ArticleCell2013
Xenobiotics shape the physiology and gene expression of the active human gut microbiome.
Article in Cell, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 427 papers, 2 of them syntheses 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.
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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
427 citing papers in PubMed, 2 syntheses or guidelines pooled it.
- [Advances in the Application of Forensic Microbiome Analysis in Tissue Source Inference].Sichuan da xue xue bao. Yi xue ban = Journal of Sichuan University. Medical science edition · 2025Pooled it
- Diet, Microbes, and Cancer Across the Tree of Life: a Systematic Review.Current nutrition reports · 2022Pooled it
- From gut dysbiosis to eubiosis: understanding microbiome recovery as an ecological process.Gut microbes · 2026Review
- Recent advances and clinical relevance of microbiome dynamics in health and disease.Gut microbes · 2026Review
- Eggerthella lenta: metabolism, pathogenesis and therapeutic implications.Nature reviews. Microbiology · 2026Review
- The microbiota at the interface of environmental toxicants and the brain.Cell metabolism · 2026Review
- Community-wide adaptive evolution of gut bacteria during dietary transitions.bioRxiv : the preprint server for biology · 2026Article
- Antisense transcription reveals disease-associated adaptations in the human gut microbiome.Nature microbiology · 2026Article
- Reconsidering the Use of Dimethyl Sulfoxide for Xenobiotic-Gut Microbiota Interaction Studies.bioRxiv : the preprint server for biology · 2026Article
- Synergistic genomic design and thermal processing mitigate anti-nutritional constraints to enhance the nutritional efficacy of diploid potatoes.NPJ science of food · 2026Article
- Responses of skin and salivary microbiome to different environmental exposures.International journal of legal medicine · 2026Article
- Impact of Two Common Beekeeper-Applied Chemicals on Honey Bee Queen Fecundity and Gut Microbial Communities.Microbial ecology · 2026Article
- Integration of human microbiota (SIHUMIx) and zebrafish models reveals microbiome-mediated host responses to azoxystrobin.Toxicological sciences : an official journal of the Society of Toxicology · 2026Article
- Widespread effects of catecholamines on growth of human gut bacteria.NPJ biofilms and microbiomes · 2026Article
- Flow Cytometric Screening Reveals Nucleic Acid Dyes Aberrantly Stain Peptidoglycan Sacculi.ACS infectious diseases · 2026Article
- Gut phages are linked to off-target antimicrobial resistance genes in orthopedic patients receiving peri-surgical antibiotics.Frontiers in microbiology · 2026Article
- Dynamics of the gut microbiome and resistome in response to prophylactic antibiotic treatment in post-surgical giant pandas.Scientific reports · 2025Article
- Best practices for developing microbiome-based disease diagnostic classifiers through machine learning.Gut microbes · 2025Article
- The gut microbiota: an emerging modulator of drug resistance in hepatocellular carcinoma.Gut microbes · 2025Review
- The presence and induction of regioselective dehydroxylases dictate urolithin metabolism by Enterocloster species.NPJ biofilms and microbiomes · 2025Article
367 more citing papers are in PubMed but not listed here.
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3 authors.
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Abstract
The human gut contains trillions of microorganisms that influence our health by metabolizing xenobiotics, including host-targeted drugs and antibiotics. Recent efforts have characterized the diversity of this host-associated community, but it remains unclear which microorganisms are active and what perturbations influence this activity. Here, we combine flow cytometry, 16S rRNA gene sequencing, and metatranscriptomics to demonstrate that the gut contains a distinctive set of active microorganisms, primarily Firmicutes. Short-term exposure to a panel of xenobiotics significantly affected the physiology, structure, and gene expression of this active gut microbiome. Xenobiotic-responsive genes were found across multiple bacterial phyla, encoding antibiotic resistance, drug metabolism, and stress response pathways. These results demonstrate the power of moving beyond surveys of microbial diversity to better understand metabolic activity, highlight the unintended consequences of xenobiotics, and suggest that attempts at personalized medicine should consider interindividual variations in the active human gut microbiome.
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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.