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Ríos-Reina R, Callejón R, Amigo J. Feasibility of a rapid and non-destructive methodology for the study and discrimination of pine nuts using near-infrared hyperspectral analysis and chemometrics. Food Control 2021. [DOI: 10.1016/j.foodcont.2021.108365] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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2
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Hunter ES, Literman R, Handy SM. Utilizing Big Data to Identify Tiny Toxic Components: Digitalis. Foods 2021; 10:1794. [PMID: 34441571 PMCID: PMC8391216 DOI: 10.3390/foods10081794] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Revised: 07/22/2021] [Accepted: 07/27/2021] [Indexed: 12/23/2022] Open
Abstract
The botanical genus Digitalis is equal parts colorful, toxic, and medicinal, and its bioactive compounds have a long history of therapeutic use. However, with an extremely narrow therapeutic range, even trace amounts of Digitalis can cause adverse effects. Using chemical methods, the United States Food and Drug Administration traced a 1997 case of Digitalis toxicity to a shipment of Plantago (a common ingredient in dietary supplements marketed to improve digestion) contaminated with Digitalis lanata. With increased accessibility to next generation sequencing technology, here we ask whether this case could have been cracked rapidly using shallow genome sequencing strategies (e.g., genome skims). Using a modified implementation of the Site Identification from Short Read Sequences (SISRS) bioinformatics pipeline with whole-genome sequence data, we generated over 2 M genus-level single nucleotide polymorphisms in addition to species-informative single nucleotide polymorphisms. We simulated dietary supplement contamination by spiking low quantities (0-10%) of Digitalis whole-genome sequence data into a background of commonly used ingredients in products marketed for "digestive cleansing" and reliably detected Digitalis at the genus level while also discriminating between Digitalis species. This work serves as a roadmap for the development of novel DNA-based assays to quickly and reliably detect the presence of toxic species such as Digitalis in food products or dietary supplements using genomic methods and highlights the power of harnessing the entire genome to identify botanical species.
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Affiliation(s)
| | | | - Sara M. Handy
- Center for Food Safety and Applied Nutrition, Office of Regulatory Science, U.S. Food and Drug Administration, College Park, MD 20740, USA; (E.S.H.); (R.L.)
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3
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Handy SM, Pawar RS, Ottesen AR, Ramachandran P, Sagi S, Zhang N, Hsu E, Erickson DL. HPLC-UV, Metabarcoding and Genome Skims of Botanical Dietary Supplements: A Case Study in Echinacea. PLANTA MEDICA 2021; 87:314-324. [PMID: 33445185 DOI: 10.1055/a-1336-1685] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
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.
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Affiliation(s)
- Sara M Handy
- Center for Food Safety and Applied Nutrition, Office of Regulatory Science, U. S. Food and Drug Administration, College Park, Maryland, United States
| | - Rahul S Pawar
- 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
- Center for Food Safety and Applied Nutrition, Office of Regulatory Science, U. S. Food and Drug Administration, College Park, Maryland, United States
| | - Padmini Ramachandran
- Center for Food Safety and Applied Nutrition, Office of Regulatory Science, U. S. Food and Drug Administration, College Park, Maryland, United States
| | - Satyanarayanaraju Sagi
- Center for Food Safety and Applied Nutrition, Office of Regulatory Science, U. S. Food and Drug Administration, College Park, Maryland, United States
| | - Ning Zhang
- Center for Food Safety and Applied Nutrition, Office of Regulatory Science, U. S. Food and Drug Administration, College Park, Maryland, United States
| | - Erica Hsu
- Joint Institute of Food Safety and Applied Nutrition, University of Maryland, College Park, Maryland, United States
| | - David L Erickson
- Joint Institute of Food Safety and Applied Nutrition, University of Maryland, College Park, Maryland, United States
- DNA4 Technologies LLC, Halethorpe, Maryland, United States
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Puente-Lelievre C, Eischeid AC. Development and validation of a duplex real-time PCR assay with locked nucleic acid (LNA) probes for the specific detection of allergenic walnut in complex food matrices. Food Control 2021. [DOI: 10.1016/j.foodcont.2020.107644] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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5
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Handy SM, Ott BM, Hunter ES, Zhang S, Erickson DL, Wolle MM, Conklin SD, Lane CE. Suitability of DNA Sequencing Tools for Identifying Edible Seaweeds Sold in the United States. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2020; 68:15516-15525. [PMID: 33334103 DOI: 10.1021/acs.jafc.0c03734] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Seaweeds have been consumed by billions of people around the world and are increasingly popular in United States (US) diets. Some seaweed species have been associated with adverse health effects-such as heavy metal toxicity-and higher priced seaweeds may be more prone to adulteration. Knowing which species of seaweeds are being marketed in the US is important for protecting human health and preventing economic adulteration. Therefore, the United States Food and Drug Administration is developing new DNA-based species identification tools to complement established chemical methods for verifying the accurate labeling of products. Here, seaweed products available in the United States were surveyed using a tiered approach to evaluate a variety of DNA extraction techniques followed by traditional DNA barcoding via Sanger sequencing; if needed, genome skimming of total extracted nuclear DNA via next-generation sequencing was performed. This two-tiered approach of DNA barcoding and genome skimming could identify most seaweed samples (41/46), even those in blends (2/2, 1 out of 3 labeled species in each). Only two commercial samples appeared to be mislabeled or to contain unintended algal species. Five samples, labeled as "hijiki" or "arame", could not be confirmed by these DNA-based identification methods.
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Affiliation(s)
- Sara M Handy
- Center for Food Safety and Applied Nutrition, Office of Regulatory Science, U.S. Food and Drug Administration, College Park 20740, Maryland, United States
| | - Brittany M Ott
- Center for Food Safety and Applied Nutrition, Office of Regulatory Science, U.S. Food and Drug Administration, College Park 20740, Maryland, United States
- Joint Institute for Food Safety and Applied Nutrition, University of Maryland, College Park 20742, Maryland, United States
| | - Elizabeth Sage Hunter
- Department of Biological Sciences, University of Rhode Island, Kingston 02881, Rhode Island, United States
| | - Shu Zhang
- DNA4 Technologies LLC, Baltimore 21227, Maryland, United States
| | - David L Erickson
- Joint Institute for Food Safety and Applied Nutrition, University of Maryland, College Park 20742, Maryland, United States
- DNA4 Technologies LLC, Baltimore 21227, Maryland, United States
| | - Mesay Mulugeta Wolle
- Center for Food Safety and Applied Nutrition, Office of Regulatory Science, U.S. Food and Drug Administration, College Park 20740, Maryland, United States
| | - Sean D Conklin
- Center for Food Safety and Applied Nutrition, Office of Regulatory Science, U.S. Food and Drug Administration, College Park 20740, Maryland, United States
| | - Christopher E Lane
- Department of Biological Sciences, University of Rhode Island, Kingston 02881, Rhode Island, United States
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6
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Zhang N, Erickson DL, Ramachandran P, Ottesen AR, Timme RE, Funk VA, Luo Y, Handy SM. An analysis of Echinacea chloroplast genomes: Implications for future botanical identification. Sci Rep 2017; 7:216. [PMID: 28303008 PMCID: PMC5428300 DOI: 10.1038/s41598-017-00321-6] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2016] [Accepted: 02/21/2017] [Indexed: 12/14/2022] Open
Abstract
Echinacea is a common botanical used in dietary supplements, primarily to treat upper respiratory tract infections and to support immune function. There are currently thought to be nine species in the genus Echinacea. Due to very low molecular divergence among sister species, traditional DNA barcoding has not been successful for differentiation of Echinacea species. Here, we present the use of full chloroplast genomes to distinguish between all 9 reported species. Total DNA was extracted from specimens stored at the National Museum of Natural History, Smithsonian Institution, which had been collected from the wild with species identification documented by experts in the field. We used Next Generation Sequencing (NGS) and CLC Genomics Workbench to assemble complete chloroplast genomes for all nine species. Full chloroplasts unambiguously differentiated all nine species, compared with the very few single nucleotide polymorphisms (SNPs) available with core DNA barcoding markers. SNPs for any two Echinacea chloroplast genomes ranged from 181 to 910, and provided robust data for unambiguous species delimitation. Implications for DNA-based species identification assays derived from chloroplast genome sequences are discussed in light of product safety, adulteration and quality issues.
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Affiliation(s)
- Ning Zhang
- Center for Food Safety and Applied Nutrition, Office of Regulatory Science, US Food and Drug Administration, College Park, Maryland, 20740, United States.
| | - David L Erickson
- Center for Food Safety and Applied Nutrition, Office of Regulatory Science, US Food and Drug Administration, College Park, Maryland, 20740, United States
| | - Padmini Ramachandran
- Center for Food Safety and Applied Nutrition, Office of Regulatory Science, US Food and Drug Administration, College Park, Maryland, 20740, United States
| | - Andrea R Ottesen
- Center for Food Safety and Applied Nutrition, Office of Regulatory Science, US Food and Drug Administration, College Park, Maryland, 20740, United States
| | - Ruth E Timme
- Center for Food Safety and Applied Nutrition, Office of Regulatory Science, US Food and Drug Administration, College Park, Maryland, 20740, United States
| | - Vicki A Funk
- Department of Botany, National Museum of Natural History, MRC-166, Smithsonian Institution, PO Box 37012, Washington, DC, 20013-0166, USA
| | - Yan Luo
- Center for Food Safety and Applied Nutrition, Office of Regulatory Science, US Food and Drug Administration, College Park, Maryland, 20740, United States
| | - Sara M Handy
- Center for Food Safety and Applied Nutrition, Office of Regulatory Science, US Food and Drug Administration, College Park, Maryland, 20740, United States
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7
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Discriminant analysis of Mediterranean pine nuts ( Pinus pinea L.) from Chilean plantations by near infrared spectroscopy (NIRS). Food Control 2017. [DOI: 10.1016/j.foodcont.2016.09.012] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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8
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Ballin NZ, Mikkelsen K. Polymerase chain reaction and chemometrics detected several Pinus species including Pinus armandii involved in pine nut syndrome. Food Control 2016. [DOI: 10.1016/j.foodcont.2015.12.036] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Garber EAE, Parker CH, Handy SM, Cho CY, Panda R, Samadpour M, Reynaud DH, Ziobro GC. Presence of Undeclared Food Allergens in Cumin: The Need for Multiplex Methods. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2016; 64:1202-1211. [PMID: 26769163 DOI: 10.1021/acs.jafc.5b05497] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Beginning in the autumn of 2014, millions of dollars of food and over 675 products were recalled in the United States due to the presence of undeclared peanut, attributed to cumin used in the manufacture of the products. Initial analyses also indicated the presence of almond. Subsequent research showed that the presence of peanut and almond did not fully explain the analytical results for the cumin samples. Using a combination of mass spectrometry, DNA-based methods (i.e., PCR and Sanger DNA Sequencing), microscopy, and antibody-based technologies (i.e., ELISA, Western blot analysis, and a novel xMAP multiplex assay) the presence of peanut was confirmed. Screening for secondary sources of adulteration (e.g., tree nuts, mahleb, peach, and cherry) supported the assessment that the cumin contained multiple contaminants. These results demonstrate the limitations of single analyte-specific assays and the need for orthogonal multiplex methods to detect food allergens irrespective of varietal or other differences.
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Affiliation(s)
- Eric A E Garber
- Office of Regulatory Science, Center for Food Safety and Applied Nutrition, Food and Drug Administration , College Park, Maryland 20740, United States
| | - Christine H Parker
- Office of Regulatory Science, Center for Food Safety and Applied Nutrition, Food and Drug Administration , College Park, Maryland 20740, United States
| | - Sara M Handy
- Office of Regulatory Science, Center for Food Safety and Applied Nutrition, Food and Drug Administration , College Park, Maryland 20740, United States
| | - Chung Y Cho
- Office of Regulatory Science, Center for Food Safety and Applied Nutrition, Food and Drug Administration , College Park, Maryland 20740, United States
| | - Rakhi Panda
- Office of Regulatory Science, Center for Food Safety and Applied Nutrition, Food and Drug Administration , College Park, Maryland 20740, United States
| | - Mansour Samadpour
- IEH Laboratories and Consulting Group, Inc. , Lake Forest Park, Washington 98155, United States
| | - Danica H Reynaud
- AuthenTechnologies LLC , Richmond, California 94806, United States
| | - George C Ziobro
- Office of Food Safety, Center for Food Safety and Applied Nutrition, Food and Drug Administration , College Park, Maryland 20740, United States
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Risso DS, Howard L, VanWaes C, Drayna D. A potential trigger for pine mouth: a case of a homozygous phenylthiocarbamide taster. Nutr Res 2015; 35:1122-5. [PMID: 26463018 DOI: 10.1016/j.nutres.2015.09.011] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2015] [Revised: 09/11/2015] [Accepted: 09/17/2015] [Indexed: 11/26/2022]
Abstract
Pine mouth, also known as pine nut syndrome, is an uncommon dysgeusia that generally begins 12 to 48 hours after consuming pine nuts. It is characterized by a bitter metallic taste, usually amplified by the consumption of other foods, which lasts 2 to 4 weeks. Recent findings have correlated this disorder with the consumption of nuts of the species Pinus armandii, but no potential triggers or common underlying medical causes have been identified in individuals affected by this syndrome. We report a 23-year-old patient affected by pine mouth who also underwent a phenylthiocarbamide taste test and was found to be a taster for this compound. TAS2R38 genotyping demonstrated that this subject was a homozygous carrier of the proline-alanine-valine taster haplotype. We, therefore, hypothesize that homozygous phenylthiocarbamide taster status may be a potential contributor for pine mouth events. Although based on a single observation, this research suggests a connection between genetically determined bitter taste perception and the occurrence of pine nut dysgeusia events.
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Affiliation(s)
- Davide S Risso
- National Institute on Deafness and Other Communication Disorders, National Institutes of Health, Bethesda, MD 20892; Department of BiGeA, Laboratory of Molecular Anthropology and Centre for Genome Biology, University of Bologna, 40126 Bologna, Italy.
| | - Louisa Howard
- National Institute of Allergy and Infectious Disease, National Institutes of Health, Bethesda, MD 20892
| | - Carter VanWaes
- Clinical Genomics Unit and Tumor Biology Section, Head and Neck Surgery Branch, National Institute on Deafness and Other Communication Disorders, National Institutes of Health, Bethesda, MD 20892
| | - Dennis Drayna
- National Institute on Deafness and Other Communication Disorders, National Institutes of Health, Bethesda, MD 20892
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Boulinguez S, Mularcyk M, Viraben R. Dysgueusie amère aux pignons de pin. Ann Dermatol Venereol 2014; 141:220-2. [DOI: 10.1016/j.annder.2014.01.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2013] [Revised: 12/06/2013] [Accepted: 01/09/2014] [Indexed: 11/26/2022]
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