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Unexplored microbial diversity from 2,500 food metagenomes and links with the human microbiome

Affiliations
  • 1Department of Cellular, Computational and Integrative Biology, University of Trento, Trento, Italy.
  • 2Scuola Universitaria Superiore IUSS Pavia, Pavia, Italy; Centre for Agriculture Food Environment, University of Trento, Trento, Italy; Research and Innovation Centre, Fondazione Edmund Mach, San Michele All’Adige, Italy.
  • 3Department of Agricultural Sciences, Division of Microbiology, University of Naples Federico II, Portici, Italy.
  • 4Department of Food Hygiene and Technology, Universidad de León, León, Spain.
  • 5Teagasc Food Research Centre, Moorepark, Fermoy, Co. Cork, Ireland; APC Microbiome Ireland, University College Cork, Cork, Ireland.
  • 6Teagasc Food Research Centre, Moorepark, Fermoy, Co. Cork, Ireland; Department of Biotechnology, Institute of Agrochemistry and Food Technology – National Research Council (IATA-CSIC), Paterna, Valencia, Spain.
  • 7Department of Microbiology and Biochemistry of Dairy Products, Instituto de Productos Lácteos de Asturias – Consejo Superior de Investigaciones Científicas (IPLA-CSIC), Villaviciosa, Spain; Microhealth Group, Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Oviedo, Spain.
  • 8Teagasc Food Research Centre, Moorepark, Fermoy, Co. Cork, Ireland.
  • 9Department of Agricultural Sciences, Division of Microbiology, University of Naples Federico II, Portici, Italy; Task Force on Microbiome Studies, University of Naples Federico II, Portici, Italy.
  • 10BaseClear B.V., Leiden, the Netherlands.
  • 11Microbiology Research Group, Matís, Reykjavík, Iceland.
  • 12QIAGEN GmbH, Hilden, Germany.
  • 13Austrian Competence Centre for Feed and Food Quality, Safety, and Innovation, FFoQSI GmbH, Tulln an der Donau, Austria; Unit of Food Microbiology, Institute of Food Safety, Food Technology and Veterinary Public Health, Department for Farm Animals and Veterinary Public Health, University of Veterinary Medicine Vienna, Vienna, Austria; Institute for Agribiotechnology Research (CIALE), Department of Microbiology and Genetics, University of Salamanca, Salamanca, Spain.
  • 14Teagasc Food Research Centre, Moorepark, Fermoy, Co. Cork, Ireland; APC Microbiome Ireland, University College Cork, Cork, Ireland; School of Microbiology, University College Cork, Cork, Ireland.
  • 15Microbiology Research Group, Matís, Reykjavík, Iceland; University of Iceland, Faculty of Food Science and Nutrition, Reykjavík, Iceland.
  • 16Centre for Agriculture Food Environment, University of Trento, Trento, Italy; Research and Innovation Centre, Fondazione Edmund Mach, San Michele All’Adige, Italy.
  • 17Teagasc Food Research Centre, Moorepark, Fermoy, Co. Cork, Ireland; APC Microbiome Ireland, University College Cork, Cork, Ireland; VistaMilk SFI Research Centre, Teagasc, Moorepark, Fermoy, Co. Cork, Ireland.
  • 18Department of Cellular, Computational and Integrative Biology, University of Trento, Trento, Italy; IEO, Istituto Europeo di Oncologia IRCSS, Milan, Italy; Department of Twins Research and Genetic Epidemiology, King’s College London, London, UK. Electronic address: nicola.segata@unitn.it.

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August 30, 2024

Abstract

Complex microbiomes are part of the food we eat and influence our own microbiome, but their diversity remains largely unexplored. Here, we generated the open access curatedFoodMetagenomicData (cFMD) resource by integrating 1,950 newly sequenced and 583 public food metagenomes. We produced 10,899 metagenome-assembled genomes spanning 1,036 prokaryotic and 108 eukaryotic species-level genome bins (SGBs), including 320 previously undescribed taxa. Food SGBs displayed significant microbial diversity within and between food categories. Extension to >20,000 human metagenomes revealed that food SGBs accounted on average for 3% of the adult gut microbiome. Strain-level analysis highlighted potential instances of food-to-gut transmission and intestinal colonization (e.g., Lacticaseibacillus paracasei) as well as SGBs with divergent genomic structures in food and humans (e.g., Streptococcus gallolyticus and Limosilactobabillus mucosae). The cFMD expands our knowledge on food microbiomes, their role in shaping the human microbiome, and supports future uses of metagenomics for food quality, safety, and authentication.

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