ArticleNature biotechnology2023
Genome-scale metabolic reconstruction of 7,302 human microorganisms for personalized medicine.
Article in Nature biotechnology, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 168 papers, 2 of them syntheses that pooled it.
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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
168 citing papers in PubMed, 2 syntheses or guidelines pooled it.
- A human gut metagenome-assembled genome catalogue spanning 41 countries supports genome-scale metabolic models.Nature microbiology · 2026Pooled it
- Leveraging genome-scale metabolic models to understand aerobic methanotrophs.The ISME journal · 2024Pooled it
- Trial
- Recent advances and clinical relevance of microbiome dynamics in health and disease.Gut microbes · 2026Review
- Multi-omic modelling of body mass index response to a dietary weight loss intervention.Gut microbes · 2026Article
- Personalized whole-body modeling links gut microbiota to metabolic perturbations in Alzheimer's disease.Gut microbes · 2026Article
- The cervicovaginal gut microbiota axis as a key determinant of systemic physiology.Gut microbes · 2026Review
- Eggerthella lenta: metabolism, pathogenesis and therapeutic implications.Nature reviews. Microbiology · 2026Review
- Review
- The FERM guild: a differentially correlated microbial module drives hypertension via metabolic flux perturbations.mSystems · 2026Article
- Longitudinal Stability of the Gut Microbiota in Relapsing-Remitting Multiple Sclerosis: A Prospective Observational Study.Microorganisms · 2026Article
- Drug-microbiome-host interactions: antimicrobial effects of non-antibiotic compounds.Nature reviews. Gastroenterology & hepatology · 2026Review
- Article
- Next-generation probiotics: an outlook into current applications and future developments.Nature reviews. Microbiology · 2026Review
- Genome-resolved gut microbial guild and fecal metabolic signatures associated with post-weaning estrus return in sows.Animal microbiome · 2026Article
- A historical journey of metabolite-protein interaction discovery: from data harmonization to AI-driven prediction.Briefings in bioinformatics · 2026Review
- Diet, Gut Microbiome, and Microbial Metabolites in Inflammatory Bowel Disease: From Functional Dysbiosis to Precision Nutrition.International journal of molecular sciences · 2026Review
- Machine learning model to identify gut microbiome-derived metabolites as potential biomarkers of autism spectrum disorder: a pilot study.BMC psychiatry · 2026Article
- Nutrient control enables metabolic reconstruction ofbioRxiv : the preprint server for biology · 2026Article
- Selecting methods for draft GEM generation in multicellular eukaryotes: a comparative analysis.BMC bioinformatics · 2026Article
108 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
15 authors.
Funding
Abstract
The human microbiome influences the efficacy and safety of a wide variety of commonly prescribed drugs. Designing precision medicine approaches that incorporate microbial metabolism would require strain- and molecule-resolved, scalable computational modeling. Here, we extend our previous resource of genome-scale metabolic reconstructions of human gut microorganisms with a greatly expanded version. AGORA2 (assembly of gut organisms through reconstruction and analysis, version 2) accounts for 7,302 strains, includes strain-resolved drug degradation and biotransformation capabilities for 98 drugs, and was extensively curated based on comparative genomics and literature searches. The microbial reconstructions performed very well against three independently assembled experimental datasets with an accuracy of 0.72 to 0.84, surpassing other reconstruction resources and predicted known microbial drug transformations with an accuracy of 0.81. We demonstrate that AGORA2 enables personalized, strain-resolved modeling by predicting the drug conversion potential of the gut microbiomes from 616 patients with colorectal cancer and controls, which greatly varied between individuals and correlated with age, sex, body mass index and disease stages. AGORA2 serves as a knowledge base for the human microbiome and paves the way to personalized, predictive analysis of host-microbiome metabolic interactions.
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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.