ArticleNature ecology & evolution2023
Statistically learning the functional landscape of microbial communities.
Article in Nature ecology & evolution, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 38 papers, 1 of them a synthesis that pooled it.
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Who cites it
38 citing papers in PubMed, 1 synthesis or guideline pooled it, 64 citations in OpenAlex.
- Coexistence Theory for Microbial Ecology, and Vice Versa.Environmental microbiology · 2025Pooled it
- Synergistic degradation of fucoidans in the ocean.Nature · 2026Article
- SubCom analysis: dissecting microbial community functions into taxon-specific contributions and interaction contexts.Microbiome · 2026Article
- Epistatic interactions inform rational design of synthetic microbial communities for bioremediation.Nature microbiology · 2026Article
- Article
- Global epistasis in ecosystems arises from resource constraints.bioRxiv : the preprint server for biology · 2026Article
- Statistical design of a synthetic microbiome that suppresses diverse gut pathogens.bioRxiv : the preprint server for biology · 2025Article
- Scarce data, noisy inferences and overfitting: the hidden flaws in ecological dynamics modelling.Journal of the Royal Society, Interface · 2025Article
- Applying ecological principles to microbiome engineering.Nature microbiology · 2025Review
- Article
- Integrative systems biology approaches for analyzing microbiome dysbiosis and species interactions.Briefings in bioinformatics · 2025Review
- Linear scaling reveals low-dimensional structure in observable microbial dynamics.bioRxiv : the preprint server for biology · 2025Article
- Microbiome determinants of productivity in aquaculture of whiteleg shrimp.Applied and environmental microbiology · 2025Article
- Macroecological patterns in experimental microbial communities.PLoS computational biology · 2025Article
- Soft Modes as a Predictive Framework for Low-Dimensional Biological Systems Across Scales.Annual review of biophysics · 2025Review
- Replicating community dynamics reveals how initial composition shapes the functional outcomes of bacterial communities.Nature communications · 2025Article
- Collective Microbial Effects Drive Toxin Bioremediation and Enable Rational Design.bioRxiv : the preprint server for biology · 2025Article
- Competition for shared resources increases dependence on initial population size during coalescence of gut microbial communities.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Ecology and Evolutionary Biology as Frameworks to Study Wine Fermentations.Microbial biotechnology · 2025Review
- A data-driven modeling framework for mapping genotypes to synthetic microbial community functions.bioRxiv : the preprint server for biology · 2025Article
Corrections and comments
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Authors and funding
8 authors at 4 institutions in 2 countries.
Funding
Abstract
Microbial consortia exhibit complex functional properties in contexts ranging from soils to bioreactors to human hosts. Understanding how community composition determines function is a major goal of microbial ecology. Here we address this challenge using the concept of community-function landscapes-analogues to fitness landscapes-that capture how changes in community composition alter collective function. Using datasets that represent a broad set of community functions, from production/degradation of specific compounds to biomass generation, we show that statistically inferred landscapes quantitatively predict community functions from knowledge of species presence or absence. Crucially, community-function landscapes allow prediction without explicit knowledge of abundance dynamics or interactions between species and can be accurately trained using measurements from a small subset of all possible community compositions. The success of our approach arises from the fact that empirical community-function landscapes appear to be not rugged, meaning that they largely lack high-order epistatic contributions that would be difficult to fit with limited data. Finally, we show that this observation holds across a wide class of ecological models, suggesting community-function landscapes can be efficiently inferred across a broad range of ecological regimes. Our results open the door to the rational design of consortia without detailed knowledge of abundance dynamics or interactions.
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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.