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Microbial Systems Ecology to Understand Cross-Feeding in Microbiomes

Understanding how microorganism-microorganism interactions shape microbial assemblages is a key to deciphering the evolution of dependencies and co-existence in complex microbiomes. Metabolic dependencies in cross-feeding exist in microbial communities and can at least partially determine microbial...

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Autores principales: Mataigne, Victor, Vannier, Nathan, Vandenkoornhuyse, Philippe, Hacquard, Stéphane
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Frontiers Media S.A. 2021
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8721230/
https://www.ncbi.nlm.nih.gov/pubmed/34987488
http://dx.doi.org/10.3389/fmicb.2021.780469
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author Mataigne, Victor
Vannier, Nathan
Vandenkoornhuyse, Philippe
Hacquard, Stéphane
author_facet Mataigne, Victor
Vannier, Nathan
Vandenkoornhuyse, Philippe
Hacquard, Stéphane
author_sort Mataigne, Victor
collection PubMed
description Understanding how microorganism-microorganism interactions shape microbial assemblages is a key to deciphering the evolution of dependencies and co-existence in complex microbiomes. Metabolic dependencies in cross-feeding exist in microbial communities and can at least partially determine microbial community composition. To parry the complexity and experimental limitations caused by the large number of possible interactions, new concepts from systems biology aim to decipher how the components of a system interact with each other. The idea that cross-feeding does impact microbiome assemblages has developed both theoretically and empirically, following a systems biology framework applied to microbial communities, formalized as microbial systems ecology (MSE) and relying on integrated-omics data. This framework merges cellular and community scales and offers new avenues to untangle microbial coexistence primarily by metabolic modeling, one of the main approaches used for mechanistic studies. In this mini-review, we first give a concise explanation of microbial cross-feeding. We then discuss how MSE can enable progress in microbial research. Finally, we provide an overview of a MSE framework mostly based on genome-scale metabolic-network reconstruction that combines top-down and bottom-up approaches to assess the molecular mechanisms of deterministic processes of microbial community assembly that is particularly suitable for use in synthetic biology and microbiome engineering.
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spelling pubmed-87212302022-01-04 Microbial Systems Ecology to Understand Cross-Feeding in Microbiomes Mataigne, Victor Vannier, Nathan Vandenkoornhuyse, Philippe Hacquard, Stéphane Front Microbiol Microbiology Understanding how microorganism-microorganism interactions shape microbial assemblages is a key to deciphering the evolution of dependencies and co-existence in complex microbiomes. Metabolic dependencies in cross-feeding exist in microbial communities and can at least partially determine microbial community composition. To parry the complexity and experimental limitations caused by the large number of possible interactions, new concepts from systems biology aim to decipher how the components of a system interact with each other. The idea that cross-feeding does impact microbiome assemblages has developed both theoretically and empirically, following a systems biology framework applied to microbial communities, formalized as microbial systems ecology (MSE) and relying on integrated-omics data. This framework merges cellular and community scales and offers new avenues to untangle microbial coexistence primarily by metabolic modeling, one of the main approaches used for mechanistic studies. In this mini-review, we first give a concise explanation of microbial cross-feeding. We then discuss how MSE can enable progress in microbial research. Finally, we provide an overview of a MSE framework mostly based on genome-scale metabolic-network reconstruction that combines top-down and bottom-up approaches to assess the molecular mechanisms of deterministic processes of microbial community assembly that is particularly suitable for use in synthetic biology and microbiome engineering. Frontiers Media S.A. 2021-12-20 /pmc/articles/PMC8721230/ /pubmed/34987488 http://dx.doi.org/10.3389/fmicb.2021.780469 Text en Copyright © 2021 Mataigne, Vannier, Vandenkoornhuyse and Hacquard. https://creativecommons.org/licenses/by/4.0/This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
spellingShingle Microbiology
Mataigne, Victor
Vannier, Nathan
Vandenkoornhuyse, Philippe
Hacquard, Stéphane
Microbial Systems Ecology to Understand Cross-Feeding in Microbiomes
title Microbial Systems Ecology to Understand Cross-Feeding in Microbiomes
title_full Microbial Systems Ecology to Understand Cross-Feeding in Microbiomes
title_fullStr Microbial Systems Ecology to Understand Cross-Feeding in Microbiomes
title_full_unstemmed Microbial Systems Ecology to Understand Cross-Feeding in Microbiomes
title_short Microbial Systems Ecology to Understand Cross-Feeding in Microbiomes
title_sort microbial systems ecology to understand cross-feeding in microbiomes
topic Microbiology
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8721230/
https://www.ncbi.nlm.nih.gov/pubmed/34987488
http://dx.doi.org/10.3389/fmicb.2021.780469
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