基因组
微生物群
生物
选择(遗传算法)
公制(单位)
基因
基因组
自然选择
计算生物学
功能(生物学)
适应度函数
人类微生物组计划
进化生物学
遗传学
计算机科学
机器学习
遗传算法
运营管理
经济
作者
Teng Wang,Andrea Weiss,You Li
标识
DOI:10.1073/pnas.2318380121
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 community-wide 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.
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