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Gut metagenome associations with extensive digital health data in a volunteer-based Estonian microbiome cohort

Author

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  • Oliver Aasmets

    (Estonian Genome Centre, Institute of Genomics, University of Tartu)

  • Kertu Liis Krigul

    (Estonian Genome Centre, Institute of Genomics, University of Tartu)

  • Kreete Lüll

    (Estonian Genome Centre, Institute of Genomics, University of Tartu)

  • Andres Metspalu

    (Estonian Genome Centre, Institute of Genomics, University of Tartu
    Institute of Cell and Molecular Biology, University of Tartu)

  • Elin Org

    (Estonian Genome Centre, Institute of Genomics, University of Tartu)

Abstract

Microbiome research is starting to move beyond the exploratory phase towards interventional trials and therefore well-characterized cohorts will be instrumental for generating hypotheses and providing new knowledge. As part of the Estonian Biobank, we established the Estonian Microbiome Cohort which includes stool, oral and plasma samples from 2509 participants and is supplemented with multi-omic measurements, questionnaires, and regular linkages to national electronic health records. Here we analyze stool data from deep metagenomic sequencing together with rich phenotyping, including 71 diseases, 136 medications, 21 dietary questions, 5 medical procedures, and 19 other factors. We identify numerous relationships (n = 3262) with different microbiome features. In this study, we extend the understanding of microbiome-host interactions using electronic health data and show that long-term antibiotic usage, independent from recent administration, has a significant impact on the microbiome composition, partly explaining the common associations between diseases.

Suggested Citation

  • Oliver Aasmets & Kertu Liis Krigul & Kreete Lüll & Andres Metspalu & Elin Org, 2022. "Gut metagenome associations with extensive digital health data in a volunteer-based Estonian microbiome cohort," Nature Communications, Nature, vol. 13(1), pages 1-11, December.
    • Handle: RePEc:nat:natcom:v:13:y:2022:i:1:d:10.1038_s41467-022-28464-9
    DOI: 10.1038/s41467-022-28464-9
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    1. Victoria E. Ruiz & Thomas Battaglia & Zachary D. Kurtz & Luc Bijnens & Amy Ou & Isak Engstrand & Xuhui Zheng & Tadasu Iizumi & Briana J. Mullins & Christian L. Müller & Ken Cadwell & Richard Bonneau &, 2017. "A single early-in-life macrolide course has lasting effects on murine microbial network topology and immunity," Nature Communications, Nature, vol. 8(1), pages 1-14, December.
    2. Lisa Maier & Mihaela Pruteanu & Michael Kuhn & Georg Zeller & Anja Telzerow & Exene Erin Anderson & Ana Rita Brochado & Keith Conrad Fernandez & Hitomi Dose & Hirotada Mori & Kiran Raosaheb Patil & Pe, 2018. "Extensive impact of non-antibiotic drugs on human gut bacteria," Nature, Nature, vol. 555(7698), pages 623-628, March.
    3. Arnau Vich Vila & Valerie Collij & Serena Sanna & Trishla Sinha & Floris Imhann & Arno R. Bourgonje & Zlatan Mujagic & Daisy M. A. E. Jonkers & Ad A. M. Masclee & Jingyuan Fu & Alexander Kurilshikov &, 2020. "Impact of commonly used drugs on the composition and metabolic function of the gut microbiota," Nature Communications, Nature, vol. 11(1), pages 1-11, December.
    4. Matthew A. Jackson & Serena Verdi & Maria-Emanuela Maxan & Cheol Min Shin & Jonas Zierer & Ruth C. E. Bowyer & Tiphaine Martin & Frances M. K. Williams & Cristina Menni & Jordana T. Bell & Tim D. Spec, 2018. "Gut microbiota associations with common diseases and prescription medications in a population-based cohort," Nature Communications, Nature, vol. 9(1), pages 1-8, December.
    5. Vinod K. Gupta & Minsuk Kim & Utpal Bakshi & Kevin Y. Cunningham & John M. Davis & Konstantinos N. Lazaridis & Heidi Nelson & Nicholas Chia & Jaeyun Sung, 2020. "A predictive index for health status using species-level gut microbiome profiling," Nature Communications, Nature, vol. 11(1), pages 1-16, December.
    6. Verónica Lloréns-Rico & Sara Vieira-Silva & Pedro J. Gonçalves & Gwen Falony & Jeroen Raes, 2021. "Benchmarking microbiome transformations favors experimental quantitative approaches to address compositionality and sampling depth biases," Nature Communications, Nature, vol. 12(1), pages 1-12, December.
    7. Zachary D Kurtz & Christian L Müller & Emily R Miraldi & Dan R Littman & Martin J Blaser & Richard A Bonneau, 2015. "Sparse and Compositionally Robust Inference of Microbial Ecological Networks," PLOS Computational Biology, Public Library of Science, vol. 11(5), pages 1-25, May.
    8. Manimozhiyan Arumugam & Jeroen Raes & Eric Pelletier & Denis Le Paslier & Takuji Yamada & Daniel R. Mende & Gabriel R. Fernandes & Julien Tap & Thomas Bruls & Jean-Michel Batto & Marcelo Bertalan & Na, 2011. "Enterotypes of the human gut microbiome," Nature, Nature, vol. 473(7346), pages 174-180, May.
    9. Manimozhiyan Arumugam & Jeroen Raes & Eric Pelletier & Denis Le Paslier & Takuji Yamada & Daniel R. Mende & Gabriel R. Fernandes & Julien Tap & Thomas Bruls & Jean-Michel Batto & Marcelo Bertalan & Na, 2011. "Erratum: Enterotypes of the human gut microbiome," Nature, Nature, vol. 474(7353), pages 666-666, June.
    10. Les Dethlefsen & Sue Huse & Mitchell L Sogin & David A Relman, 2008. "The Pervasive Effects of an Antibiotic on the Human Gut Microbiota, as Revealed by Deep 16S rRNA Sequencing," PLOS Biology, Public Library of Science, vol. 6(11), pages 1-18, November.
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