ArticleCell reports methods2023
A computational method to dissect colonization resistance of the gut microbiota against pathogens.
Article in Cell reports methods, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
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Who cites it
14 citing papers in PubMed.
- Microbiome-based therapeutics forGut microbes · 2026Review
- Review
- Intrapartum caesarean delivery and childhood BMI trajectories in relation to the infant gut microbiome in the VDAART prospective birth cohort.EBioMedicine · 2026Article
- A triangulation and neural network approach reveals the microbe-metabolite-sensory associations of fermented milk.Current research in food science · 2026Article
- Toward the Next Generation of In Silico Modeling of Dynamic Host-Microbiota Interactions in the Skin.JID innovations : skin science from molecules to population health · 2025Review
- Rational Design of Live Biotherapeutic Products for the Prevention of Clostridioides difficile Infection.The Journal of infectious diseases · 2025Article
- Seasonal Change in Microbial Diversity: Bile Microbiota and Antibiotics Resistance in Patients with Bilio-Pancreatic Tumors: A Retrospective Monocentric Study (2010-2020).Antibiotics (Basel, Switzerland) · 2025Article
- Metabolic tug-of-war: Microbial metabolism shapes colonization resistance against enteric pathogens.Cell chemical biology · 2025Review
- The gut microbiome: an emerging epicenter of antimicrobial resistance?Frontiers in microbiology · 2025Review
- High-proportions of tailwater discharge alter microbial community composition and assembly in receiving sediments.Scientific reports · 2024Article
- Rational Design of Live Biotherapeutic Products for the Prevention ofbioRxiv : the preprint server for biology · 2024Article
- Promiscuous, persistent and problematic: insights into current enterococcal genomics to guide therapeutic strategy.BMC microbiology · 2024Review
- Association of Probable Post-Traumatic Stress Disorder with Dietary Pattern and Gut Microbiome in a Cohort of Women.Nature. Mental health · 2023Article
- Dissecting the role of the human microbiome in COVID-19 via metagenome-assembled genomes.Nature communications · 2022Article
Corrections and comments
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Authors and funding
6 authors.
Funding
Abstract
The mammalian gut microbiome protects the host through colonization resistance (CR) against the incursion of exogenous and often harmful microorganisms, but identifying the exact microbes responsible for the gut microbiota-mediated CR against a particular pathogen remains a challenge. To address this limitation, we developed a computational method: generalized microbe-phenotype triangulation (GMPT). We first systematically validated GMPT using a classical population dynamics model in community ecology and demonstrated its superiority over baseline methods. We then tested GMPT on simulated data generated from the ecological network inferred from a real community (GnotoComplex microflora) and real microbiome data on two mouse studies on Clostridioides difficile infection. We demonstrated GMPT's ability to streamline the discovery of microbes that are potentially responsible for microbiota-mediated CR against pathogens. GMPT holds promise to advance our understanding of CR mechanisms and facilitate the rational design of microbiome-based therapies for preventing and treating enteric infections.
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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.