Journal retracts botanical DNA barcoding paper by Newmaster

By Stephen Daniells contact

- Last updated on GMT

© Olena Yepifanova / Getty Images
© Olena Yepifanova / Getty Images

Related tags: Dna barcoding, botanical extracts, science, peer-review journals

A paper that concluded that DNA barcoding techniques were more cost-effective than traditional practices for identification of vegetation species has been retracted after the lead researcher – Dr Steven Newmaster – failed to respond to questions about the validity of the data.

The paper, “Molecular taxonomic tools provide more accurate estimates of species richness at less cost than traditional morphology based taxonomic practices in a vegetation survey”​ was authored by Ken Thompson and Steven Newmaster of the University of Guelph and published in 2014 in Biodiversity and Conservation​.

In an October 27, 2021 notice, the journal’s Editor-in-Chief​ confirmed the paper has been retracted after Thompson voiced concerns about the validity of the data and Newmaster failed to respond to the journal’s editor and publisher.  

Retractions of papers published in peer reviewed scientific journals are rare, with only about four articles per 10,000 published estimated to be retracted (Science​, 2018, doi: 10.1126/science.aav8384​).

It should be stressed that this is related to only one paper focused on a vegetation survey and not botanical extracts or dietary supplements.

The news will be of interest to many industry stakeholders, however, since DNA barcoding technology burst into the industry’s collective consciousness in 2015​ when then New York Attorney General Eric Schneiderman sent letters to GNC, Target, Walmart, and Walgreens telling them to stop selling some herbal supplements after DNA tests found 79% didn’t contain the labeled substance or contained other non-listed ingredients.

The prompt for the NY AG’s investigation was a report in the New York Times​ in 2013 of a paper by Dr Newmaster and his group in the open access journal BMC Medicine​. That paper was widely criticized by analytical and botanical experts, and the American Botanical Council called for it to be retracted​. That 2013 paper was not retracted.

Newmaster also founded the NHP Research Alliance​ which aims to advance the use of DNA testing and molecular diagnostics in quality assurance of natural health products, including dietary supplements.

Retraction

The retraction of the paper by Thompson and Newmaster was initiated by Thompson when he became concerned about the availability of the data, the sources of the data, and reproducibility.

“Post-publication review of the article confirmed concerns with the data availability, and the validity of the data included in the article could not be confirmed,”​ states the retraction notice in the journal.

NutraIngredients-USA attempted to contact Dr Newmaster but did not receive a response prior to publication. Repeated attempts by the editor and publisher of Biodiversity and Conservation​, and journalists at Science​ also reportedly went unanswered.

Thompson’s efforts to shine a light on his concerns were the subject of two articles published in Science​ over the past several months. Those articles are available via the links below.  According to the first Science​ article, Thompson, who was a graduate student at the time the 2014 paper was written, has had suspicions about the data used in the paper for a while, but feared raising the issue would harm his career.

Science​, June 15, 2021: “When his suspicions went unanswered, this biologist decided to disavow his own study”

Science​, October 28, 2021: “DNA barcoding paper retracted after its first author flags serious problems”

The technology

As reported by NutraIngredients-USA in 2013​, DNA barcoding to test botanicals is reliable, but only when performed on appropriate material. Botanical extracts are problematic because, while some extracts may contain DNA, it is often of low quality or degraded to a point that makes it impossible to perform proper authentication.

Other limitations of DNA technology are that, i) it cannot determine between plant parts (leaf, stem, root – the DNA is the same), ii) it’s not very useful for quantification, and iii) there is no definitive library of reference standards.

Michael McGuffin, President of the American Herbal Products Association (AHPA), told us that DNA technology is one tool that industry is using and is investing in. The retraction in no way undermines the use of DNA analysis when used appropriately, he said.

Commenting on the technology itself, Dr Ikhlas Khan, Director of the National Center for Natural Products Research at the University of Mississippi, told NutraIngredients-USA that DNA technology is fit for purpose if used appropriately, but it did not match the hype as a magic bullet to resolve the identity issue required by GMPs in the wake of the New York AG’s findings.

“Like any other technology, it should be understood as a tool and we should generate enough data to justify its purpose,”​ said Dr Khan. “DNA barcoding has potential uses if we focus on generating the data and have resources available to do it.”

“Genetic testing is here to stay”

Stefan Gafner, PhD, Chief Science Officer at the American Botanical Council, told NutraIngredients-USA that, at least from an industry side, the classic methods of authentication (macroscopic, microscopic, and chemical methods) are still the backbone of identity testing.

“Some industry members are using genetic testing at the source, i.e., the plants once they are harvested, since some manufacturers require that the raw material is authenticated by DNA,” ​he said. “But if you know your supply chain and have a good control over it, then such testing seems mostly superfluous. And once the plant material is extracted, filtered, and sterilized, getting good results by genetic testing becomes tricky.

“There are some obvious strengths to genetic testing as well, of course. Most notably, it can identify the adulterating species in many cases, especially for cut or powdered plant material. This is usually much more challenging with other methods. Interestingly (at least for me), Steven Newmaster has more and more embraced nuclear magnetic resonance (NMR) as a means of plant authentication. But overall, I think that genetic authentication is a very useful tool.”

Dr Gafner continued: “While genetic test methods for botanical identity assessment have been around for a while, assays to authenticate botanical dietary supplement ingredients with DNA technology are relatively new. But the technology advances at a very rapid pace, and researchers are now working on methods to answer some questions that a few years ago seemed impossible to figure out by genetic means. As such, a number of papers have shown that DNA can be found in most extracts, albeit at shorter length (more fragmented) and of lower quality, but often good enough to identify the species.

“Some strides have also been made to get qualitative or semi-qualitative results using quantitative PCR. As such, genetic testing is here to stay, but I don’t foresee it replacing any of the classical quality control methods currently used in the dietary supplement industry, at least not in the near future.”

 

Related topics: Research, GMPs, QA & QC, Botanicals

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