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Towards an Ecosystem Approach to Cheese Microbiology

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  • Authors: Benjamin E. Wolfe1, Rachel J. Dutton2
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    Affiliations: 1: FAS Center for Systems Biology, Harvard University, Cambridge, MA 02138; 2: FAS Center for Systems Biology, Harvard University, Cambridge, MA 02138; 3: University of Vermont, Burlington, VT
  • Source: microbiolspec October 2013 vol. 1 no. 1 doi:10.1128/microbiolspec.CM-0012-12
  • Received 15 April 2011 Accepted 04 April 2012 Published 31 October 2013
  • Rachel J. Dutton, rdutton@cgr.harvard.edu
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  • Abstract:

    Cheese is an ideal environment to serve as a model for the behavior of microbes in complex communities and at the same time allow detailed genetic analysis. Linking organisms, and their genes, to their role in the environment becomes possible in the case of cheese since cheese microbial communities have been “in culture” for thousands of years, with the knowledge of how to grow these organisms passed down by generations of cheesemakers. Recent reviews have described several emerging approaches to link molecular systems biology to ecosystem-scale processes, known as ecosystems biology. These approaches integrate massive datasets now available through high-throughput sequencing technologies with measurements of ecosystem properties. High-throughput datasets uncover the “parts list” (e.g., the species and all the genes within each species) of an ecosystem as well as the molecular basis of interactions within this parts list. Novel computational frameworks make it possible to link species and their interactions to ecosystem properties. Applying these approaches across multiple temporal and spatial scales makes it possible to understand how changes in the parts lists over space and time lead to changes in ecosystems processes. By manipulating the species present within model systems, we can test hypotheses related to the role of microbes in ecosystem function. Due to the tractability of cheese microbial communities, we have the opportunity to use an ecosystems biology approach from the scale of individual microbial cells within a cheese to replicated cheese microbial communities across continents. Using cheese as a model microbial ecosystem can provide a way to answer important questions concerning the form, function, and evolution of microbial communities.

  • Citation: Wolfe B, Dutton R. 2013. Towards an Ecosystem Approach to Cheese Microbiology. Microbiol Spectrum 1(1):CM-0012-12. doi:10.1128/microbiolspec.CM-0012-12.

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2013-10-31
2017-07-23

Abstract:

Cheese is an ideal environment to serve as a model for the behavior of microbes in complex communities and at the same time allow detailed genetic analysis. Linking organisms, and their genes, to their role in the environment becomes possible in the case of cheese since cheese microbial communities have been “in culture” for thousands of years, with the knowledge of how to grow these organisms passed down by generations of cheesemakers. Recent reviews have described several emerging approaches to link molecular systems biology to ecosystem-scale processes, known as ecosystems biology. These approaches integrate massive datasets now available through high-throughput sequencing technologies with measurements of ecosystem properties. High-throughput datasets uncover the “parts list” (e.g., the species and all the genes within each species) of an ecosystem as well as the molecular basis of interactions within this parts list. Novel computational frameworks make it possible to link species and their interactions to ecosystem properties. Applying these approaches across multiple temporal and spatial scales makes it possible to understand how changes in the parts lists over space and time lead to changes in ecosystems processes. By manipulating the species present within model systems, we can test hypotheses related to the role of microbes in ecosystem function. Due to the tractability of cheese microbial communities, we have the opportunity to use an ecosystems biology approach from the scale of individual microbial cells within a cheese to replicated cheese microbial communities across continents. Using cheese as a model microbial ecosystem can provide a way to answer important questions concerning the form, function, and evolution of microbial communities.

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FIGURE 1

Cheese as a model for microbial ecosystems biology. A conceptual overview of the fundamental biological processes that occur within cheese microbial ecosystems is shown. Emerging systems biology approaches provide the potential to dissect these processes across multiple spatial scales, ranging from individual microbial cells growing within a cheese to microbial communities distributed across a cheesemaking region. doi:10.1128/microbiolspec.CM-0012-2012.f1

Source: microbiolspec October 2013 vol. 1 no. 1 doi:10.1128/microbiolspec.CM-0012-12
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