Using Cultivated Microbial Communities To Dissect Microbiome Assembly: Challenges, Limitations, and the Path Ahead

ABSTRACT As troves of microbiome sequencing data provide improved resolution of patterns of microbial diversity, new approaches are needed to understand what controls these patterns. Many microbial ecologists are using cultivated model microbial communities to address this challenge. These systems p...

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Autor principal:	Benjamin E. Wolfe
Formato:	article
Lenguaje:	EN
Publicado:	American Society for Microbiology 2018
Materias:	cultivated microbial communities model system microbiome assembly metagenomics Microbiology QR1-502
Acceso en línea:	https://doaj.org/article/47f5fefb7f3641408dbd0b31c242a87d
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id	oai:doaj.org-article:47f5fefb7f3641408dbd0b31c242a87d
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spelling	oai:doaj.org-article:47f5fefb7f3641408dbd0b31c242a87d2021-12-02T19:46:20ZUsing Cultivated Microbial Communities To Dissect Microbiome Assembly: Challenges, Limitations, and the Path Ahead10.1128/mSystems.00161-172379-5077https://doaj.org/article/47f5fefb7f3641408dbd0b31c242a87d2018-04-01T00:00:00Zhttps://journals.asm.org/doi/10.1128/mSystems.00161-17https://doaj.org/toc/2379-5077ABSTRACT As troves of microbiome sequencing data provide improved resolution of patterns of microbial diversity, new approaches are needed to understand what controls these patterns. Many microbial ecologists are using cultivated model microbial communities to address this challenge. These systems provide opportunities to identify drivers of microbiome assembly, but key challenges and limitations need to be carefully considered in their development, implementation, and interpretation. How well do model microbial communities mimic in vitro communities in terms of taxonomic diversity, trophic levels, intraspecific diversity, and the abiotic environment? What are the best ways to manipulate and measure inputs and outputs in model community experiments? In this perspective, I briefly address some of these challenges on the basis of our experience developing fermented food model communities. Future work integrating genetic and molecular approaches with cultivated model microbial communities will allow microbial ecology to develop a more mechanistic understanding of microbiome diversity.Benjamin E. WolfeAmerican Society for Microbiologyarticlecultivatedmicrobial communitiesmodel systemmicrobiome assemblymetagenomicsMicrobiologyQR1-502ENmSystems, Vol 3, Iss 2 (2018)
institution	DOAJ
collection	DOAJ
language	EN
topic	cultivated microbial communities model system microbiome assembly metagenomics Microbiology QR1-502
spellingShingle	cultivated microbial communities model system microbiome assembly metagenomics Microbiology QR1-502 Benjamin E. Wolfe Using Cultivated Microbial Communities To Dissect Microbiome Assembly: Challenges, Limitations, and the Path Ahead
description	ABSTRACT As troves of microbiome sequencing data provide improved resolution of patterns of microbial diversity, new approaches are needed to understand what controls these patterns. Many microbial ecologists are using cultivated model microbial communities to address this challenge. These systems provide opportunities to identify drivers of microbiome assembly, but key challenges and limitations need to be carefully considered in their development, implementation, and interpretation. How well do model microbial communities mimic in vitro communities in terms of taxonomic diversity, trophic levels, intraspecific diversity, and the abiotic environment? What are the best ways to manipulate and measure inputs and outputs in model community experiments? In this perspective, I briefly address some of these challenges on the basis of our experience developing fermented food model communities. Future work integrating genetic and molecular approaches with cultivated model microbial communities will allow microbial ecology to develop a more mechanistic understanding of microbiome diversity.
format	article
author	Benjamin E. Wolfe
author_facet	Benjamin E. Wolfe
author_sort	Benjamin E. Wolfe
title	Using Cultivated Microbial Communities To Dissect Microbiome Assembly: Challenges, Limitations, and the Path Ahead
title_short	Using Cultivated Microbial Communities To Dissect Microbiome Assembly: Challenges, Limitations, and the Path Ahead
title_full	Using Cultivated Microbial Communities To Dissect Microbiome Assembly: Challenges, Limitations, and the Path Ahead
title_fullStr	Using Cultivated Microbial Communities To Dissect Microbiome Assembly: Challenges, Limitations, and the Path Ahead
title_full_unstemmed	Using Cultivated Microbial Communities To Dissect Microbiome Assembly: Challenges, Limitations, and the Path Ahead
title_sort	using cultivated microbial communities to dissect microbiome assembly: challenges, limitations, and the path ahead
publisher	American Society for Microbiology
publishDate	2018
url	https://doaj.org/article/47f5fefb7f3641408dbd0b31c242a87d
work_keys_str_mv	AT benjaminewolfe usingcultivatedmicrobialcommunitiestodissectmicrobiomeassemblychallengeslimitationsandthepathahead
_version_	1718376023080304640

Using Cultivated Microbial Communities To Dissect Microbiome Assembly: Challenges, Limitations, and the Path Ahead

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