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Related Experiment Video

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Strain-Level Diversity Impacts Cheese Rind Microbiome Assembly and Function.

Brittany A Niccum1, Erik K Kastman1, Nicole Kfoury2

  • 1Tufts University, Department of Biology, Medford, Massachusetts, USA.

Msystems
|June 18, 2020
PubMed
Summary
This summary is machine-generated.

Microbial strain diversity significantly impacts microbiome assembly, function, and response to environmental changes. Understanding strain-level differences is crucial for predicting community dynamics and product quality in systems like cheese rinds.

Keywords:
cheesegenomicsmicrobial communitiesmicrobiome assemblystrain diversity

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Area of Science:

  • Microbial Ecology
  • Systems Microbiology
  • Food Microbiology

Background:

  • Microbial strain diversity (microdiversity) is known at the genomic and phenotypic levels within species.
  • The community-level impacts of this strain diversity remain poorly understood.
  • Previous studies often overlook strain-level variations when analyzing microbial communities.

Purpose of the Study:

  • To investigate how strain diversity within microbial communities affects their assembly dynamics.
  • To determine the impact of strain diversity on functional outputs and responses to perturbations.
  • To assess the role of strain diversity in model microbial systems, specifically cheese rinds.

Main Methods:

  • Isolated three bacterial species (Staphylococcus equorum, Brevibacterium auranticum, Brachybacterium alimentarium) from nine different cheeses.
  • Constructed nine synthetic microbial communities using distinct strains of these species.
  • Employed comparative genomics, assembled communities, and subjected them to abiotic (high salt) and biotic (fungal) perturbations.

Main Results:

  • Comparative genomics revealed distinct phylogenetic clusters and varied genome content among synthetic communities.
  • Community structure diverged over time, leading to different dominant taxa despite identical initial compositions.
  • Communities exhibited varied responses to perturbations, with some showing significant shifts and others remaining stable.
  • Functional outputs, including pigment production and volatile organic compound profiles, differed significantly across communities.

Conclusions:

  • The specific microbial strains used in a microbiome construction critically influence species composition, perturbation responses, and functional outcomes.
  • 16S rRNA gene-based taxonomic profiles may be insufficient for predicting microbial community dynamics due to their inability to capture strain-level diversity.
  • Strain-level diversity can drive variability in the quality and aesthetics of surface-ripened products like cheese.