ArticleNature ecology & evolution2021
Engineering complex communities by directed evolution.
Article in Nature ecology & evolution, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 51 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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Who cites it
51 citing papers in PubMed, 104 citations in OpenAlex.
- Top-down/bottom-up consortia achieve robust γ-HCH degradation and reduced methanogenic contribution in wetlands.Applied and environmental microbiology · 2026Article
- SynComs should be rigorously defined, not renamed.Nature communications · 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
- Review
- Novel artificial selection method improves function of simulated microbial communities.PLoS computational biology · 2026Article
- Ecological drift simulations reveal key factors influencing minimal microbiome engineering and community assembly.ISME communications · 2026Article
- Breeding of microbiomes conferring salt tolerance to plants.Microbiome · 2025Article
- Selection and transmission of the gut microbiome alone can shift mammalian behavior.Nature communications · 2025Article
- The success of artificial selection for collective composition hinges on initial and target values.eLife · 2025Article
- Applying ecological principles to microbiome engineering.Nature microbiology · 2025Review
- The engineering of TBBPA-degrading synthetic microbiomes with integrated strategies.NPJ biofilms and microbiomes · 2025Article
- Directed Evolution of Microbial Communities in Fermented Foods: Strategies, Mechanisms, and Challenges.Foods (Basel, Switzerland) · 2025Review
- Ecological design of high-performance synthetic microbial communities: from theoretical foundations to functional optimization.ISME communications · 2025Review
- Engineering Microbial Consortia as Living Materials: Advances and Prospectives.ACS synthetic biology · 2024Review
- The evolution of autonomy from two cooperative specialists in fluctuating environments.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- Microeukaryote community coalescence strengthens community stability and elevates diversity.FEMS microbiology ecology · 2024Article
- Engineering natural microbiomes toward enhanced bioremediation by microbiome modeling.Nature communications · 2024Article
- Enhancing phosphate-solubilising microbial communities through artificial selection.Nature communications · 2024Article
- Serial cultures in invert emulsion and monophase systems for microbial community shaping and propagation.Microbial cell factories · 2024Article
- Top-down and bottom-up microbiome engineering approaches to enable biomanufacturing from waste biomass.Journal of industrial microbiology & biotechnology · 2024Review
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Authors and funding
15 authors at 7 institutions in 2 countries.
Funding
Abstract
Directed evolution has been used for decades to engineer biological systems at or below the organismal level. Above the organismal level, a small number of studies have attempted to artificially select microbial ecosystems, with uneven and generally modest success. Our theoretical understanding of artificial ecosystem selection is limited, particularly for large assemblages of asexual organisms, and we know little about designing efficient methods to direct their evolution. Here, we have developed a flexible modelling framework that allows us to systematically probe any arbitrary selection strategy on any arbitrary set of communities and selected functions. By artificially selecting hundreds of in silico microbial metacommunities under identical conditions, we first show that the main breeding methods used to date, which do not necessarily let communities reach their ecological equilibrium, are outperformed by a simple screen of sufficiently mature communities. We then identify a range of alternative directed evolution strategies that, particularly when applied in combination, are well suited for the top-down engineering of large, diverse and stable microbial consortia. Our results emphasize that directed evolution allows an ecological structure-function landscape to be navigated in search of dynamically stable and ecologically resilient communities with desired quantitative attributes.
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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.