ArticleeLife2025
Microbes with higher metabolic independence are enriched in human gut microbiomes under stress.
Article in eLife, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 44 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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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
44 citing papers in PubMed.
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- A transfer RNA inosine modification drives genome-wide synonymous recoding across human commensal bacterial families.PNAS nexus · 2026Article
- Comorbid Alzheimer's Disease and Type 2 Diabetes Microbiota Shape Age-Associated Gut-Brain Axis Profiles.Aging cell · 2026Article
- Environmental disturbances and cyanobacterial traits shape prokaryotic dynamics in a eutrophic Mediterranean coastal lagoon.Environmental microbiome · 2026Article
- Unique ecology of co-occurring functionally and phylogenetically undescribed species in the infant oral microbiome.PLoS computational biology · 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
- Genomic insights into the functional and metabolic versatility of gut microbiomeMicrobial genomics · 2026Article
- Lactobacillus-vectored nanobodies improve broiler productivity under sub-clinical necrotic enteritis with associated microbiome and transcriptome changes.NPJ biofilms and microbiomes · 2026Article
- Oral dysbiosis: methodological evolution, the mobile resistome and the future of machine learning in dentistry.Journal of oral microbiology · 2026Review
- Functional gut microbiota dynamics of generalist and specialist bacteria in association with chicken growth.ISME communications · 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
- Article
- Complete genome sequences of five aquaticMicrobiology resource announcements · 2025Article
- Microbial model communities exhibit widespread metabolic interdependencies.Communications biology · 2025Article
- The Gut-Joint Connection: Microbiome's Role in Rheumatic Disease.Archives of rheumatology · 2025Review
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13 authors.
Funding
Abstract
A wide variety of human diseases are associated with loss of microbial diversity in the human gut, inspiring a great interest in the diagnostic or therapeutic potential of the microbiota. However, the ecological forces that drive diversity reduction in disease states remain unclear, rendering it difficult to ascertain the role of the microbiota in disease emergence or severity. One hypothesis to explain this phenomenon is that microbial diversity is diminished as disease states select for microbial populations that are more fit to survive environmental stress caused by inflammation or other host factors. Here, we tested this hypothesis on a large scale, by developing a software framework to quantify the enrichment of microbial metabolisms in complex metagenomes as a function of microbial diversity. We applied this framework to over 400 gut metagenomes from individuals who are healthy or diagnosed with inflammatory bowel disease (IBD). We found that high metabolic independence (HMI) is a distinguishing characteristic of microbial communities associated with individuals diagnosed with IBD. A classifier we trained using the normalized copy numbers of 33 HMI-associated metabolic modules not only distinguished states of health vs IBD, but also tracked the recovery of the gut microbiome following antibiotic treatment, suggesting that HMI is a hallmark of microbial communities in stressed gut environments.
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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.