Get Involved
About Us
Our Members
‘Strengths and Limitations of DNA Barcoding’ Article Published in Planta Medica
ABC Chief Science Officer Co-authors Review of DNA Barcoding Analysis

Editor’s note: American Botanical Council (ABC) Chief Science Officer Stefan Gafner, PhD, co-authored the Planta Medica article with Iffat Parveen, PhD, Natascha Techen, PhD, and Ikhlas Khan, PhD, all researchers at the internationally respected National Center for Natural Products Research (NCNPR) at the University of Mississippi (a US Food and Drug Administration [FDA]-funded Center of Excellence in the area of medicinal plant analysis), and Susan Murch, PhD, an expert in the analysis of botanical ingredients at the University of British Columbia in Canada. Interested parties are encouraged to obtain the original article from the journal.


In July 2016, the respected, peer-reviewed medicinal plant journal Planta Medica published an online paper1 written by various experts in medicinal plant analysis. The paper reviews the strengths and limitations of DNA barcoding analytical methods — a subject that has received significant global attention since the New York attorney general’s (NY AG’s) now-infamous and highly flawed DNA analysis of various herbal dietary supplements, which was covered by The New York Times and other major news outlets in 2015.

Based on the DNA analysis, the NY AG took regulatory action against four major retailers for allegedly selling mislabeled herbal supplements. (The products produced and sold by retailer GNC were later deemed by the NY AG to be compliant with state and federal regulations and allowed back onto retail shelves in New York; actions against Target, Walgreens, and Walmart are still pending.) The NY AG has been criticized for relying solely on DNA barcoding analysis as the basis for his regulatory actions. These criticisms have come from a variety of sources: from plant analytical experts in academia, government, and industry, to industry sources and ABC publications.

As noted in the paper, DNA barcoding methods should not be used as the sole analytical method to determine the identity of botanical ingredients in finished herbal formulations (e.g., dietary supplements). Rather, DNA barcoding should be used as part of a larger array of methodologies, including microscopic and chemical methods.

Article Summary

The authors of the Planta Medica article begin with an overview of DNA barcoding and discuss the steps (extraction, amplification, and sequencing) involved in the technology, as well as its strengths and limitations for plant identification.

DNA barcoding, which involves the use of short genomic regions to distinguish species of animals, plants, fungi, bacteria, and other organisms, has become an increasingly popular technology to determine the authenticity of botanical ingredients in herbal medicines and dietary supplements. Plant DNA barcoding, initially used predominantly in academia to determine the relationship among species (phylogeny), is now used by many groups, including dietary supplement manufacturers, contract analytical laboratories, government agencies (e.g., the FDA), and, as noted previously, the office of the NY AG. The outcome of DNA barcoding varies depending on the method of DNA extraction, primer choice, amplification, and sequencing. In addition, the success of the technology depends on the presence of high-quality DNA and the absence of interfering compounds in the material analyzed.

A number of extraction methods are used in practice. The choice of the method depends on the material to be analyzed. Different plant parts (DNA is more difficult to obtain from bark or root compared to leaves or flowers) and metabolite compositions (e.g., presence of polysaccharides or polyphenols) will affect the extraction efficiency. The choice of the genomic region is crucial for the successful outcome of the approach. Some regions are difficult to amplify in certain plants (e.g., matK) or have a low resolving power (i.e., they do not adequately distinguish among certain species). Others, like the widely used ITS region, may differentiate plants readily, but there may be several copies with varying DNA sequences within the same plant (e.g., in valerian [Valeriana officinalis, Caprifoliaceae] and related species). For example, ITS regions from fungal species that may be present as an endophyte (living within the plant) or ectophyte (living at the surface of the plant) may be preferentially amplified.

The quality of DNA present in botanical material is highly dependent on the various steps used to process the material (e.g., drying, grinding, sterilization, storage, extraction, etc.). In many cases, DNA is degraded or absent altogether. The universal primers used for DNA barcoding are designed to amplify the target genomic region of as many plant species as possible, but variations in the sequence in which the primers anneal (bind) may introduce an amplification bias (i.e., in a mixture of botanically derived ingredients, one material is amplified preferentially over the other). The presence of plant polyphenols, such as tannins, in the amplification step also may be problematic, since these metabolites inhibit the polymerases that amplify the DNA.

The final step in DNA barcoding is the sequencing of the DNA. The Sanger sequencing method has been the method of choice in the past, and works well in cases in which a single botanical ingredient is present. Drawbacks of the Sanger sequencing method include the difficulty of obtaining accurate results for mixtures of ingredients, the low throughput, and the need for greater amounts of DNA compared to next-generation sequencing (NGS). NGS allows simultaneous analysis of multiple DNA fragments (e.g., when multiple plant species are present, such as in herbal preparations used in traditional Chinese medicine or Ayurvedic medicine).

There are, however, some notable advantages to using DNA barcoding compared to other methods of plant species identification. While botanical taxonomy remains the basis of plant classification when a whole plant can be examined in its natural habitat (or as a pressed herbarium species), botanical ingredients are predominantly sold in cut, powdered, or extracted form. For cut or powdered crude raw material, DNA barcoding offers a reliable way to authenticate samples in addition to methods such as organoleptic evaluation, botanical microscopy, and chemical analysis, especially in cases in which species distinction may be challenging.

For materials with fragmented DNA, the amplification of shorter genomic regions, so-called mini-barcodes, may enable identification of the plant material. In order for mini-barcoding to be successful, the analyst has to design species-specific primers resulting in a much shorter amplicon (the piece of DNA that is amplified) compared to the universal barcoding. To apply mini-barcoding, the analyst has to have an idea of the composition of the material, and by using species-specific primers may fail to detect adulterant material. Some plant materials may not be suitable for the design of mini-barcodes (i.e., a small amplicon may not contain sufficient sequence variation to distinguish among species).

The main limitations of current DNA barcoding techniques are the possibility of erroneous results when DNA is degraded (or when large amounts of DNA from other species is present), the reliance on databases in which the material from which the DNA sequence was obtained may not have been authenticated properly, and its inability to distinguish plant parts, which is a legal requirement specified in the FDA’s current good manufacturing practices (cGMPs) for dietary supplements.

As with every analytical method used for quality control of botanical ingredients, DNA barcoding methods need to be properly validated in order to ensure that the results are accurate and reproducible. Validation requirements specific to DNA barcoding of plant ingredients are a matter of debate, and the establishment of guidelines to validate such methods is much-needed.

Overall, DNA barcoding is a helpful tool to determine the authenticity of botanical material in whole, cut or powdered form. However, based on its inherent limitations, it should be used in combination with other identification methods, such as microscopic, macroscopic, organoleptic, and chemical methods of analysis.

—Stefan Gafner, PhD


  1. Parveen I, Gafner S, Techen N, Murch SJ, Khan IA. DNA barcoding for the identification of botanicals in herbal medicine and dietary supplements: strengths and limitations [published online July 8, 2016]. Planta Med. 2016. doi:10.1055/s-0042-111208. Available at: Accessed August 10, 2016.