Experimental Microbiomes: Models Not to Scale

ABSTRACT Low-cost, high-throughput nucleic acid sequencing ushered the field of microbial ecology into a new era in which the microbial composition of nearly every conceivable environment on the planet is under examination. However, static “screenshots” derived from sequence-only approaches belie th...

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Autores principales:	Marc G. Chevrette, Jennifer R. Bratburd, Cameron R. Currie, Reed M. Stubbendieck
Formato:	article
Lenguaje:	EN
Publicado:	American Society for Microbiology 2019
Materias:	interactions microbial communities microbiome model systems Microbiology QR1-502
Acceso en línea:	https://doaj.org/article/0be3c0962e11410181976f3effaa8a48
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id	oai:doaj.org-article:0be3c0962e11410181976f3effaa8a48
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spelling	oai:doaj.org-article:0be3c0962e11410181976f3effaa8a482021-12-02T19:46:18ZExperimental Microbiomes: Models Not to Scale10.1128/mSystems.00175-192379-5077https://doaj.org/article/0be3c0962e11410181976f3effaa8a482019-08-01T00:00:00Zhttps://journals.asm.org/doi/10.1128/mSystems.00175-19https://doaj.org/toc/2379-5077ABSTRACT Low-cost, high-throughput nucleic acid sequencing ushered the field of microbial ecology into a new era in which the microbial composition of nearly every conceivable environment on the planet is under examination. However, static “screenshots” derived from sequence-only approaches belie the underlying complexity of the microbe-microbe and microbe-host interactions occurring within these systems. Reductionist experimental models are essential to identify the microbes involved in interactions and to characterize the molecular mechanisms that manifest as complex host and environmental phenomena. Herein, we focus on three models (Bacillus-Streptomyces, Aliivibrio fischeri-Hawaiian bobtail squid, and gnotobiotic mice) at various levels of taxonomic complexity and experimental control used to gain molecular insight into microbe-mediated interactions. We argue that when studying microbial communities, it is crucial to consider the scope of questions that experimental systems are suited to address, especially for researchers beginning new projects. Therefore, we highlight practical applications, limitations, and tradeoffs inherent to each model.Marc G. ChevretteJennifer R. BratburdCameron R. CurrieReed M. StubbendieckAmerican Society for Microbiologyarticleinteractionsmicrobial communitiesmicrobiomemodel systemsMicrobiologyQR1-502ENmSystems, Vol 4, Iss 4 (2019)
institution	DOAJ
collection	DOAJ
language	EN
topic	interactions microbial communities microbiome model systems Microbiology QR1-502
spellingShingle	interactions microbial communities microbiome model systems Microbiology QR1-502 Marc G. Chevrette Jennifer R. Bratburd Cameron R. Currie Reed M. Stubbendieck Experimental Microbiomes: Models Not to Scale
description	ABSTRACT Low-cost, high-throughput nucleic acid sequencing ushered the field of microbial ecology into a new era in which the microbial composition of nearly every conceivable environment on the planet is under examination. However, static “screenshots” derived from sequence-only approaches belie the underlying complexity of the microbe-microbe and microbe-host interactions occurring within these systems. Reductionist experimental models are essential to identify the microbes involved in interactions and to characterize the molecular mechanisms that manifest as complex host and environmental phenomena. Herein, we focus on three models (Bacillus-Streptomyces, Aliivibrio fischeri-Hawaiian bobtail squid, and gnotobiotic mice) at various levels of taxonomic complexity and experimental control used to gain molecular insight into microbe-mediated interactions. We argue that when studying microbial communities, it is crucial to consider the scope of questions that experimental systems are suited to address, especially for researchers beginning new projects. Therefore, we highlight practical applications, limitations, and tradeoffs inherent to each model.
format	article
author	Marc G. Chevrette Jennifer R. Bratburd Cameron R. Currie Reed M. Stubbendieck
author_facet	Marc G. Chevrette Jennifer R. Bratburd Cameron R. Currie Reed M. Stubbendieck
author_sort	Marc G. Chevrette
title	Experimental Microbiomes: Models Not to Scale
title_short	Experimental Microbiomes: Models Not to Scale
title_full	Experimental Microbiomes: Models Not to Scale
title_fullStr	Experimental Microbiomes: Models Not to Scale
title_full_unstemmed	Experimental Microbiomes: Models Not to Scale
title_sort	experimental microbiomes: models not to scale
publisher	American Society for Microbiology
publishDate	2019
url	https://doaj.org/article/0be3c0962e11410181976f3effaa8a48
work_keys_str_mv	AT marcgchevrette experimentalmicrobiomesmodelsnottoscale AT jenniferrbratburd experimentalmicrobiomesmodelsnottoscale AT cameronrcurrie experimentalmicrobiomesmodelsnottoscale AT reedmstubbendieck experimentalmicrobiomesmodelsnottoscale
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Experimental Microbiomes: Models Not to Scale

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