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<p>Bacterial growth dynamics, typically represented by growth curves, are fundamental yet complex features of living populations. Traditional analyses focusing on specific parameters often overlook the full temporal patterns of growth. Here, we systematically investigated how genomic and environmental factors shape bacterial growth dynamics by analyzing 870 growth curves from five <i>Escherichia coli</i> strains with varying genome sizes cultured in 29 chemically defined media. Using dynamic time warping, clustering, and gradient boosting decision trees, we found that environmental components, especially glucose, primarily determine overall growth curve patterns, while genome size governs detailed growth parameters such as lag time, growth rate, and carrying capacity. Notably, finer clustering revealed increased genomic influence and decreased environmental impact, suggesting a hierarchical interaction where the environment modulates broad growth behavior and the genome fine-tunes specific growth responses. These findings provide insights into the coordinated roles of genome and environment in bacterial population dynamics, advancing our understanding of microbial growth regulation.</p>

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Data-driven analysis reveals distinct genomic and environmental contributions to bacterial growth curves

  • 期刊论文

  • 出版模式：

    开放获取

  • 发表日期：

    2025年12月12日

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  • Jiarun Gong,
  • Bei-Wen Ying

摘要

Bacterial growth dynamics, typically represented by growth curves, are fundamental yet complex features of living populations. Traditional analyses focusing on specific parameters often overlook the full temporal patterns of growth. Here, we systematically investigated how genomic and environmental factors shape bacterial growth dynamics by analyzing 870 growth curves from five Escherichia coli strains with varying genome sizes cultured in 29 chemically defined media. Using dynamic time warping, clustering, and gradient boosting decision trees, we found that environmental components, especially glucose, primarily determine overall growth curve patterns, while genome size governs detailed growth parameters such as lag time, growth rate, and carrying capacity. Notably, finer clustering revealed increased genomic influence and decreased environmental impact, suggesting a hierarchical interaction where the environment modulates broad growth behavior and the genome fine-tunes specific growth responses. These findings provide insights into the coordinated roles of genome and environment in bacterial population dynamics, advancing our understanding of microbial growth regulation.