Trial reportBMC biology2019
Distinct impact of antibiotics on the gut microbiome and resistome: a longitudinal multicenter cohort study.
Trial report in BMC biology, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. It is linked to trial NCT02058888 (Self-controlled Cohort Study of the Amplification and Selection of Antimicrobial Resistance in the Human Intestine), which is not on this map. Cited by 87 papers, 1 of them a synthesis that pooled it.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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.
Self-controlled Cohort Study of the Amplification and Selection of Antimicrobial Resistance in the Human Intestine
Who cites it
87 citing papers in PubMed, 1 synthesis or guideline pooled it, 168 citations in OpenAlex.
- Variability of strain engraftment and predictability of microbiome composition after fecal microbiota transplantation across different diseases.Nature medicine · 2022Pooled it
- Potential of Fecal Microbiota Transplantation to Prevent Acute GVHD: Analysis from a Phase II Trial.Clinical cancer research : an official journal of the American Association for Cancer Research · 2023Trial
- Alterations of human skin microbiome and expansion of antimicrobial resistance after systemic antibiotics.Science translational medicine · 2021Trial
- Microbiome recovery in adult females with uncomplicated urinary tract infections in a randomised phase 2A trial of the novel antibiotic gepotidacin (GSK140944).BMC microbiology · 2021Trial
- Distinct impact of antibiotics on the gut microbiome and resistome: a longitudinal multicenter cohort study.BMC biology · 2019Trial
- From gut dysbiosis to eubiosis: understanding microbiome recovery as an ecological process.Gut microbes · 2026Review
- A genotoxin associated with colorectal cancer linked to gut dysbiosis in children with cystic fibrosis.Journal of bacteriology · 2026Article
- Review
- Safety of Fluoroquinolones and Cotrimoxazole in Urinary Tract Infections in Older Males.Open forum infectious diseases · 2026Article
- Bacterial fecal microbiome composition associated with HIV stage among rural and peri-urban adults living with HIV in Uganda.BMC infectious diseases · 2026Article
- Antibiotic exposure impairs the efficacy of first-line chemoimmunotherapy in non-small cell lung cancer through the regulation of gut microbiome and bile acid metabolism.Precision clinical medicine · 2026Article
- Article
- Broad-spectrum antibiotic treatment reshapes the gut microbiome, resistome, and colonization potential of opportunistic pathogens: a metagenomics study.Gut pathogens · 2026Article
- Gut microbiome resistotypes reflect chronological age andFrontiers in microbiology · 2026Article
- The role of the gut microbiome in antibiotic-driven antimicrobial resistance.Frontiers in microbiology · 2026Review
- Early Antibiotic Use and Retinopathy of Prematurity: A Single-Center Retrospective Cohort Study.Ophthalmology science · 2026Article
- Antibiotic-induced gut microbiota dysbiosis and bile acid metabolism: implications for intestinal health, immune regulation, and disease susceptibility.Frontiers in microbiology · 2026Review
- Early trajectories of antibiotic exposure and colonization pressure and risk of ICU-acquired carbapenem-resistant Gram-negative bacteria: A prospective cohort study.Annals of intensive care · 2026Article
- Quantifying the bystander effect of antimicrobial use on the gut microbiome and resistome in Malawian adults.Nature communications · 2025Article
- Effects of commonly used antibiotics on children's developing gut microbiomes and resistomes in peri-urban Lima, Peru.The Journal of antimicrobial chemotherapy · 2025Article
27 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
9 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundThe selection pressure exercised by antibiotic drugs is an important consideration for the wise stewardship of antimicrobial treatment programs. Treatment decisions are currently based on crude assumptions, and there is an urgent need to develop a more quantitative knowledge base that can enable predictions of the impact of individual antibiotics on the human gut microbiome and resistome.
resultsUsing shotgun metagenomics, we quantified changes in the gut microbiome in two cohorts of hematological patients receiving prophylactic antibiotics; one cohort was treated with ciprofloxacin in a hospital in Tübingen and the other with cotrimoxazole in a hospital in Cologne. Analyzing this rich longitudinal dataset, we found that gut microbiome diversity was reduced in both treatment cohorts to a similar extent, while effects on the gut resistome differed. We observed a sharp increase in the relative abundance of sulfonamide antibiotic resistance genes (ARGs) by 148.1% per cumulative defined daily dose of cotrimoxazole in the Cologne cohort, but not in the Tübingen cohort treated with ciprofloxacin. Through multivariate modeling, we found that factors such as individual baseline microbiome, resistome, and plasmid diversity; liver/kidney function; and concurrent medication, especially virostatic agents, influence resistome alterations. Strikingly, we observed different effects on the plasmidome in the two treatment groups. There was a substantial increase in the abundance of ARG-carrying plasmids in the cohort treated with cotrimoxazole, but not in the cohort treated with ciprofloxacin, indicating that cotrimoxazole might contribute more efficiently to the spread of resistance.
conclusionsOur study represents a step forward in developing the capability to predict the effect of individual antimicrobials on the human microbiome and resistome. Our results indicate that to achieve this, integration of the individual baseline microbiome, resistome, and mobilome status as well as additional individual patient factors will be required. Such personalized predictions may in the future increase patient safety and reduce the spread of resistance.
trial registrationClinicalTrials.gov, NCT02058888 . Registered February 10 2014.
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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.