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Mottola A, Piredda R, Lorusso L, Ranieri L, Intermite C, Barresi C, Galli C, Di Pinto A. Decoding Seafood: Multi-Marker Metabarcoding for Authenticating Processed Seafood. Foods 2024; 13:2382. [PMID: 39123573 PMCID: PMC11311639 DOI: 10.3390/foods13152382] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2024] [Revised: 07/22/2024] [Accepted: 07/25/2024] [Indexed: 08/12/2024] Open
Abstract
Given the recognized nutritional value of fish and shifting consumer lifestyles, processed seafood has become increasingly prevalent, comprising a significant portion of global food production. Although current European Union labeling regulations do not require species declaration for these products, food business operators often voluntarily provide this information on ingredient lists. Next Generation Sequencing (NGS) approaches are currently the most effective methods for verifying the accuracy of species declarations on processed seafood labels. This study examined the species composition of 20 processed seafood products, each labeled as containing a single species, using two DNA metabarcoding markers targeting the mitochondrial cytochrome c oxidase I (COI) and 16S rRNA genes. The combined use of these markers revealed that the majority of the products contained multiple species. Furthermore, two products were found to be mislabeled, as the declared species were not detected. These findings underscore that NGS is a robust technique that could be adopted to support routine food industry activities and official control programs, thereby enhancing the 'From Boat to Plate' strategy and combating fraudulent practices in the complex fisheries supply chain.
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Affiliation(s)
- Anna Mottola
- Department of Veterinary Medicine, University of Bari Aldo Moro, Prov. le Casamassima 62, Km 3, 70010 Valenzano, Italy; (A.M.); (R.P.); (L.R.); (C.I.); (A.D.P.)
| | - Roberta Piredda
- Department of Veterinary Medicine, University of Bari Aldo Moro, Prov. le Casamassima 62, Km 3, 70010 Valenzano, Italy; (A.M.); (R.P.); (L.R.); (C.I.); (A.D.P.)
| | - Lucilia Lorusso
- Department of Veterinary Medicine, University of Bari Aldo Moro, Prov. le Casamassima 62, Km 3, 70010 Valenzano, Italy; (A.M.); (R.P.); (L.R.); (C.I.); (A.D.P.)
| | - Lucia Ranieri
- Department of Veterinary Medicine, University of Bari Aldo Moro, Prov. le Casamassima 62, Km 3, 70010 Valenzano, Italy; (A.M.); (R.P.); (L.R.); (C.I.); (A.D.P.)
| | - Chiara Intermite
- Department of Veterinary Medicine, University of Bari Aldo Moro, Prov. le Casamassima 62, Km 3, 70010 Valenzano, Italy; (A.M.); (R.P.); (L.R.); (C.I.); (A.D.P.)
| | - Concettina Barresi
- Laboratory of Modena, Department of Central Inspectorate for Fraud Repression and Quality Protection of the Agri-Food Products and Foodstuffs, Ministry of Agriculture, Food Sovereignty and Forests (ICQRF-MASAF), Via Domenico Cucchiari, 12, 41124 Modena, Italy;
| | - Carmela Galli
- Laboratory of Salerno, Department of Central Inspectorate for Fraud Repression and Quality Protection of the Agri-Food Products and Foodstuffs, Ministry of Agriculture, Food Sovereignty and Forests (ICQRF-MASAF), Via Frà Giacomo Acquaviva n. 1, 84135 Salerno, Italy;
| | - Angela Di Pinto
- Department of Veterinary Medicine, University of Bari Aldo Moro, Prov. le Casamassima 62, Km 3, 70010 Valenzano, Italy; (A.M.); (R.P.); (L.R.); (C.I.); (A.D.P.)
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Yan R, Abdullah, Ahmed I, Jiang L, Tuliebieke T, Xing Z, Li H, Zhang Y, Zhang T, Tian X, Zhang H. The metabarcoding of Grubs: Traditional herbal medicine of Scarabaeidae larvae. Gene 2024; 910:148303. [PMID: 38401835 DOI: 10.1016/j.gene.2024.148303] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2023] [Revised: 02/04/2024] [Accepted: 02/19/2024] [Indexed: 02/26/2024]
Abstract
Grubs, called Qicao in China, have a long tradition as herbal medicine in East Asia. These larvae belong to the diverse family Scarabaeidae and are typically harvested from the wild during their immature stage based on morphological characteristics. However, rapid and accurate identification becomes challenging when relying solely on external morphological features, as the lack of clarity on biological sources raises safety concerns for clinical applications. The application of DNA metabarcoding provides a solution by enabling the determination of the biological source of a large sample. In the current study, we collected 19 batches of Grubs, consisting of 11,539 individuals, from the market and analyzed their biological composition through metabarcoding. We identified 49 Amplicon Sequence Variants (ASVs), 21 of which were Grubs. The 21 ASVs were classified into seven Molecular Operational Taxonomic Units (MOTUs) through species delimitation, which revealed that commercially available Grubs are predominantly sourced from Protaetia brevitarsis seulensis, while species of Rutelinae, Anomala, and Holotrichia were also abundant in some commercial batches. Among the identified ASVs, 28 belonged to non-Grub species and indicated adulteration from different animal families; high abundances of these ASVs were detected for Bombycidae, Tabanidae, and Viviparidae. Our findings underscore the complexity of Grubs' species composition and advocate for a deeper understanding of the wildlife sources contributing to herbal products. This research contributes valuable insights into the molecular identification of Grubs, paving the way for enhanced quality assurance in traditional medicine applications to provide safe and effective medicines for humanity.
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Affiliation(s)
- Rushan Yan
- State Key Laboratory of Component-Based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China; Haihe Laboratory of Modern Chinese Medicine, Tianjin 301617, China
| | - Abdullah
- State Key Laboratory of Component-Based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China; Haihe Laboratory of Modern Chinese Medicine, Tianjin 301617, China.
| | - Ibrar Ahmed
- Alpha Genomics Private Limited, Islamabad 45710, Pakistan; Microbiological Analysis Team, Group for Biometrology, Korea Research Institute of Standards Band Science (KRISS), Daejeon 34113, Republic of Korea
| | - Lu Jiang
- Key Laboratory of Economic and Applied Entomology of Liaoning Province, College of Plant Protection, Shenyang Agricultural University, Shenyang Liaoning, 110866, China.
| | - Tenukeguli Tuliebieke
- State Key Laboratory of Component-Based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China; Haihe Laboratory of Modern Chinese Medicine, Tianjin 301617, China.
| | - Zhimei Xing
- State Key Laboratory of Component-Based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China; Haihe Laboratory of Modern Chinese Medicine, Tianjin 301617, China.
| | - Hui Li
- State Key Laboratory of Component-Based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China; Haihe Laboratory of Modern Chinese Medicine, Tianjin 301617, China.
| | - Yue Zhang
- State Key Laboratory of Component-Based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China; Haihe Laboratory of Modern Chinese Medicine, Tianjin 301617, China.
| | - Tingting Zhang
- State Key Laboratory of Component-Based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China; Haihe Laboratory of Modern Chinese Medicine, Tianjin 301617, China.
| | - Xiaoxuan Tian
- State Key Laboratory of Component-Based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China; Haihe Laboratory of Modern Chinese Medicine, Tianjin 301617, China.
| | - Huanyu Zhang
- State Key Laboratory of Component-Based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China; School of Pharmaceutical Science and Technology, Tianjin University, Tianjin 300072, China.
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3
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Mück F, Scotti F, Mauvisseau Q, Thorbek BLG, Wangensteen H, de Boer HJ. Three-tiered authentication of herbal traditional Chinese medicine ingredients used in women's health provides progressive qualitative and quantitative insight. Front Pharmacol 2024; 15:1353434. [PMID: 38375033 PMCID: PMC10875096 DOI: 10.3389/fphar.2024.1353434] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2023] [Accepted: 01/16/2024] [Indexed: 02/21/2024] Open
Abstract
Traditional Chinese Medicine (TCM) herbal products are increasingly used in Europe, but prevalent authentication methods have significant gaps in detection. In this study, three authentication methods were tested in a tiered approach to improve accuracy on a collection of 51 TCM plant ingredients obtained on the European market. We show the relative performance of conventional barcoding, metabarcoding and standardized chromatographic profiling for TCM ingredients used in one of the most diagnosed disease patterns in women, endometriosis. DNA barcoding using marker ITS2 and chromatographic profiling are methods of choice reported by regulatory authorities and relevant national pharmacopeias. HPTLC was shown to be a valuable authentication tool, combined with metabarcoding, which gives an increased resolution on species diversity, despite dealing with highly processed herbal ingredients. Conventional DNA barcoding as a recommended method was shown to be an insufficient tool for authentication of these samples, while DNA metabarcoding yields an insight into biological contaminants. We conclude that a tiered identification strategy can provide progressive qualitative and quantitative insight in an integrative approach for quality control of processed herbal ingredients.
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Affiliation(s)
- Felicitas Mück
- Section for Pharmaceutical Chemistry, Department of Pharmacy, University of Oslo, Oslo, Norway
| | - Francesca Scotti
- Department of Pharmaceutical and Biological Chemistry, School of Pharmacy, University College London, London, United Kingdom
| | | | | | - Helle Wangensteen
- Section for Pharmaceutical Chemistry, Department of Pharmacy, University of Oslo, Oslo, Norway
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Giusti A, Malloggi C, Magagna G, Filipello V, Armani A. Is the metabarcoding ripe enough to be applied to the authentication of foodstuff of animal origin? A systematic review. Compr Rev Food Sci Food Saf 2024; 23:e13256. [PMID: 38284609 DOI: 10.1111/1541-4337.13256] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Revised: 09/25/2023] [Accepted: 10/02/2023] [Indexed: 01/30/2024]
Abstract
Food authentication using molecular techniques is of great importance to fight food fraud. Metabarcoding, based on the next-generation sequencing (NGS) technologies, allowing large-scale taxonomic identification of complex samples via massive parallel sequencing of fragments (called DNA barcodes) simultaneously, has become increasingly popular in many scientific fields. A systematic review to answer the question "Is the metabarcoding ripe enough to be applied to the authentication of foodstuff of animal origin?" is presented. The inclusion criteria were focused on the selection of scientific papers (SPs) only applying metabarcoding to foodstuff of animal origin collected on the market. The 23 included SPs were first analyzed with respect to the metabarcoding phases: library preparation (target genes, primer pairs, and fragment length), sequencing (NGS platforms), and final data analysis (bioinformatic pipelines). Given the importance of primer selection, the taxonomic coverage of the used primers was also evaluated. In addition, the SPs were scored based on the use of quality control measures (procedural blanks, positive controls, replicates, curated databases, and thresholds to filter the data). A lack of standardized protocols, especially with respect to the target barcode/s and the universal primer/s, and the infrequent application of the quality control measures, leads to answer that metabarcoding is not ripe enough for authenticating foodstuff of animal origin. However, the observed trend of the SP quality improvement over the years is encouraging. Concluding, a proper protocol standardization would allow a wider use of metabarcoding by both official and private laboratories, enabling this method to become the primary for the authentication of foodstuffs of animal origin.
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Affiliation(s)
- Alice Giusti
- FishLab, Department of Veterinary Sciences, University of Pisa, Pisa, Italy
| | - Chiara Malloggi
- FishLab, Department of Veterinary Sciences, University of Pisa, Pisa, Italy
| | - Giulia Magagna
- Istituto Zooprofilattico Sperimentale della Lombardia e dell'Emilia Romagna "Bruno Ubertini", Brescia, Italy
| | - Virginia Filipello
- Istituto Zooprofilattico Sperimentale della Lombardia e dell'Emilia Romagna "Bruno Ubertini", Brescia, Italy
| | - Andrea Armani
- FishLab, Department of Veterinary Sciences, University of Pisa, Pisa, Italy
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Mück F, Scotti F, Mauvisseau Q, Raclariu-Manolică AC, Schrøder-Nielsen A, Wangensteen H, de Boer HJ. Complementary authentication of Chinese herbal products to treat endometriosis using DNA metabarcoding and HPTLC shows a high level of variability. Front Pharmacol 2023; 14:1305410. [PMID: 38116075 PMCID: PMC10728824 DOI: 10.3389/fphar.2023.1305410] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2023] [Accepted: 11/14/2023] [Indexed: 12/21/2023] Open
Abstract
Traditional Chinese Medicine (TCM) is popular for the treatment of endometriosis, a complex gynecological disease that affects 10% of women globally. The growing market for TCMs has yielded a significant incentive for product adulteration, and although emerging technologies show promise to improve their quality control, many challenges remain. We tested the authenticity of two traditional Chinese herbal formulae used in women's healthcare for the treatment of endometriosis, known as Gui Zhi Fu Ling Wan (FL) and Ge Xia Zhu Yu Tang (GX). Dual-locus DNA metabarcoding analysis coupled with high-performance thin-layer chromatography (HPTLC) were used to authenticate 19 FL and six GX commercial herbal products, as well as three ad hoc prepared artificial mixtures. HPTLC was able to detect most of the expected ingredients via comparative component analysis. DNA metabarcoding was able to detect an unexpected species diversity in the products, including 38 unexpected taxa. Chromatography has a resolution for all species indirectly through the identification of marker compounds for the different species ingredients. Metabarcoding on the other hand yields an overview of species diversity in each sample, but interpretation of the results can be challenging. Detected species might not be present in quantities that matter, and without validated quantification, some detected species can be hard to interpret. Comparative analysis of the two analytical approaches also reveals that DNA for species might be absent or too fragmented to amplify as the relevant chemical marker compounds can be detected but no amplicons are assigned to the same species. Our study emphasizes that integrating DNA metabarcoding with phytochemical analysis brings valuable data for the comprehensive authentication of Traditional Chinese Medicines ensuring their quality and safe use.
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Affiliation(s)
- Felicitas Mück
- Section for Pharmaceutical Chemistry, Department of Pharmacy, University of Oslo, Oslo, Norway
| | - Francesca Scotti
- Department of Pharmaceutical and Biological Chemistry, UCL School of Pharmacy, University College London, London, United Kingdom
| | | | - Ancuţa Cristina Raclariu-Manolică
- Natural History Museum, University of Oslo, Oslo, Norway
- Stejarul Research Centre for Biological Sciences, National Institute of Research and Development for Biological Sciences, Piatra Neamț, Romania
| | | | - Helle Wangensteen
- Section for Pharmaceutical Chemistry, Department of Pharmacy, University of Oslo, Oslo, Norway
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Wizenberg SB, Newburn LR, Pepinelli M, Conflitti IM, Richardson RT, Hoover SER, Currie RW, Giovenazzo P, Zayed A. Validating a multi-locus metabarcoding approach for characterizing mixed-pollen samples. PLANT METHODS 2023; 19:120. [PMID: 37925401 PMCID: PMC10625703 DOI: 10.1186/s13007-023-01097-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Accepted: 10/21/2023] [Indexed: 11/06/2023]
Abstract
BACKGROUND The mutualistic interaction between entomophilous plants and pollinators is fundamental to the structure of most terrestrial ecosystems. The sensitive nature of this relationship has been disrupted by anthropogenic modifications to natural landscapes, warranting development of new methods for exploring this trophic interaction. Characterizing the composition of pollen collected by pollinators, e.g. Apis mellifera, is a common means of exploring this relationship, but traditional methods of microscopic pollen assessment are laborious and limited in their scope. The development of pollen metabarcoding as a method of rapidly characterizing the abundance and diversity of pollen within mixed samples presents a new frontier for this type of work, but metabarcoding may have limitations, and validation is warranted before any suite of primers can be confidently used in a research program. We set out to evaluate the utility of an integrative approach, using a set of established primers (ITS2 and rbcL) versus melissopalynological analysis for characterizing 27 mixed-pollen samples from agricultural sites across Canada. RESULTS Both individual markers performed well relative to melissopalynology at the family level with decreases in the strength of correlation and linear model fits at the genus level. Integrating data from both markers together via a multi-locus approach provided the best rank-based correlation between metagenetic and melissopalynological data at both the genus (ρ = 0.659; p < 0.001) and family level (ρ = 0.830; p < 0.001). Species accumulation curves indicated that, after controlling for sampling effort, melissopalynological characterization provides similar or higher species richness estimates than either marker. The higher number of plant species discovered via the metabarcoding approach simply reflects the vastly greater sampling effort in comparison to melissopalynology. CONCLUSIONS Pollen metabarcoding performed well at characterizing the composition of mixed pollen samples relative to a traditional melissopalynological approach. Limitations to the quantitative application of this method can be addressed by adopting a multi-locus approach that integrates information from multiple markers.
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Affiliation(s)
- Sydney B Wizenberg
- Department of Biology, York University, 4700 Keele St., Toronto, ON, M3J 1P3, Canada
| | - Laura R Newburn
- Department of Biology, York University, 4700 Keele St., Toronto, ON, M3J 1P3, Canada
| | - Mateus Pepinelli
- Department of Biology, York University, 4700 Keele St., Toronto, ON, M3J 1P3, Canada
| | - Ida M Conflitti
- Department of Biology, York University, 4700 Keele St., Toronto, ON, M3J 1P3, Canada
| | - Rodney T Richardson
- Appalachian Laboratory, University of Maryland Center for Environmental Science, Frostburg, MD, 21613, USA
| | - Shelley E R Hoover
- Department of Biological Sciences, University of Lethbridge, 4401 University Drive W, Lethbridge, AB, T1K3M4, Canada
| | - Robert W Currie
- Department of Entomology, University of Manitoba, 12 Dafoe Road, Winnipeg, MB, R3T2N2, Canada
| | - Pierre Giovenazzo
- Département de Biologie, Université Laval, 2325 Rue de l'Université, Québec City, Québec, G1V0A6, Canada
| | - Amro Zayed
- Department of Biology, York University, 4700 Keele St., Toronto, ON, M3J 1P3, Canada.
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Dziedzic E, Sidlauskas B, Cronn R, Anthony J, Cornwell T, Friesen TA, Konstantinidis P, Penaluna BE, Stein S, Levi T. Creating, curating and evaluating a mitogenomic reference database to improve regional species identification using environmental DNA. Mol Ecol Resour 2023; 23:1880-1904. [PMID: 37602732 DOI: 10.1111/1755-0998.13855] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Revised: 07/11/2023] [Accepted: 08/02/2023] [Indexed: 08/22/2023]
Abstract
Species detection using eDNA is revolutionizing global capacity to monitor biodiversity. However, the lack of regional, vouchered, genomic sequence information-especially sequence information that includes intraspecific variation-creates a bottleneck for management agencies wanting to harness the complete power of eDNA to monitor taxa and implement eDNA analyses. eDNA studies depend upon regional databases of mitogenomic sequence information to evaluate the effectiveness of such data to detect and identify taxa. We created the Oregon Biodiversity Genome Project to create a database of complete, nearly error-free mitogenomic sequences for all of Oregon's fishes. We have successfully assembled the complete mitogenomes of 313 specimens of freshwater, anadromous and estuarine fishes representing 24 families, 55 genera and 129 species and lineages. Comparative analyses of these sequences illustrate that many regions of the mitogenome are taxonomically informative, that the short (~150 bp) mitochondrial 'barcode' regions typically used for eDNA assays do not consistently diagnose for species and that complete single or multiple genes of the mitogenome are preferable for identifying Oregon's fishes. This project provides a blueprint for other researchers to follow as they build regional databases, illustrates the taxonomic value and limits of complete mitogenomic sequences and offers clues as to how current eDNA assays and environmental genomics methods of the future can best leverage this information.
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Affiliation(s)
- Emily Dziedzic
- Department of Fisheries, Wildlife, and Conservation Sciences, Oregon State University, Corvallis, Oregon, USA
| | - Brian Sidlauskas
- Department of Fisheries, Wildlife, and Conservation Sciences, Oregon State University, Corvallis, Oregon, USA
| | - Richard Cronn
- Pacific Northwest Research Station, US Department of Agriculture Forest Service, Corvallis, Oregon, USA
| | - James Anthony
- Oregon Department of Fish and Wildlife, Corvallis Research Laboratory, Corvallis, Oregon, USA
| | - Trevan Cornwell
- Oregon Department of Fish and Wildlife, Corvallis Research Laboratory, Corvallis, Oregon, USA
| | - Thomas A Friesen
- Oregon Department of Fish and Wildlife, Corvallis Research Laboratory, Corvallis, Oregon, USA
| | - Peter Konstantinidis
- Department of Fisheries, Wildlife, and Conservation Sciences, Oregon State University, Corvallis, Oregon, USA
| | - Brooke E Penaluna
- Pacific Northwest Research Station, US Department of Agriculture Forest Service, Corvallis, Oregon, USA
| | - Staci Stein
- Oregon Department of Fish and Wildlife, Corvallis Research Laboratory, Corvallis, Oregon, USA
| | - Taal Levi
- Department of Fisheries, Wildlife, and Conservation Sciences, Oregon State University, Corvallis, Oregon, USA
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Shah AP, Travadi T, Sharma S, Pandit R, Joshi C, Joshi M. Comprehensive analysis using DNA metabarcoding, SCAR marker based PCR assay, and HPLC unveils the adulteration in Brahmi herbal products. Mol Biol Rep 2023; 50:7605-7618. [PMID: 37532919 DOI: 10.1007/s11033-023-08653-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Accepted: 06/28/2023] [Indexed: 08/04/2023]
Abstract
BACKGROUND Brahmi is one of the important nootropic botanicals, widely sold in the market, with the name "Brahmi'' being used to describe both Bacopa monnieri and Centella asiatica species. The Brahmi herbal products market is expanding; hence, economically motivated adulteration is highly prevalent. METHODS AND RESULTS This study aimed to develop DNA-based methods, including SCAR marker-based PCR and metabarcoding, to authenticate Brahmi herbal products and compare these methods with HPLC. These methods have been validated using mock controls (in-house blended formulations). All targeted plant species in mock controls were detected successfully with all three methods, whereas, in market samples, only 22.2%, 55.6%, and 50.0% were found positive for Brahmi by PCR assay, DNA metabarcoding, and HPLC, respectively. Metabarcoding can detect the presence of non-labeled plants together with targeted species, which is an advantage over PCR assay or HPLC. CONCLUSION SCAR marker-based PCR is a rapid and cost-effective method for detecting the presence of B. monnieri and C. asiatica. However, in this study, the success rate of PCR amplification was relatively low because the primers targeted either RAPD or ITS-based SCAR markers. HPLC assay, although an alternative, was unable to detect the presence of other botanicals, just like the SCAR marker-based PCR assay. On the other hand, metabarcoding can be utilized to identify the target plants, even in very small quantities, while also providing simulated identification of other botanicals. This study successfully addressed the need for quality control of Brahmi herbal products and provided the first-time report of DNA metabarcoding for such products.
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Affiliation(s)
- Abhi P Shah
- Gujarat Biotechnology Research Centre (GBRC), Department of Science and Technology, Government of Gujarat, Gandhinagar, India
| | - Tasnim Travadi
- Gujarat Biotechnology Research Centre (GBRC), Department of Science and Technology, Government of Gujarat, Gandhinagar, India
| | - Sonal Sharma
- Gujarat Biotechnology Research Centre (GBRC), Department of Science and Technology, Government of Gujarat, Gandhinagar, India
| | - Ramesh Pandit
- Gujarat Biotechnology Research Centre (GBRC), Department of Science and Technology, Government of Gujarat, Gandhinagar, India
| | - Chaitanya Joshi
- Gujarat Biotechnology Research Centre (GBRC), Department of Science and Technology, Government of Gujarat, Gandhinagar, India
| | - Madhvi Joshi
- Gujarat Biotechnology Research Centre (GBRC), Department of Science and Technology, Government of Gujarat, Gandhinagar, India.
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Cock PJA, Cooke DEL, Thorpe P, Pritchard L. THAPBI PICT-a fast, cautious, and accurate metabarcoding analysis pipeline. PeerJ 2023; 11:e15648. [PMID: 37609440 PMCID: PMC10441533 DOI: 10.7717/peerj.15648] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Accepted: 06/06/2023] [Indexed: 08/24/2023] Open
Abstract
THAPBI PICT is an open source software pipeline for metabarcoding analysis of Illumina paired-end reads, including cases of multiplexing where more than one amplicon is amplified per DNA sample. Initially a Phytophthora ITS1 Classification Tool (PICT), we demonstrate using worked examples with our own and public data sets how, with appropriate primer settings and a custom database, it can be applied to other amplicons and organisms, and used for reanalysis of existing datasets. The core dataflow of the implementation is (i) data reduction to unique marker sequences, often called amplicon sequence variants (ASVs), (ii) dynamic thresholds for discarding low abundance sequences to remove noise and artifacts (rather than error correction by default), before (iii) classification using a curated reference database. The default classifier assigns a label to each query sequence based on a database match that is either perfect, or a single base pair edit away (substitution, deletion or insertion). Abundance thresholds for inclusion can be set by the user or automatically using per-batch negative or synthetic control samples. Output is designed for practical interpretation by non-specialists and includes a read report (ASVs with classification and counts per sample), sample report (samples with counts per species classification), and a topological graph of ASVs as nodes with short edit distances as edges. Source code available from https://github.com/peterjc/thapbi-pict/ with documentation including installation instructions.
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Affiliation(s)
- Peter J. A. Cock
- Information and Computational Sciences, The James Hutton Institute, Dundee, United Kingdom
| | - David E. L. Cooke
- Cell and Molecular Sciences, The James Hutton Institute, Dundee, United Kingdom
| | - Peter Thorpe
- Cell and Molecular Sciences, The James Hutton Institute, Dundee, United Kingdom
- The Data Analysis Group, School of Life Sciences, The University of Dundee, Dundee, United Kingdom
| | - Leighton Pritchard
- Information and Computational Sciences, The James Hutton Institute, Dundee, United Kingdom
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Glasgow, United Kingdom
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10
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Travadi T, Shah AP, Pandit R, Sharma S, Joshi C, Joshi M. A combined approach of DNA metabarcoding collectively enhances the detection efficiency of medicinal plants in single and polyherbal formulations. FRONTIERS IN PLANT SCIENCE 2023; 14:1169984. [PMID: 37255553 PMCID: PMC10225634 DOI: 10.3389/fpls.2023.1169984] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Accepted: 04/17/2023] [Indexed: 06/01/2023]
Abstract
Introduction Empirical research has refined traditional herbal medicinal systems. The traditional market is expanding globally, but inadequate regulatory guidelines, taxonomic knowledge, and resources are causing herbal product adulteration. With the widespread adoption of barcoding and next-generation sequencing, metabarcoding is emerging as a potential tool for detecting labeled and unlabeled plant species in herbal products. Methods This study validated newly designed rbcL and ITS2 metabarcode primers for metabarcoding using in-house mock controls of medicinal plant gDNA pools and biomass pools. The applicability of the multi-barcode sequencing approach was evaluated on 17 single drugs and 15 polyherbal formulations procured from the Indian market. Results The rbcL metabarcode demonstrated 86.7% and 71.7% detection efficiencies in gDNA plant pools and biomass mock controls, respectively, while the ITS2 metabarcode demonstrated 82.2% and 69.4%. In the gDNA plant pool and biomass pool mock controls, the cumulative detection efficiency increased by 100% and 90%, respectively. A 79% cumulative detection efficiency of both metabarcodes was observed in single drugs, while 76.3% was observed in polyherbal formulations. An average fidelity of 83.6% was observed for targeted plant species present within mock controls and in herbal formulations. Discussion In the present study, we achieved increasing cumulative detection efficiency by combining the high universality of the rbcL locus with the high-resolution power of the ITS2 locus in medicinal plants, which shows applicability of multilocus strategies in metabarcoding as a potential tool for the Pharmacovigilance of labeled and unlabeled plant species in herbal formulations.
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11
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Raclariu-Manolică AC, Mauvisseau Q, de Boer HJ. Horizon scan of DNA-based methods for quality control and monitoring of herbal preparations. Front Pharmacol 2023; 14:1179099. [PMID: 37214460 PMCID: PMC10193163 DOI: 10.3389/fphar.2023.1179099] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Accepted: 04/20/2023] [Indexed: 05/24/2023] Open
Abstract
Herbal medicines and preparations are widely used in healthcare systems globally, but concerns remain about their quality and safety. New herbal products are constantly being introduced to the market under varying regulatory frameworks, with no global consensus on their definition or characterization. These biologically active mixtures are sold through complex globalized value chains, which create concerns around contamination and profit-driven adulteration. Industry, academia, and regulatory bodies must collaborate to develop innovative strategies for the identification and authentication of botanicals and their preparations to ensure quality control. High-throughput sequencing (HTS) has significantly improved our understanding of the total species diversity within DNA mixtures. The standard concept of DNA barcoding has evolved over the last two decades to encompass genomic data more broadly. Recent research in DNA metabarcoding has focused on developing methods for quantifying herbal product ingredients, yielding meaningful results in a regulatory framework. Techniques, such as loop-mediated isothermal amplification (LAMP), DNA barcode-based Recombinase Polymerase Amplification (BAR-RPA), DNA barcoding coupled with High-Resolution Melting (Bar-HRM), and microfluidics-based methods, offer more affordable tests for the detection of target species. While target capture sequencing and genome skimming are considerably increasing the species identification resolution in challenging plant clades, ddPCR enables the quantification of DNA in samples and could be used to detect intended and unwanted ingredients in herbal medicines. Here, we explore the latest advances in emerging DNA-based technologies and the opportunities they provide as taxa detection tools for evaluating the safety and quality of dietary supplements and herbal medicines.
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Affiliation(s)
- Ancuța Cristina Raclariu-Manolică
- Stejarul Research Centre for Biological Sciences, National Institute of Research and Development for Biological Sciences, Piatra Neamț, Romania
- Natural History Museum, University of Oslo, Oslo, Norway
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12
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Species identification of culinary spices with two-locus DNA barcoding. Food Control 2023. [DOI: 10.1016/j.foodcont.2023.109742] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/17/2023]
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13
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Yang P, Lang J, Li H, Lu J, Lin H, Tian G, Bai H, Yang J, Ning K. TCM-Suite: A comprehensive and holistic platform for Traditional Chinese Medicine component identification and network pharmacology analysis. IMETA 2022; 1:e47. [PMID: 38867910 PMCID: PMC10989960 DOI: 10.1002/imt2.47] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Revised: 07/05/2022] [Accepted: 07/20/2022] [Indexed: 06/14/2024]
Abstract
DNA-based biological ingredient identification and downstream pharmacology network analysis are commonly used in research for Traditional Chinese Medicine preparations (TCM formulas). Advancements in bioinformatics tools and the accumulation of related data have become driving forces for progress in this field. However, a lack of a platform integrating biological ingredient identification and downstream pharmacology network analysis hinders the deep understanding of TCM. In this study, we developed the TCM-Suite platform composed of two sub-databases, Holmes-Suite and Watson-Suite, for TCM biological ingredient identification and network pharmacology investigation, respectively, both are among the most complete: In the Holmes-Suite, we collected and processed six types of marker gene sequences, accounting for 1,251,548 marker gene sequences. In the Watson-Suite, we curated and integrated a massive number of entries from more than 10 public databases. Importantly, we developed a comprehensive pipeline to integrate TCM biological ingredient identification and downstream network pharmacology research, allowing users to simultaneously identify components of a TCM formula and analyze its potential pharmacology mechanism. Furthermore, we designed search engines and a user-friendly platform to better search and visualize these rich resources. TCM-Suite is a comprehensive and holistic platform for TCM-based drug discovery and repurposing. TCM-Suite website: http://TCM-Suite.AImicrobiome.cn.
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Affiliation(s)
- Pengshuo Yang
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular‐imaging, Center for Artificial Intelligence Biology, Department of Bioinformatics and Systems BiologyCollege of Life Science and Technology, Huazhong University of Science and TechnologyWuhanChina
| | - Jidong Lang
- Geneis Beijing Co., Ltd.BeijingChina
- Department of sciencesQingdao Genesis Institute of Big Data Mining and PrecisionQingdaoShandongChina
- Academician WorkstationChangsha Medical UniversityChangshaChina
| | - Hongjun Li
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular‐imaging, Center for Artificial Intelligence Biology, Department of Bioinformatics and Systems BiologyCollege of Life Science and Technology, Huazhong University of Science and TechnologyWuhanChina
| | - Jinxiang Lu
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular‐imaging, Center for Artificial Intelligence Biology, Department of Bioinformatics and Systems BiologyCollege of Life Science and Technology, Huazhong University of Science and TechnologyWuhanChina
| | - Hanyang Lin
- Sequenxe Biological Technology Co., Ltd.XiamenChina
| | - Geng Tian
- Geneis Beijing Co., Ltd.BeijingChina
- Department of sciencesQingdao Genesis Institute of Big Data Mining and PrecisionQingdaoShandongChina
| | - Hong Bai
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular‐imaging, Center for Artificial Intelligence Biology, Department of Bioinformatics and Systems BiologyCollege of Life Science and Technology, Huazhong University of Science and TechnologyWuhanChina
| | - Jialiang Yang
- Geneis Beijing Co., Ltd.BeijingChina
- Department of sciencesQingdao Genesis Institute of Big Data Mining and PrecisionQingdaoShandongChina
- Academician WorkstationChangsha Medical UniversityChangshaChina
| | - Kang Ning
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular‐imaging, Center for Artificial Intelligence Biology, Department of Bioinformatics and Systems BiologyCollege of Life Science and Technology, Huazhong University of Science and TechnologyWuhanChina
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14
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Gold Z, Wall AR, Schweizer TM, Pentcheff ND, Curd EE, Barber PH, Meyer RS, Wayne R, Stolzenbach K, Prickett K, Luedy J, Wetzer R. A manager's guide to using eDNA metabarcoding in marine ecosystems. PeerJ 2022; 10:e14071. [PMID: 36405018 PMCID: PMC9673773 DOI: 10.7717/peerj.14071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Accepted: 08/27/2022] [Indexed: 11/16/2022] Open
Abstract
Environmental DNA (eDNA) metabarcoding is a powerful tool that can enhance marine ecosystem/biodiversity monitoring programs. Here we outline five important steps managers and researchers should consider when developing eDNA monitoring program: (1) select genes and primers to target taxa; (2) assemble or develop comprehensive barcode reference databases; (3) apply rigorous site occupancy based decontamination pipelines; (4) conduct pilot studies to define spatial and temporal variance of eDNA; and (5) archive samples, extracts, and raw sequence data. We demonstrate the importance of each of these considerations using a case study of eDNA metabarcoding in the Ports of Los Angeles and Long Beach. eDNA metabarcoding approaches detected 94.1% (16/17) of species observed in paired trawl surveys while identifying an additional 55 native fishes, providing more comprehensive biodiversity inventories. Rigorous benchmarking of eDNA metabarcoding results improved ecological interpretation and confidence in species detections while providing archived genetic resources for future analyses. Well designed and validated eDNA metabarcoding approaches are ideally suited for biomonitoring applications that rely on the detection of species, including mapping invasive species fronts and endangered species habitats as well as tracking range shifts in response to climate change. Incorporating these considerations will enhance the utility and efficacy of eDNA metabarcoding for routine biomonitoring applications.
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Affiliation(s)
- Zachary Gold
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, Los Angeles, CA, United States of America
| | - Adam R. Wall
- Diversity Initiative for the Southern California Ocean (DISCO), Natural History Museum of Los Angeles County, Los Angeles, CA, United States of America
| | - Teia M. Schweizer
- Department of Fish and Wildlife Conservation Biology, Colorado State University, Fort Collins, CO, United States of America
| | - N. Dean Pentcheff
- Diversity Initiative for the Southern California Ocean (DISCO), Natural History Museum of Los Angeles County, Los Angeles, CA, United States of America
| | - Emily E. Curd
- Department of Natural Sciences, Landmark College, Putney, VT, United States of America
| | - Paul H. Barber
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, Los Angeles, CA, United States of America
| | - Rachel S. Meyer
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, Los Angeles, CA, United States of America,Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, Santa Cruz, CA, United States of America
| | - Robert Wayne
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, Los Angeles, CA, United States of America
| | - Kevin Stolzenbach
- Wood Environment and Infrastructure, Inc., San Diego, CA, United States of America
| | - Kat Prickett
- Port of Los Angeles, Los Angeles, CA, United States of America
| | - Justin Luedy
- Port of Long Beach, Long Beach, CA, United States of America
| | - Regina Wetzer
- Diversity Initiative for the Southern California Ocean (DISCO), Natural History Museum of Los Angeles County, Los Angeles, CA, United States of America
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15
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Sarkis CM, Hoenig BD, Seney EE, Gaspar SA, Forsman AM. Sea Snacks from DNA Tracks: Using DNA Metabarcoding to Characterize The Diet of Green Turtles (Chelonia Mydas). Integr Comp Biol 2022; 62:223-236. [PMID: 35679089 DOI: 10.1093/icb/icac080] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Revised: 05/20/2022] [Accepted: 05/23/2022] [Indexed: 11/12/2022] Open
Abstract
The green turtle (Chelonia mydas) is a circumglobal species with a wide dietary breadth that varies among regions and life history stages. Comprehensive understanding of foraging ecology over space and time is critical to inform conservation and management of this species and its habitats. Here, we used DNA metabarcoding to test candidate primer sets with 39 gut content homogenates from stranded green turtles (FL, USA) to identify primer sets that maximize detection of food items and specificity of taxonomic classifications. We tested six existing universal primer sets to detect plants, animals, and eukaryotes more broadly (CO1, 18SV1-V3, 18SV4, rbcL, UPA, ITS). The CO1 and 18SV4 primer sets produced the greatest number of dietary amplicon sequence variants (ASVs) and unique taxonomic classifications, and they were the only primer sets to amplify taxa from all three kingdoms relevant to green turtle diet (Animalia, Chromista, and Plantae). Even though the majority of CO1-derived reads were of host origin (>90%), this primer set still produced the largest number of dietary ASVs classified to species among the six primer sets. However, because the CO1 primer set failed to detect both vascular plants and green algae, we do not recommend the use of this primer set on its own to characterize green turtle diet. Instead, our findings support previous research highlighting the utility of using multiple primer sets, specifically targeting CO1 and the V4 region of the 18S gene, as doing so will provide the most comprehensive understanding of green turtle diet. More generally, our results highlight the importance of primer and loci selection and the need to validate primer sets against the study system of interest. The addition of DNA metabarcoding with optimized primer sets to the sea turtle researcher's toolbox will both increase our understanding of foraging ecology and better inform science-based conservation and ecosystem management.
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Affiliation(s)
- Christine M Sarkis
- Department of Biology, University of Central Florida, Orlando, Florida, USA
| | - Brandon D Hoenig
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, USA
| | - Erin E Seney
- Department of Biology, University of Central Florida, Orlando, Florida, USA.,Marine Turtle Research Group, Department of Biology, University of Central Florida, Orlando, Florida, USA
| | - Stephanie A Gaspar
- Department of Biology, University of Central Florida, Orlando, Florida, USA
| | - Anna M Forsman
- Department of Biology, University of Central Florida, Orlando, Florida, USA.,Genomics & Bioinformatics Cluster, University of Central Florida, Orlando, Florida, USA
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16
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Rapid in situ identification of biological specimens via DNA amplicon sequencing using miniaturized laboratory equipment. Nat Protoc 2022; 17:1415-1443. [DOI: 10.1038/s41596-022-00682-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Accepted: 01/04/2022] [Indexed: 12/24/2022]
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17
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Wu HY, Shaw PC. Strategies for molecular authentication of herbal products: from experimental design to data analysis. Chin Med 2022; 17:38. [PMID: 35317843 PMCID: PMC8939074 DOI: 10.1186/s13020-022-00590-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Accepted: 03/02/2022] [Indexed: 12/22/2022] Open
Abstract
Molecular herbal authentication has gained worldwide popularity in the past decade. DNA-based methods, including DNA barcoding and species-specific amplification, have been adopted for herbal identification by various pharmacopoeias. Development of next-generating sequencing (NGS) drastically increased the throughput of sequencing process and has sped up sequence collection and assembly of organelle genomes, making more and more reference sequences/genomes available. NGS allows simultaneous sequencing of multiple reads, opening up the opportunity of identifying multiple species from one sample in one go. Two major experimental approaches have been applied in recent publications of identification of herbal products by NGS, the PCR-dependent DNA metabarcoding and PCR-free genome skimming/shotgun metagenomics. This review provides a brief introduction of the use of DNA metabarcoding and genome skimming/shotgun metagenomics in authentication of herbal products and discusses some important considerations in experimental design for botanical identification by NGS, with a specific focus on quality control, reference sequence database and different taxon assignment programs. The potential of quantification or abundance estimation by NGS is discussed and new scientific findings that could potentially interfere with accurate taxon assignment and/or quantification is presented.
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Affiliation(s)
- Hoi-Yan Wu
- Li Dak Sum Yip Yio Chin R & D Centre for Chinese Medicine, The Chinese University of Hong Kong, Shatin, Hong Kong, China
| | - Pang-Chui Shaw
- Li Dak Sum Yip Yio Chin R & D Centre for Chinese Medicine, The Chinese University of Hong Kong, Shatin, Hong Kong, China. .,School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong, China. .,State Key Laboratory of Research on Bioactivities and Clinical Applications of Medicinal Plants (The Chinese University of Hong Kong) and Institute of Chinese Medicine, The Chinese University of Hong Kong, Hong Kong, China.
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18
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Development of a DNA Metabarcoding Method for the Identification of Bivalve Species in Seafood Products. Foods 2021; 10:foods10112618. [PMID: 34828894 PMCID: PMC8617786 DOI: 10.3390/foods10112618] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Revised: 10/20/2021] [Accepted: 10/23/2021] [Indexed: 11/16/2022] Open
Abstract
The production of bivalve species has been increasing in the last decades. In spite of strict requirements for species declaration, incorrect labelling of bivalve products has repeatedly been detected. We present a DNA metabarcoding method allowing the identification of bivalve species belonging to the bivalve families Mytilidae (mussels), Pectinidae (scallops), and Ostreidae (oysters) in foodstuffs. The method, developed on Illumina instruments, targets a 150 bp fragment of mitochondrial 16S rDNA. We designed seven primers (three primers for mussel species, two primers for scallop species and a primer pair for oyster species) and combined them in a triplex PCR assay. In each of eleven reference samples, the bivalve species was identified correctly. In ten DNA extract mixtures, not only the main component (97.0-98.0%) but also the minor components (0.5-1.5%) were detected correctly, with only a few exceptions. The DNA metabarcoding method was found to be applicable to complex and processed foodstuffs, allowing the identification of bivalves in, e.g., marinated form, in sauces, in seafood mixes and even in instant noodle seafood. The method is highly suitable for food authentication in routine analysis, in particular in combination with a DNA metabarcoding method for mammalian and poultry species published recently.
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19
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Mori C, Matsumura S. Development and validation of simultaneous identification of 26 mammalian and poultry species by a multiplex assay. Int J Legal Med 2021; 136:1-12. [PMID: 34626212 DOI: 10.1007/s00414-021-02711-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Accepted: 09/24/2021] [Indexed: 11/29/2022]
Abstract
A multiplex PCR assay was developed to simultaneously identify 22 mammalian species (alpaca, Asiatic black bear, Bactrian camel, brown rat, cat, cattle, common raccoon, dog, European rabbit, goat, horse, house mouse, human, Japanese badger, Japanese wild boar, masked palm civet, pig, raccoon dog, red fox, sheep, Siberian weasel, and sika deer) and four poultry species (chicken, domestic turkey, Japanese quail, and mallard), even from a biological sample containing a DNA mixture of multiple species. The assay was designed to identify species through multiplex PCR and capillary electrophoresis, with a combination of amplification of a partial region of the mitochondrial D-loop by universal primer sets and a partial region of the cytochrome b (cyt b) gene by species-specific primer sets. The assay was highly sensitive, with a detection limit of 100 copies of mitochondrial DNA. The assay's ability to identify species from complex DNA mixtures was demonstrated using an experimental sample consisting of 10 species. Efficacy, accuracy, and reliability of the assay were validated for use in forensic analysis with the guidelines of Scientific Working Group on DNA Analysis Methods (SWGDAM). The multiplex PCR assay developed in this study enables cost-effective, highly sensitive, and simultaneous species identification without massively parallel sequencing (MPS) platforms. Thus, the technique described is straightforward and suitable for routine forensic investigations.
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Affiliation(s)
- Chikahiro Mori
- The United Graduate School of Agricultural Science, Gifu University, 1-1 Yanagido, Gifu, 501-1193, Japan. .,Forensic Science Laboratory, Gifu Prefectural Police Headquarters, 2-1-1 Yabutaminami, Gifu, 500-8501, Japan.
| | - Shuichi Matsumura
- Faculty of Applied Biological Sciences, Gifu University, 1-1 Yanagido, Gifu, 501-1193, Japan
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20
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Chiara B, Francesco C, Fulvio B, Paola M, Annalisa G, Stefania S, Luigi AP, Simone P. Exploring the botanical composition of polyfloral and monofloral honeys through DNA metabarcoding. Food Control 2021. [DOI: 10.1016/j.foodcont.2021.108175] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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21
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Ghemrawi M, Fischinger F, Duncan G, Dukes MJ, Guilliano M, McCord B. Developmental validation of SpeID: A pyrosequencing-based assay for species identification. Forensic Sci Int Genet 2021; 55:102560. [PMID: 34507077 DOI: 10.1016/j.fsigen.2021.102560] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Revised: 06/16/2021] [Accepted: 06/30/2021] [Indexed: 11/19/2022]
Abstract
In crime scenes, biological exhibits are often human in origin, yet biological stains from other fauna may also be present at a crime scene, creating confusion during an investigation. Furthermore, identifying the source of a biological sample can be critical during an investigation. To identify the presence of biological material from non-human sources, it is common to use genetic markers within mitochondrial DNA such as cytochrome b, 16S rRNA, and 12S rRNA genes. This process usually requires DNA sequencing, a process that is neither quick nor easy. In general, a faster, more standardized method for species identification from tissue and body fluids is desirable.For this reason, we have developed a vertebrate specific real-time quantitation method that is followed by an automated pyrosequencing-based procedure that sequences a short fragment within the 12S rRNA gene. Using no more than 35 bases, the assay can distinguish between 32 different species commonly found in and around a household with a turnaround time of 6 h from extraction to sequencing. -Using this procedure, up to 48 samples can be run at a time without the need for expensive reagents or bioinformatic skills.
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Affiliation(s)
- Mirna Ghemrawi
- Department of Chemistry and Biochemistry, Florida International University, Miami, FL 33199, United States
| | | | - George Duncan
- Nova Southeastern University, Dania Beach, Fl 33004, United State
| | | | | | - Bruce McCord
- Department of Chemistry and Biochemistry, Florida International University, Miami, FL 33199, United States.
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22
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Xie H, Zhao Q, Shi M, Kong W, Mu W, Li B, Zhao J, Zhao C, Jia J, Liu J, Shi L. Biological Ingredient Analysis of Traditional Herbal Patent Medicine Fuke Desheng Wan Using the Shotgun Metabarcoding Approach. Front Pharmacol 2021; 12:607197. [PMID: 34483893 PMCID: PMC8416078 DOI: 10.3389/fphar.2021.607197] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Accepted: 08/06/2021] [Indexed: 12/15/2022] Open
Abstract
With the widespread use of traditional medicine around the world, the safety and efficacy of traditional herbal patent medicine have become an increasing concern to the public. However, it is difficult to supervise the authenticity of herbal materials in mixed herbal products according to the current quality standards, especially for traditional herbal patent medicine, with a distinct variance in the dosage of herbal materials. This study utilized the shotgun metabarcoding approach to analyze the biological ingredients of Fuke Desheng Wan (FKDSW), which is an effective traditional herbal product for the treatment of dysmenorrhea. Six herbal materials were collected, and a lab-made mock FKDSW sample was produced to establish a method for the authentication assessment of biological ingredients in traditional herbal patent medicine based on shotgun metabarcoding. Furthermore, four commercial FKDSW samples were collected to verify the practicality of the shotgun metabarcoding approach. Then, a total of 52.16 Gb raw data for 174 million paired-end reads was generated using the Illumina NovaSeq sequencing platform. Meanwhile, 228, 23, and 14 operational taxonomic units (OTUs) were obtained for the ITS2, matK, and rbcL regions, respectively, after bioinformatic analysis. Moreover, no differences were evident between the assembly sequences obtained via shotgun metabarcoding and their corresponding reference sequences of the same species obtained via Sanger sequencing, except for part of the ITS2 and matK assembly sequences of Paeonia lactiflora Pall., Saussurea costus (Falc.) Lipsch. and Bupleurum chinense DC. with 1–6 different bases. The identification results showed that all six prescribed ingredients were successfully detected and that the non-authentic ingredient of Bupleuri Radix (Chaihu, Bupleurum chinense DC. or Bupleurum scorzonerifolium Willd.) was found in all the commercial samples, namely Bupleurum falcatum L. Here, 25 weed species representing 16 genera of ten families were detected. Moreover, 26 fungal genera belonging to 17 families were found in both lab-made and commercial FKDSW samples. This study demonstrated that the shotgun metabarcoding approach could overcome the biased PCR amplification and authenticate the biological ingredients of traditional herbal patent medicine with a distinct variance in the dosage of the herbal materials. Therefore, this provides an appropriate evaluation method for improving the safety and efficacy of traditional herbal patent medicine.
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Affiliation(s)
- Hongbo Xie
- Hebei Key Laboratory of Study and Exploitation of Chinese Medicine, Chengde Medical University, Chengde, China
| | - Qing Zhao
- Hebei Key Laboratory of Study and Exploitation of Chinese Medicine, Chengde Medical University, Chengde, China.,Department of Pharmacy, Baoding First Central Hospital, Baoding, China
| | - Mengmeng Shi
- Hebei Key Laboratory of Study and Exploitation of Chinese Medicine, Chengde Medical University, Chengde, China
| | - Weijun Kong
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China
| | - Weishan Mu
- Hebei Key Laboratory of Study and Exploitation of Chinese Medicine, Chengde Medical University, Chengde, China
| | - Baoli Li
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China
| | - Jingyi Zhao
- Hebei Key Laboratory of Study and Exploitation of Chinese Medicine, Chengde Medical University, Chengde, China
| | - Chunying Zhao
- Hebei Key Laboratory of Study and Exploitation of Chinese Medicine, Chengde Medical University, Chengde, China
| | - Jing Jia
- Department of Pharmacy, Affiliated Hospital of Shandong University of Traditional Chinese Medicine, Jinan, China
| | - Jinxin Liu
- Hebei Key Laboratory of Study and Exploitation of Chinese Medicine, Chengde Medical University, Chengde, China.,Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China
| | - Linchun Shi
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China
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23
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Pandit R, Travadi T, Sharma S, Joshi C, Joshi M. DNA meta-barcoding using rbcL based mini-barcode revealed presence of unspecified plant species in Ayurvedic polyherbal formulations. PHYTOCHEMICAL ANALYSIS : PCA 2021; 32:804-810. [PMID: 33527609 DOI: 10.1002/pca.3026] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Revised: 12/09/2020] [Accepted: 12/10/2020] [Indexed: 06/12/2023]
Abstract
INTRODUCTION Ayurveda takes advantage of the beneficial properties of medicinal plants. High demands in combination with inadequate availability of botanicals and a lack of knowledge with respect to their precise identification lead to adulterations in herbal products. Identification becomes more difficult in complex herbal formulations. Four different polyherbal formulations have been analyzed for the present paper. The targeted plants have different pharmacological properties for various ailments. OBJECTIVE We aimed to examine the rbcL gene based plant DNA mini-barcode to identify target and non-target plants in polyherbal formulations by using high-throughput next generation sequencing. METHODS Degenerate primers of the selected mini-barcode region have been identified from the literature. A blend of 30 authentic medicinal plant species was used to examine the species resolution capacity of the mini-barcode. DNA was isolated from herbal formulations, an amplicon library was prepared, and sequencing was performed on an IonS5 system. Data were analyzed using various bioinformatics tools. RESULTS Analysis of control pooled samples revealed the optimum resolving power of the DNA mini-barcode. Data analysis of the commercial samples revealed that only one herbal formulation contained all plants and matched with listed contents. In two formulations, only 10 out of 21 and 11 out of 20 plants were detected, respectively. Additionally, several non-listed plants were also detected in these formulations. Two formulations contained >20% reads assigned to non-target plants. Overall, 21.98% of the reads were assigned to non-target plants. CONCLUSION The present study clearly demonstrated the successful application and potential of meta-barcoding in the quality control of complex herbal matrices. The results strongly suggest that this approach can be used in pharmacovigilance of processed herbal products.
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Affiliation(s)
- Ramesh Pandit
- Department of Science and Technology, Gov. of Gujarat, Gujarat Biotechnology Research Centre (GBRC), Gandhinagar, India
| | - Tasnim Travadi
- Department of Science and Technology, Gov. of Gujarat, Gujarat Biotechnology Research Centre (GBRC), Gandhinagar, India
| | - Sonal Sharma
- Department of Science and Technology, Gov. of Gujarat, Gujarat Biotechnology Research Centre (GBRC), Gandhinagar, India
| | - Chaitanya Joshi
- Department of Science and Technology, Gov. of Gujarat, Gujarat Biotechnology Research Centre (GBRC), Gandhinagar, India
| | - Madhvi Joshi
- Department of Science and Technology, Gov. of Gujarat, Gujarat Biotechnology Research Centre (GBRC), Gandhinagar, India
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24
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Nanopore sequencing in non-human forensic genetics. Emerg Top Life Sci 2021; 5:465-473. [PMID: 34002773 PMCID: PMC8457772 DOI: 10.1042/etls20200287] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Revised: 04/21/2021] [Accepted: 04/29/2021] [Indexed: 12/28/2022]
Abstract
The past decade has seen a rapid expansion of non-human forensic genetics coinciding with the development of 2nd and 3rd generation DNA sequencing technologies. Nanopore sequencing is one such technology that offers massively parallel sequencing at a fraction of the capital cost of other sequencing platforms. The application of nanopore sequencing to species identification has already been widely demonstrated in biomonitoring studies and has significant potential for non-human forensic casework, particularly in the area of wildlife forensics. This review examines nanopore sequencing technology and assesses its potential applications, advantages and drawbacks for use in non-human forensics, alongside other next-generation sequencing platforms and as a possible replacement to Sanger sequencing. We assess the specific challenges of sequence error rate and the standardisation of consensus sequence production, before discussing recent progress in the validation of nanopore sequencing for use in forensic casework. We conclude that nanopore sequencing may be able to play a considerable role in the future of non-human forensic genetics, especially for applications to wildlife law enforcement within emerging forensic laboratories.
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Batovska J, Piper AM, Valenzuela I, Cunningham JP, Blacket MJ. Developing a non-destructive metabarcoding protocol for detection of pest insects in bulk trap catches. Sci Rep 2021; 11:7946. [PMID: 33846382 PMCID: PMC8041782 DOI: 10.1038/s41598-021-85855-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Accepted: 03/02/2021] [Indexed: 01/04/2023] Open
Abstract
Metabarcoding has the potential to revolutionise insect surveillance by providing high-throughput and cost-effective species identification of all specimens within mixed trap catches. Nevertheless, incorporation of metabarcoding into insect diagnostic laboratories will first require the development and evaluation of protocols that adhere to the specialised regulatory requirements of invasive species surveillance. In this study, we develop a multi-locus non-destructive metabarcoding protocol that allows sensitive detection of agricultural pests, and subsequent confirmation using traditional diagnostic techniques. We validate this protocol for the detection of tomato potato psyllid (Bactericera cockerelli) and Russian wheat aphid (Diuraphis noxia) within mock communities and field survey traps. We find that metabarcoding can reliably detect target insects within mixed community samples, including specimens that morphological identification did not initially detect, but sensitivity appears inversely related to community size and is impacted by primer biases, target loci, and sample indexing strategy. While our multi-locus approach allowed independent validation of target detection, lack of reference sequences for 18S and 12S restricted its usefulness for estimating diversity in field samples. The non-destructive DNA extraction proved invaluable for resolving inconsistencies between morphological and metabarcoding identification results, and post-extraction specimens were suitable for both morphological re-examination and DNA re-extraction for confirmatory barcoding.
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Affiliation(s)
- Jana Batovska
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, 5 Ring Road, Bundoora, VIC, 3083, Australia. .,School of Applied Systems Biology, La Trobe University, Bundoora, VIC, 3086, Australia.
| | - Alexander M Piper
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, 5 Ring Road, Bundoora, VIC, 3083, Australia.,School of Applied Systems Biology, La Trobe University, Bundoora, VIC, 3086, Australia
| | - Isabel Valenzuela
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, 5 Ring Road, Bundoora, VIC, 3083, Australia
| | - John Paul Cunningham
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, 5 Ring Road, Bundoora, VIC, 3083, Australia.,School of Applied Systems Biology, La Trobe University, Bundoora, VIC, 3086, Australia
| | - Mark J Blacket
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, 5 Ring Road, Bundoora, VIC, 3083, Australia
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Nakanishi H, Yoneyama K, Hara M, Takada A, Saito K. Estimating included animal species in mixed crude drugs derived from animals using massively parallel sequencing. Sci Rep 2021; 11:6257. [PMID: 33739020 PMCID: PMC7973747 DOI: 10.1038/s41598-021-85803-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Accepted: 03/05/2021] [Indexed: 11/09/2022] Open
Abstract
We developed a method that can detect each animal species of origin for crude drugs derived from multiple animal species based on massively parallel sequencing analysis of mitochondrial genes. The crude drugs derived from animals investigated in this study were Cervi Parvum Cornu and Trogopterorum feces, which are derived from a mix of different animal species, two chopped cicada sloughs, and two commercial Kampo drugs. The mitochondrial 12S rRNA, 16S rRNA, and cytochrome oxidase subunit I gene regions were amplified and sequenced using MiSeq. The ratios of haplotype to total number of sequences reads were calculated after sequence extraction and trimming. Haplotypes that exceeded the threshold were defined as positive haplotypes, which were compared with all available sequences using BLAST. In the Cervi Parvum Cornu and Trogopterorum feces samples, the haplotype ratios corresponded roughly to the mixture ratios, although there was a slight difference from mixture ratios depending on the gene examined. This method could also roughly estimate the compositions of chopped cicada sloughs and Kampo drugs. This analysis, whereby the sequences of several genes are elucidated, is better for identifying the included animal species. This method should be useful for quality control of crude drugs and Kampo drugs.
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Affiliation(s)
- Hiroaki Nakanishi
- Department of Forensic Medicine, Juntendo University School of Medicine, 2-1-1, Hongo, Bunkyo-Ku, Tokyo, 113-8421, Japan.
| | - Katsumi Yoneyama
- Department of Forensic Medicine, Saitama Medical University, 38 Morohongo, Moroyama, Saitama, 350-0495, Japan
| | - Masaaki Hara
- Department of Forensic Medicine, Saitama Medical University, 38 Morohongo, Moroyama, Saitama, 350-0495, Japan
| | - Aya Takada
- Department of Forensic Medicine, Saitama Medical University, 38 Morohongo, Moroyama, Saitama, 350-0495, Japan
| | - Kazuyuki Saito
- Department of Forensic Medicine, Juntendo University School of Medicine, 2-1-1, Hongo, Bunkyo-Ku, Tokyo, 113-8421, Japan
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Vasiljevic N, Lim M, Humble E, Seah A, Kratzer A, Morf NV, Prost S, Ogden R. Developmental validation of Oxford Nanopore Technology MinION sequence data and the NGSpeciesID bioinformatic pipeline for forensic genetic species identification. Forensic Sci Int Genet 2021; 53:102493. [PMID: 33770699 DOI: 10.1016/j.fsigen.2021.102493] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Revised: 02/09/2021] [Accepted: 03/03/2021] [Indexed: 12/14/2022]
Abstract
Species identification of non-human biological evidence through DNA nucleotide sequencing is routinely used for forensic genetic analysis to support law enforcement. The gold standard for forensic genetics is conventional Sanger sequencing; however, this is gradually being replaced by high-throughput sequencing (HTS) approaches which can generate millions of individual reads in a single experiment. HTS sequencing, which now dominates molecular biology research, has already been demonstrated for use in a number of forensic genetic analysis applications, including species identification. However, the generation of HTS data to date requires expensive equipment and is cost-effective only when large numbers of samples are analysed simultaneously. The Oxford Nanopore Technologies (ONT) MinION™ is an affordable and small footprint DNA sequencing device with the potential to quickly deliver reliable and cost effective data. However, there has been no formal validation of forensic species identification using high-throughput (deep read) sequence data from the MinION making it currently impractical for many wildlife forensic end-users. Here, we present a MinION deep read sequence data validation study for species identification. First, we tested whether the clustering-based bioinformatics pipeline NGSpeciesID can be used to generate an accurate consensus sequence for species identification. Second, we systematically evaluated the read variation distribution around the generated consensus sequences to understand what confidence we have in the accuracy of the resulting consensus sequence and to determine how to interpret individual sample results. Finally, we investigated the impact of differences between the MinION consensus and Sanger control sequences on correct species identification to understand the ability and accuracy of the MinION consensus sequence to differentiate the true species from the next most similar species. This validation study establishes that ONT MinION sequence data used in conjunction with the NGSpeciesID pipeline can produce consensus DNA sequences of sufficient accuracy for forensic genetic species identification.
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Affiliation(s)
- Nina Vasiljevic
- Institute of Forensic Medicine, University of Zurich, Zurich, Switzerland.
| | - Marisa Lim
- Wildlife Conservation Society, Zoological Health Program, Bronx, NY, USA
| | - Emily Humble
- Royal (Dick) School of Veterinary Studies and the Roslin Institute, University of Edinburgh, UK
| | - Adeline Seah
- Wildlife Conservation Society, Zoological Health Program, Bronx, NY, USA
| | - Adelgunde Kratzer
- Institute of Forensic Medicine, University of Zurich, Zurich, Switzerland
| | - Nadja V Morf
- Institute of Forensic Medicine, University of Zurich, Zurich, Switzerland
| | - Stefan Prost
- LOEWE-Centre for Translational Biodiversity Genomics, Senckenberg, Frankfurt, Germany; South African National Biodiversity Institute, National Zoological Garden, Pretoria, South Africa
| | - Rob Ogden
- Royal (Dick) School of Veterinary Studies and the Roslin Institute, University of Edinburgh, UK; TRACE Wildlife Forensics Network, Edinburgh, UK
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Liu J, Mu W, Shi M, Zhao Q, Kong W, Xie H, Shi L. The Species Identification in Traditional Herbal Patent Medicine, Wuhu San, Based on Shotgun Metabarcoding. Front Pharmacol 2021; 12:607200. [PMID: 33664667 PMCID: PMC7921783 DOI: 10.3389/fphar.2021.607200] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Accepted: 01/18/2021] [Indexed: 12/15/2022] Open
Abstract
Traditional herbal patent medicine typically consists of multiple ingredients, making it challenging to supervise contamination by impurities and the improper use of raw materials. This study employed shotgun metabarcoding for the species identification of biological ingredients in traditional herbal patent medicine, Wuhu San. The five prescribed herbal materials found in Wuhu San were collected, and their reference sequences were obtained by traditional DNA barcoding using Sanger sequencing. Two lab-made and three commercial Wuhu San samples were collected, and a total of 37.14 Gb of shotgun sequencing data was obtained for these five samples using the Illumina sequencing platform. A total of 1,421,013 paired-end reads were enriched for the Internal Transcribed Spacer 2 (ITS2), psbA and trnH intergenic spacer region (psbA-trnH), maturase k (matK), and ribulose-1, 5-bisphosphate carboxylase (rbcL) regions. Furthermore, 80, 11, 9, and 8 operational taxonomic units were obtained for the ITS2, psbA-trnH, matK, and rbcL regions, respectively, after metagenomic assembly, annotation, and chimeric detection. In the two lab-made mock samples, all labeled ingredients in the Wuhu San prescription were successfully detected, and the positive control, Panax quinquefolius L., was detected in the HSZY172 mock sample. Three species, namely Angelica sinensis (Oliv.) Diels, Saposhnikovia divaricata (Turcz. ex Ledeb.) Schischk., and Carthamus tinctorius L., belonging to three labeled ingredients, Angelicae Sinensis Radix (Danggui), Saposhnikoviae Radix (Fangfeng), and Carthami Flos (Honghua), were detected in the three commercial samples. Angelica dahurica (Hoffm.) Benth. & Hook. f. ex Franch. & Sav., the original Angelicae Dahuricae Radix (Baizhi) species, was only detected in WHS003. Arisaema erubescens (Wall.) Schott, Arisaema heterophyllum Blume, or Arisaema amurense Maxim., the original Arisaematis Rhizoma (Tiannanxing) species, were not detected in any of the commercial samples, which could be attributed to the fact that this medicinal material underwent extensive processing. In addition, the Saposhnikovia divaricata adulterant was detected in all the commercial samples, while 24 fungal genera, including Aspergillus, were identified in both the lab-made and commercial samples. This study showed that shotgun metabarcoding provided alternative strategy and technical means for identifying prescribed ingredients in traditional herbal patent medicine and displayed the potential to effectively complement traditional methods.
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Affiliation(s)
- Jinxin Liu
- Hebei Key Laboratory of Study and Exploitation of Chinese Medicine, Chengde Medical University, Chengde, China.,Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China
| | - Weishan Mu
- Hebei Key Laboratory of Study and Exploitation of Chinese Medicine, Chengde Medical University, Chengde, China
| | - Mengmeng Shi
- Hebei Key Laboratory of Study and Exploitation of Chinese Medicine, Chengde Medical University, Chengde, China
| | - Qing Zhao
- Hebei Key Laboratory of Study and Exploitation of Chinese Medicine, Chengde Medical University, Chengde, China
| | - Weijun Kong
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China
| | - Hongbo Xie
- Hebei Key Laboratory of Study and Exploitation of Chinese Medicine, Chengde Medical University, Chengde, China
| | - Linchun Shi
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China
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Yu J, Wu X, Liu C, Newmaster S, Ragupathy S, Kress WJ. Progress in the use of DNA barcodes in the identification and classification of medicinal plants. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2021; 208:111691. [PMID: 33396023 DOI: 10.1016/j.ecoenv.2020.111691] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Revised: 11/03/2020] [Accepted: 11/17/2020] [Indexed: 05/27/2023]
Abstract
DNA barcoding is an emerging molecular identification and classification technology that has been applied to medicinal plants since 2008. The application of this technique has greatly ensured the safety and effectiveness of medicinal materials. In this paper, we review the application of DNA barcoding and some related technologies over the past 10 years with respect to improving our knowledge of medicinal plant identification and authentication. From single locus-based DNA barcodes to combined markers to genome-scale levels, DNA barcodes contribute more and more genetic information. At the same time, other technologies, such as high-resolution melting (HRM), have been combined with DNA barcoding. With the development of next-generation sequencing (NGS), metabarcoding technology has also been shown to identify species in mixed samples successfully. As a widely used and effective tool, DNA barcoding will become more useful over time in the field of medicinal plants.
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Affiliation(s)
- Jie Yu
- College of Horticulture and Landscape Architecture, Southwest University, Chongqing 400716, China.
| | - Xi Wu
- Herbal Medicine from Ministry of Education, Engineering Research Center of Chinese Medicine Resources from Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing 100193, China
| | - Chang Liu
- Herbal Medicine from Ministry of Education, Engineering Research Center of Chinese Medicine Resources from Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing 100193, China
| | - Steve Newmaster
- Centre for Biodiversity Genomics, Biodiversity Institute of Ontario (BIO), University of Guelph, Guelph, Ontario N1G2W1, Canada
| | - Subramanyam Ragupathy
- Centre for Biodiversity Genomics, Biodiversity Institute of Ontario (BIO), University of Guelph, Guelph, Ontario N1G2W1, Canada
| | - W John Kress
- Department of Botany, MRC-166, National Museum of Natural History, Smithsonian Institution, P. O. Box 37012, Washington, DC 20013-7012, United States.
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30
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Kowal K, Tkaczyk A, Pierzchała M, Bownik A, Ślaska B. Identification of Mitochondrial DNA (NUMTs) in the Nuclear Genome of Daphnia magna. Int J Mol Sci 2020; 21:E8725. [PMID: 33218217 PMCID: PMC7699184 DOI: 10.3390/ijms21228725] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Revised: 11/06/2020] [Accepted: 11/16/2020] [Indexed: 01/30/2023] Open
Abstract
This is the first study in which the Daphnia magna (D. magna) nuclear genome (nDNA) obtained from the GenBank database was analyzed for pseudogene sequences of mitochondrial origin. To date, there is no information about pseudogenes localized in D. magna genome. This study aimed to identify NUMTs, their length, homology, and location for potential use in evolutionary studies and to check whether their occurrence causes co-amplification during mitochondrial genome (mtDNA) analyses. Bioinformatic analysis showed 1909 fragments of the mtDNA of D. magna, of which 1630 were located in ten linkage groups (LG) of the nDNA. The best-matched NUMTs covering >90% of the gene sequence have been identified for two mt-tRNA genes, and they may be functional nuclear RNA molecules. Isolating the total DNA in mtDNA studies, co-amplification of nDNA fragments is unlikely in the case of amplification of the whole tRNA genes as well as fragments of other genes. It was observed that TRNA-MET fragments had the highest level of sequence homology, thus they could be evolutionarily the youngest. The lowest homology was found in the D-loop-derived pseudogene. It may probably be the oldest NUMT incorporated into the nDNA; however, further analysis is necessary.
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Affiliation(s)
- Krzysztof Kowal
- Faculty of Animal Sciences and Bioeconomy, Institute of Biological Bases of Animal Production, University of Life Sciences in Lublin, Akademicka 13 Str., 20-950 Lublin, Poland; (K.K.); (A.T.)
| | - Angelika Tkaczyk
- Faculty of Animal Sciences and Bioeconomy, Institute of Biological Bases of Animal Production, University of Life Sciences in Lublin, Akademicka 13 Str., 20-950 Lublin, Poland; (K.K.); (A.T.)
| | - Mariusz Pierzchała
- Department of Genomics and Biodiversity, Institute of Genetics and Animal Biotechnology of the Polish Academy of Sciences, Postępu 36a Str., 05-552 Jastrzębiec, Poland;
| | - Adam Bownik
- Faculty of Environmental Biology, Department of Hydrobiology and Protection of Ecosystems, University of Life Sciences in Lublin, Dobrzańskiego 37 Str., 20-262 Lublin, Poland;
| | - Brygida Ślaska
- Faculty of Animal Sciences and Bioeconomy, Institute of Biological Bases of Animal Production, University of Life Sciences in Lublin, Akademicka 13 Str., 20-950 Lublin, Poland; (K.K.); (A.T.)
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Cui W, Jin X, Guo Y, Chen C, Zhang W, Wang Y, Lan J, Zhu B. Development and Validation of a Novel Five-Dye Short Tandem Repeat Panel for Forensic Identification of 11 Species. Front Genet 2020; 11:1005. [PMID: 33193588 PMCID: PMC7541953 DOI: 10.3389/fgene.2020.01005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Accepted: 08/06/2020] [Indexed: 01/16/2023] Open
Abstract
Species identification of unknown biological samples is of fundamental importance for forensic applications, especially in crime detection, poaching, and illegal trade of endangered animals as well as meat fraud. In this study, a novel panel was developed to simultaneously identify 10 different animal species (Gallus domesticus, Anas platyrhynchos domesticus, Ovis aries, Sus scrofa domesticus, Bos taurus, Equus caballus, Columba livia domestica, Rattus norvegicus, Mus musculus, and Canis lupus familiaris) and human beings by amplifying 22 short tandem repeat (STR) loci in a multiplex PCR using a set of five fluorescently labeled dyes. This novel 22-STR panel was validated by optimization of PCR conditions as well as species specificity, sensitivity, reproducibility, precision, DNA mixture, and tissue/organ consistency. The results of developmental validation showed that the 22-STR loci achieved high species specificity among 10 animal species and human beings, and the sensitivity of this panel was 0.09 ng. This 22-STR panel identified different meats in mixed samples, and the minimum detected mixture ratio in the current test was 10% (0.1 ng/1 ng). This sensitive, accurate, and specific 22-STR panel can be used for forensic species identification and the detection of meat fraud and adulteration.
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Affiliation(s)
- Wei Cui
- Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi'an Jiaotong University, Xi'an, China.,Clinical Research Center of Shaanxi Province for Dental and Maxillofacial Diseases, College of Stomatology, Xi'an Jiaotong University, Xi'an, China.,College of Medicine and Forensics, Xi'an Jiaotong University Health Science Center, Xi'an, China
| | - Xiaoye Jin
- Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi'an Jiaotong University, Xi'an, China.,Clinical Research Center of Shaanxi Province for Dental and Maxillofacial Diseases, College of Stomatology, Xi'an Jiaotong University, Xi'an, China.,College of Medicine and Forensics, Xi'an Jiaotong University Health Science Center, Xi'an, China
| | - Yuxin Guo
- Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi'an Jiaotong University, Xi'an, China.,Clinical Research Center of Shaanxi Province for Dental and Maxillofacial Diseases, College of Stomatology, Xi'an Jiaotong University, Xi'an, China.,College of Medicine and Forensics, Xi'an Jiaotong University Health Science Center, Xi'an, China
| | - Chong Chen
- Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi'an Jiaotong University, Xi'an, China.,Clinical Research Center of Shaanxi Province for Dental and Maxillofacial Diseases, College of Stomatology, Xi'an Jiaotong University, Xi'an, China.,College of Medicine and Forensics, Xi'an Jiaotong University Health Science Center, Xi'an, China
| | - Wenqing Zhang
- Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi'an Jiaotong University, Xi'an, China.,Clinical Research Center of Shaanxi Province for Dental and Maxillofacial Diseases, College of Stomatology, Xi'an Jiaotong University, Xi'an, China
| | - Yijie Wang
- Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi'an Jiaotong University, Xi'an, China.,Clinical Research Center of Shaanxi Province for Dental and Maxillofacial Diseases, College of Stomatology, Xi'an Jiaotong University, Xi'an, China
| | - Jiangwei Lan
- Multi-Omics Innovative Research Center of Forensic Identification, Department of Forensic Genetics, School of Forensic Medicine, Southern Medical University, Guangzhou, China
| | - Bofeng Zhu
- Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi'an Jiaotong University, Xi'an, China.,Clinical Research Center of Shaanxi Province for Dental and Maxillofacial Diseases, College of Stomatology, Xi'an Jiaotong University, Xi'an, China.,Multi-Omics Innovative Research Center of Forensic Identification, Department of Forensic Genetics, School of Forensic Medicine, Southern Medical University, Guangzhou, China
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DNA metabarcoding to unravel plant species composition in selected herbal medicines on the National List of Essential Medicines (NLEM) of Thailand. Sci Rep 2020; 10:18259. [PMID: 33106579 PMCID: PMC7588419 DOI: 10.1038/s41598-020-75305-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Accepted: 09/28/2020] [Indexed: 01/25/2023] Open
Abstract
Traditional medicines are widely traded across the globe and have received considerable attention in the recent past, with expectations of heightened demand in the future. However, there are increasing global concerns over admixture, which can affect the quality, safety, and efficacy of herbal medicinal products. In this study, we aimed to use DNA metabarcoding to identify 39 Thai herbal products on the Thai National List of Essential Medicines (NLEM) and assess species composition and admixture. Among the products, 24 samples were in-house-prepared formulations, and 15 samples were registered formulations. In our study, DNA metabarcoding analysis using ITS2 and rbcL barcode regions were employed to identify herbal ingredients mentioned in the products. The nuclear region, ITS2, was able to identify herbal ingredients in the products at the genus- and family-levels in 55% and 63% of cases, respectively. The chloroplast gene, rbcL, enabled genus- and family-level identifications in 58% and 73% of cases, respectively. In addition, plant species were detected in larger numbers (Family identified, absolute %) in registered herbal products than in in-house-prepared formulations. The level of fidelity increases concerns about the reliability of the products. This study highlights that DNA metabarcoding is a useful analytical tool when combined with advanced chemical techniques for the identification of plant species in highly processed, multi-ingredient herbal products.
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Mader M, Schroeder H, Schott T, Schöning-Stierand K, Leite Montalvão AP, Liesebach H, Liesebach M, Fussi B, Kersten B. Mitochondrial Genome of Fagus sylvatica L. as a Source for Taxonomic Marker Development in the Fagales. PLANTS (BASEL, SWITZERLAND) 2020; 9:E1274. [PMID: 32992588 PMCID: PMC7650814 DOI: 10.3390/plants9101274] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Revised: 09/23/2020] [Accepted: 09/24/2020] [Indexed: 11/16/2022]
Abstract
European beech, Fagus sylvatica L., is one of the most important and widespread deciduous tree species in Central Europe and is widely managed for its hard wood. The complete DNA sequence of the mitochondrial genome of Fagus sylvatica L. was assembled and annotated based on Illumina MiSeq reads and validated using long reads from nanopore MinION sequencing. The genome assembled into a single DNA sequence of 504,715 bp in length containing 58 genes with predicted function, including 35 protein-coding, 20 tRNA and three rRNA genes. Additionally, 23 putative protein-coding genes were predicted supported by RNA-Seq data. Aiming at the development of taxon-specific mitochondrial genetic markers, the tool SNPtax was developed and applied to select genic SNPs potentially specific for different taxa within the Fagales. Further validation of a small SNP set resulted in the development of four CAPS markers specific for Fagus, Fagaceae, or Fagales, respectively, when considering over 100 individuals from a total of 69 species of deciduous trees and conifers from up to 15 families included in the marker validation. The CAPS marker set is suitable to identify the genus Fagus in DNA samples from tree tissues or wood products, including wood composite products.
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Affiliation(s)
- Malte Mader
- Thünen Institute of Forest Genetics, D-22927 Grosshansdorf, Germany; (M.M.); (H.S.); (T.S.); (K.S.-S.); (A.P.L.M.); (H.L.); (M.L.)
| | - Hilke Schroeder
- Thünen Institute of Forest Genetics, D-22927 Grosshansdorf, Germany; (M.M.); (H.S.); (T.S.); (K.S.-S.); (A.P.L.M.); (H.L.); (M.L.)
| | - Thomas Schott
- Thünen Institute of Forest Genetics, D-22927 Grosshansdorf, Germany; (M.M.); (H.S.); (T.S.); (K.S.-S.); (A.P.L.M.); (H.L.); (M.L.)
| | - Katrin Schöning-Stierand
- Thünen Institute of Forest Genetics, D-22927 Grosshansdorf, Germany; (M.M.); (H.S.); (T.S.); (K.S.-S.); (A.P.L.M.); (H.L.); (M.L.)
- Center for Bioinformatics, Universität Hamburg, 20146 Hamburg, Germany
| | - Ana Paula Leite Montalvão
- Thünen Institute of Forest Genetics, D-22927 Grosshansdorf, Germany; (M.M.); (H.S.); (T.S.); (K.S.-S.); (A.P.L.M.); (H.L.); (M.L.)
| | - Heike Liesebach
- Thünen Institute of Forest Genetics, D-22927 Grosshansdorf, Germany; (M.M.); (H.S.); (T.S.); (K.S.-S.); (A.P.L.M.); (H.L.); (M.L.)
| | - Mirko Liesebach
- Thünen Institute of Forest Genetics, D-22927 Grosshansdorf, Germany; (M.M.); (H.S.); (T.S.); (K.S.-S.); (A.P.L.M.); (H.L.); (M.L.)
| | - Barbara Fussi
- Bavarian Office for Forest Genetics, 83317 Teisendorf, Germany;
| | - Birgit Kersten
- Thünen Institute of Forest Genetics, D-22927 Grosshansdorf, Germany; (M.M.); (H.S.); (T.S.); (K.S.-S.); (A.P.L.M.); (H.L.); (M.L.)
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Matthes N, Pietsch K, Rullmann A, Näumann G, Pöpping B, Szabo K. The Barcoding Table of Animal Species (BaTAnS): a new tool to select appropriate methods for animal species identification using DNA barcoding. Mol Biol Rep 2020; 47:6457-6461. [PMID: 32710387 DOI: 10.1007/s11033-020-05675-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Accepted: 07/19/2020] [Indexed: 12/15/2022]
Abstract
Food and feed products derived from animal materials have a long history of being adulterated. Methods for the identification of animal samples based on DNA barcoding are very potent tools to reveal species substitution. Since numerous DNA barcoding methods are available for different taxa, it is challenging to choose an appropriate and verified method for each sample in question. To overcome this obstacle the working group "Molecular biological methods for plant and animal species differentiation" developed the "Barcoding Table of Animal Species". This working group is established through the German food and feed law and is mandated to validate standard methods, especially for the official food and feed control laboratories in Germany. In this paper, a collection of currently available and verified DNA barcoding methods for the identification of animal species is presented as a Microsoft Excel® file-"The Barcoding Table of Animal Species (BaTAnS)". It consists of several components: The method collection, the results collection and a section for reporting new entries and problems. It is focusing on the validity and applicability of DNA barcoding methods to test food and feed products for correct species declaration. Each method is listed with its reference and is verified by at least two laboratories for their applicability. Since additional information will be available in future, this table will be updated regularly. The BaTAnS is an easy tool that helps to choose the right verified method to identify a certain specimen to taxon, genus or species level in food samples.
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Affiliation(s)
- Nele Matthes
- State Office for Agriculture, Food Safety and Fishery Mecklenburg-Vorpommern, Thierfelderstraße 18, 18059, Rostock, Germany.
| | - Klaus Pietsch
- State Institute for Chemical and Veterinary Analysis Freiburg, Bissierstr. 5, 79114, Freiburg, Germany
| | - Anke Rullmann
- State Institute for Chemical and Veterinary Analysis Karlsruhe, Weissenburgerstr. 3, 76187, Karlsruhe, Germany
| | - Gabriele Näumann
- Institute for Hygiene and Environment Hamburg, Markmannstr. 129b, 20539, Hamburg, Germany
| | - Bert Pöpping
- FOCOS - Food Consulting Strategically, Zum Kälterhaus 6b, 63755, Alzenau, Germany
| | - Kathrin Szabo
- Federal Office of Consumer Protection and Food Safety, Mauerstr. 39-42, 10117, Berlin, Germany
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Mori C, Matsumura S. Current issues for mammalian species identification in forensic science: a review. Int J Legal Med 2020; 135:3-12. [PMID: 32562039 DOI: 10.1007/s00414-020-02341-w] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Accepted: 06/09/2020] [Indexed: 12/21/2022]
Abstract
Mammalian species identification is one of the important issues in forensic science. Determining the origins of non-human biological material found at crime scenes can increase the possibility of identifying the true culprit by narrowing down the range of suspects. Although many techniques based on mitochondrial DNA (mtDNA) have been developed, challenges remain to cost-effectively identify species from degraded samples containing a mixture of DNA from multiple species and to standardize procedures for mammalian species identification. This review evaluates the reliability and versatility of mtDNA-based techniques to reveal obstacles to the establishment of standard analytical methods, with a particular focus on DNA mixtures. When samples contain a mixture of DNA from multiple species, the interpretation of sequencing analysis results is difficult. Although DNA metabarcoding using next-generation sequencing (NGS) technologies can overcome the DNA mixture problem, DNA metabarcoding is not suitable for the type of small-scale analysis routinely performed by local forensic laboratories, primarily because it is costly and time-consuming. By contrast, fluorescent multiplex PCR analysis enables cost-effective and simultaneous species identification from suboptimal samples, although the number of identifiable species is currently limited in comparison with sequencing techniques. The advantages and limitations of current techniques presented in this review indicate that multiplex PCR analysis will continue to be important for mammalian species identification in forensic casework analysis. Further developments in multiplex PCR analysis that enable the identification of an increased number of species will play a key step for standardization efforts among forensic laboratories.
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Affiliation(s)
- Chikahiro Mori
- The United Graduate School of Agricultural Science, Gifu University, 1-1 Yanagido, Gifu, 501-1193, Japan. .,Forensic Science Laboratory, Gifu Prefectural Police Headquarters, 2-1-1 Yabutaminami, Gifu, 500-8501, Japan.
| | - Shuichi Matsumura
- Faculty of Applied Biological Sciences, Gifu University, 1-1 Yanagido, Gifu, 501-1193, Japan
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Gostel MR, Zúñiga JD, Kress WJ, Funk VA, Puente-Lelievre C. Microfluidic Enrichment Barcoding (MEBarcoding): a new method for high throughput plant DNA barcoding. Sci Rep 2020; 10:8701. [PMID: 32457375 PMCID: PMC7250904 DOI: 10.1038/s41598-020-64919-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2019] [Accepted: 04/20/2020] [Indexed: 11/24/2022] Open
Abstract
DNA barcoding is a valuable tool to support species identification with broad applications from traditional taxonomy, ecology, forensics, food analysis, and environmental science. We introduce Microfluidic Enrichment Barcoding (MEBarcoding) for plant DNA Barcoding, a cost-effective method for high-throughput DNA barcoding. MEBarcoding uses the Fluidigm Access Array to simultaneously amplify targeted regions for 48 DNA samples and hundreds of PCR primer pairs (producing up to 23,040 PCR products) during a single thermal cycling protocol. As a proof of concept, we developed a microfluidic PCR workflow using the Fluidigm Access Array and Illumina MiSeq. We tested 96 samples for each of the four primary DNA barcode loci in plants: rbcL, matK, trnH-psbA, and ITS. This workflow was used to build a reference library for 78 families and 96 genera from all major plant lineages - many currently lacking in public databases. Our results show that this technique is an efficient alternative to traditional PCR and Sanger sequencing to generate large amounts of plant DNA barcodes and build more comprehensive barcode databases.
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Affiliation(s)
- Morgan R Gostel
- Botanical Research Institute of Texas, Fort Worth, Texas, 76107-3400, USA.
| | - Jose D Zúñiga
- Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases (NIAID), NIH, Bethesda, MD, 20892, USA
| | - W John Kress
- Department of Botany, National Museum of Natural History, MRC 166, Smithsonian Institution, Washington, DC, 20013-7012, USA
| | - Vicki A Funk
- Department of Botany, National Museum of Natural History, MRC 166, Smithsonian Institution, Washington, DC, 20013-7012, USA
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Deressa BT, Cihoric N, Tefesse E, Assefa M, Zemenfes D. Multidisciplinary Cancer Management of Colorectal Cancer in Tikur Anbessa Specialized Hospital, Ethiopia. J Glob Oncol 2020; 5:1-7. [PMID: 31589543 PMCID: PMC6825246 DOI: 10.1200/jgo.19.00014] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
PURPOSE Multidisciplinary cancer care is currently considered worldwide as standard for the management of patients with cancer. It improves patient diagnostic and staging accuracy and provides patients the benefit of having physicians of various specialties participating in their treatment plan. The purpose of this study was to describe the profile of patients discussed in the Tikur Anbessa Multidisciplinary Tumor Board (MTB) and the potential benefits brought by multidisciplinary care. METHODS The study involved the retrospective assessment of all patient cases presented to the Tikur Anbessa Hospital colorectal cancers MTB between March 2016 and November 2017. The data were collected from the MTB medical summary documents and were analyzed using SPSS version 20 (SPSS, Chicago, IL). RESULTS Of 147 patients with colorectal cancer, 96 (65%) were men. The median age at presentation was 46 years (range, 17-78 years). The predominant cancer was rectal (n = 101; 69%), followed by colon (n = 24; 16%). Of these, 68 (45%) and 22 (15%) had stage III and IV disease, respectively, on presentation to the MTB. The oncology department presented the majority of the patients for discussion. Most patients had undergone surgery before the MTB discussion but had no proper preoperative clinical staging information. The majority of patients with rectal cancer treated before the MTB discussion had undergone surgery upfront; however, most of the patients who were treatment naive before MTB received neoadjuvant chemoradiotherapy before surgery. CONCLUSION Decisions made by tumor boards are more likely to conform to evidence-based guidelines than are those made by individual clinicians. Therefore, early referral of patients to MTB before any treatment should be encouraged. Finally, other hospitals in Ethiopia should take a lesson from the Tikur Anbessa Hospital colorectal cancers MTB and adopt multidisciplinary cancer management.
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Affiliation(s)
- Biniyam Tefera Deressa
- Addis Ababa University, Addis Ababa, Ethiopia.,Bern University Hospital, University of Bern, Bern, Switzerland
| | - Nikola Cihoric
- Bern University Hospital, University of Bern, Bern, Switzerland
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Grazina L, Amaral JS, Mafra I. Botanical origin authentication of dietary supplements by DNA‐based approaches. Compr Rev Food Sci Food Saf 2020; 19:1080-1109. [DOI: 10.1111/1541-4337.12551] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2019] [Revised: 01/22/2020] [Accepted: 02/06/2020] [Indexed: 12/14/2022]
Affiliation(s)
- Liliana Grazina
- REQUIMTE‐LAQV, Faculdade de FarmáciaUniversidade do Porto Porto Portugal
| | - Joana S. Amaral
- Centro de Investigação de Montanha (CIMO)Instituto Politécnico de Bragança Bragança Portugal
| | - Isabel Mafra
- REQUIMTE‐LAQV, Faculdade de FarmáciaUniversidade do Porto Porto Portugal
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39
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Lo YT, Shaw PC. Application of next-generation sequencing for the identification of herbal products. Biotechnol Adv 2019; 37:107450. [DOI: 10.1016/j.biotechadv.2019.107450] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2019] [Revised: 09/10/2019] [Accepted: 09/10/2019] [Indexed: 12/17/2022]
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Leray M, Ho SL, Lin IJ, Machida RJ. MIDORI server: a webserver for taxonomic assignment of unknown metazoan mitochondrial-encoded sequences using a curated database. Bioinformatics 2019; 34:3753-3754. [PMID: 29878054 PMCID: PMC6198853 DOI: 10.1093/bioinformatics/bty454] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2018] [Accepted: 06/01/2018] [Indexed: 12/16/2022] Open
Abstract
Summary We present MIDORI server, a user-friendly web platform that uses a curated reference dataset, MIDORI, for high throughput taxonomic classification of unknown metazoan mitochondrial-encoded gene sequences. Currently three methods of taxonomic assignments: RDP Classifier, SPINGO and SINTAX, are implemented. Availability and implementation The web server is freely available at {http://reference-midori.info/server.php}.
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Affiliation(s)
- Matthieu Leray
- Smithsonian Tropical Research Institute, Smithsonian Institution, Panama City, Republic of Panama
| | - Shian-Lei Ho
- Biodiversity Research Centre, Academia Sinica, Taipei, Taiwan
| | - I-Jeng Lin
- Biodiversity Research Centre, Academia Sinica, Taipei, Taiwan
| | - Ryuji J Machida
- Biodiversity Research Centre, Academia Sinica, Taipei, Taiwan
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41
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Zhu X, Wu HY, Shaw PC, Peng W, Su W. Specific DNA identification of Pheretima in the Naoxintong capsule. Chin Med 2019; 14:41. [PMID: 31583012 PMCID: PMC6767644 DOI: 10.1186/s13020-019-0264-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2019] [Accepted: 09/23/2019] [Indexed: 12/28/2022] Open
Abstract
Background Pheretima is a minister drug in Naoxintong capsule (NXTC), a well-known traditional Chinese medicine (TCM) formula for the treatment of cardiovascular and cerebrovascular diseases. Owing to the loss of morphological and microscopic characteristics and the lack of recognized chemical marker, it is difficult to identify Pheretima in NXTC. This study aims to evaluate the feasibility of using DNA techniques to authenticate Pheretima, especially when it is processed into NXTC. Methods DNA was extracted from crude drugs of the genuine and adulterant species, as well as nine batches of NXTCs. Based on mitochondrial cytochrome c oxidase subunit I (COI) gene, specific primers were designed for two genera of genuine species, Metaphire and Amynthas, respectively. PCR amplification was performed with the designed primers on crude drugs of Pheretima and NXTCs. The purified PCR products were sequenced and the obtained sequences were identified to species level with top hit of similarity with BLAST against GenBank nucleotide database. Results Primers MF2R2 and AF3R1 could amplify specific DNA fragments with sizes around 230–250 bp, both in crude drugs and NXTC. With sequencing and the BLAST search, identities of the tested samples were found. Conclusion This study indicated that the molecular approach is effective for identifying Pheretima in NXTC. Therefore, DNA identification may contribute to the quality control and assurance of NXTC.
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Affiliation(s)
- Xiaoxiao Zhu
- 1Guangdong Engineering and Technology Research Center for Quality and Efficacy Reevaluation of Post-Market Traditional Chinese Medicine, Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275 China
| | - Hoi-Yan Wu
- 2Li Dak Sum Yip Yio Chin R & D Centre for Chinese Medicine, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong China
| | - Pang-Chui Shaw
- 2Li Dak Sum Yip Yio Chin R & D Centre for Chinese Medicine, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong China.,3Institute of Chinese Medicine, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong China.,4School of Life Sciences, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong China
| | - Wei Peng
- 1Guangdong Engineering and Technology Research Center for Quality and Efficacy Reevaluation of Post-Market Traditional Chinese Medicine, Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275 China
| | - Weiwei Su
- 1Guangdong Engineering and Technology Research Center for Quality and Efficacy Reevaluation of Post-Market Traditional Chinese Medicine, Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275 China
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42
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Dunham-Cheatham SM, Klingler K, Peacock M, Teglas MB, Gustin MS. What is in commercial cat and dog food? The case for mercury and ingredient testing. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 684:276-280. [PMID: 31153074 DOI: 10.1016/j.scitotenv.2019.05.337] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Revised: 05/19/2019] [Accepted: 05/22/2019] [Indexed: 06/09/2023]
Abstract
Commercial pet foods should be safe for long-term feeding. However, recent recalls and lawsuits have eroded public trust in pet food companies and products. Recent studies have identified high concentrations of mercury, a potent neurotoxin, in pet food products. Here we posit that pet food products require independent testing to verify safety and compliance with developed Food and Drug Administration and Association of American Feed Control Officials standards, and initiate a discussion as to why including quantification of mercury and methylmercury, as well as the identification of adulteration, are important to such testing protocols. The outcomes of these discussions will be multi-faceted: initiating the impetus to investigate the quality and label accuracy of pet foods; ensuring product safety; promoting transparency within the pet food industry; informing veterinary practices regarding pet food recommendations; providing data for evidence-based policy and regulatory enforcement; and working toward fulfilling the National Research Council's call for research that identifies levels of contaminants in animal feeds and residues in human foods.
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Affiliation(s)
- Sarrah M Dunham-Cheatham
- Department of Natural Resources and Environmental Science, University of Nevada, Reno, NV 89557, USA.
| | - Kelly Klingler
- Department of Biology, University of Nevada, Reno, NV 89557, USA
| | - Mary Peacock
- Department of Biology, University of Nevada, Reno, NV 89557, USA
| | - Michael B Teglas
- Department of Agriculture, Veterinary and Range Sciences, University of Nevada, Reno, NV 89557, USA
| | - Mae Sexauer Gustin
- Department of Natural Resources and Environmental Science, University of Nevada, Reno, NV 89557, USA.
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43
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Piper AM, Batovska J, Cogan NOI, Weiss J, Cunningham JP, Rodoni BC, Blacket MJ. Prospects and challenges of implementing DNA metabarcoding for high-throughput insect surveillance. Gigascience 2019; 8:giz092. [PMID: 31363753 PMCID: PMC6667344 DOI: 10.1093/gigascience/giz092] [Citation(s) in RCA: 82] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Revised: 06/25/2019] [Accepted: 07/09/2019] [Indexed: 12/21/2022] Open
Abstract
Trap-based surveillance strategies are widely used for monitoring of invasive insect species, aiming to detect newly arrived exotic taxa as well as track the population levels of established or endemic pests. Where these surveillance traps have low specificity and capture non-target endemic species in excess of the target pests, the need for extensive specimen sorting and identification creates a major diagnostic bottleneck. While the recent development of standardized molecular diagnostics has partly alleviated this requirement, the single specimen per reaction nature of these methods does not readily scale to the sheer number of insects trapped in surveillance programmes. Consequently, target lists are often restricted to a few high-priority pests, allowing unanticipated species to avoid detection and potentially establish populations. DNA metabarcoding has recently emerged as a method for conducting simultaneous, multi-species identification of complex mixed communities and may lend itself ideally to rapid diagnostics of bulk insect trap samples. Moreover, the high-throughput nature of recent sequencing platforms could enable the multiplexing of hundreds of diverse trap samples on a single flow cell, thereby providing the means to dramatically scale up insect surveillance in terms of both the quantity of traps that can be processed concurrently and number of pest species that can be targeted. In this review of the metabarcoding literature, we explore how DNA metabarcoding could be tailored to the detection of invasive insects in a surveillance context and highlight the unique technical and regulatory challenges that must be considered when implementing high-throughput sequencing technologies into sensitive diagnostic applications.
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Affiliation(s)
- Alexander M Piper
- Agriculture Victoria Research, AgriBio Centre, 5 Ring Road, Bundoora 3083, VIC, Australia
- School of Applied Systems Biology, La Trobe University, Bundoora 3083, VIC, Australia
| | - Jana Batovska
- Agriculture Victoria Research, AgriBio Centre, 5 Ring Road, Bundoora 3083, VIC, Australia
- School of Applied Systems Biology, La Trobe University, Bundoora 3083, VIC, Australia
| | - Noel O I Cogan
- Agriculture Victoria Research, AgriBio Centre, 5 Ring Road, Bundoora 3083, VIC, Australia
- School of Applied Systems Biology, La Trobe University, Bundoora 3083, VIC, Australia
| | - John Weiss
- Agriculture Victoria Research, AgriBio Centre, 5 Ring Road, Bundoora 3083, VIC, Australia
| | - John Paul Cunningham
- Agriculture Victoria Research, AgriBio Centre, 5 Ring Road, Bundoora 3083, VIC, Australia
| | - Brendan C Rodoni
- Agriculture Victoria Research, AgriBio Centre, 5 Ring Road, Bundoora 3083, VIC, Australia
- School of Applied Systems Biology, La Trobe University, Bundoora 3083, VIC, Australia
| | - Mark J Blacket
- Agriculture Victoria Research, AgriBio Centre, 5 Ring Road, Bundoora 3083, VIC, Australia
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Haynes E, Jimenez E, Pardo MA, Helyar SJ. The future of NGS (Next Generation Sequencing) analysis in testing food authenticity. Food Control 2019. [DOI: 10.1016/j.foodcont.2019.02.010] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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45
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Curd EE, Gold Z, Kandlikar GS, Gomer J, Ogden M, O'Connell T, Pipes L, Schweizer TM, Rabichow L, Lin M, Shi B, Barber PH, Kraft N, Wayne R, Meyer RS. Anacapa Toolkit
: An environmental DNA toolkit for processing multilocus metabarcode datasets. Methods Ecol Evol 2019. [DOI: 10.1111/2041-210x.13214] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Emily E. Curd
- Department of Ecology and Evolutionary Biology University of California Los Angeles
| | - Zack Gold
- Department of Ecology and Evolutionary Biology University of California Los Angeles
| | - Gaurav S. Kandlikar
- Department of Ecology and Evolutionary Biology University of California Los Angeles
| | - Jesse Gomer
- Department of Ecology and Evolutionary Biology University of California Los Angeles
| | - Max Ogden
- Code for Science and Society Portland Oregon
| | - Taylor O'Connell
- Department of Ecology and Evolutionary Biology University of California Los Angeles
| | - Lenore Pipes
- Department of Ecology and Evolutionary Biology University of California Berkeley
| | | | - Laura Rabichow
- Department of Ecology and Evolutionary Biology University of California Los Angeles
| | - Meixi Lin
- Department of Ecology and Evolutionary Biology University of California Los Angeles
| | - Baochen Shi
- Department of Molecular and Medical Pharmacology University of California Los Angeles
| | - Paul H. Barber
- Department of Ecology and Evolutionary Biology University of California Los Angeles
| | - Nathan Kraft
- Department of Ecology and Evolutionary Biology University of California Los Angeles
| | - Robert Wayne
- Department of Ecology and Evolutionary Biology University of California Los Angeles
| | - Rachel S. Meyer
- Department of Ecology and Evolutionary Biology University of California Los Angeles
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Boggs LM, Scheible MKR, Machado G, Meiklejohn KA. Single Fragment or Bulk Soil DNA Metabarcoding: Which is Better for Characterizing Biological Taxa Found in Surface Soils for Sample Separation? Genes (Basel) 2019; 10:E431. [PMID: 31174412 PMCID: PMC6627524 DOI: 10.3390/genes10060431] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2019] [Revised: 06/02/2019] [Accepted: 06/05/2019] [Indexed: 12/18/2022] Open
Abstract
In forensic geology casework, sample size typically limits routine characterization of material using bulk approaches. To address this, DNA-based characterization of biological taxa has received attention, as the taxa present can be useful for sample-to-sample comparisons and source attribution. In our initial work, low biodiversity was captured when DNA barcodes were Sanger-sequenced from plant and insect fragments isolated from 10 forensic-type surface soils. Considering some forensic laboratories now have access to massively parallel sequencing platforms, we assessed whether biological taxa present in the same surface soils could be better characterized using DNA metabarcoding. To achieve this, plant and animal barcodes were amplified and sequenced on an Illumina MiniSeq for three different DNA sample types (n = 50): individual fragments used in our initial study, and 250 and 100 mg of bulk soil (from the 10 sites used in the initial study). A total of 572 unique target barcode sequences passed quality filtering and were used in downstream statistical analyses: 54, 321, and 285 for individual fragments, 100 mg, and 250 mg bulk soil samples, respectively. Plant barcodes permitted some spatial separation of sample sites in non-metric multidimensional scaling plots; better separation was obtained for samples prepared from bulk soil. This study confirmed that bulk soil DNA metabarcoding is a better approach for characterizing biological taxa present in surface soils, which could supplement traditional geologic examinations.
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Affiliation(s)
- Laura M Boggs
- Department of Population Health and Pathobiology, North Carolina State University, 1060 William Moore Drive, Raleigh, NC 27607, USA.
| | - Melissa K R Scheible
- Department of Population Health and Pathobiology, North Carolina State University, 1060 William Moore Drive, Raleigh, NC 27607, USA.
| | - Gustavo Machado
- Department of Population Health and Pathobiology, North Carolina State University, 1060 William Moore Drive, Raleigh, NC 27607, USA.
| | - Kelly A Meiklejohn
- Department of Population Health and Pathobiology, North Carolina State University, 1060 William Moore Drive, Raleigh, NC 27607, USA.
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Voorhuijzen-Harink MM, Hagelaar R, van Dijk JP, Prins TW, Kok EJ, Staats M. Toward on-site food authentication using nanopore sequencing. FOOD CHEMISTRY-X 2019; 2:100035. [PMID: 31432019 PMCID: PMC6694865 DOI: 10.1016/j.fochx.2019.100035] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Revised: 04/25/2019] [Accepted: 05/23/2019] [Indexed: 11/03/2022]
Abstract
•MinION DNA metabarcoding is a promising tool for species identification in food.•MinION and Illumina MiSeq sequencing platforms perform equally accurate.•Species identification with MinION sequencing requires dedicated bioinformatics.
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Affiliation(s)
| | - Rico Hagelaar
- Princess Máxima Center for Pediatric Oncology, Netherlands
| | - Jeroen P van Dijk
- Wageningen University & Research - Wageningen Food Safety Research (WFSR), Netherlands
| | - Theo W Prins
- Wageningen University & Research - Wageningen Food Safety Research (WFSR), Netherlands
| | - Esther J Kok
- Wageningen University & Research - Wageningen Food Safety Research (WFSR), Netherlands
| | - Martijn Staats
- Wageningen University & Research - Wageningen Food Safety Research (WFSR), Netherlands
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48
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49
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McCord BR, Gauthier Q, Cho S, Roig MN, Gibson-Daw GC, Young B, Taglia F, Zapico SC, Mariot RF, Lee SB, Duncan G. Forensic DNA Analysis. Anal Chem 2019; 91:673-688. [PMID: 30485738 DOI: 10.1021/acs.analchem.8b05318] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Bruce R McCord
- Department of Chemistry , Florida International University , Miami , Florida 33199 , United States
| | - Quentin Gauthier
- Department of Chemistry , Florida International University , Miami , Florida 33199 , United States
| | - Sohee Cho
- Department of Forensic Medicine , Seoul National University , Seoul , 08826 , South Korea
| | - Meghan N Roig
- Department of Chemistry , Florida International University , Miami , Florida 33199 , United States
| | - Georgiana C Gibson-Daw
- Department of Chemistry , Florida International University , Miami , Florida 33199 , United States
| | - Brian Young
- Niche Vision, Inc. , Akron , Ohio 44311 , United States
| | - Fabiana Taglia
- Department of Chemistry , Florida International University , Miami , Florida 33199 , United States
| | - Sara C Zapico
- Department of Chemistry , Florida International University , Miami , Florida 33199 , United States
| | - Roberta Fogliatto Mariot
- Department of Chemistry , Florida International University , Miami , Florida 33199 , United States
| | - Steven B Lee
- Forensic Science Program, Justice Studies Department , San Jose State University , San Jose , California 95192 , United States
| | - George Duncan
- Department of Chemistry , Florida International University , Miami , Florida 33199 , United States
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50
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Arulandhu AJ, van Dijk J, Staats M, Hagelaar R, Voorhuijzen M, Molenaar B, van Hoof R, Li R, Yang L, Shi J, Scholtens I, Kok E. NGS-based amplicon sequencing approach; towards a new era in GMO screening and detection. Food Control 2018. [DOI: 10.1016/j.foodcont.2018.06.014] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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