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Conceptual Exchanges for Understanding Free-Living and Host-Associated Microbiomes

Whether a microbe is free-living or associated with a host from across the tree of life, its existence depends on a limited number of elements and electron donors and acceptors. Yet divergent approaches have been used by investigators from different fields. The “environment first” research tradition...

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Autores principales: Pfister, Catherine A., Light, Samuel H., Bohannan, Brendan, Schmidt, Thomas, Martiny, Adam, Hynson, Nicole A., Devkota, Suzanne, David, Lawrence, Whiteson, Katrine
Formato: Online Artículo Texto
Lenguaje:English
Publicado: American Society for Microbiology 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8751383/
https://www.ncbi.nlm.nih.gov/pubmed/35014872
http://dx.doi.org/10.1128/msystems.01374-21
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author Pfister, Catherine A.
Light, Samuel H.
Bohannan, Brendan
Schmidt, Thomas
Martiny, Adam
Hynson, Nicole A.
Devkota, Suzanne
David, Lawrence
Whiteson, Katrine
author_facet Pfister, Catherine A.
Light, Samuel H.
Bohannan, Brendan
Schmidt, Thomas
Martiny, Adam
Hynson, Nicole A.
Devkota, Suzanne
David, Lawrence
Whiteson, Katrine
author_sort Pfister, Catherine A.
collection PubMed
description Whether a microbe is free-living or associated with a host from across the tree of life, its existence depends on a limited number of elements and electron donors and acceptors. Yet divergent approaches have been used by investigators from different fields. The “environment first” research tradition emphasizes thermodynamics and biogeochemical principles, including the quantification of redox environments and elemental stoichiometry to identify transformations and thus an underlying microbe. The increasingly common “microbe first” research approach benefits from culturing and/or DNA sequencing methods to first identify a microbe and encoded metabolic functions. Here, the microbe itself serves as an indicator for environmental conditions and transformations. We illustrate the application of both approaches to the study of microbiomes and emphasize how both can reveal the selection of microbial metabolisms across diverse environments, anticipate alterations to microbiomes in host health, and understand the implications of a changing climate for microbial function.
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spelling pubmed-87513832022-01-24 Conceptual Exchanges for Understanding Free-Living and Host-Associated Microbiomes Pfister, Catherine A. Light, Samuel H. Bohannan, Brendan Schmidt, Thomas Martiny, Adam Hynson, Nicole A. Devkota, Suzanne David, Lawrence Whiteson, Katrine mSystems Perspective Whether a microbe is free-living or associated with a host from across the tree of life, its existence depends on a limited number of elements and electron donors and acceptors. Yet divergent approaches have been used by investigators from different fields. The “environment first” research tradition emphasizes thermodynamics and biogeochemical principles, including the quantification of redox environments and elemental stoichiometry to identify transformations and thus an underlying microbe. The increasingly common “microbe first” research approach benefits from culturing and/or DNA sequencing methods to first identify a microbe and encoded metabolic functions. Here, the microbe itself serves as an indicator for environmental conditions and transformations. We illustrate the application of both approaches to the study of microbiomes and emphasize how both can reveal the selection of microbial metabolisms across diverse environments, anticipate alterations to microbiomes in host health, and understand the implications of a changing climate for microbial function. American Society for Microbiology 2022-01-11 /pmc/articles/PMC8751383/ /pubmed/35014872 http://dx.doi.org/10.1128/msystems.01374-21 Text en Copyright © 2022 Pfister et al. https://creativecommons.org/licenses/by/4.0/This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International license (https://creativecommons.org/licenses/by/4.0/) .
spellingShingle Perspective
Pfister, Catherine A.
Light, Samuel H.
Bohannan, Brendan
Schmidt, Thomas
Martiny, Adam
Hynson, Nicole A.
Devkota, Suzanne
David, Lawrence
Whiteson, Katrine
Conceptual Exchanges for Understanding Free-Living and Host-Associated Microbiomes
title Conceptual Exchanges for Understanding Free-Living and Host-Associated Microbiomes
title_full Conceptual Exchanges for Understanding Free-Living and Host-Associated Microbiomes
title_fullStr Conceptual Exchanges for Understanding Free-Living and Host-Associated Microbiomes
title_full_unstemmed Conceptual Exchanges for Understanding Free-Living and Host-Associated Microbiomes
title_short Conceptual Exchanges for Understanding Free-Living and Host-Associated Microbiomes
title_sort conceptual exchanges for understanding free-living and host-associated microbiomes
topic Perspective
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8751383/
https://www.ncbi.nlm.nih.gov/pubmed/35014872
http://dx.doi.org/10.1128/msystems.01374-21
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