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Background <p>Quantifying bacteria’s growth rates is essential for understanding their ecological roles and for building predictive models in environmental and clinical settings. Peak-to-trough ratios (PTRs) derived from shotgun metagenomes offer a culture-independent proxy for in situ growth rates of bacterial species, yet their reliable computation remains challenging.</p> Results <p>We introduce Pilea&#xa0;(<a href="https://github.com/xinehc/pilea">https://github.com/xinehc/pilea</a>), an alignment-free, sketching-based method that incorporates statistical models for robust PTR estimation. Pilea achieves speed improvements over existing methods while also enhancing accuracy, as demonstrated on both simulated and real datasets.</p> Conclusions <p>By scaling efficiently to comprehensive reference collections such as the Genome Taxonomy Database (GTDB), Pilea enables large-scale analyses of bacterial growth dynamics across biomes, unlocking new insights for ecological research.</p> <p><MediaObject ID="MOESM2"> <VideoObject FileRef="MediaObjects/40168_2026_2374_MOESM2_ESM.mp4" VideoID="EGAjoD9S2FpW8PX5gEf-Wz"> <Caption Language="En" xml:lang="en"> <CaptionContent> <p>Video Abstract</p> </CaptionContent> </Caption> </VideoObject> </MediaObject></p>

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Pilea: profiling bacterial growth dynamics from metagenomes with sketching

  • 期刊论文

  • 出版模式：

    开放获取

  • 发表日期：

    2026年3月14日

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  • Xi Chen,
  • Xiaoqing Xu,
  • Yunqi Lin,
  • Xianghui Shi,
  • Dou Wang,
  • Tong Zhang

摘要

Background

Quantifying bacteria’s growth rates is essential for understanding their ecological roles and for building predictive models in environmental and clinical settings. Peak-to-trough ratios (PTRs) derived from shotgun metagenomes offer a culture-independent proxy for in situ growth rates of bacterial species, yet their reliable computation remains challenging.

Results

We introduce Pilea (https://github.com/xinehc/pilea), an alignment-free, sketching-based method that incorporates statistical models for robust PTR estimation. Pilea achieves speed improvements over existing methods while also enhancing accuracy, as demonstrated on both simulated and real datasets.

Conclusions

By scaling efficiently to comprehensive reference collections such as the Genome Taxonomy Database (GTDB), Pilea enables large-scale analyses of bacterial growth dynamics across biomes, unlocking new insights for ecological research.

Video Abstract