A generic approach to infer communitylevel fitness of microbial genes

• 成果类型: Article
• 署名作者: Wang, Teng; Weiss, Andrea; You, Lingchong
• 署名单位: Duke University; Duke University; Duke University
• 刊物名称: PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
• ISSN/ISSBN: 0027-15394
• DOI: 10.1073/pnas.2318380121
• 发表日期: 2024-04-23
• 关键词: evolution; communities; distributions; selection; ELEMENTS; catalog

摘要

The gene content in a metagenomic pool defines the function potential of a microbial community. Natural selection, operating on the level of genomes or genes, shapes the evolution of community functions by enriching some genes while depriving the others. Despite the importance of microbiomes in the environment and health, a general metric to evaluate the communitywide fitness of microbial genes remains lacking. In this work, we adapt the classic neutral model of species and use it to predict how the abundances of different genes will be shaped by selection, regardless of at which level the selection acts. We establish a simple metric that quantitatively infers the average survival capability of each gene in a microbiome. We then experimentally validate the predictions using synthetic communities of barcoded Escherichia coli strains undergoing neutral assembly and competition. We further show that this approach can be applied to publicly available metagenomic datasets to gain insights into the environment - function interplay of natural microbiomes.