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Large-scale genome-wide analysis links lactic acid bacteria from food with the gut microbiome

Author

Listed:
  • Edoardo Pasolli

    (University of Naples Federico II
    University of Naples Federico II)

  • Francesca Filippis

    (University of Naples Federico II
    University of Naples Federico II)

  • Italia E. Mauriello

    (University of Naples Federico II)

  • Fabio Cumbo

    (University of Trento)

  • Aaron M. Walsh

    (Teagasc Food Research Centre
    APC Microbiome Ireland)

  • John Leech

    (Teagasc Food Research Centre
    APC Microbiome Ireland)

  • Paul D. Cotter

    (Teagasc Food Research Centre
    APC Microbiome Ireland)

  • Nicola Segata

    (University of Trento)

  • Danilo Ercolini

    (University of Naples Federico II
    University of Naples Federico II)

Abstract

Lactic acid bacteria (LAB) are fundamental in the production of fermented foods and several strains are regarded as probiotics. Large quantities of live LAB are consumed within fermented foods, but it is not yet known to what extent the LAB we ingest become members of the gut microbiome. By analysis of 9445 metagenomes from human samples, we demonstrate that the prevalence and abundance of LAB species in stool samples is generally low and linked to age, lifestyle, and geography, with Streptococcus thermophilus and Lactococcus lactis being most prevalent. Moreover, we identify genome-based differences between food and gut microbes by considering 666 metagenome-assembled genomes (MAGs) newly reconstructed from fermented food microbiomes along with 154,723 human MAGs and 193,078 reference genomes. Our large-scale genome-wide analysis demonstrates that closely related LAB strains occur in both food and gut environments and provides unprecedented evidence that fermented foods can be indeed regarded as a possible source of LAB for the gut microbiome.

Suggested Citation

  • Edoardo Pasolli & Francesca Filippis & Italia E. Mauriello & Fabio Cumbo & Aaron M. Walsh & John Leech & Paul D. Cotter & Nicola Segata & Danilo Ercolini, 2020. "Large-scale genome-wide analysis links lactic acid bacteria from food with the gut microbiome," Nature Communications, Nature, vol. 11(1), pages 1-12, December.
    • Handle: RePEc:nat:natcom:v:11:y:2020:i:1:d:10.1038_s41467-020-16438-8
    DOI: 10.1038/s41467-020-16438-8
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    Cited by:

    1. Vincent Somerville & Nadine Thierer & Remo S. Schmidt & Alexandra Roetschi & Lauriane Braillard & Monika Haueter & Hélène Berthoud & Noam Shani & Ueli Ah & Florent Mazel & Philipp Engel, 2024. "Genomic and phenotypic imprints of microbial domestication on cheese starter cultures," Nature Communications, Nature, vol. 15(1), pages 1-12, December.

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