ArticleProceedings of the National Academy of Sciences of the United States of America2024
Learning beyond-pairwise interactions enables the bottom-up prediction of microbial community structure.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers.
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Who cites it
22 citing papers in PubMed.
- Interaction matrices as unifying tools for navigating ecological complexity.Nature ecology & evolution · 2026Review
- SynComs should be rigorously defined, not renamed.Nature communications · 2026Article
- Systematic profiling of growth interactions in human gut microbiome species.Nature communications · 2026Article
- SubCom analysis: dissecting microbial community functions into taxon-specific contributions and interaction contexts.Microbiome · 2026Article
- Interspecies interactions drive bacterial proteome reorganization and emergent metabolism.Nature ecology & evolution · 2026Article
- Microbial biotechnology meets ecological theory: a unified framework to design industrial microbial consortia.International microbiology : the official journal of the Spanish Society for Microbiology · 2026Review
- Subinhibitory concentrations of antibiotics mediate primary metabolism and shape diverse species interactions among coevolved soil Streptomyces.The ISME journal · 2026Article
- Substrate complexity and species number jointly shift the balance between competition and facilitation in a chitin-degrading bacterial consortium.ISME communications · 2026Article
- Emerging microbiome-directed therapies in inflammatory bowel disease: beyond diet modification and FMT.Seminars in immunopathology · 2025Review
- Exploration of Core Microorganisms and Synthetic Microbial Communities in Low-TemperatureMicroorganisms · 2025Review
- Structural and functional properties of bacterial communities associated with rootless duckweed (Wolffia globosa) and their effect on the Wolffia growth.Environmental microbiome · 2025Article
- 7th International Conference on Duckweed Research and Applications: Depicting an Era of Advancing Research Translation Toward Practical Applications.Plants (Basel, Switzerland) · 2025Article
- Diversity-disease relationships in natural microscopic nematode communities.Royal Society open science · 2025Article
- Directing microbial co-culture composition using cybernetic control.Cell reports methods · 2025Article
- Decoding emergent properties of microbial community functions through subcommunity observations and interpretable machine learning.The ISME journal · 2025Article
- Strong pairwise interactions do not drive interactions in a plant leaf associated microbial community.ISME communications · 2025Article
- A Continuum From Positive to Negative Interactions Drives Plant Species' Performance in a Diverse Community.Ecology letters · 2025Article
- A systematic discussion and comparison of the construction methods of synthetic microbial community.Synthetic and systems biotechnology · 2024Review
- Multispecies interactions and the community context of the evolution of virulence.Proceedings. Biological sciences · 2024Article
- Interspecies interactions in dairy biofilms drive community structure and response against cleaning and disinfection.Biofilm · 2024Article
Corrections and comments
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Authors and funding
5 authors.
Funding
Abstract
Understanding the assembly of multispecies microbial communities represents a significant challenge in ecology and has wide applications in agriculture, wastewater treatment, and human healthcare domains. Traditionally, studies on the microbial community assembly focused on analyzing pairwise relationships among species; however, neglecting higher-order interactions, i.e., the change of pairwise relationships in the community context, may lead to substantial deviation from reality. Herein, we have proposed a simple framework that incorporates higher-order interactions into a bottom-up prediction of the microbial community assembly and examined its accuracy using a seven-member synthetic bacterial community on a host plant, duckweed. Although the synthetic community exhibited emergent properties that cannot be predicted from pairwise coculturing results, our results demonstrated that incorporating information from three-member combinations allows the acceptable prediction of the community structure and actual interaction forces within it. This reflects that the occurrence of higher-order effects follows consistent patterns, which can be predicted even from trio combinations, the smallest unit of higher-order interactions. These results highlight the possibility of predicting, explaining, and understanding the microbial community structure from the bottom-up by learning interspecies interactions from simple beyond-pairwise combinations.
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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.