‘All authors agree’ to retraction of Nature article linking microbial DNA to cancer

A 2020 paper that claimed to find a link between microbial genomes in tissue and cancer has been retracted following an analysis that called the results into question. 

The paper, “Microbiome analyses of blood and tissues suggest cancer diagnostic approach,” was published in March 2020 and has been cited 610 times, according to Clarivate’s Web of Science. It was retracted June 26. The study was also key to the formation of biotech start-up Micronoma, which did not immediately respond to our request for comment. 

Rob Knight, corresponding author and researcher at the University of California San Diego, also did not immediately respond to our request for comment. 

In October 2023, mBio, a journal from the American Society for Microbiology, published “Major data analysis errors invalidate cancer microbiome findings.” The paper pointed out several major flaws in the the earlier article by Knight’s group. 

After downloading and analyzing the original data, “we found almost right away that the authors of the Nature paper had made some huge mistakes – that most of the bacteria they found simply weren’t there, or else were present in quantities that were 100s of times smaller than they reported. Oops,” Steven Salzberg, a researcher at Johns Hopkins in Baltimore, and corresponding author of the 2023 paper, told Retraction Watch in an email. 

Salzberg and his colleagues found “some of these species were ‘nonsensical,’” he told us. For example, the Knight paper found that Hepandensovirus was the most important species to identify adrenocortical carcinoma. “Well, that’s a shrimp virus! Makes no sense as it doesn’t exist in humans,” he told us.

Knight’s group responded to the criticism in a follow-up paper, “Robustness of cancer microbiome signals over a broad range of methodological variation,” published in February 2024 in Oncogene. In it, they defended their original findings: “These extensive re-analyses and updated methods validate our original conclusion that cancer type-specific microbial signatures exist in TCGA, and show they are robust to methodology.”

The retraction notice cites Salzberg’s paper and the response from the authors. It reads: 

The Editors have retracted this article. After publication, concerns about the robustness of specific microbial signatures reported as associated with cancer were brought to the attention of the Editors. The authors have provided responses to the issues in a separate publication.

Expert post-publication peer review of the issues raised and the authors’ responses has confirmed that some of the findings of the article are affected and the corresponding conclusions are no longer supported. All authors agree with this retraction.

Like Retraction Watch? You can make a tax-deductible contribution to support our work, subscribe to our free daily digest or paid weekly update, follow us on Twitter, like us on Facebook, or add us to your RSS reader. If you find a retraction that’s not in The Retraction Watch Database, you can let us know here. For comments or feedback, email us at [email protected].