Abstract
Microbial safety is fundamental to ensuring water quality, particularly in the Yangtze River Basin, China’s most critical drinking water source. Despite its ecological and economic importance, the basin faces significant anthropogenic pressures, including wastewater discharge, which may elevate the risk of pathogenic contamination. However, fragmented sampling efforts and limited coverage have hindered a systematic understanding of pathogenic microbial diversity and distribution across this vast ecosystem. A novel bioinformatic pipeline leveraging Genome-Specific Markers to accurately identify and quantify potential pathogenic taxa in metagenomic data was applied to 625 publicly available metagenomes, spanning water, sediments, and riparian soils along the 6,300 km Yangtze River continuum. We reconstructed a potential pathogen catalog comprising 403 taxa, largely expanding the pathogen diversity in the large river ecosystem. We also generate the Richness distribution maps of potential pathogens for water, sediments and soils along Yangtze River. The basin-scale pathogen inventory not only establishes a baseline for potential pathogenic bacteria communities in the Yangtze Basin but also serves as a reference library for quick biosurveillance and risk management from genomic resolution.
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Data availability
Data are available at the figshare repository (https://doi.org/10.6084/m9.figshare.30196462)29. The repository contains four datasets, including the spatial distribution maps for water, sediment and soils; S1. Metadata of samples for pathogen detection analysis; S2. Pathogens identified by GSMer in the Yangtze River Basin and their potential hosts and S3. Georeferenced sampling locations and pathogen richness used in spatial mapping. Dataset S1 contains the sources of the original metagenomic sequencing data used in this study. Dataset S2 provides potential pathogen species identified by the GSM-based matching and their host information.
Code availability
The parameters of all programs used for the analysis are described in the main text. GSM library construction code was available at https://github.com/yedeng-lab/humanpathogen-GSM.
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Acknowledgements
This work was supported by Opening Project of State Key Laboratory of Geomicrobiology and Environmental Changes (51830100303), the National Key Research and Development Program of China (Grant 2022YFC3204703) and the National Natural Science Foundation of China (Grant 42277104).
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J.W. generated the data and contributed to manuscript writing and revision. S.W. and Y.D designed the study and organized the research, manuscript writing and revision. T.L. contributed to the code writing and data analysis. W.G.H. contributed to manuscript revision.
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Supplementary information
S1. Metadata of samples for pathogen detection analysis
S2. Pathogens identified by GSMer in the Yangtze River Basin and their potential hosts
S3. Georeferenced sampling locations and pathogen richness used in spatial mapping
the spatial distribution maps for water, sediment and soils
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Wang, J., Wang, S., Li, T. et al. A watershed-scale potential pathogenic bacteria dataset from the Yangtze River Basin.
Sci Data (2026). https://doi.org/10.1038/s41597-026-06983-0
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DOI: https://doi.org/10.1038/s41597-026-06983-0
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