ArticleCell host & microbe2024
Discovery of disease-adapted bacterial lineages in inflammatory bowel diseases.
Article in Cell host & microbe, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 36 papers, 1 of them a synthesis 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
36 citing papers in PubMed, 1 synthesis or guideline pooled it.
- A meta-analysis of the gut microbiome in inflammatory bowel disease patients identifies disease-associated small molecules.Cell host & microbe · 2025Pooled it
- Eggerthella lenta: metabolism, pathogenesis and therapeutic implications.Nature reviews. Microbiology · 2026Review
- Community-wide adaptive evolution of gut bacteria during dietary transitions.bioRxiv : the preprint server for biology · 2026Article
- Global gut microbiome atlas identifies epidemiologic-stage-specific signatures in inflammatory bowel disease.Cell reports. Medicine · 2026Article
- Integrated Multi-Omics Reveals Complementary Luminal and Mucosal Host-Microbiome Interactions Associated with Disease Activity and Phenotype in Paediatric Inflammatory Bowel Disease.Microorganisms · 2026Article
- Hesperetin mitigates IBD-associated bone loss viaJournal of orthopaedic translation · 2026Article
- Simulating the host niche: balancing complexity and control in the experimental evolution of antibiotic resistance and pathoadaptation.Microbiology (Reading, England) · 2026Review
- Review
- Human-Centered Innovation: Precision Nutrition and the Future of Food.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Review
- Multi-kingdom gut microbiota analyses define bacterial-fungal interplay in multiple type 2 diabetes cohorts.Science China. Life sciences · 2026Article
- Article
- Article
- A widespread gut bacterial lineage distinguished by redox metabolism and phage defense.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
- The Japanese gut microbiome: ecology, uniqueness, and impact on health and disease.Proceedings of the Japan Academy. Series B, Physical and biological sciences · 2026Review
- Evaluation of electroacupuncture acupoint selection's potential in the treatment of inflammatory bowel disease: an investigation using a mouse gut microbiome and metabolomics model.Frontiers in cellular and infection microbiology · 2026Article
- A temporal-aware machine learning framework enables microbial community dynamics prediction with personalized precision.Microbiome · 2025Article
- The Dual Role of Gut Microbiota and Their Metabolites in Hepatocellular Carcinoma: A Context-Dependent Framework.Microorganisms · 2025Review
- Synergy between culturomics and metagenomics of health status-associated gut bacteria originating from non-IBD and IBD populations.Scientific reports · 2025Article
- A noncanonical polyamine from bacteria antagonizes host mitochondrial function.Nature communications · 2025Article
Corrections and comments
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Authors and funding
9 authors.
Funding
Abstract
Gut bacteria are implicated in inflammatory bowel disease (IBD), but the strains driving these associations are unknown. Large-scale studies of microbiome evolution could reveal the imprint of disease on gut bacteria, thus pinpointing the strains and genes that may underlie inflammation. Here, we use stool metagenomes of thousands of IBD patients and healthy controls to reconstruct 140,000 strain genotypes, revealing hundreds of lineages enriched in IBD. We demonstrate that these strains are ancient, taxonomically diverse, and ubiquitous in humans. Moreover, disease-associated strains outcompete their healthy counterparts during inflammation, implying long-term adaptation to disease. Strain genetic differences map onto known axes of inflammation, including oxidative stress, nutrient biosynthesis, and immune evasion. Lastly, the loss of health-associated strains of Eggerthella lenta was predictive of fecal calprotectin, a biomarker of disease severity. Our work identifies reservoirs of strain diversity that may impact inflammatory disease and can be extended to other microbiome-associated diseases.
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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.