Pilea: profiling bacterial growth dynamics from metagenomes with sketching.

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

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In one paragraph

Article in Microbiome, 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.

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5 · Who and what money

Authors and funding

6 authors.

Xi ChenEnvironmental Microbiome Engineering and Biotechnology Lab, Department of Civil Engineering, The University of Hong Kong, Hong Kong SAR, China.

Xiaoqing XuEnvironmental Microbiome Engineering and Biotechnology Lab, Department of Civil Engineering, The University of Hong Kong, Hong Kong SAR, China.

Yunqi LinEnvironmental Microbiome Engineering and Biotechnology Lab, Department of Civil Engineering, The University of Hong Kong, Hong Kong SAR, China.

Xianghui ShiEnvironmental Microbiome Engineering and Biotechnology Lab, Department of Civil Engineering, The University of Hong Kong, Hong Kong SAR, China.

Dou WangEnvironmental Microbiome Engineering and Biotechnology Lab, Department of Civil Engineering, The University of Hong Kong, Hong Kong SAR, China.

Tong ZhangEnvironmental Microbiome Engineering and Biotechnology Lab, Department of Civil Engineering, The University of Hong Kong, Hong Kong SAR, China. zhangt@hku.hk.

Funding

University Grants Committee T21-705/20-N

6 · The paper itself

Abstract

backgroundQuantifying 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.

resultsWe 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.

conclusionsBy 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.

Indexed as

BacteriaComputational BiologyMetagenomeMetagenomicsMicrobiotaSoftware

Identifiers

PMID41827056

DOI10.1186/s40168-026-02374-0

PMCPMC13123247

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LicenceCC BY-NC-ND

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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.