Other Major data analysis errors invalidate cancer microbiome findings (Oct 2023) Critique of "Microbiome analyses of blood and tissues suggest cancer diagnostic approach"

Michael Harrop

Active member
Jul 6, 2023


We re-analyzed the data from a recent large-scale study that reported strong correlations between DNA signatures of microbial organisms and 33 different cancer types and that created machine-learning predictors with near-perfect accuracy at distinguishing among cancers. We found at least two fundamental flaws in the reported data and in the methods: (i) errors in the genome database and the associated computational methods led to millions of false-positive findings of bacterial reads across all samples, largely because most of the sequences identified as bacteria were instead human; and (ii) errors in the transformation of the raw data created an artificial signature, even for microbes with no reads detected, tagging each tumor type with a distinct signal that the machine-learning programs then used to create an apparently accurate classifier. Each of these problems invalidates the results, leading to the conclusion that the microbiome-based classifiers for identifying cancer presented in the study are entirely wrong. These flaws have subsequently affected more than a dozen additional published studies that used the same data and whose results are likely invalid as well.


Recent reports showing that human cancers have a distinctive microbiome have led to a flurry of papers describing microbial signatures of different cancer types. Many of these reports are based on flawed data that, upon re-analysis, completely overturns the original findings. The re-analysis conducted here shows that most of the microbes originally reported as associated with cancer were not present at all in the samples. The original report of a cancer microbiome and more than a dozen follow-up studies are, therefore, likely to be invalid.

The referenced study:
Microbiome analyses of blood and tissues suggest cancer diagnostic approach (March 2020) https://www.nature.com/articles/s41586-020-2095-1

Pubpeer discussion https://pubpeer.com/publications/C5FB84438097C5A408B6D6A3648539

I think most of the studies listed here https://humanmicrobiome.info/cancer/ should be unaffected by this discovery.
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