Antibiotic perturbation of the human gut phageome preserves its individuality and promotes blooms of virulent phages
Antibiotic use disrupts the gut microbiota, posing risks of long-term health issues and resistance. To study its impact on gut phages, we followed 22 healthy individuals 2 weeks before and up to 6 months after a 3-day course of 3<sup>rd</sup>-generation cephalosporins. Our results show that gut phages rarely encode antibiotic resistance genes and are mostly temperate, including many phage plasmids. Furthermore, phage populations remain individual-specific even after microbiome perturbation. Yet, we report a 20% decline in phage diversity the day after treatment, alongside blooms of a few, mostly virulent, phages. We suggest that some of these phages contribute to the recovery of bacterial diversity via "kill-the-winner" dynamics. This is supported by (temporarily) dominant phages targeting Parabacteroides distasonis, a bacterium that thrives post-treatment only in the absence of these phages. Our findings suggest gut phages are crucial to the microbiome response to antibiotics, aiding the restoration of balance and diversity.
Authors
- Rémi Denise (ORCID: https://orcid.org/0000-0003-2277-689X)
- Charles Burdet (ORCID: https://orcid.org/0000-0003-4138-0794)
- Marie Touchon (ORCID: https://orcid.org/0000-0001-7389-447X)
- Camille d’Humières (ORCID: https://orcid.org/0000-0001-5912-863X)
- Quentin Lamy-Besnier (ORCID: https://orcid.org/0000-0002-7141-6340)
- Eduardo P. C. Rocha (ORCID: https://orcid.org/0000-0001-7704-822X)
- France Mentré (ORCID: https://orcid.org/0000-0002-7045-1275)
- Bénédicte Condamine (ORCID: https://orcid.org/0000-0002-3513-7168)
- Laurence Ma (ORCID: https://orcid.org/0000-0003-4050-1814)
- Erick Denamur
- Eugen Pfeifer (ORCID: https://orcid.org/0000-0002-4554-3696)
- Florian Plaza Oñate (ORCID: https://orcid.org/0000-0001-6036-0989)
- Sara Dion
Institutions
- Délégation Paris 5 (FR)
- Centre National de la Recherche Scientifique (FR)
- Inserm (FR)
- Institut Pasteur (FR)
- Université Paris Cité (FR)
- AgroParisTech (FR)
- Université Paris-Saclay (FR)
- Microbiologie de l’alimentation au service de la santé (FR)
- Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement (FR)
- Sorbonne Paris Cité (FR)
- Evolutionary Genomics (United States) (US)
Publication Details
- Journal
- Cell Reports
- Published
- 2025-07-21
- DOI
- https://doi.org/10.1016/j.celrep.2025.116020
- Citations
- 3
- Primary Topic
- Bacteriophages and microbial interactions
- Type
- article
- Field-Weighted Citation Impact
- 5.15
Funders
- Agence Nationale de la Recherche