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Arulandhu AJ, Staats M, Hagelaar R, Voorhuijzen MM, Prins TW, Scholtens I, Costessi A, Duijsings D, Rechenmann F, Gaspar FB, Barreto Crespo MT, Holst-Jensen A, Birck M, Burns M, Haynes E, Hochegger R, Klingl A, Lundberg L, Natale C, Niekamp H, Perri E, Barbante A, Rosec JP, Seyfarth R, Sovová T, Van Moorleghem C, van Ruth S, Peelen T, Kok E. Development and validation of a multi-locus DNA metabarcoding method to identify endangered species in complex samples. Gigascience 2018; 6:1-18. [PMID: 29020743 PMCID: PMC5632295 DOI: 10.1093/gigascience/gix080] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2017] [Accepted: 08/15/2017] [Indexed: 11/19/2022] Open
Abstract
DNA metabarcoding provides great potential for species identification in complex samples such as food supplements and traditional medicines. Such a method would aid Convention on International Trade in Endangered Species of Wild Fauna and Flora (CITES) enforcement officers to combat wildlife crime by preventing illegal trade of endangered plant and animal species. The objective of this research was to develop a multi-locus DNA metabarcoding method for forensic wildlife species identification and to evaluate the applicability and reproducibility of this approach across different laboratories. A DNA metabarcoding method was developed that makes use of 12 DNA barcode markers that have demonstrated universal applicability across a wide range of plant and animal taxa and that facilitate the identification of species in samples containing degraded DNA. The DNA metabarcoding method was developed based on Illumina MiSeq amplicon sequencing of well-defined experimental mixtures, for which a bioinformatics pipeline with user-friendly web-interface was developed. The performance of the DNA metabarcoding method was assessed in an international validation trial by 16 laboratories, in which the method was found to be highly reproducible and sensitive enough to identify species present in a mixture at 1% dry weight content. The advanced multi-locus DNA metabarcoding method assessed in this study provides reliable and detailed data on the composition of complex food products, including information on the presence of CITES-listed species. The method can provide improved resolution for species identification, while verifying species with multiple DNA barcodes contributes to an enhanced quality assurance.
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Affiliation(s)
- Alfred J Arulandhu
- RIKILT Wageningen University & Research, P.O. Box 230, 6700 AE Wageningen, The Netherlands.,Food Quality and Design Group, Wageningen University and Research, P.O. Box 8129, 6700 EV Wageningen, The Netherlands
| | - Martijn Staats
- RIKILT Wageningen University & Research, P.O. Box 230, 6700 AE Wageningen, The Netherlands
| | - Rico Hagelaar
- RIKILT Wageningen University & Research, P.O. Box 230, 6700 AE Wageningen, The Netherlands
| | - Marleen M Voorhuijzen
- RIKILT Wageningen University & Research, P.O. Box 230, 6700 AE Wageningen, The Netherlands
| | - Theo W Prins
- RIKILT Wageningen University & Research, P.O. Box 230, 6700 AE Wageningen, The Netherlands
| | - Ingrid Scholtens
- RIKILT Wageningen University & Research, P.O. Box 230, 6700 AE Wageningen, The Netherlands
| | | | - Danny Duijsings
- Baseclear B. V, Einsteinweg 5, 2333 CC Leiden, The Netherlands
| | - François Rechenmann
- GenoStar Bioinformatics Solutions, 60 rue Lavoisier, 38330 Montbonnot Saint Martin, France
| | - Frédéric B Gaspar
- iBET, Instituto de Biologia Experimental e Tecnológica, Apartado 12, 2780-901 Oeiras, Portugal
| | | | - Arne Holst-Jensen
- Norwegian Veterinary Institute, Ullevaalsveien 68, P.O. Box 750 Sentrum, 0106 Oslo, Norway
| | - Matthew Birck
- U.S. Customs and Border Protection Laboratory, 1100 Raymond Blvd Newark, NJ 07102 USA
| | - Malcolm Burns
- LGC, Queens Road, Teddington, Middlesex, TW11 0LY, UK
| | | | - Rupert Hochegger
- Austrian Agency for Health and Food Safety, Spargelfeldstrasse 191, 1220 Vienna, Austria
| | - Alexander Klingl
- Generalzolldirektion, Direktion IX, Bildungs- und Wissenschaftszentrum der Bundesfinanzverwaltung, Dienstort Hamburg, Baumacker 3, D-22523 Hamburg, Germany
| | - Lisa Lundberg
- Livsmedelsverket, Att. Lisa Lundberg, Strandbodgatan 4, SE 75323 Uppsala, Sweden
| | - Chiara Natale
- AGENZIA DELLE DOGANE E DEI MONOPOLI, Laboratori e servizi chimici - Laboratorio Chimico di Genova, 16126 Genova, Via Rubattino n. 6, Italy
| | - Hauke Niekamp
- Eurofins GeneScan GmbH, Engesserstrasse 4 79108 Freiburg, Germany
| | - Elena Perri
- CREA-SCS sede di Tavazzano - Laboratorio via Emilia, Km 307, 26838 Tavazzano, Italy
| | - Alessandra Barbante
- CREA-SCS sede di Tavazzano - Laboratorio via Emilia, Km 307, 26838 Tavazzano, Italy
| | - Jean-Philippe Rosec
- Service Commun des Laboratoires, Laboratoire de Montpellier, Parc Euromédecine, 205 rue de la Croix Verte, 34196 Montpellier Cedex 5, France
| | - Ralf Seyfarth
- Biolytix AG, Benkenstrasse 254, 4108 Witterswil, Switzerland
| | - Tereza Sovová
- Crop Research Institute, Department of Molecular Genetics, Drnovská 507, 161 06 Prague, Czech Republic
| | | | - Saskia van Ruth
- RIKILT Wageningen University & Research, P.O. Box 230, 6700 AE Wageningen, The Netherlands.,Food Quality and Design Group, Wageningen University and Research, P.O. Box 8129, 6700 EV Wageningen, The Netherlands
| | - Tamara Peelen
- Dutch Customs Laboratory, Kingsfordweg 1, 1043 GN, Amsterdam, The Netherlands
| | - Esther Kok
- RIKILT Wageningen University & Research, P.O. Box 230, 6700 AE Wageningen, The Netherlands
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55
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Yang F, Ding F, Chen H, He M, Zhu S, Ma X, Jiang L, Li H. DNA Barcoding for the Identification and Authentication of Animal Species in Traditional Medicine. EVIDENCE-BASED COMPLEMENTARY AND ALTERNATIVE MEDICINE : ECAM 2018; 2018:5160254. [PMID: 29849709 PMCID: PMC5937547 DOI: 10.1155/2018/5160254] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/19/2017] [Accepted: 03/11/2018] [Indexed: 02/06/2023]
Abstract
Animal-based traditional medicine not only plays a significant role in therapeutic practices worldwide but also provides a potential compound library for drug discovery. However, persistent hunting and illegal trade markedly threaten numerous medicinal animal species, and increasing demand further provokes the emergence of various adulterants. As the conventional methods are difficult and time-consuming to detect processed products or identify animal species with similar morphology, developing novel authentication methods for animal-based traditional medicine represents an urgent need. During the last decade, DNA barcoding offers an accurate and efficient strategy that can identify existing species and discover unknown species via analysis of sequence variation in a standardized region of DNA. Recent studies have shown that DNA barcoding as well as minibarcoding and metabarcoding is capable of identifying animal species and discriminating the authentics from the adulterants in various types of traditional medicines, including raw materials, processed products, and complex preparations. These techniques can also be used to detect the unlabelled and threatened animal species in traditional medicine. Here, we review the recent progress of DNA barcoding for the identification and authentication of animal species used in traditional medicine, which provides a reference for quality control and trade supervision of animal-based traditional medicine.
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Affiliation(s)
- Fan Yang
- Institute of Forensic Science, Ministry of Public Security, Beijing 100038, China
- Beijing Engineering Research Center of Crime Scene Evidence Examination, Institute of Forensic Science, Beijing 100038, China
| | - Fei Ding
- Center for Bioresources & Drug Discovery and School of Biosciences & Biopharmaceutics, Guangdong Pharmaceutical University, Guangzhou, Guangdong 510006, China
| | - Hong Chen
- Center for Bioresources & Drug Discovery and School of Biosciences & Biopharmaceutics, Guangdong Pharmaceutical University, Guangzhou, Guangdong 510006, China
| | - Mingqi He
- Center for Bioresources & Drug Discovery and School of Biosciences & Biopharmaceutics, Guangdong Pharmaceutical University, Guangzhou, Guangdong 510006, China
| | - Shixin Zhu
- Center for Bioresources & Drug Discovery and School of Biosciences & Biopharmaceutics, Guangdong Pharmaceutical University, Guangzhou, Guangdong 510006, China
| | - Xin Ma
- Institute of Forensic Science, Ministry of Public Security, Beijing 100038, China
- Beijing Engineering Research Center of Crime Scene Evidence Examination, Institute of Forensic Science, Beijing 100038, China
| | - Li Jiang
- Institute of Forensic Science, Ministry of Public Security, Beijing 100038, China
- Beijing Engineering Research Center of Crime Scene Evidence Examination, Institute of Forensic Science, Beijing 100038, China
| | - Haifeng Li
- Center for Bioresources & Drug Discovery and School of Biosciences & Biopharmaceutics, Guangdong Pharmaceutical University, Guangzhou, Guangdong 510006, China
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56
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Sekse C, Holst-Jensen A, Dobrindt U, Johannessen GS, Li W, Spilsberg B, Shi J. High Throughput Sequencing for Detection of Foodborne Pathogens. Front Microbiol 2017; 8:2029. [PMID: 29104564 PMCID: PMC5655695 DOI: 10.3389/fmicb.2017.02029] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2017] [Accepted: 10/04/2017] [Indexed: 12/23/2022] Open
Abstract
High-throughput sequencing (HTS) is becoming the state-of-the-art technology for typing of microbial isolates, especially in clinical samples. Yet, its application is still in its infancy for monitoring and outbreak investigations of foods. Here we review the published literature, covering not only bacterial but also viral and Eukaryote food pathogens, to assess the status and potential of HTS implementation to inform stakeholders, improve food safety and reduce outbreak impacts. The developments in sequencing technology and bioinformatics have outpaced the capacity to analyze and interpret the sequence data. The influence of sample processing, nucleic acid extraction and purification, harmonized protocols for generation and interpretation of data, and properly annotated and curated reference databases including non-pathogenic "natural" strains are other major obstacles to the realization of the full potential of HTS in analytical food surveillance, epidemiological and outbreak investigations, and in complementing preventive approaches for the control and management of foodborne pathogens. Despite significant obstacles, the achieved progress in capacity and broadening of the application range over the last decade is impressive and unprecedented, as illustrated with the chosen examples from the literature. Large consortia, often with broad international participation, are making coordinated efforts to cope with many of the mentioned obstacles. Further rapid progress can therefore be prospected for the next decade.
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Affiliation(s)
- Camilla Sekse
- Department of Animal Health and Food Safety, Norwegian Veterinary Institute, Oslo, Norway
| | - Arne Holst-Jensen
- Department of Animal Health and Food Safety, Norwegian Veterinary Institute, Oslo, Norway
| | - Ulrich Dobrindt
- Institute of Hygiene, University of Münster, Münster, Germany
| | - Gro S. Johannessen
- Department of Animal Health and Food Safety, Norwegian Veterinary Institute, Oslo, Norway
| | - Weihua Li
- Joint International Research Laboratory of Metabolic and Developmental Sciences, Shanghai Jiao Tong University–University of Adelaide Joint Centre for Agriculture and Health, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Bjørn Spilsberg
- Department of Analysis and Diagnostics, Norwegian Veterinary Institute, Oslo, Norway
| | - Jianxin Shi
- Joint International Research Laboratory of Metabolic and Developmental Sciences, Shanghai Jiao Tong University–University of Adelaide Joint Centre for Agriculture and Health, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
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