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Extensive impact of non-antibiotic drugs on human gut bacteria

Author

Listed:
  • Lisa Maier

    (European Molecular Biology Laboratory, Genome Biology Unit)

  • Mihaela Pruteanu

    (European Molecular Biology Laboratory, Genome Biology Unit
    Humboldt University Berlin)

  • Michael Kuhn

    (European Molecular Biology Laboratory, Structural and Computational Biology Unit)

  • Georg Zeller

    (European Molecular Biology Laboratory, Structural and Computational Biology Unit)

  • Anja Telzerow

    (European Molecular Biology Laboratory, Genome Biology Unit)

  • Exene Erin Anderson

    (European Molecular Biology Laboratory, Genome Biology Unit)

  • Ana Rita Brochado

    (European Molecular Biology Laboratory, Genome Biology Unit)

  • Keith Conrad Fernandez

    (European Molecular Biology Laboratory, Genome Biology Unit)

  • Hitomi Dose

    (Graduate School of Biological Sciences, Nara Institute of Science and Technology)

  • Hirotada Mori

    (Graduate School of Biological Sciences, Nara Institute of Science and Technology)

  • Kiran Raosaheb Patil

    (European Molecular Biology Laboratory, Structural and Computational Biology Unit)

  • Peer Bork

    (European Molecular Biology Laboratory, Structural and Computational Biology Unit
    Max-Delbrück-Centre for Molecular Medicine
    Molecular Medicine Partnership Unit
    Biocenter, University of Würzburg)

  • Athanasios Typas

    (European Molecular Biology Laboratory, Genome Biology Unit
    European Molecular Biology Laboratory, Structural and Computational Biology Unit)

Abstract

A few commonly used non-antibiotic drugs have recently been associated with changes in gut microbiome composition, but the extent of this phenomenon is unknown. Here, we screened more than 1,000 marketed drugs against 40 representative gut bacterial strains, and found that 24% of the drugs with human targets, including members of all therapeutic classes, inhibited the growth of at least one strain in vitro. Particular classes, such as the chemically diverse antipsychotics, were overrepresented in this group. The effects of human-targeted drugs on gut bacteria are reflected on their antibiotic-like side effects in humans and are concordant with existing human cohort studies. Susceptibility to antibiotics and human-targeted drugs correlates across bacterial species, suggesting common resistance mechanisms, which we verified for some drugs. The potential risk of non-antibiotics promoting antibiotic resistance warrants further exploration. Our results provide a resource for future research on drug–microbiome interactions, opening new paths for side effect control and drug repurposing, and broadening our view of antibiotic resistance.

Suggested Citation

  • 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.
    • Handle: RePEc:nat:nature:v:555:y:2018:i:7698:d:10.1038_nature25979
    DOI: 10.1038/nature25979
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    Cited by:

    1. 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.
    2. Karolína Ondrová & Iveta Zůvalová & Barbora Vyhlídalová & Kristýna Krasulová & Eva Miková & Radim Vrzal & Petr Nádvorník & Binod Nepal & Sandhya Kortagere & Martina Kopečná & David Kopečný & Marek Šeb, 2023. "Monoterpenoid aryl hydrocarbon receptor allosteric antagonists protect against ultraviolet skin damage in female mice," Nature Communications, Nature, vol. 14(1), pages 1-15, December.
    3. Xuanji Li & Asker Brejnrod & Jonathan Thorsen & Trine Zachariasen & Urvish Trivedi & Jakob Russel & Gisle Alberg Vestergaard & Jakob Stokholm & Morten Arendt Rasmussen & Søren Johannes Sørensen, 2023. "Differential responses of the gut microbiome and resistome to antibiotic exposures in infants and adults," Nature Communications, Nature, vol. 14(1), pages 1-16, December.
    4. Lu Wu & Xu-Wen Wang & Zining Tao & Tong Wang & Wenlong Zuo & Yu Zeng & Yang-Yu Liu & Lei Dai, 2024. "Data-driven prediction of colonization outcomes for complex microbial communities," Nature Communications, Nature, vol. 15(1), pages 1-15, December.
    5. Cédric Diot & Aurian P. García-González & Andre F. Vieira & Melissa Walker & Megan Honeywell & Hailey Doyle & Olga Ponomarova & Yomari Rivera & Huimin Na & Hefei Zhang & Michael Lee & Carissa P. Olsen, 2022. "Bacterial diet modulates tamoxifen-induced death via host fatty acid metabolism," Nature Communications, Nature, vol. 13(1), pages 1-15, December.
    6. Yonggan Sun & Qixing Nie & Shanshan Zhang & Huijun He & Sheng Zuo & Chunhua Chen & Jingrui Yang & Haihong Chen & Jielun Hu & Song Li & Jiaobo Cheng & Baojie Zhang & Zhitian Zheng & Shijie Pan & Ping H, 2023. "Parabacteroides distasonis ameliorates insulin resistance via activation of intestinal GPR109a," Nature Communications, Nature, vol. 14(1), pages 1-16, December.
    7. Daniel P. Newton & Po-Yi Ho & Kerwyn Casey Huang, 2023. "Modulation of antibiotic effects on microbial communities by resource competition," Nature Communications, Nature, vol. 14(1), pages 1-12, December.

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