An international team led by researchers from the Yong Loo Lin School of Medicine, National University of Singapore (NUS Medicine) and A*STAR Genome Institute of Singapore (A*STAR GIS), has published a new paper in Nature Cancer highlighting the importance of greater care, consistency, and rigour in studies reporting microbes in human tumours.
In recent years, advances in DNA sequencing have enabled researchers to detect traces of bacterial, fungal, and viral genetic material in diverse samples. Some studies have reported microbes even in sites traditionally considered microbe-free, such as the brain or the placenta, and findings on microbes in tumours from diverse organs have generated interest in how tumour-associated microbes could influence cancer growth, spread, or response to treatment. However, the researchers caution that interpreting such signals can be complex. Tumour tissues from diverse organs typically contain extremely low amounts of microbial material or none, making them especially vulnerable to contamination introduced during surgery, sample handling, storage, laboratory processing, or sequencing. Limitations in data analysis and reference databases can further complicate interpretation, leading to microbial signals that may not reflect true biological presence.
“Finding microbial DNA in tumours is like finding a needle in a haystack,” said Associate Professor Niranjan Nagarajan, Department of Biochemistry and Infectious Diseases Translational Research Programme (TRP), NUS Medicine, a lead author of this report. “If appropriate checks and additional validation are not built into the analysis, it becomes very difficult to distinguish genuine microbial signals from background noise.” Associate Professor Nagarajan is also Associate Director, AI and Compute, and Senior Group Leader, Laboratory of Metagenomic Technologies and Microbial Systems at A*STAR GIS.
The team reviewed current practices across the rapidly growing field of cancer microbiome research and identified recurring methodological challenges, including insufficient use of negative controls, heavy reliance on bioinformatic analysis alone, and limited validation using independent or complementary methods. They drew parallels with early challenges in ancient DNA research, where the adoption of stringent standards helped mature that field into a reliable scientific discipline.
Importantly, the researchers stress that their report does not question the role of cancer-associated microbes in general. Microorganisms are already known to contribute to certain cancers, particularly in tissues exposed to abundant microbes, such as the gastrointestinal tract. Rather, the paper encourages careful evaluation of claims of diverse tumour-resident microbiomes in low-biomass tissues, especially where supporting evidence is limited.
To help the field move forward, the researchers propose a practical checklist of best practices covering the entire research pipeline—from sample collection and handling, to sequencing, data analysis, and biological validation. A more detailed explanation can be found below, in Annexe A .
These recommendations emphasise preventing contamination, incorporating appropriate controls, validating findings with multiple independent approaches, and being transparent about data limitations. This work reflects an international collaboration involving scientists from Singapore, the United States, the Netherlands, Denmark, and Australia, bringing together expertise in genomics, computational biology, microbiome science, pathology, and immunology.
“When researchers work with very small signals, even minor background noise can influence the outcome,” said Dr Chia Minghao, Senior Scientist at A*STAR GIS, and co-author of the study. “By putting stronger safeguards in place and confirming results through multiple approaches, the scientific community can improve reproducibility and ensure that future discoveries about microbes and cancer rest on solid foundations.”
Microbes associated with tumours could provide important insights into cancer biology and inform future diagnostics or therapies. At the same time, inconclusive or weakly supported findings can slow progress. By encouraging higher and more consistent standards across the field, the researchers hope to strengthen confidence in cancer microbiome research and support future findings that are reliable, reproducible, and clinically relevant.
ANNEXE A
List of proposed best practices
1. Prevent contamination during sample collection
2. Maintain clean handling and storage procedures
3. Use strict laboratory and sequencing controls
4. Ensure sequencing quality and transparency
5. Apply conservative and transparent bioinformatic analysis
6. Validate findings using independent experimental methods
7. Provide transparent reporting and multiple lines of evidence
Please refer to their published study for the checklist and the reasoning behind those items:
https://www.nature.com/articles/s43018-026-01121-6
Nature Cancer
Setting higher standards for reports of microbial species in human cancers
19-Feb-2026