ArticleThe ISME journal2016
The initial state of the human gut microbiome determines its reshaping by antibiotics.
Article in The ISME journal, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 189 papers, 5 of them syntheses that pooled it.
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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
189 citing papers in PubMed, 5 syntheses or guidelines pooled it, 359 citations in OpenAlex.
- Identification of robust and generalizable biomarkers for microbiome-based stratification in lifestyle interventions.Microbiome · 2023Pooled it
- Identification of robust and generalizable biomarkers for microbiome-based stratification in lifestyle interventions.Microbiome · 2023Pooled it
- Host phenotype classification from human microbiome data is mainly driven by the presence of microbial taxa.PLoS computational biology · 2022Pooled it
- Systematic review of human gut resistome studies revealed variable definitions and approaches.Gut microbes · 2020Pooled it
- Individualized recovery of gut microbial strains post antibiotics.NPJ biofilms and microbiomesPooled it
- Gut microbial diversity at baseline conditions the clinical, microbiome, and metabolic response to paraprobioticGut microbes · 2026Trial
- Influence of diet on acute endocannabinoidome mediator levels post exercise in active women, a crossover randomized study.Scientific reports · 2022Trial
- Luminal microbiota related to Crohn's disease recurrence after surgery.Gut microbes · 2020Trial
- Trial
- Gut Microbial Diversity in Antibiotic-Naive Children After Systemic Antibiotic Exposure: A Randomized Controlled Trial.Clinical infectious diseases : an official publication of the Infectious Diseases Society of America · 2017Trial
- From gut dysbiosis to eubiosis: understanding microbiome recovery as an ecological process.Gut microbes · 2026Review
- Dietary and nutritional strategies for reducing disease risk associated with antibiotic-induced dysbiosis.Gut microbes · 2026Review
- Distinct Basal Gut Microbiota Profiles Are Associated with Strain-Specific Lung Responses toBiology · 2026Article
- Strain transmission links human microbiomes along the oral-gut axis and across cohabiting individuals.Cell press blue · 2026Article
- High early-life gut Bacteroides links to microbiome stability, resilience, and risk for childhood infections.NPJ biofilms and microbiomes · 2026Article
- Antibiotic-induced gut microbiome dysbiosis: risks and strategies for mitigation.The EMBO journal · 2026Review
- Article
- Dietary intake of enrofloxacin promotes the spread of antibiotic resistance from food to simulated human gut.The ISME journal · 2026Article
- South African Honey: Anti-International journal of food science · 2026Article
- Antibiotic: a boon to mankind and doom to the environment - an insight on biological and non-biological degradation processes.Frontiers in microbiology · 2026Review
129 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
22 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Microbiome studies have demonstrated the high inter-individual diversity of the gut microbiota. However, how the initial composition of the microbiome affects the impact of antibiotics on microbial communities is relatively unexplored. To specifically address this question, we administered a second-generation cephalosporin, cefprozil, to healthy volunteers. Stool samples gathered before antibiotic exposure, at the end of the treatment and 3 months later were analysed using shotgun metagenomic sequencing. On average, 15 billion nucleotides were sequenced for each sample. We show that standard antibiotic treatment can alter the gut microbiome in a specific, reproducible and predictable manner. The most consistent effect of the antibiotic was the increase of Lachnoclostridium bolteae in 16 out of the 18 cefprozil-exposed participants. Strikingly, we identified a subgroup of participants who were enriched in the opportunistic pathogen Enterobacter cloacae after exposure to the antibiotic, an effect linked to lower initial microbiome diversity and to a Bacteroides enterotype. Although the resistance gene content of participants' microbiomes was altered by the antibiotic, the impact of cefprozil remained specific to individual participants. Resistance genes that were not detectable prior to treatment were observed after a 7-day course of antibiotic administration. Specifically, point mutations in beta-lactamase blaCfxA-6 were enriched after antibiotic treatment in several participants. This suggests that monitoring the initial composition of the microbiome before treatment could assist in the prevention of some of the adverse effects associated with antibiotics or other treatments.
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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.