Planta Med 2021; 87(04): 314-324
DOI: 10.1055/a-1336-1685
Natural Product Chemistry and Analytical Studies
Original Papers

HPLC-UV, Metabarcoding and Genome Skims of Botanical Dietary Supplements: A Case Study in Echinacea

1   Center for Food Safety and Applied Nutrition, Office of Regulatory Science, U. S. Food and Drug Administration, College Park, Maryland, United States
1   Center for Food Safety and Applied Nutrition, Office of Regulatory Science, U. S. Food and Drug Administration, College Park, Maryland, United States
Andrea R. Ottesen*
1   Center for Food Safety and Applied Nutrition, Office of Regulatory Science, U. S. Food and Drug Administration, College Park, Maryland, United States
Padmini Ramachandran
1   Center for Food Safety and Applied Nutrition, Office of Regulatory Science, U. S. Food and Drug Administration, College Park, Maryland, United States
Satyanarayanaraju Sagi
1   Center for Food Safety and Applied Nutrition, Office of Regulatory Science, U. S. Food and Drug Administration, College Park, Maryland, United States
Ning Zhang
1   Center for Food Safety and Applied Nutrition, Office of Regulatory Science, U. S. Food and Drug Administration, College Park, Maryland, United States
Erica Hsu
2   Joint Institute of Food Safety and Applied Nutrition, University of Maryland, College Park, Maryland, United States
David L. Erickson
2   Joint Institute of Food Safety and Applied Nutrition, University of Maryland, College Park, Maryland, United States
3   DNA4 Technologies LLC, Halethorpe, Maryland, United States
› Author Affiliations


The use of DNA-based methods to authenticate botanical dietary supplements has been vigorously debated for a variety of reasons. More comparisons of DNA-based and chemical methods are needed, and concordant evaluation of orthogonal approaches on the same products will provide data to better understand the strengths and weaknesses of both approaches. The overall application of DNA-based methods is already firmly integrated into a wide array of continually modernizing stand alone and complementary authentication protocols. Recently, the use of full-length chloroplast genome sequences provided enhanced discriminatory capacity for closely related species of Echinacea compared to traditional DNA barcoding approaches (matK and rbcL). Here, two next-generation sequencing approaches were used: (1) genome skimming and (2) PCR amplicon (metabarcoding). The two genetic approaches were then combined with HPLC-UV to evaluate 20 commercially available dietary supplements of Echinacea representing “finished” products. The trade-offs involved in different DNA approaches were discussed, with a focus on how DNA methods support existing, accepted chemical methods. In most of the products (19/20), HPLC-UV suggested the presence of Echinacea spp. While metabarcoding was not useful with this genus and instead only resolved 7 products to the family level, genome skimming was able to resolve to species (9) or genus (1) with the 10/20 products where it was successful. Additional ingredients that HPLC-UV was unable to identify were also found in four products along with the relative sequence proportion of the constituents. Additionally, genome skimming was able to identify one product that was a different Echinacea species entirely.

* Current address: Center for Veterinary Medicine, U. S. Food and Drug Administration, College Park, Maryland, United States

Supporting Information

Publication History

Received: 10 July 2020

Accepted after revision: 11 December 2020

Article published online:
14 January 2021

© 2021. Thieme. All rights reserved.

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