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Design of synthetic human gut microbiome assembly and butyrate production

The capability to design microbiomes with predictable functions would enable new technologies for applications in health, agriculture, and bioprocessing. Towards this goal, we develop a model-guided approach to design synthetic human gut microbiomes for production of the health-relevant metabolite b...

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Autores principales: Clark, Ryan L., Connors, Bryce M., Stevenson, David M., Hromada, Susan E., Hamilton, Joshua J., Amador-Noguez, Daniel, Venturelli, Ophelia S.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Nature Publishing Group UK 2021
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8166853/
https://www.ncbi.nlm.nih.gov/pubmed/34059668
http://dx.doi.org/10.1038/s41467-021-22938-y
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author Clark, Ryan L.
Connors, Bryce M.
Stevenson, David M.
Hromada, Susan E.
Hamilton, Joshua J.
Amador-Noguez, Daniel
Venturelli, Ophelia S.
author_facet Clark, Ryan L.
Connors, Bryce M.
Stevenson, David M.
Hromada, Susan E.
Hamilton, Joshua J.
Amador-Noguez, Daniel
Venturelli, Ophelia S.
author_sort Clark, Ryan L.
collection PubMed
description The capability to design microbiomes with predictable functions would enable new technologies for applications in health, agriculture, and bioprocessing. Towards this goal, we develop a model-guided approach to design synthetic human gut microbiomes for production of the health-relevant metabolite butyrate. Our data-driven model quantifies microbial interactions impacting growth and butyrate production separately, providing key insights into ecological mechanisms driving butyrate production. We use our model to explore a vast community design space using a design-test-learn cycle to identify high butyrate-producing communities. Our model can accurately predict community assembly and butyrate production across a wide range of species richness. Guided by the model, we identify constraints on butyrate production by high species richness and key molecular factors driving butyrate production, including hydrogen sulfide, environmental pH, and resource competition. In sum, our model-guided approach provides a flexible and generalizable framework for understanding and accurately predicting community assembly and metabolic functions.
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spelling pubmed-81668532021-06-17 Design of synthetic human gut microbiome assembly and butyrate production Clark, Ryan L. Connors, Bryce M. Stevenson, David M. Hromada, Susan E. Hamilton, Joshua J. Amador-Noguez, Daniel Venturelli, Ophelia S. Nat Commun Article The capability to design microbiomes with predictable functions would enable new technologies for applications in health, agriculture, and bioprocessing. Towards this goal, we develop a model-guided approach to design synthetic human gut microbiomes for production of the health-relevant metabolite butyrate. Our data-driven model quantifies microbial interactions impacting growth and butyrate production separately, providing key insights into ecological mechanisms driving butyrate production. We use our model to explore a vast community design space using a design-test-learn cycle to identify high butyrate-producing communities. Our model can accurately predict community assembly and butyrate production across a wide range of species richness. Guided by the model, we identify constraints on butyrate production by high species richness and key molecular factors driving butyrate production, including hydrogen sulfide, environmental pH, and resource competition. In sum, our model-guided approach provides a flexible and generalizable framework for understanding and accurately predicting community assembly and metabolic functions. Nature Publishing Group UK 2021-05-31 /pmc/articles/PMC8166853/ /pubmed/34059668 http://dx.doi.org/10.1038/s41467-021-22938-y Text en © The Author(s) 2021 https://creativecommons.org/licenses/by/4.0/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/ (https://creativecommons.org/licenses/by/4.0/) .
spellingShingle Article
Clark, Ryan L.
Connors, Bryce M.
Stevenson, David M.
Hromada, Susan E.
Hamilton, Joshua J.
Amador-Noguez, Daniel
Venturelli, Ophelia S.
Design of synthetic human gut microbiome assembly and butyrate production
title Design of synthetic human gut microbiome assembly and butyrate production
title_full Design of synthetic human gut microbiome assembly and butyrate production
title_fullStr Design of synthetic human gut microbiome assembly and butyrate production
title_full_unstemmed Design of synthetic human gut microbiome assembly and butyrate production
title_short Design of synthetic human gut microbiome assembly and butyrate production
title_sort design of synthetic human gut microbiome assembly and butyrate production
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8166853/
https://www.ncbi.nlm.nih.gov/pubmed/34059668
http://dx.doi.org/10.1038/s41467-021-22938-y
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