnetworkanalysistofunctionalmetabolicmodelingofthehumangutmicrobiota AT inesthiele fromnetworkanalysistofunctionalmetabolicmodelingofthehumangutmicrobiota
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From Network Analysis to Functional Metabolic Modeling of the Human Gut Microbiota

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