Weill Cornell Medical College's Christopher Mason and his colleagues have issued a correction for their study that examined the microbiome of the New York City subway system and other metropolitan locales, Retraction Watch reports.
As they reported in a February Cell Systems article, much of the DNA they collected from all over the city didn't belong to any known organisms, and most of the rest came from rather harmless bacteria, archaea, and viruses, especially bacterial genera associated with human skin.
However, the researchers also reported that they found evidence of pathogens like Bacillus anthracis and Yersinia pestis, which they suggested might just be part of a healthy city microbiome. Health officials and others took issue with these findings.
In a subsequent blog post, Mason had countered that the study only presented evidence that DNA from these pathogens could be present and that he and his colleagues had hedged their bets by noting the low levels of their DNA and by including phrases like "if truly present." He also noted that the study's reliance on Blast for comparison limited it.
In the erratum, Mason and his colleagues report that the article has been "revised to remove and clarify misleading and speculative text about pathogenic organisms." They add "that although all our metagenomic analysis tools identified reads with similarity to B. anthracis and Y. pestis sequences, there is minimal coverage to the backbone genome of these organisms, and there is no strong evidence to suggest these organisms are in fact present, and no evidence of pathogenicity." They also revised an error in a figure regarding coverage of the murine toxin gene.
Mason tells Retraction Watch in a statement that "[e]ven though all of the most widely used tools for DNA mapping and metagenomics reported the presence of putative pathogens, (including BLAST, MetaPhlAn, SURPI, PhyloSift, and others), we felt it was important to unequivocally state the difference between matching fragments of DNA from a species and a pathogen."
He adds that much of the criticism of the work centered on the interpretation, not the analysis, of the data. "[T]here is not a retraction of our paper and there won't be — our main results have been validated by several groups already and publicized," Mason says. "The question is not about the data analysis — it is about interpretation of the results."