Extensive impact of non-antibiotic drugs on human gut bacteria

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 (), Peer Bork () and Athanasios Typas ()
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Lisa Maier: European Molecular Biology Laboratory, Genome Biology Unit
Mihaela Pruteanu: European Molecular Biology Laboratory, Genome Biology Unit
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
Athanasios Typas: European Molecular Biology Laboratory, Genome Biology Unit

Nature, 2018, vol. 555, issue 7698, 623-628

Abstract: 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.

Date: 2018
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DOI: 10.1038/nature25979

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