<p>Bacterial growth is fundamental to understanding microbial survival strategies and optimizing microbial culture systems, yet the variation in these dynamics across bacteria and environments remains largely unexplored. Here, we present a bacterial growth dataset comprising 11,686 growth curves, including six representative model bacteria (<i>Escherichia coli, Lactiplantibacillus plantarum, Yersinia bercovieri, Brevundimonas subvibrioides, Aeromonas salmonicida subsp. masoucida</i>, and <i>Staphylococcus arlettae</i>) and 664 variations of compositionally defined media. The media were formulated with 11 to 56 components from a total of 80, including pure chemical compounds and natural ingredients. High-throughput bacterial monocultures were performed in 251 to 664 media for the six bacteria, with four biological replicates per condition. Temporal changes in bacterial population size were monitored by measuring optical density at 600 nm (OD<sub>600</sub>) over 24–48 hours at 30-minute intervals. Growth rate, carrying capacity, and lag time were also provided as quantitative traits of population dynamics for downstream analyses, including species-specific fitness landscapes, ecological niches, and other growth-related phenotypic patterns. This dataset provides a comprehensive resource linking population dynamics across bacterial species to medium compositions, facilitating data-driven comparison and modeling of bacterial growth in response to environmental dimensions. It serves as a foundation for studies in microbial ecology, systems biology, and culture medium design.</p>

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Population dynamics of six representative bacteria across hundreds of compositionally defined media

  • Shuyang Zhang,
  • Kai Sawamura,
  • Bei-Wen Ying

摘要

Bacterial growth is fundamental to understanding microbial survival strategies and optimizing microbial culture systems, yet the variation in these dynamics across bacteria and environments remains largely unexplored. Here, we present a bacterial growth dataset comprising 11,686 growth curves, including six representative model bacteria (Escherichia coli, Lactiplantibacillus plantarum, Yersinia bercovieri, Brevundimonas subvibrioides, Aeromonas salmonicida subsp. masoucida, and Staphylococcus arlettae) and 664 variations of compositionally defined media. The media were formulated with 11 to 56 components from a total of 80, including pure chemical compounds and natural ingredients. High-throughput bacterial monocultures were performed in 251 to 664 media for the six bacteria, with four biological replicates per condition. Temporal changes in bacterial population size were monitored by measuring optical density at 600 nm (OD600) over 24–48 hours at 30-minute intervals. Growth rate, carrying capacity, and lag time were also provided as quantitative traits of population dynamics for downstream analyses, including species-specific fitness landscapes, ecological niches, and other growth-related phenotypic patterns. This dataset provides a comprehensive resource linking population dynamics across bacterial species to medium compositions, facilitating data-driven comparison and modeling of bacterial growth in response to environmental dimensions. It serves as a foundation for studies in microbial ecology, systems biology, and culture medium design.