ArticleNature microbiology2018
Recovery of gut microbiota of healthy adults following antibiotic exposure.
Article in Nature microbiology, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 482 papers, 4 of them syntheses that pooled it.
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The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
482 citing papers in PubMed, 4 syntheses or guidelines pooled it.
- The impact of estrogen status on the gut microbiome: a systematic review and meta-analysis.Frontiers in endocrinology · 2026Pooled it
- Meta-Analysis of 16S rRNA Sequencing Reveals Altered Fecal but Not Vaginal Microbial Composition and Function in Women with Endometriosis.Medicina (Kaunas, Lithuania) · 2025Pooled it
- Assessing the impact of probiotics on immunotherapy effectiveness and antibiotic-mediated resistance in cancer: a systematic review and meta-analysis.Frontiers in immunology · 2025Pooled it
- A gut microbial signature for combination immune checkpoint blockade across cancer types.Nature medicine · 2024Pooled it
- Modulation of the gut microbiome and resistome by antibiotic use, but not by subsequent 2'-fucosyllactose intake, in adults with overweight or obesity.Gut microbes · 2026Trial
- A retrospectively registered pilot randomized controlled trial of postbiotic administration during antibiotic treatment increases microbiome diversity and enriches health-associated taxa.Infection and immunity · 2026Trial
- Trial
- Dysbiosis in the Gut Microbiome of Pembrolizumab-Treated Non-Small Lung Cancer Patients Compared to Healthy Controls Characterized Through Opportunistic Sampling.Thoracic cancer · 2025Trial
- Dietary and nutritional strategies for reducing disease risk associated with antibiotic-induced dysbiosis.Gut microbes · 2026Review
- A network dynamical simulation model for the study of antibiotic resistance in microbial communities.Gut microbes · 2026Article
- Pre-existing β-lactamase gene diversity is associated with lower risk of ESBL-producing Enterobacterales colonization in patients exposed to ceftriaxone.Gut microbes · 2026Article
- From gut dysbiosis to eubiosis: understanding microbiome recovery as an ecological process.Gut microbes · 2026Review
- Modulation of the response to immunotherapy in triple-negative breast cancer: the role of the microbiota and microbial metabolites in the tumor microenvironment.Gut microbes · 2026Review
- Article
- Prebiotics in sport and exercise: current evidence, practical applications, and methodological considerations.Journal of the International Society of Sports Nutrition · 2026Review
- Microbiome interactions in renal cell carcinoma: evidence, challenges and opportunities.Nature reviews. Urology · 2026Review
- Longitudinal ecological disruption and metabolite associations of the gut microbiome during acute myeloid leukemia therapy.Microbiology spectrum · 2026Article
- Comparative impact of imipenem and meropenem on intestinal carriage and relative fecal abundance of multidrug-resistant bacteria, with detection of residual antibiotics in rectal swabs.Microbiology spectrum · 2026Observational
- Microbiome ecology and antibiotic treatment failure: resistance spread, microbial competition and community engineering.Microbial genomics · 2026Review
- Gut microbiome dynamics in acute infectious diarrhea: A conceptual framework from acute dysbiosis toward precision restoration (Review).Experimental and therapeutic medicine · 2026Review
422 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
24 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
To minimize the impact of antibiotics, gut microorganisms harbour and exchange antibiotics resistance genes, collectively called their resistome. Using shotgun sequencing-based metagenomics, we analysed the partial eradication and subsequent regrowth of the gut microbiota in 12 healthy men over a 6-month period following a 4-day intervention with a cocktail of 3 last-resort antibiotics: meropenem, gentamicin and vancomycin. Initial changes included blooms of enterobacteria and other pathobionts, such as Enterococcus faecalis and Fusobacterium nucleatum, and the depletion of Bifidobacterium species and butyrate producers. The gut microbiota of the subjects recovered to near-baseline composition within 1.5 months, although 9 common species, which were present in all subjects before the treatment, remained undetectable in most of the subjects after 180 days. Species that harbour β-lactam resistance genes were positively selected for during and after the intervention. Harbouring glycopeptide or aminoglycoside resistance genes increased the odds of de novo colonization, however, the former also decreased the odds of survival. Compositional changes under antibiotic intervention in vivo matched results from in vitro susceptibility tests. Despite a mild yet long-lasting imprint following antibiotics exposure, the gut microbiota of healthy young adults are resilient to a short-term broad-spectrum antibiotics intervention and their antibiotics resistance gene carriage modulates their recovery processes.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.