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Antibiotic use and gut microbiome composition links from individual-level prescription data of 14,979 individuals

Baldanzi, Gabriel LU ; Larsson, Anna LU ; Sayols-Baixeras, Sergi ; Dekkers, Koen F ; Hammar, Ulf ; Nguyen, Diem ; Graells, Tíscar ; Ahmad, Shafqat ; Gazolla Volpiano, Camila and Meric, Guillaume , et al. (2026) In Nature Medicine
Abstract

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... (More)

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.

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publishing date
type
Contribution to journal
publication status
epub
subject
keywords
Antibiotics, Epidemiolgy, Metagenomics
in
Nature Medicine
pages
25 pages
publisher
Nature Publishing Group
external identifiers
  • scopus:105033295683
  • pmid:41814006
ISSN
1546-170X
DOI
10.1038/s41591-026-04284-y
language
English
LU publication?
yes
additional info
© 2026. The Author(s).
id
0eaaf9f8-765f-4ebc-8115-875d860ff59c
date added to LUP
2026-03-16 14:18:31
date last changed
2026-05-17 04:58:21
@article{0eaaf9f8-765f-4ebc-8115-875d860ff59c,
  abstract     = {{<p>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 &lt;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.</p>}},
  author       = {{Baldanzi, Gabriel and Larsson, Anna and Sayols-Baixeras, Sergi and Dekkers, Koen F and Hammar, Ulf and Nguyen, Diem and Graells, Tíscar and Ahmad, Shafqat and Gazolla Volpiano, Camila and Meric, Guillaume and Järhult, Josef D and Tängdén, Thomas and Ludvigsson, Jonas F and Lind, Lars and Sundström, Johan and Michaëlsson, Karl and Ärnlöv, Johan and Kennedy, Beatrice and Orho-Melander, Marju and Fall, Tove}},
  issn         = {{1546-170X}},
  keywords     = {{Antibiotics; Epidemiolgy; Metagenomics}},
  language     = {{eng}},
  month        = {{03}},
  publisher    = {{Nature Publishing Group}},
  series       = {{Nature Medicine}},
  title        = {{Antibiotic use and gut microbiome composition links from individual-level prescription data of 14,979 individuals}},
  url          = {{http://dx.doi.org/10.1038/s41591-026-04284-y}},
  doi          = {{10.1038/s41591-026-04284-y}},
  year         = {{2026}},
}