ArticleNature communications2021
Gene-level metagenomic architectures across diseases yield high-resolution microbiome diagnostic indicators.
Article in Nature communications, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 40 papers, 1 of them a synthesis that pooled it.
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Who cites it
40 citing papers in PubMed, 1 synthesis or guideline pooled it, 61 citations in OpenAlex.
- Meta-analysis of the human gut microbiome uncovers shared and distinct microbial signatures between diseases.mSystems · 2024Pooled it
- Phylogenize2: robust phylogenetic methods link genes to phenotypes across host-associated and environmental microbiomes.bioRxiv : the preprint server for biology · 2026Article
- The Oral Microbiome Is a Population-Scale Readout of the Exposome, Age, and Systemic Health.bioRxiv : the preprint server for biology · 2026Article
- Duodenal Fluid Microbiome Diversity and Pancreatic Cyst Status Among Patients Undergoing Pancreatic Surveillance.Gastro hep advances · 2026Article
- Comparative metagenomics using pan-metagenomic graphs.bioRxiv : the preprint server for biology · 2025Article
- Immunotherapy-mediated modulation of the gut microbiota in multiple sclerosis and associations with diet and clinical response-the effect of dimethyl fumarate therapy.Therapeutic advances in neurological disorders · 2025Article
- Unraveling the role of gut microbiome in predicting adverse events in neoadjuvant therapy for rectal cancer.Human vaccines & immunotherapeutics · 2024Observational
- Exploring the Frontier: The Human Microbiome's Role in Rare Childhood Neurological Diseases and Epilepsy.Brain sciences · 2024Review
- The Gut Microbiome Advances Precision Medicine and Diagnostics for Inflammatory Bowel Diseases.International journal of molecular sciences · 2024Review
- Towards geospatially-resolved public-health surveillance via wastewater sequencing.Nature communications · 2024Article
- Longitudinal multi-omics analysis of host microbiome architecture and immune responses during short-term spaceflight.Nature microbiology · 2024Article
- The human microbiome and immune response shift during spaceflight.Nature microbiology · 2024Article
- Co-evolution of vaginal microbiome and cervical cancer.Journal of translational medicine · 2024Article
- Single-cell multi-ome and immune profiles of the Inspiration4 crew reveal conserved, cell-type, and sex-specific responses to spaceflight.Nature communications · 2024Article
- Meta-analysis of the human gut microbiome uncovers shared and distinct microbial signatures between diseases.bioRxiv : the preprint server for biology · 2024Article
- The Next Generation Fecal Microbiota Transplantation: To Transplant Bacteria or Virome.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2023Review
- Multimodal metagenomic analysis reveals microbial single nucleotide variants as superior biomarkers for early detection of colorectal cancer.Gut microbes · 2023Article
- Viral activation and ecological restructuring characterize a microbiome axis of spaceflight-associated immune activation.Research square · 2023Article
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Authors and funding
4 authors at 2 institutions in 1 country.
Funding
Abstract
We propose microbiome disease "architectures": linking >1 million microbial features (species, pathways, and genes) to 7 host phenotypes from 13 cohorts using a pipeline designed to identify associations that are robust to analytical model choice. Here, we quantify conservation and heterogeneity in microbiome-disease associations, using gene-level analysis to identify strain-specific, cross-disease, positive and negative associations. We find coronary artery disease, inflammatory bowel diseases, and liver cirrhosis to share gene-level signatures ascribed to the Streptococcus genus. Type 2 diabetes, by comparison, has a distinct metagenomic signature not linked to any one specific species or genus. We additionally find that at the species-level, the prior-reported connection between Solobacterium moorei and colorectal cancer is not consistently identified across models-however, our gene-level analysis unveils a group of robust, strain-specific gene associations. Finally, we validate our findings regarding colorectal cancer and inflammatory bowel diseases in independent cohorts and identify that features inversely associated with disease tend to be less reproducible than features enriched in disease. Overall, our work is not only a step towards gene-based, cross-disease microbiome diagnostic indicators, but it also illuminates the nuances of the genetic architecture of the human microbiome, including tension between gene- and species-level associations.
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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.