ArticleGenome biology2023
Metabolic independence drives gut microbial colonization and resilience in health and disease.
Article in Genome biology, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 63 papers, 5 of them syntheses that pooled it.
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Who cites it
63 citing papers in PubMed, 5 syntheses or guidelines pooled it, 95 citations in OpenAlex.
- A human gut metagenome-assembled genome catalogue spanning 41 countries supports genome-scale metabolic models.Nature microbiology · 2026Pooled it
- Multi-omics time-series analysis in microbiome research: a systematic review.Briefings in bioinformatics · 2025Pooled it
- Engrafting gut bacteriophages have potential to modulate microbial metabolism in fecal microbiota transplantation.Microbiome · 2025Pooled it
- Spleen volume in relation to ulcerative colitis and Crohn's disease: a Mendelian randomization study.Scientific reports · 2025Pooled it
- A meta-analysis of the gut microbiome in inflammatory bowel disease patients identifies disease-associated small molecules.Cell host & microbe · 2025Pooled it
- Gut Microbial Species and Endotypes Associate with Remission in Ulcerative Colitis Patients Treated with Anti-TNF or Anti-integrin Therapy.Journal of Crohn's & colitis · 2024Trial
- Higher alpha diversity and Lactobacillus blooms are associated with better engraftment after fecal microbiota transplant in inflammatory bowel disease.Scientific reports · 2024Trial
- Multi-omics analysis of saccharomyces boulardii supplementation reveals coordinated microbiome, metabolic, and immune signaling changes accompanying tumor suppression.Gut microbes · 2026Article
- From gut dysbiosis to eubiosis: understanding microbiome recovery as an ecological process.Gut microbes · 2026Review
- Article
- A clinic-responder-derived defined microbial consortium enhances anti-PD-1 immunotherapy efficacy in mice.Nature microbiology · 2026Article
- Human DNA levels in feces reflect gut inflammation and associate with presence of gut species in IBD patients across the age spectrum.Microbiome · 2026Article
- Gut dysbiosis in oncology: a risk factor for immunoresistance.Cell research · 2026Review
- Genome-wide association analysis reveals specialization to hosts and niches in multiple species of the Lactobacillaceae.The ISME journal · 2026Article
- Functional gut microbiota dynamics of generalist and specialist bacteria in association with chicken growth.ISME communications · 2026Article
- Bacteroides thetaiotaomicron and Human Health: A Bibliometric Analysis of Global Research Trends.Iranian biomedical journal · 2026Article
- Topological characteristics and longitudinal dynamics of co-abundance networks involving beneficial commensal bacteria in the pig gut microbiome and its association with average daily gain.Frontiers in microbiology · 2026Article
- Association between oral microbiome alpha and beta diversity and MASLD risk: a large-scale, population-based retrospective study.Frontiers in cellular and infection microbiology · 2026Article
- Core rumen microbes are functional generalists that sustain host metabolism and gut ecosystem function.Nature ecology & evolution · 2026Article
- Beyond the core microbiome: endemic bacteria drive functional and microdiversity differences across salamander populations.ISME communications · 2026Article
3 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
20 authors at 9 institutions in 5 countries.
Funding
Abstract
backgroundChanges in microbial community composition as a function of human health and disease states have sparked remarkable interest in the human gut microbiome. However, establishing reproducible insights into the determinants of microbial succession in disease has been a formidable challenge.
resultsHere we use fecal microbiota transplantation (FMT) as an in natura experimental model to investigate the association between metabolic independence and resilience in stressed gut environments. Our genome-resolved metagenomics survey suggests that FMT serves as an environmental filter that favors populations with higher metabolic independence, the genomes of which encode complete metabolic modules to synthesize critical metabolites, including amino acids, nucleotides, and vitamins. Interestingly, we observe higher completion of the same biosynthetic pathways in microbes enriched in IBD patients.
conclusionsThese observations suggest a general mechanism that underlies changes in diversity in perturbed gut environments and reveal taxon-independent markers of "dysbiosis" that may explain why widespread yet typically low-abundance members of healthy gut microbiomes can dominate under inflammatory conditions without any causal association with disease.
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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.