Strain-Level Diversity Impacts Cheese Rind Microbiome Assembly and Function

ABSTRACT Diversification can generate genomic and phenotypic strain-level diversity within microbial species. This microdiversity is widely recognized in populations, but the community-level consequences of microbial strain-level diversity are poorly characterized. Using the cheese rind model system...

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Autores principales:	Brittany A. Niccum, Erik K. Kastman, Nicole Kfoury, Albert Robbat, Benjamin E. Wolfe
Formato:	article
Lenguaje:	EN
Publicado:	American Society for Microbiology 2020
Materias:	cheese genomics microbial communities microbiome assembly strain diversity Microbiology QR1-502
Acceso en línea:	https://doaj.org/article/999b064f706841d68065b1e0aca5286a
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spelling	oai:doaj.org-article:999b064f706841d68065b1e0aca5286a2021-12-02T19:46:20ZStrain-Level Diversity Impacts Cheese Rind Microbiome Assembly and Function10.1128/mSystems.00149-202379-5077https://doaj.org/article/999b064f706841d68065b1e0aca5286a2020-06-01T00:00:00Zhttps://journals.asm.org/doi/10.1128/mSystems.00149-20https://doaj.org/toc/2379-5077ABSTRACT Diversification can generate genomic and phenotypic strain-level diversity within microbial species. This microdiversity is widely recognized in populations, but the community-level consequences of microbial strain-level diversity are poorly characterized. Using the cheese rind model system, we tested whether strain diversity across microbiomes from distinct geographic regions impacts assembly dynamics and functional outputs. We first isolated the same three bacterial species (Staphylococcus equorum, Brevibacterium auranticum, and Brachybacterium alimentarium) from nine cheeses produced in different regions of the United States and Europe to construct nine synthetic microbial communities consisting of distinct strains of the same three bacterial species. Comparative genomics identified distinct phylogenetic clusters and significant variation in genome content across the nine synthetic communities. When we assembled each synthetic community with initially identical compositions, community structure diverged over time, resulting in communities with different dominant taxa. The taxonomically identical communities showed differing responses to abiotic (high salt) and biotic (the fungus Penicillium) perturbations, with some communities showing no response and others substantially shifting in composition. Functional differences were also observed across the nine communities, with significant variation in pigment production (light yellow to orange) and in composition of volatile organic compound profiles emitted from the rinds (nutty to sulfury). IMPORTANCE Our work demonstrated that the specific microbial strains used to construct a microbiome could impact the species composition, perturbation responses, and functional outputs of that system. These findings suggest that 16S rRNA gene taxonomic profiles alone may have limited potential to predict the dynamics of microbial communities because they usually do not capture strain-level diversity. Observations from our synthetic communities also suggest that strain-level diversity has the potential to drive variability in the aesthetics and quality of surface-ripened cheeses.Brittany A. NiccumErik K. KastmanNicole KfouryAlbert RobbatBenjamin E. WolfeAmerican Society for Microbiologyarticlecheesegenomicsmicrobial communitiesmicrobiome assemblystrain diversityMicrobiologyQR1-502ENmSystems, Vol 5, Iss 3 (2020)
institution	DOAJ
collection	DOAJ
language	EN
topic	cheese genomics microbial communities microbiome assembly strain diversity Microbiology QR1-502
spellingShingle	cheese genomics microbial communities microbiome assembly strain diversity Microbiology QR1-502 Brittany A. Niccum Erik K. Kastman Nicole Kfoury Albert Robbat Benjamin E. Wolfe Strain-Level Diversity Impacts Cheese Rind Microbiome Assembly and Function
description	ABSTRACT Diversification can generate genomic and phenotypic strain-level diversity within microbial species. This microdiversity is widely recognized in populations, but the community-level consequences of microbial strain-level diversity are poorly characterized. Using the cheese rind model system, we tested whether strain diversity across microbiomes from distinct geographic regions impacts assembly dynamics and functional outputs. We first isolated the same three bacterial species (Staphylococcus equorum, Brevibacterium auranticum, and Brachybacterium alimentarium) from nine cheeses produced in different regions of the United States and Europe to construct nine synthetic microbial communities consisting of distinct strains of the same three bacterial species. Comparative genomics identified distinct phylogenetic clusters and significant variation in genome content across the nine synthetic communities. When we assembled each synthetic community with initially identical compositions, community structure diverged over time, resulting in communities with different dominant taxa. The taxonomically identical communities showed differing responses to abiotic (high salt) and biotic (the fungus Penicillium) perturbations, with some communities showing no response and others substantially shifting in composition. Functional differences were also observed across the nine communities, with significant variation in pigment production (light yellow to orange) and in composition of volatile organic compound profiles emitted from the rinds (nutty to sulfury). IMPORTANCE Our work demonstrated that the specific microbial strains used to construct a microbiome could impact the species composition, perturbation responses, and functional outputs of that system. These findings suggest that 16S rRNA gene taxonomic profiles alone may have limited potential to predict the dynamics of microbial communities because they usually do not capture strain-level diversity. Observations from our synthetic communities also suggest that strain-level diversity has the potential to drive variability in the aesthetics and quality of surface-ripened cheeses.
format	article
author	Brittany A. Niccum Erik K. Kastman Nicole Kfoury Albert Robbat Benjamin E. Wolfe
author_facet	Brittany A. Niccum Erik K. Kastman Nicole Kfoury Albert Robbat Benjamin E. Wolfe
author_sort	Brittany A. Niccum
title	Strain-Level Diversity Impacts Cheese Rind Microbiome Assembly and Function
title_short	Strain-Level Diversity Impacts Cheese Rind Microbiome Assembly and Function
title_full	Strain-Level Diversity Impacts Cheese Rind Microbiome Assembly and Function
title_fullStr	Strain-Level Diversity Impacts Cheese Rind Microbiome Assembly and Function
title_full_unstemmed	Strain-Level Diversity Impacts Cheese Rind Microbiome Assembly and Function
title_sort	strain-level diversity impacts cheese rind microbiome assembly and function
publisher	American Society for Microbiology
publishDate	2020
url	https://doaj.org/article/999b064f706841d68065b1e0aca5286a
work_keys_str_mv	AT brittanyaniccum strainleveldiversityimpactscheeserindmicrobiomeassemblyandfunction AT erikkkastman strainleveldiversityimpactscheeserindmicrobiomeassemblyandfunction AT nicolekfoury strainleveldiversityimpactscheeserindmicrobiomeassemblyandfunction AT albertrobbat strainleveldiversityimpactscheeserindmicrobiomeassemblyandfunction AT benjaminewolfe strainleveldiversityimpactscheeserindmicrobiomeassemblyandfunction
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Strain-Level Diversity Impacts Cheese Rind Microbiome Assembly and Function

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