Directed microbial evolution harnesses evolutionary processes in the laboratory to construct microorganisms with enhanced or novel functional traits. Attempting to direct evolutionary processes for applied goals is fundamental to evolutionary computation, which harnesses the principles of Darwinian evolution as a general purpose search engine for solutions to challenging computational problems. Despite their overlapping approaches, artificial selection methods from evolutionary computing are not commonly applied to living systems in the laboratory. In this work, we ask if parent selection algorithms-procedures for choosing promising progenitors-from evolutionary computation might be useful for directing the evolution of microbial populations when selecting for multiple functional traits. To do so, we introduce an agent-based model of directed microbial evolution, which we used to evaluate how well three selection algorithms from evolutionary computing (tournament selection, lexicase selection, and non-dominated elite selection) performed relative to methods commonly used in the laboratory (elite and top-10% selection). We found that multi-objective selection techniques from evolutionary computing (lexicase and non-dominated elite) generally outperformed the commonly used directed evolution approaches when selecting for multiple traits of interest. Our results motivate ongoing work transferring these multi-objective selection procedures into the laboratory and a continued evaluation of more sophisticated artificial selection methods.
Our source code for experiments, analyses, and visualizations is publicly available on GitHub (https://github.com/amlalejini/directed-digital-evolution). Our GitHub repository is publicly archived using Zenodo with the following DOI: 10.5281/zenodo.6403135.The data produced by our computational experiments are publicly available and archived on the Open Science Framework: https://osf.io/zn63x/ (DOI: 10.17605/OSF.IO/ZN63X).
Data from: Selection schemes from evolutionary computing show promise for directed evolution of microbesOpen Science Framework, 10.17605/OSF.IO/ZN63X.
- Luis Zaman
- Anya E Vostinar
The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.
- C Brandon Ogbunugafor, Yale University, United States
- Received: April 21, 2022
- Accepted: August 1, 2022
- Accepted Manuscript published: August 2, 2022 (version 1)
© 2022, Lalejini et al.
This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.
Reducing the microbial diversity in a type of fermented tea reveals the core metabolic interactions responsible for the drink’s signature taste and characteristics.
One defining goal of microbiome research is to uncover mechanistic causation that dictates the emergence of structural and functional traits of microbiomes. However, the extraordinary degree of ecosystem complexity has hampered the realization of the goal. Here, we developed a systematic, complexity-reducing strategy to mechanistically elucidate the compositional and metabolic characteristics of microbiome by using the kombucha tea microbiome as an example. The strategy centered around a two-species core that was abstracted from but recapitulated the native counterpart. The core was convergent in its composition, coordinated on temporal metabolic patterns, and capable for pellicle formation. Controlled fermentations uncovered the drivers of these characteristics, which were also demonstrated translatable to provide insights into the properties of communities with increased complexity and altered conditions. This work unravels the pattern and process underlying the kombucha tea microbiome, providing a potential conceptual framework for mechanistic investigation of microbiome behaviors.