ArticleNature communications2021
Steering ecological-evolutionary dynamics to improve artificial selection of microbial communities.
Article in Nature communications, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
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Who cites it
17 citing papers in PubMed.
- Novel artificial selection method improves function of simulated microbial communities.PLoS computational biology · 2026Article
- The success of artificial selection for collective composition hinges on initial and target values.eLife · 2025Article
- Evolutionary dynamics of nascent multicellular lineages.Proceedings. Biological sciences · 2025Article
- Article
- 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
- Engineering is evolution: a perspective on design processes to engineer biology.Nature communications · 2024Article
- Enhancing phosphate-solubilising microbial communities through artificial selection.Nature communications · 2024Article
- Strategies for tailoring functional microbial synthetic communities.The ISME journal · 2024Review
- Steering and controlling evolution - from bioengineering to fighting pathogens.Nature reviews. Genetics · 2023Review
- Partner-assisted artificial selection of a secondary function for efficient bioremediation.iScience · 2023Article
- Ecological Drivers of Community Cohesion.mSystems · 2023Article
- The effectiveness of artificial microbial community selection: a conceptual framework and a meta-analysis.Frontiers in microbiology · 2023Article
- Ecological landscapes guide the assembly of optimal microbial communities.PLoS computational biology · 2023Article
- Guided by the principles of microbiome engineering: Accomplishments and perspectives for environmental use.mLife · 2022Review
- Review
- Artificial selection methods from evolutionary computing show promise for directed evolution of microbes.eLife · 2022Article
- Dynamic proteome allocation regulates the profile of interaction of auxotrophic bacterial consortia.Royal Society open science · 2022Article
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Authors and funding
2 authors.
Funding
Abstract
Microbial communities often perform important functions that depend on inter-species interactions. To improve community function via artificial selection, one can repeatedly grow many communities to allow mutations to arise, and "reproduce" the highest-functioning communities by partitioning each into multiple offspring communities for the next cycle. Since improvement is often unimpressive in experiments, we study how to design effective selection strategies in silico. Specifically, we simulate community selection to improve a function that requires two species. With a "community function landscape", we visualize how community function depends on species and genotype compositions. Due to ecological interactions that promote species coexistence, the evolutionary trajectory of communities is restricted to a path on the landscape. This restriction can generate counter-intuitive evolutionary dynamics, prevent the attainment of maximal function, and importantly, hinder selection by trapping communities in locations of low community function heritability. We devise experimentally-implementable manipulations to shift the path to higher heritability, which speeds up community function improvement even when landscapes are high dimensional or unknown. Video walkthroughs: https://go.nature.com/3GWwS6j ; https://online.kitp.ucsb.edu/online/ecoevo21/shou2/ .
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