Antibiotic use and gut microbiome composition links from individual-level prescription data of 14,979 individuals
Disruptions in gut microbiome are implicated in cardiometabolic disorders and other health outcomes. Antibiotics are known gut microbiome disruptors, but their long-term consequences remain underexplored. Here we combined individual-level data from the Swedish Prescribed Drug Register with fecal metagenomes of 14,979 adults to examine the association between oral antibiotic use over 8 years and gut microbiome. In multivariable confounder-adjusted regression models, antibiotic use <1 year before fecal sampling was associated with the greatest reduction in species diversity, but significant associations were also observed for use 1-4 and 4-8 years earlier. Clindamycin, fluoroquinolones and flucloxacillin accounted for most of the associations with the abundance of individual species. Use of these antibiotics 4-8 years earlier was associated with altered abundance of 10-15% of the species studied; penicillin V, extended-spectrum penicillins and nitrofurantoin were associated with only a few species. Similar results were found comparing one antibiotic course 4-8 years before sampling versus none in the past 8 years. These findings indicate that antibiotics may have long-lasting consequences for the gut microbiome.
Authors
- Sergi Sayols-Baixeras (ORCID: https://orcid.org/0000-0002-1181-6262)
- Gabriel Baldanzi (ORCID: https://orcid.org/0000-0003-3962-3953)
- Beatrice Kennedy (ORCID: https://orcid.org/0000-0002-0066-4814)
- Camila Gazolla Volpiano (ORCID: https://orcid.org/0000-0002-8251-1685)
- Josef D. Järhult (ORCID: https://orcid.org/0000-0002-7075-1059)
- Guillaume Méric (ORCID: https://orcid.org/0000-0001-6288-9958)
- Koen F. Dekkers (ORCID: https://orcid.org/0000-0002-4074-7235)
- Johan Sundström (ORCID: https://orcid.org/0000-0003-2247-8454)
- Tíscar Graells (ORCID: https://orcid.org/0000-0002-2376-3559)
- Shafqat Ahmad (ORCID: https://orcid.org/0000-0002-3873-7943)
- Thomas Tängdén (ORCID: https://orcid.org/0000-0001-7142-9849)
- Lars Lind
- Ulf Hammar
- Diem Nguyen
- Marju Orho-Melander
- Johan Ärnlöv
- Karl Michaëlsson
- Anna Larsson
- Tove Fall
- Jonas F. Ludvigsson
Institutions
- Dalarna University (SE)
- Uppsala University (SE)
- Brigham and Women's Hospital (US)
- Södertörn University (SE)
- Baker Heart and Diabetes Institute (AU)
- The University of Melbourne (AU)
- Lund University (SE)
- La Trobe University (AU)
- Columbia University Irving Medical Center (US)
- Science for Life Laboratory (SE)
- Instituto de Salud Carlos III (ES)
- Karolinska Institutet (SE)
- UNSW Sydney (AU)
- The George Institute for Global Health (AU)
- Örebro University Hospital (SE)
- Center for Clinical Research Dalarna (SE)
- University of Bath (GB)
Publication Details
- Journal
- Nature Medicine
- Published
- 2026-03-11
- DOI
- https://doi.org/10.1038/s41591-026-04284-y
- Citations
- 1
- Primary Topic
- Gut microbiota and health
- Type
- article
- Field-Weighted Citation Impact
- 22.24
Funders
- Göran Gustafssons Stiftelser
- Stiftelsen för Strategisk Forskning
- VINNOVA
- Svenska Forskningsrådet Formas
- Lunds Universitet
- Hjärt-Lungfonden
- Linköpings Universitet
- Karolinska Institutet
- Knut och Alice Wallenbergs Stiftelse
- Novo Nordisk
- Stiftelsen Olle Engkvist Byggmästare
- Vetenskapsrådet
- Umeå Universitet
- Akademiska Sjukhuset
- Sahlgrenska Universitetssjukhuset
- Göteborgs Universitet
- Uppsala Universitet
- Novo Nordisk Fonden
- Ernhold Lundströms stiftelse
- Skånes universitetssjukhus
- Uppsala Multidisciplinary Center for Advanced Computational Science