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Volume 11, Issue 1

Ecological insights into the microbiology of food using metagenomics and its potential surveillance applications Open Access

Abstract

A diverse array of micro-organisms can be found on food, including those that are pathogenic or resistant to antimicrobial drugs. Metagenomics involves extracting and sequencing the DNA of all micro-organisms on a sample, and here, we used a combination of culture and culture-independent approaches to investigate the microbial ecology of food to assess the potential application of metagenomics for the microbial surveillance of food. We cultured common foodborne pathogens and other organisms including , spp., spp. and spp. from five different food commodities and compared their genomes to the microbial communities obtained by metagenomic sequencing following host (food) DNA depletion. The microbial populations of retail food were found to be predominated by psychrotrophic bacteria, driven by the cool temperatures in which the food products are stored. Pathogens accounted for a small percentage of the food metagenome compared to the psychrotrophic bacteria, and cultured pathogens were inconsistently identified in the metagenome data. The microbial composition of food varied amongst different commodities, and metagenomics was able to classify the taxonomic origin of 59% of antimicrobial resistance genes (ARGs) found on food to the genus level, but it was unclear what percentage of ARGs were associated with mobile genetic elements and thus transferable to other bacteria. Metagenomics may be used to survey the ARG burden, composition and carriage on foods to which consumers are exposed. However, food metagenomics, even after depleting host DNA, inconsistently identifies pathogens without enrichment or further bait capture.

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): antimicrobial resistance , food , metagenomes and pathogens
Funding
This study was supported by the:
  • H2020 European Research Council (Award erc-stg-948219, EPYC)
    • Principle Award Recipient: FalkHildebrand
  • Biotechnology and Biological Sciences Research Council (Award BBS/E/ER/230002A)
    • Principle Award Recipient: FalkHildebrand
  • Biotechnology and Biological Sciences Research Council (Award BBX011089/1)
    • Principle Award Recipient: FalkHildebrand
  • Biotechnology and Biological Sciences Research Council (Award BBS/E/ F/000PR13631)
    • Principle Award Recipient: FalkHildebrand
  • Biotechnology and Biological Sciences Research Council (Award BB/X011054/1)
    • Principle Award Recipient: FalkHildebrand
  • Biotechnology and Biological Sciences Research Council (Award BB/V01823X/1)
    • Principle Award Recipient: AlisonE Mather
  • Food Standards Agency (Award FS101185)
    • Principle Award Recipient: AlisonE Mather
  • Biotechnology and Biological Sciences Research Council (Award BBS/E/F/000PR13634)
    • Principle Award Recipient: AlisonE Mather
  • Biotechnology and Biological Sciences Research Council (Award BB/X011011/1)
    • Principle Award Recipient: AlisonE Mather
  • Biotechnology and Biological Sciences Research Council (Award BBS/E/F/000PR10348)
    • Principle Award Recipient: AlisonE Mather
  • Biotechnology and Biological Sciences Research Council (Award BB/R012504/1)
    • Principle Award Recipient: AlisonE Mather
© 2025 The Authors
  • This is an open-access article distributed under the terms of the Creative Commons Attribution License. This article was made open access via a Publish and Read agreement between the Microbiology Society and the corresponding author’s institution.
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2025-01-14
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Ecological insights into the microbiology of food using metagenomics and its potential surveillance applications
M Gen 11, 001337 (2025); https://doi.org/10.1099/mgen.0.001337
/content/journal/mgen/10.1099/mgen.0.001337
/content/journal/mgen/10.1099/mgen.0.001337
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