Data availability
The processed non-human reads from tumor and NAT tissues of 937 CRC patients in the U-CAN study are deposited at the European Nucleotide Archive (ENA, PRJEB86036) and the China National GeneBank Sequence Archive (CNSA87, CNP0007001) of the China National GeneBank DataBase (CNGBdb)88. Genomic variations and gene expression profiles from the U-CAN study are available at the European Variation Archive[89](http…
Data availability
The processed non-human reads from tumor and NAT tissues of 937 CRC patients in the U-CAN study are deposited at the European Nucleotide Archive (ENA, PRJEB86036) and the China National GeneBank Sequence Archive (CNSA87, CNP0007001) of the China National GeneBank DataBase (CNGBdb)88. Genomic variations and gene expression profiles from the U-CAN study are available at the European Variation Archive89 (EVA, PRJEB61514), and at the ArrayExpress90 (E-MTAB-12862), and available at the CNSA (CNP0004160). The raw WGS data can be accessed by directing to the U-CAN cancer biobank at Uppsala University (https://www.uu.se/forskning/u-can/)9. Non-human WGS reads from tumor tissues of 167 colon cancer patients in the AC-ICAM study10 are publicly available via the Sequence Read Archive (SRA) (PRJNA941834). A genus-level 16S rRNA amplicon-based abundance matrix for tumor and matched healthy colon tissues from 246 patients in the AC-ICAM study were retrieved from Figshare (https://figshare.com/articles/dataset/Supplementary_Data_AC-ICAM/16944775). Clinical and gene expression data for the AC-ICAM study are available from Supplementary Source Data of the study. Source data are provided with this paper.
Code availability
The source code for generating the main figures and constructing the Microbial Risk Score (MRS) is available to use on GitHub under the MIT License (https://github.com/rusher321/UCAN_Microbiome). The repository has been archived on Zenodo (https://doi.org/10.5281/zenodo.17588313, version v1.0)91.
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Acknowledgements
The U-CAN tumor biobank was funded by a grant from the Swedish Government (CancerUU) to Uppsala University, Umeå University, KTH Royal Institute of Technology, and Stockholm University (2010-ongoing). This study was also funded by the National Science and Technology Major Project (No. 2025ZD0551700 to K.W.) and the Guangdong Provincial Key Laboratory of Human Disease Genomics (2020B1212070028 to K.W.). Data handling and storage was enabled by resources in project sens2019031 provided by the National Academic Infrastructure for Supercomputing in Sweden (NAISS) at UPPMAX, funded by the Swedish Research Council through grant agreement no. 2022-06725.
Author information
Author notes
These authors contributed equally: Zhun Shi, Huahui Ren, Cong Lin, Fuqiang Li.
Authors and Affiliations
BGI Genomics, Shenzhen, China
Zhun Shi, Huahui Ren, Meizhen Wu, Fangming Yang, Tian Luo, Shida Zhu, Yiyi Zhong, Kui Wu & Huanzi Zhong 1.
HIM-BGI Omics Center, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, BGI Research, Hangzhou, China
Cong Lin & Fuqiang Li 1.
Guangdong Provincial Key Laboratory of Human Disease Genomics, BGI Research, Shenzhen, China
Cong Lin & Fuqiang Li 1.
Department of Molecular Oncology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
Luís Nunes 1.
Science for Life Laboratory, Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
Luís Nunes, Anders Isaksson, Klara Hammarström, Bengt Glimelius & Tobias Sjöblom 1.
College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
Ting Zhu 1.
BGI Precision Nutrition, Shenzhen, China
Yiyi Zhong & Huanzi Zhong 1.
Department of Radiation Sciences, Oncology, Umeå University, Umeå, Sweden
Ingrid Ljuslinder 1.
Science for Life Laboratory, Department of Protein Science, KTH-Royal Institute of Technology, Stockholm, Sweden
Mathias Uhlén 1.
Department of Neuroscience, Karolinska Institutet, Stockholm, Sweden
Mathias Uhlén 1.
Department of Medical Biosciences, Pathology, Umeå University, Umeå, Sweden
Richard Palmqvist
Authors
- Zhun Shi
- Huahui Ren
- Cong Lin
- Fuqiang Li
- Meizhen Wu
- Fangming Yang
- Tian Luo
- Luís Nunes
- Anders Isaksson
- Klara Hammarström
- Ting Zhu
- Shida Zhu
- Yiyi Zhong
- Ingrid Ljuslinder
- Mathias Uhlén
- Richard Palmqvist
- Bengt Glimelius
- Kui Wu
- Tobias Sjöblom
- Huanzi Zhong
Contributions
Z.S., H.R., C.L., F.L., and H.Z. conceived the study; C.L., K.W., T.S., I.L., B.G., R.P., S.Z., Y.Z. M.U. and H.Z., coordinated the study; Z.S., H.R., C.L., F.L., M.W., T.L., F.Y., L.N., K.H., A.I., T.Z., B.G., and H.Z performed data curation; Z.S., H.R., and F.L., analyzed data; K.W., T.S., C.L., and H.Z. supervised the study; Z.S., H.R., C.L., F.L., T.S., and H.Z. wrote the paper with input from all other authors. All authors approved the manuscript before submission.
Corresponding authors
Correspondence to Cong Lin, Kui Wu, Tobias Sjöblom or Huanzi Zhong.
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Shi, Z., Ren, H., Lin, C. et al. Tissue-resident microbiota impacts colorectal cancer progression and prognosis. Nat Commun (2025). https://doi.org/10.1038/s41467-025-67047-2
Received: 11 August 2025
Accepted: 20 November 2025
Published: 07 December 2025
DOI: https://doi.org/10.1038/s41467-025-67047-2