ArticleGut2015
Uncovering effects of antibiotics on the host and microbiota using transkingdom gene networks.
Article in Gut, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 158 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.
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
158 citing papers in PubMed, 2 syntheses or guidelines pooled it, 301 citations in OpenAlex.
- Multi-omic network analysis identified betacellulin as a novel target of omega-3 fatty acid attenuation of western diet-induced nonalcoholic steatohepatitis.EMBO molecular medicine · 2023Pooled it
- Role of gut microbiota in type 2 diabetes pathophysiology.EBioMedicine · 2020Pooled it
- l-Carnitine in omnivorous diets induces an atherogenic gut microbial pathway in humans.The Journal of clinical investigation · 2019Trial
- Human fecal transplantation from stunted children promotes metabolic dysfunction in mice fed with a high-fat and high-fructose corn syrup diet.Gut microbes · 2026Article
- Gut dysbiosis modulates hyperoxia-induced bronchopulmonary dysplasia by promoting EMT through activating TLR4/NF-κB pathway.Molecular medicine (Cambridge, Mass.) · 2026Article
- The elephant (bird) in the room: unknown mechanisms and unresolved impacts of low DNA yields in avian microbiome research.Animal microbiome · 2026Article
- Navigating multi-omic integration methods for human microbiome research.Nature microbiology · 2026Review
- Antibiotic treatment reveals the contributions of the gut microbiome to CLN2 disease in the central and enteric nervous system.Scientific reports · 2026Article
- The hidden cost of antibiotics: microbial dysbiosis-induced SCFA imbalance and its underlying mechanisms.Frontiers in immunology · 2026Review
- Article
- Engineered an ultrasmall curcumin oral nanoformulation restores intestinal integrity and gut microbiota dysbiosis.Materials today. Bio · 2025Article
- Gut microbiota as a predictive tool for outcomes in IgA nephropathy.Renal failure · 2025Article
- Gut-larynx axis and its contribution to laryngeal immunity.mSystems · 2025Article
- Human umbilical cord mesenchymal stromal cell-derived exosomes alleviate antibiotic-induced intestinal barrier damage by regulating autophagy via the S100G/mTOR signaling pathway.Cellular & molecular biology letters · 2025Article
- The Small Intestinal Microbiota and the Gut-Brain Axis in Parkinson's Disease: A Narrative Review.Biomedicines · 2025Review
- Article
- A gut-on-a-chip incorporating human faecal samples and peristalsis predicts responses to immune checkpoint inhibitors for melanoma.Nature biomedical engineering · 2025Article
- Review
- Antibiotic-induced gut microbiota depletion enhances glucose tolerance linked to GLP-1 signaling.Frontiers in endocrinology · 2025Article
- Article
98 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
10 authors at 6 institutions in 2 countries.
Funding
Abstract
objectiveDespite widespread use of antibiotics for the treatment of life-threatening infections and for research on the role of commensal microbiota, our understanding of their effects on the host is still very limited.
designUsing a popular mouse model of microbiota depletion by a cocktail of antibiotics, we analysed the effects of antibiotics by combining intestinal transcriptome together with metagenomic analysis of the gut microbiota. In order to identify specific microbes and microbial genes that influence the host phenotype in antibiotic-treated mice, we developed and applied analysis of the transkingdom network.
resultsWe found that most antibiotic-induced alterations in the gut can be explained by three factors: depletion of the microbiota; direct effects of antibiotics on host tissues and the effects of remaining antibiotic-resistant microbes. Normal microbiota depletion mostly led to downregulation of different aspects of immunity. The two other factors (antibiotic direct effects on host tissues and antibiotic-resistant microbes) primarily inhibited mitochondrial gene expression and amounts of active mitochondria, increasing epithelial cell death. By reconstructing and analysing the transkingdom network, we discovered that these toxic effects were mediated by virulence/quorum sensing in antibiotic-resistant bacteria, a finding further validated using in vitro experiments.
conclusionsIn addition to revealing mechanisms of antibiotic-induced alterations, this study also describes a new bioinformatics approach that predicts microbial components that regulate host functions and establishes a comprehensive resource on what, why and how antibiotics affect the gut in a widely used mouse model of microbiota depletion by antibiotics.
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What OpenQuestion holds
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.