ArticleProceedings of the National Academy of Sciences of the United States of America2015
Metabolic dependencies drive species co-occurrence in diverse microbial communities.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 441 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
441 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
- Harnessing plant-microbe interactions: strategies for enhancing resilience and nutrient acquisition for sustainable agriculture.Frontiers in plant science · 2025Pooled it
- Microbiome-mediated resilience and cross-generational consequences in male Drosophila exposed to combined environmental stressors.Proceedings. Biological sciences · 2026Article
- Spatial mixed models for assessing environmental exposure effects on the microbiome.Genome medicine · 2026Article
- Ecological Engineering of the Human Gut Microbiome: A Narrative Review and Framework for Next-Generation Therapeutics.Microorganisms · 2026Review
- Metabolic cooperation supports mutual growth between the protozoan parasite Trichomonas vaginalis and dysbiotic vaginal bacteria.PLoS pathogens · 2026Article
- Decoding microbial metabolic complementarity from individual traits to community structuring.Ecology · 2026Article
- Obligate cross-feeding of metabolites is common in soil microbial communities.Nature microbiology · 2026Article
- Niche Construction: A Rational Engineering Strategy for Regulating Microbial Assembly to Enhance Flavor and Bioactivity of Fermented Foods.Comprehensive reviews in food science and food safety · 2026Review
- Describing the persistence landscape for introducing microbes into complex communities.Applied and environmental microbiology · 2026Review
- Article
- Biofilm state transitions: quorum sensing inhibition and network destabilization.Applied microbiology and biotechnology · 2026Review
- Plant growth-promoting Pseudomonas strains modulate potato tuberization signalling and development.Journal of experimental botany · 2026Article
- Microbiomic Insights into Differential Snow Mold Severity in Winter Cereal Crops.Journal of fungi (Basel, Switzerland) · 2026Article
- Metabolic set theory: a generalized model of microbial interactions.NPJ systems biology and applications · 2026Article
- Functional and ecological drivers of bacterial interactions in glacier-fed stream biofilms.mSystems · 2026Article
- Third-generation RNA Amplicon Sequencing Reveals the Dynamics of Microbial Communities in the Tidal Reach of a Subtropical Estuary.Microbial ecology · 2026Article
- Multi-omic characterization of a soil microbial consortium reveals critical role of succinate and glutamate metabolism during calcium carbonate precipitation.BMC biotechnology · 2026Article
- Article
- Biofilm synergy byBiofilm · 2026Article
381 more citing papers are in PubMed but not listed here.
Corrections and comments
- Erratum issued
Authors and funding
6 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Microbial communities populate most environments on earth and play a critical role in ecology and human health. Their composition is thought to be largely shaped by interspecies competition for the available resources, but cooperative interactions, such as metabolite exchanges, have also been implicated in community assembly. The prevalence of metabolic interactions in microbial communities, however, has remained largely unknown. Here, we systematically survey, by using a genome-scale metabolic modeling approach, the extent of resource competition and metabolic exchanges in over 800 communities. We find that, despite marked resource competition at the level of whole assemblies, microbial communities harbor metabolically interdependent groups that recur across diverse habitats. By enumerating flux-balanced metabolic exchanges in these co-occurring subcommunities we also predict the likely exchanged metabolites, such as amino acids and sugars, that can promote group survival under nutritionally challenging conditions. Our results highlight metabolic dependencies as a major driver of species co-occurrence and hint at cooperative groups as recurring modules of microbial community architecture.
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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.