Data availability
All raw metatranscriptomic sequencing data generated in this study are deposited in the NCBI Sequence Read Archive (SRA) under BioProject PRJNA119800130. The dataset contains paired-end FASTQ files (2 × 150 bp) for each wastewater sample, organized into BioSamples SAMN45825509–SAMN45825528 and corresponding SRA Experiments SRX27073143–SRX2707316231. Metadata describing sample collection dates, sample type, and sequencing platform are included in each BioSample record...
Data availability
All raw metatranscriptomic sequencing data generated in this study are deposited in the NCBI Sequence Read Archive (SRA) under BioProject PRJNA119800130. The dataset contains paired-end FASTQ files (2 × 150 bp) for each wastewater sample, organized into BioSamples SAMN45825509–SAMN45825528 and corresponding SRA Experiments SRX27073143–SRX2707316231. Metadata describing sample collection dates, sample type, and sequencing platform are included in each BioSample record. BioSample metadata follows the Genomic Standards Consortium’s “MIMS Environmental/Metagenome” metadata standard. The analysis results can be accessed in the following figshare repository: https://doi.org/10.6084/m9.figshare.28454990.v132.
Code availability
Sequencing data quality and taxonomic composition was assessed using a comprehensive computational pipeline, available under https://github.com/naobservatory/mgs-workflow/tree/2.5.1. The analysis results can be accessed in the following figshare repository: https://doi.org/10.6084/m9.figshare.28454990.v132. Code for figures and tables can be accessed under https://github.com/naobservatory/w-mgs-data-paper.
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Acknowledgements
S.L.G., J.T.K., W.J.B., K.L.W., and J.A.R. were funded for this research project by gifts from Open Philanthropy (to SecureBio). J.A.R was supported by an allocation (#BIO240238) from the National Science Foundation Advanced Cyberinfrastructure Coordination Ecosystem: Services and Support (ACCESS) program. K.L.W. and J.A.R. would like to acknowledge earlier support for wastewater monitoring from the University of California Office of the President (award R00RG2814) and the Hewitt Foundation for Biomedical Research. We thank the City of Los Angeles and the Hyperion Wastewater Reclamation Plant for sampling assistance. We also thank Seung-Ah Chung and Melanie Oaks of the University of California Irvine Genomics Research and Technology Hub (GRT Hub), parts of which are supported by NIH grants to the Comprehensive Cancer Center (P30CA-062203) and the UCI Skin Biology Resource Based Center (P30AR075047) at the University of California, Irvine, as well as to the GRT Hub for instrumentation (1S10OD010794-01 and 1S10OD021718-01).
Author information
Authors and Affiliations
Media Laboratory, Massachusetts Institute of Technology, Cambridge, USA
Simon L. Grimm, William J. Bradshaw & Jeff T. Kaufman 1.
SecureBio, Cambridge, USA
Simon L. Grimm, William J. Bradshaw & Jeff T. Kaufman 1.
Department of Microbiology and Plant Pathology, University of California, Riverside, Riverside, CA, USA
Jason A. Rothman 1.
Southern California Coastal Water Research Project, Costa Mesa, CA, USA
Kylie Langlois, Joshua A. Steele & John F. Griffith 1.
Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine, CA, USA
Katrine L. Whiteson
Authors
- Simon L. Grimm
- Jason A. Rothman
- William J. Bradshaw
- Kylie Langlois
- Joshua A. Steele
- John F. Griffith
- Jeff T. Kaufman
- Katrine L. Whiteson
Contributions
J.T.K. and J.A.R. conceived the study; K.L., J.A.S. and J.F.G. collected wastewater samples; J.A.R. ran sequencing experiments; J.T.K. imported sequencing data, with processing and analysis by S.L.G. and W.J.B. S.L.G. wrote the manuscript, with feedback from all authors. K.L.W. provided study design, project management, and oversight along with manuscript edits.
Corresponding authors
Correspondence to Jason A. Rothman or Jeff T. Kaufman.
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The authors declare no competing interests.
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Cite this article
Grimm, S.L., Rothman, J.A., Bradshaw, W.J. et al. Deep metatranscriptomic sequencing data of wastewater from Los Angeles, USA, 2023–2024. Sci Data (2025). https://doi.org/10.1038/s41597-025-06475-7
Received: 07 May 2025
Accepted: 15 December 2025
Published: 24 December 2025
DOI: https://doi.org/10.1038/s41597-025-06475-7