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A theoretical framework for controlling complex microbial communities

Microbes form complex communities that perform critical roles for the integrity of their environment or the well-being of their hosts. Controlling these microbial communities can help us restore natural ecosystems and maintain healthy human microbiota. However, the lack of an efficient and systemati...

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Autores principales: Angulo, Marco Tulio, Moog, Claude H., Liu, Yang-Yu
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Nature Publishing Group UK 2019
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6401173/
https://www.ncbi.nlm.nih.gov/pubmed/30837457
http://dx.doi.org/10.1038/s41467-019-08890-y
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author Angulo, Marco Tulio
Moog, Claude H.
Liu, Yang-Yu
author_facet Angulo, Marco Tulio
Moog, Claude H.
Liu, Yang-Yu
author_sort Angulo, Marco Tulio
collection PubMed
description Microbes form complex communities that perform critical roles for the integrity of their environment or the well-being of their hosts. Controlling these microbial communities can help us restore natural ecosystems and maintain healthy human microbiota. However, the lack of an efficient and systematic control framework has limited our ability to manipulate these microbial communities. Here we fill this gap by developing a control framework based on the new notion of structural accessibility. Our framework uses the ecological network of the community to identify minimum sets of its driver species, manipulation of which allows controlling the whole community. We numerically validate our control framework on large communities, and then we demonstrate its application for controlling the gut microbiota of gnotobiotic mice infected with Clostridium difficile and the core microbiota of the sea sponge Ircinia oros. Our results provide a systematic pipeline to efficiently drive complex microbial communities towards desired states.
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spelling pubmed-64011732019-03-07 A theoretical framework for controlling complex microbial communities Angulo, Marco Tulio Moog, Claude H. Liu, Yang-Yu Nat Commun Article Microbes form complex communities that perform critical roles for the integrity of their environment or the well-being of their hosts. Controlling these microbial communities can help us restore natural ecosystems and maintain healthy human microbiota. However, the lack of an efficient and systematic control framework has limited our ability to manipulate these microbial communities. Here we fill this gap by developing a control framework based on the new notion of structural accessibility. Our framework uses the ecological network of the community to identify minimum sets of its driver species, manipulation of which allows controlling the whole community. We numerically validate our control framework on large communities, and then we demonstrate its application for controlling the gut microbiota of gnotobiotic mice infected with Clostridium difficile and the core microbiota of the sea sponge Ircinia oros. Our results provide a systematic pipeline to efficiently drive complex microbial communities towards desired states. Nature Publishing Group UK 2019-03-05 /pmc/articles/PMC6401173/ /pubmed/30837457 http://dx.doi.org/10.1038/s41467-019-08890-y Text en © The Author(s) 2019 Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.
spellingShingle Article
Angulo, Marco Tulio
Moog, Claude H.
Liu, Yang-Yu
A theoretical framework for controlling complex microbial communities
title A theoretical framework for controlling complex microbial communities
title_full A theoretical framework for controlling complex microbial communities
title_fullStr A theoretical framework for controlling complex microbial communities
title_full_unstemmed A theoretical framework for controlling complex microbial communities
title_short A theoretical framework for controlling complex microbial communities
title_sort theoretical framework for controlling complex microbial communities
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6401173/
https://www.ncbi.nlm.nih.gov/pubmed/30837457
http://dx.doi.org/10.1038/s41467-019-08890-y
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