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Replication Study: Fusobacterium nucleatum infection is prevalent in human colorectal carcinoma

As part of the “Reproducibility Project: Cancer Biology”, a Registered Report (Repass et al., 2016) was published in 2016, that described how to replicate an experiment from the paper “Fusobacterium nucleatuminfection is prevalent in human colorectal carcinoma” (Castellarin et al., 2012). Here, the “Reproducibility Project: Cancer Biology” Team reported the results, published in eLIFE. When measuring Fusobacterium nucleatum DNA by qPCR in colorectal carcinoma (CRC), adjacent normal tissue, and separate matched control tissue, the authors did not detect a signal for F. nucleatum in most samples. When only samples with detectable F. nucleatum in CRC and adjacent normal tissue were compared, the difference was not statistically significant, while the original study reported a statistically significant increase in F. nucleatum presence in CRC compared to adjacent normal tissue.
Searching for potential explanations for this discrepancy, the authors of the replication study explained that any known differences, including reagents and protocol differences, were identified prior to conducting the experimental work. However, this was limited to what could be obtained from the original paper, which means there might be particular features of the original experimental protocol that could be critical, but unidentified. So while some aspects, such as method of qPCR and primer and probe sequences were maintained, others were unknown or not easily controlled for, including any influence of diet on the gut microbiota. Whether these or other factors influence the outcomes of this study is open to hypothesizing and further investigation, which is facilitated by direct replications and transparent reporting.
The outcome measures reported in this Replication Study will be aggregated with those from the other Replication Studies to create a dataset that will be examined to provide evidence about reproducibility of cancer biology research, and to identify factors that influence reproducibility more generally.

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