ArticleNature microbiology2024
High-throughput transcriptomics of 409 bacteria-drug pairs reveals drivers of gut microbiota perturbation.
Article in Nature microbiology, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 24 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
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.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
24 citing papers in PubMed, 27 citations in OpenAlex.
- Drug-microbiome-host interactions: antimicrobial effects of non-antibiotic compounds.Nature reviews. Gastroenterology & hepatology · 2026Review
- Eggerthella lenta: metabolism, pathogenesis and therapeutic implications.Nature reviews. Microbiology · 2026Review
- Probiotics mitigate non-antibiotic drug-induced dysbiosis via protein homology-driven competitive binding.Nature communications · 2026Article
- A class of metallohydrolases expands bile salt hydrolase activity in the gut.bioRxiv : the preprint server for biology · 2026Article
- Gut dysbiosis in oncology: a risk factor for immunoresistance.Cell research · 2026Review
- Review
- Precision microbiome medicine and therapeutics: the enabling role of in vitro gut models.FEMS microbiology reviews · 2026Review
- Beyond antibiotics: collateral damage to the gut microbiome during cancer therapy.Frontiers in microbiology · 2026Review
- Antagonistic drug interactions protect commensalGut microbes · 2025Article
- The Role of Gut Microbiota and Mucin Barrier in the Pathogenesis of Colorectal Cancer.Current issues in molecular biology · 2025Review
- Metagenomic editing of commensal bacteria in vivo using CRISPR-associated transposases.Science (New York, N.Y.) · 2025Article
- Bidirectional Interplay Between IBD Therapies and the Gut Microbiota: A Pharmacomicrobiomic Approach to Personalized Treatment.BioDrugs : clinical immunotherapeutics, biopharmaceuticals and gene therapy · 2025Review
- Article
- Impact of drugs and environmental contaminants on amine production by gut bacteria.Molecular systems biology · 2025Article
- Article
- Integrative systems biology approaches for analyzing microbiome dysbiosis and species interactions.Briefings in bioinformatics · 2025Review
- Systematic screen uncovers regulator contributions to chemical cues in Escherichia coli.PLoS biology · 2025Article
- Enabling next-generation anaerobic cultivation through biotechnology to advance functional microbiome research.Nature biotechnology · 2025Review
- MicrobeRX: a tool for enzymatic-reaction-based metabolite prediction in the gut microbiome.Microbiome · 2025Article
- The microbiome as a modulator of neurological health across the maternal-offspring interface.The Journal of clinical investigation · 2025Review
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
6 authors at 1 institution in 1 country.
Funding
Abstract
Many drugs can perturb the gut microbiome, potentially leading to negative health consequences. However, mechanisms of most microorganism-drug responses have not been elucidated at the genetic level. Using high-throughput bacterial transcriptomics, we systematically characterized the gene expression profiles of prevalent human gut bacteria exposed to the most frequently prescribed orally administered pharmaceuticals. Across >400 drug-microorganism pairs, significant and reproducible transcriptional responses were observed, including pathways involved in multidrug resistance, metabolite transport, tartrate metabolism and riboflavin biosynthesis. Importantly, we discovered that statin-mediated upregulation of the AcrAB-TolC efflux pump in Bacteroidales species enhances microbial sensitivity to vitamin A and secondary bile acids. Moreover, gut bacteria carrying acrAB-tolC genes are depleted in patients taking simvastatin, suggesting that drug-efflux interactions generate collateral toxicity that depletes pump-containing microorganisms from patient microbiomes. This study provides a resource to further understand the drivers of drug-mediated microbiota shifts for better informed clinical interventions.
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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.