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Shehata HR, Hassane B, Newmaster SG. Real-time PCR methods for identification and stability monitoring of Bifidobacterium longum subsp. longum UABl-14 during shelf life. Front Microbiol 2024; 15:1360241. [PMID: 38706967 PMCID: PMC11066167 DOI: 10.3389/fmicb.2024.1360241] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Accepted: 04/03/2024] [Indexed: 05/07/2024] Open
Abstract
Bifidobacterium longum subsp. longum UABl-14™ is an important probiotic strain that was found to support digestive health. Here we present the development and validation of real-time PCR methods for strain-specific identification and enumeration of this important strain. The identification method was evaluated for specificity using 22 target samples and 30 non-target samples. All target samples successfully amplified, while no amplification was observed from any non-target samples including other B. longum strains. The identification method was evaluated for sensitivity using three DNA dilution series and the limit of detection was 2 pg. of DNA. Coupled with a viability dye, the method was further validated for quantitative use to enumerate viable cells of UABl-14. The viability dye treatment (PMAxx) was optimized, and a final concentration of 50 μM was found as an effective concentration to inactivate DNA in dead cells from reacting in PCR. The reaction efficiency, linear dynamic range, repeatability, and reproducibility were also evaluated. The reaction efficiency was determined to be 97.2, 95.2, and 95.0% with R2 values of 99%, in three replicates. The linear dynamic range was 1.3 × 102 to 1.3 × 105 genomes. The relative standard deviation (RSD%) for repeatability ranged from 0.03 to 2.80, and for reproducibility ranged from 0.04 to 2.18. The ability of the validated enumeration method to monitor cell counts during shelf life was evaluated by determining the viable counts and total counts of strain UABl-14 in 18 multi-strain finished products. The viable counts were lower than label claims in seven products tested post-expiration and were higher than label claims in products tested pre-expiration, with a slight decrease in viable counts below label claim in three samples that were tested 2-3 months pre-expiration. Interestingly, the total counts of strain UABl-14 were consistently higher than label claims in all 18 products. Thus, the method enables strain-specific stability monitoring in finished products during shelf life, which can be difficult or impossible to achieve using the standard plate count method. The validated methods allow for simultaneous and cost-effective identification and enumeration of strain UABl-14 and represent an advancement in the quality control and quality assurance of probiotics.
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Affiliation(s)
- Hanan R. Shehata
- Purity-IQ Inc., Guelph, ON, Canada
- Department of Integrative Biology, College of Biological Science, University of Guelph, Guelph, ON, Canada
- Department of Microbiology, Faculty of Pharmacy, Mansoura University, Mansoura, Egypt
| | | | - Steven G. Newmaster
- Department of Integrative Biology, College of Biological Science, University of Guelph, Guelph, ON, Canada
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Ragupathy S, Thirugnanasambandam A, Vinayagam V, Newmaster SG. Nuclear Magnetic Resonance Fingerprints and Mini DNA Markers for the Authentication of Cinnamon Species Ingredients Used in Food and Natural Health Products. Plants (Basel) 2024; 13:841. [PMID: 38592863 PMCID: PMC10975438 DOI: 10.3390/plants13060841] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/27/2023] [Revised: 03/01/2024] [Accepted: 03/12/2024] [Indexed: 04/11/2024]
Abstract
Cinnamomum verum (syn C. zeylanicum) is considered 'true' cinnamon. However, it is reported that less expensive sources of cinnamon from C. cassia (syn C. aromaticum), C. loureiroi, and C. burmannii (toxic coumarin) may be used in the place of C. verum. We lack the quality assurance tools that are required to differentiate C. verum from other cinnamon species when verifying that the correct species is sourced from ingredient suppliers. The current research on cinnamon species authentication using DNA tools is limited to a few species and the use of high-quality DNA extracted from raw leaf materials. The cinnamon bark traded in the supply chain contains much less DNA and poorer-quality DNA than leaves. Our research advances DNA methods to authenticate cinnamon, as we utilized full-length chloroplast genomes via a genome skimming approach for C. burmannii and C. cassia to facilitate the design of optimal mini DNA markers. Furthermore, we developed and validated the use of NMR fingerprints for several commercial cinnamon species, including the quantification of 16 molecules. NMR fingerprints provided additional data that were useful for quality assessment in cinnamon extract powders and product consistency. Both the new mini DNA markers and NMR fingerprints were tested on commercial cinnamon products.
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Affiliation(s)
- Subramanyam Ragupathy
- Natural Health Products (NHP) Research Alliance, College of Biological Sciences, University of Guelph, Guelph, ON N1G 2W1, Canada; (V.V.); (S.G.N.)
| | - Arunachalam Thirugnanasambandam
- Natural Health Products (NHP) Research Alliance, College of Biological Sciences, University of Guelph, Guelph, ON N1G 2W1, Canada; (V.V.); (S.G.N.)
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Liu J, Zhang C, Jiang M, Ni Y, Xu Y, Wu W, Huang L, Newmaster SG, Kole C, Wu B, Liu C. Identification of circular RNAs of Cannabis sativa L. potentially involved in the biosynthesis of cannabinoids. Planta 2023; 257:72. [PMID: 36862222 DOI: 10.1007/s00425-023-04104-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Accepted: 02/21/2023] [Indexed: 06/18/2023]
Abstract
We identified circRNAs in the Cannabis sativa L. genome and examined their association with 28 cannabinoids in three tissues of C. sativa. Nine circRNAs are potentially involved in the biosynthesis of six cannabinoids. Cannabis sativa L. has been widely used in the production of medicine, textiles, and food for over 2500 years. The main bioactive compounds in C. sativa are cannabinoids, which have multiple important pharmacological actions. Circular RNAs (circRNAs) play essential roles in growth and development, stress resistance, and the biosynthesis of secondary metabolites. However, the circRNAs in C. sativa remain unknown. In this study, to explore the role of circRNAs in cannabinoid biosynthesis, we performed RNA-Seq and metabolomics analysis on the leaves, roots, and stems of C. sativa. We identified 741 overlapping circRNAs by three tools, of which 717, 16, and 8 circRNAs were derived from exonic, intronic, and intergenic, respectively. Functional enrichment analysis indicated that the parental genes (PGs) of circRNAs were enriched in many processes related to biological stress responses. We found that most of the circRNAs showed tissue-specific expression and 65 circRNAs were significantly correlated with their PGs (P < 0.05, |r|≥ 0.5). We also determined 28 cannabinoids by High-performance liquid chromatography-ESI-triple quadrupole-linear ion trap mass spectrometry. Ten circRNAs, including ciR0159, ciR0212, ciR0153, ciR0149, ciR0016, ciR0044, ciR0022, ciR0381, ciR0006, and ciR0025 were found to be associated with six cannabinoids by weighted gene co-expression network analysis. Twenty-nine of 53 candidate circRNAs, including 9 cannabinoids related were validated successfully using PCR amplification and Sanger sequencing. Taken together, all these results would help to enhance our acknowledge of the regulation of circRNAs, and lay the foundation for breeding new C. sativa cultivars with high cannabinoids through manipulating circRNAs.
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Affiliation(s)
- Jingting Liu
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100193, People's Republic of China
| | - Chang Zhang
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100193, People's Republic of China
| | - Mei Jiang
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100193, People's Republic of China
| | - Yang Ni
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100193, People's Republic of China
| | - Yicen Xu
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100193, People's Republic of China
| | - Wuwei Wu
- Guangxi Botanical Garden of Medicinal Plants, Nanning, 530023, People's Republic of China
| | - Linfang Huang
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100193, People's Republic of China
| | - Steven G Newmaster
- Natural Health Product Research Alliance, College of Biological Sciences, University of Guelph, Guelph, ON, N1G2W1, Canada
| | - Chittaranjan Kole
- International Climate Resilient Crop Genomics Consortium and International Phytomedomics and Nutriomics Consortium, Kolkata, 700094, India
| | - Bin Wu
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100193, People's Republic of China.
| | - Chang Liu
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100193, People's Republic of China.
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Shehata HR, Hassane B, Newmaster SG. Real-time polymerase chain reaction methods for strain specific identification and enumeration of strain Lacticaseibacillus paracasei 8700:2. Front Microbiol 2023; 13:1076631. [PMID: 36741903 PMCID: PMC9889646 DOI: 10.3389/fmicb.2022.1076631] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Accepted: 12/21/2022] [Indexed: 01/19/2023] Open
Abstract
Introduction Reliable and accurate methods for probiotic identification and enumeration, at the strain level plays a major role in confirming product efficacy since probiotic health benefits are strain-specific and dose-dependent. In this study, real-time PCR methods were developed for strain specific identification and enumeration of L. paracasei 8700:2, a probiotic strain that plays a role in fighting the common cold. Methods The assay was designed to target a unique region in L. paracasei 8700:2 genome sequence to achieve strain level specificity. The identification assay was evaluated for specificity and sensitivity. The enumeration viability real-time PCR (v-qPCR) method was first optimized for the viability treatment, then the method was evaluated for efficiency, limit of quantification, precision, and its performance was compared to plate count (PC) and viability droplet digital PCR (v-ddPCR) methods. Results The identification method proved to be strain specific and highly sensitive with a limit of detection of 0.5 pg of DNA. The optimal viability dye (PMAxx) concentration was 50 μM. The method was efficient (> 90% with R 2 values > 0.99), with a linear dynamic range between 6*102 and 6*105 copies. The method was highly precise with a relative standard deviation below 5%. The Pearson correlation coefficient (r) was 0.707 for PC and v-qPCR methods, and 0.922 for v-qPCR and v-ddPCR. Bland-Altman method comparison showed that v-qPCR always gave higher values compared to PC method (relative difference ranging from 119% to 184%) and showed no consistent trend (relative difference ranging from -20% to 22%) when comparing v-qPCR and v-ddPCR methods. Discussion The difference between PC and v-PCR methods can potentially be attributed to the proportion of cells that exist in a viable but non culturable (VBNC) state, which can be count by v-PCR but not with PC. The developed v-qPCR method was confirmed to be strain specific, sensitive, efficient, with low variance, able to count VBNC cells, and has shorter time to results compared to plate count methods. Thus, the identification and enumeration methods developed for L. paracasei 8700:2 will be of great importance to achieve high quality and efficacious probiotic products.
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Affiliation(s)
- Hanan R. Shehata
- Natural Health Product Research Alliance, Department of Integrative Biology, College of Biological Science, University of Guelph, Guelph, ON, Canada,Department of Microbiology, Faculty of Pharmacy, Mansoura University, Mansoura, Egypt,Purity-IQ Inc., Guelph, ON, Canada,*Correspondence: Hanan R. Shehata,
| | | | - Steven G. Newmaster
- Natural Health Product Research Alliance, Department of Integrative Biology, College of Biological Science, University of Guelph, Guelph, ON, Canada
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Shehata HR, Newmaster SG. The power of DNA based methods in probiotic authentication. Front Microbiol 2023; 14:1158440. [PMID: 37138639 PMCID: PMC10150049 DOI: 10.3389/fmicb.2023.1158440] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Accepted: 03/24/2023] [Indexed: 05/05/2023] Open
Abstract
Introduction The global probiotic market is growing rapidly, and strict quality control measures are required to ensure probiotic product efficacy and safety. Quality assurance of probiotic products involve confirming the presence of specific probiotic strains, determining the viable cell counts, and confirming the absence of contaminant strains. Third-party evaluation of probiotic quality and label accuracy is recommended for probiotic manufacturers. Following this recommendation, multiple batches of a top selling multi-strain probiotic product were evaluated for label accuracy. Methods A total of 55 samples (five multi-strain finished products and 50 single-strain raw ingredients) containing a total of 100 probiotic strains were evaluated using a combination of molecular methods including targeted PCR, non-targeted amplicon-based High Throughput Sequencing (HTS), and non-targeted Shotgun Metagenomic Sequencing (SMS). Results Targeted testing using species-specific or strain-specific PCR methods confirmed the identity of all strains/species. While 40 strains were identified to strain level, 60 strains were identified to species level only due to lack of strain-specific identification methods. In amplicon based HTS, two variable regions of 16S rRNA gene were targeted. Based on V5-V8 region data, ~99% of total reads per sample corresponded to target species, and no undeclared species were detected. Based on V3-V4 region data, ~95%-97% of total reads per sample corresponded to target species, while ~2%-3% of reads matched undeclared species (Proteus species), however, attempts to culture Proteus confirmed that all batches were free from viable Proteus species. Reads from SMS assembled to the genomes of all 10 target strains in all five batches of the finished product. Discussion While targeted methods enable quick and accurate identification of target taxa in probiotic products, non-targeted methods enable the identification of all species in a product including undeclared species, with the caveats of complexity, high cost, and long time to result.
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Affiliation(s)
- Hanan R. Shehata
- Natural Health Product Research Alliance, Department of Integrative Biology, College of Biological Science, University of Guelph, Guelph, ON, Canada
- Department of Microbiology, Faculty of Pharmacy, Mansoura University, Mansoura, Egypt
- *Correspondence: Hanan R. Shehata,
| | - Steven G. Newmaster
- Natural Health Product Research Alliance, Department of Integrative Biology, College of Biological Science, University of Guelph, Guelph, ON, Canada
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Shehata HR, Kiefer A, Morovic W, Newmaster SG. Locked Nucleic Acid Hydrolysis Probes for the Specific Identification of Probiotic Strains Bifidobacterium animalis subsp. lactis DSM 15954 and Bi-07™. Front Microbiol 2022; 12:801795. [PMID: 35003031 PMCID: PMC8733699 DOI: 10.3389/fmicb.2021.801795] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Accepted: 11/25/2021] [Indexed: 11/13/2022] Open
Abstract
Probiotic health benefits are now well-recognized to be strain specific. Probiotic strain characterization and identification is thus important in clinical research and in the probiotic industry. This is becoming especially important with reports of probiotic products failing to meet the declared strain content, potentially compromising their efficacy. Availability of reliable identification methods is essential for strain authentication during discovery, evaluation and commercialization of a probiotic strain. This study aims to develop identification methods for strains Bifidobacterium animalis subsp. lactis DSM 15954 and Bi-07 (Bi-07™) based on real-time PCR, targeting single nucleotide polymorphisms (SNPs). The SNPs were targeted by PCR assays with locked nucleic acid (LNA) probes, which is a novel application in probiotic identification. The assays were then validated following the guidelines for validating qualitative real-time PCR assays. Each assay was evaluated for specificity against 22 non-target strains including closely related Bifidobacterium animalis subsp. lactis strains and were found to achieve 100% true positive and 0% false positive rates. To determine reaction sensitivity and efficiency, three standard curves were established for each strain. Reaction efficiency values were 86, 91, and 90% (R square values > 0.99), and 87, 84, and 86% (R square values > 0.98) for B. animalis subsp. lactis DSM 15954 and Bi-07 assays, respectively. The limit of detection (LOD) was 5.0 picograms and 0.5 picograms of DNA for DSM 15954 and Bi-07 assays, respectively. Each assay was evaluated for accuracy using five samples tested at three different DNA concentrations and both assays proved to be highly repeatable and reproducible. Standard deviation of Cq values between two replicates was always below 1.38 and below 1.68 for DSM 15954 and Bi-07 assays, respectively. The assays proved to be applicable to mono-strain and multi-strain samples as well as for samples in various matrices of foods or dietary supplement ingredients. Overall, the methods demonstrated high specificity, sensitivity, efficiency and precision and broad applicability to sample, matrix and machine types. These methods facilitate strain level identification of the highly monophyletic strains B. animalis subsp. lactis DSM 15954 and Bi-07 to ensure probiotic efficacy and provide a strategy to identify other closely related probiotics organisms.
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Affiliation(s)
- Hanan R Shehata
- Natural Health Product Research Alliance, College of Biological Science, University of Guelph, Guelph, ON, Canada.,Department of Microbiology, Faculty of Pharmacy, Mansoura University, Mansoura, Egypt
| | - Anthony Kiefer
- IFF Health & Biosciences, International Flavors and Fragrances, Inc., Madison, WI, United States
| | - Wesley Morovic
- IFF Health & Biosciences, International Flavors and Fragrances, Inc., Madison, WI, United States
| | - Steven G Newmaster
- Natural Health Product Research Alliance, College of Biological Science, University of Guelph, Guelph, ON, Canada
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Shehata HR, Newmaster SG. Enumeration of Probiotic Strain Lacticaseibacillus rhamnosus GG (ATCC 53103) Using Viability Real-time PCR. Probiotics Antimicrob Proteins 2021; 13:1611-1620. [PMID: 34591288 DOI: 10.1007/s12602-021-09849-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/21/2021] [Indexed: 12/18/2022]
Abstract
Probiotic health benefits are strain specific and are dose dependent. Hence, administering the correct strains, at the recommended doses is essential to achieve probiotic health benefits. Reliable methods are needed to facilitate probiotic strain identification and enumeration. Plate count methods are the most commonly used methods for probiotic enumeration. However, these methods are time-consuming, laborious, highly variable, and non-specific. Here, we developed a real-time PCR method for enumeration of a commonly used strain, Lacticaseibacillus rhamnosus GG. The method utilizes PMAxx as a viability dye to enumerate viable cells only. Optimization of viability treatment showed that PMAxx at a final concentration of 50 μM was effective in inactivating DNA from dead cells, and that bead beating for 5 min at 3000 rpm was effective in liberating DNA. The assay demonstrated high efficiency between 93 and 102%, with R2 values > 0.99. The assay showed high precision with relative standard deviation (RSD%) below 2.3%. Assay performance was compared to a plate count method in which there was a strong correlation between both methods (Pearson r = 0.8443). This method offers a 10 × shorter time for results and a higher precision compared to plate count methods. Furthermore, this method enables specific enumeration of L. rhamnosus GG in multi-strain products, which is not possible to achieve using plate count methods. This novel method facilitates faster and more accurate enumeration of L. rhamnosus GG as a raw ingredient as well as in finished products which enables better quality assurance and efficacy of probiotics for consumers.
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Affiliation(s)
- Hanan R Shehata
- College of Biological Science, NHP Research Alliance, University of Guelph, Guelph, ON, N1G 2W1, Canada.
- Department of Microbiology, Faculty of Pharmacy, Mansoura University, Mansoura, Egypt.
| | - Steven G Newmaster
- College of Biological Science, NHP Research Alliance, University of Guelph, Guelph, ON, N1G 2W1, Canada
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Singh M, Sadat A, Abdi R, Colaruotolo LA, Francavilla A, Petker K, Nasr P, Moraveji M, Cruz G, Huang Y, Arora A, Chao A, Walker S, Wang X, Rathnayake S, Ragupathy S, Newmaster SG, Hanner RH, Goodridge LD, Corradini MG. Detection of SAR-CoV-2 on surfaces in food retailers in Ontario. Curr Res Food Sci 2021; 4:598-602. [PMID: 34485928 PMCID: PMC8406517 DOI: 10.1016/j.crfs.2021.08.009] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Revised: 08/09/2021] [Accepted: 08/23/2021] [Indexed: 12/23/2022] Open
Abstract
The COVID-19 pandemic has generated increased interest in potential transmission routes. In food retail settings, transmission from infected customers and workers and customers through surfaces has been deemed plausible. However, limited information exists on the presence and survival of SARS-CoV-2 on surfaces, particularly outside laboratory settings. Therefore, the purpose of this project was to assess the presence of the virus at commonly found surfaces at food retail stores and the potential role that these spaces play in virus transmission. Samples (n=957) were collected twice a week for a month in food-retail stores within Ontario, Canada. High-touch surfaces were identified and surveyed in 4 zones within the store (payment stations, deli counters, refrigerated food section and carts and baskets). The samples were analyzed using a molecular method, i.e., reverse transcriptase quantitative Polymerase Chain Reaction (RT-qPCR). Regardless of the store's location, the sampling day or time, the location of the surface within the store or the surface material, all samples tested negative for SARS-CoV-2. These results suggest that the risk of exposure from contaminated high-touch surfaces within a food retailer store is low if preventive measures and recommended sanitizing routines are maintained.
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Affiliation(s)
- Maleeka Singh
- Food Science Department, University of Guelph, Guelph, ON, Canada
| | - Azin Sadat
- Food Science Department, University of Guelph, Guelph, ON, Canada
| | - Reihaneh Abdi
- Food Science Department, University of Guelph, Guelph, ON, Canada
| | | | | | - Katherine Petker
- Food Science Department, University of Guelph, Guelph, ON, Canada
| | - Pedram Nasr
- Food Science Department, University of Guelph, Guelph, ON, Canada
| | - Maryam Moraveji
- Food Science Department, University of Guelph, Guelph, ON, Canada
| | - Gyllian Cruz
- Food Science Department, University of Guelph, Guelph, ON, Canada
| | - Yinan Huang
- Food Science Department, University of Guelph, Guelph, ON, Canada
| | - Aditi Arora
- Food Science Department, University of Guelph, Guelph, ON, Canada
| | - Aleana Chao
- Food Science Department, University of Guelph, Guelph, ON, Canada
| | - Sarah Walker
- Food Science Department, University of Guelph, Guelph, ON, Canada
| | - Xinya Wang
- Food Science Department, University of Guelph, Guelph, ON, Canada
| | - Sujani Rathnayake
- Integrative Biology Department, University of Guelph, Guelph, ON, Canada
| | | | | | - Robert H. Hanner
- Integrative Biology Department, University of Guelph, Guelph, ON, Canada
| | | | - Maria G. Corradini
- Food Science Department, University of Guelph, Guelph, ON, Canada
- Arrell Food Institute, University of Guelph, Guelph, ON, Canada
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Urumarudappa SKJ, Gogna N, Newmaster SG, Venkatarangaiah K, Subramanyam R, Saroja SG, Gudasalamani R, Dorai K, Ramanan US. Correction to: DNA barcoding and NMR spectroscopy-based assessment of species adulteration in the raw herbal trade of Saraca asoca (Roxb.) Willd, an important medicinal plant. Int J Legal Med 2021; 135:2681. [PMID: 34370086 DOI: 10.1007/s00414-021-02669-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Affiliation(s)
- Santhosh Kumar Jayanthinagar Urumarudappa
- School of Ecology and Conservation, University of Agricultural Sciences, GKVK, Bangalore, 560065, India
- Department of Crop Physiology, University of Agricultural Sciences, GKVK, Bangalore, 560065, India
- Department of Post Graduate Studies and Research in Biotechnology, Jnanasahyadri, Kuvempu University, Shankaraghatta, Shimoga, 577451, India
| | - Navdeep Gogna
- Indian Institute of Science Education and Research (IISER) Mohali, Knowledge City Sector 81, PO Manauli, Mohali, Punjab, 140306, India
| | - Steven G Newmaster
- College of Biological Sciences, Department of Integrative Biology, University of Guelph, Toronto, N1G 2W1, Canada
| | - Krishna Venkatarangaiah
- Department of Post Graduate Studies and Research in Biotechnology, Jnanasahyadri, Kuvempu University, Shankaraghatta, Shimoga, 577451, India
| | - Ragupathy Subramanyam
- College of Biological Sciences, Department of Integrative Biology, University of Guelph, Toronto, N1G 2W1, Canada
| | | | - Ravikanth Gudasalamani
- Ashoka Trust for Research in Ecology and the Environment, Royal Enclave, Srirampura, Jakkur Post, Bangalore, 560064, India
| | - Kavita Dorai
- Indian Institute of Science Education and Research (IISER) Mohali, Knowledge City Sector 81, PO Manauli, Mohali, Punjab, 140306, India
| | - Uma Shaanker Ramanan
- School of Ecology and Conservation, University of Agricultural Sciences, GKVK, Bangalore, 560065, India.
- Department of Crop Physiology, University of Agricultural Sciences, GKVK, Bangalore, 560065, India.
- Ashoka Trust for Research in Ecology and the Environment, Royal Enclave, Srirampura, Jakkur Post, Bangalore, 560064, India.
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Shanmughanandhan J, Shanmughanandhan D, Ragupathy S, Henry TA, Newmaster SG. Validation and Optimization of qPCR Method for Identification of Actaea racemosa (Black Cohosh) NHPs. J AOAC Int 2021; 104:836-846. [PMID: 33346838 DOI: 10.1093/jaoacint/qsaa167] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Revised: 09/29/2020] [Accepted: 11/26/2020] [Indexed: 12/28/2022]
Abstract
BACKGROUND Actaea racemosa (black cohosh) herbal dietary supplements are commonly used to treat menopausal symptoms in women. However, there is a considerable risk of contamination of A. racemosa herbal products in the natural health product (NHP) industry, impacting potential efficacy. Authentication of A. racemosa products is challenging because of the standard, multi-part analytical chemistry methods that may be too costly and not appropriate for both raw and finished products. OBJECTIVE In this paper, we discuss developing and validating quick alternative biotechnology methods to authenticate A. racemosa herbal dietary supplements, based on the use of a species-specific hydrolysis PCR probe assay. METHODS A qPCR-based species-specific hydrolysis probe assay was designed, validated, and optimized for precisely identifying the species of interest using the following analytical validation criteria: (1) specificity (accuracy) in determining the target species ingredient, while not identifying other non-target species; (2) sensitivity in detecting the smallest amount of the target material; and (3) reliability (repeatability and reproducibility) in detecting the target species in raw materials on a real-time PCR platform. RESULTS The results show that the species-specific hydrolysis probe assay was successfully developed for the raw materials and powders of A. racemosa. The specificity of the test was 100% to the target species. The efficiency of the assay was observed to be 99%, and the reliability of the assay was 100% for the raw/starting and powder materials. CONCLUSION The method developed in this study can be used to authenticate and perform qualitative analysis of A. racemosa supplements.
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Affiliation(s)
- Jeevitha Shanmughanandhan
- NHP Research Alliance, College of Biological Sciences, University of Guelph, Guelph, Ontario N1G 2W1, Canada
| | - Dhivya Shanmughanandhan
- NHP Research Alliance, College of Biological Sciences, University of Guelph, Guelph, Ontario N1G 2W1, Canada
| | - Subramanyam Ragupathy
- NHP Research Alliance, College of Biological Sciences, University of Guelph, Guelph, Ontario N1G 2W1, Canada
| | - Thomas A Henry
- NHP Research Alliance, College of Biological Sciences, University of Guelph, Guelph, Ontario N1G 2W1, Canada
| | - Steven G Newmaster
- NHP Research Alliance, College of Biological Sciences, University of Guelph, Guelph, Ontario N1G 2W1, Canada
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11
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Faller AC, Shanmughanandhan D, Ragupathy S, Zhang Y, Lu Z, Chang P, Swanson G, Newmaster SG. Validation of a Triplex Quantitative Polymerase Chain Reaction Assay for Detection and Quantification of Traditional Protein Sources, Pisum sativum L. and Glycine max (L.) Merr., in Protein Powder Mixtures. Front Plant Sci 2021; 12:661770. [PMID: 34108980 PMCID: PMC8183462 DOI: 10.3389/fpls.2021.661770] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Accepted: 04/23/2021] [Indexed: 06/12/2023]
Abstract
Several botanicals have been traditionally used as protein sources, including the leguminous Pisum sativum L. and Glycine max (L.) Merr. While a rich history exists of cultivating these plants for their whole, protein-rich grain, modern use as powdered supplements present a new challenge in material authentication. The absence of clear morphological identifiers of an intact plant and the existence of long, complex supply chains behoove industry to create quick, reliable analytical tools to identify the botanical source of a protein product (many of which contain multiple sources). The utility of molecular tools for plant-based protein powder authentication is gaining traction, but few validated tools exist. Multiplex quantitative polymerase chain reaction (qPCR) can provide an economical means by which sources can be identified and relative proportions quantified. We followed established guidelines for the design, optimization, and validation of qPCR assay, and developed a triplex qPCR assay that can amplify and quantify pea and soy DNA targets, normalized by a calibrator. The assay was evaluated for analytical specificity, analytical sensitivity, efficiency, precision, dynamic range, repeatability, and reproducibility. We tested the quantitative ability of the assay using pea and soy DNA mixtures, finding exceptional quantitative linearity for both targets - 0.9983 (p < 0.0001) for soy and 0.9915 (p < 0.0001) for pea. Ratios based on mass of protein powder were also tested, resulting in non-linear patterns in data that suggested the requirement of further sample preparation optimization or algorithmic correction. Variation in fragment size within different lots of commercial protein powder samples was also analyzed, revealing low SD among lots. Ultimately, this study demonstrated the utility of qPCR in the context of protein powder mixtures and highlighted key considerations to take into account for commercial implementation.
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Affiliation(s)
- Adam C. Faller
- Natural Health Product Research Alliance, College of Biological Sciences, University of Guelph, Guelph, ON, Canada
| | - Dhivya Shanmughanandhan
- Natural Health Product Research Alliance, College of Biological Sciences, University of Guelph, Guelph, ON, Canada
| | - Subramanyam Ragupathy
- Natural Health Product Research Alliance, College of Biological Sciences, University of Guelph, Guelph, ON, Canada
| | - Yanjun Zhang
- Herbalife International, Torrance, CA, United States
| | - Zhengfei Lu
- Herbalife International, Torrance, CA, United States
| | - Peter Chang
- Herbalife International, Torrance, CA, United States
| | - Gary Swanson
- Herbalife International, Torrance, CA, United States
| | - Steven G. Newmaster
- Natural Health Product Research Alliance, College of Biological Sciences, University of Guelph, Guelph, ON, Canada
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12
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Shanmughanandhan J, Shanmughanandhan D, Ragupathy S, Henry TA, Newmaster SG. Quantification of Actaea racemosa L. (black cohosh) from some of its potential adulterants using qPCR and dPCR methods. Sci Rep 2021; 11:4331. [PMID: 33619286 PMCID: PMC7900226 DOI: 10.1038/s41598-020-80465-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Accepted: 12/21/2020] [Indexed: 12/04/2022] Open
Abstract
The demand for popular natural health products (NHPs) such as Black Cohosh is increasing considerably, which in turn challenges quality assurance (QA) throughout the supply chain. To detect and quantify the target species present in a given NHP, DNA-based molecular techniques such as Real-time quantitative PCR (qPCR) and digital PCR (dPCR) are standard tools in the food and pathogen testing industries. There is a gap in the literature concerning validated quantitative PCR methods for botanicals that can be utilized for QA and good manufacturing practices. The objective of this study is to develop an efficient quantification method using qPCR and dPCR techniques for the detection and quantification of Actaea racemosa (Black cohosh) NHPs from its potential adulterants. These developed methods are validated for applicability on commercial NHPs. Species-specific hydrolysis probe assays were designed to analyze the black cohosh NHPs using qPCR and dPCR techniques. The results confirmed that the developed qPCR and dPCR methods are highly precise for identifying and quantifying black cohosh NHPs, indicating their potential applicability in future routine industrial and laboratory testing. This enables a single qPCR test to determine not only the presence of a specific botanical, but also the amount when mixed with an adulterant.
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Affiliation(s)
- Jeevitha Shanmughanandhan
- NHP Research Alliance, College of Biological Sciences, University of Guelph, 50 Stone Road East, Guelph, ON, N1G 2W1, Canada
| | - Dhivya Shanmughanandhan
- NHP Research Alliance, College of Biological Sciences, University of Guelph, 50 Stone Road East, Guelph, ON, N1G 2W1, Canada.
| | - Subramanyam Ragupathy
- NHP Research Alliance, College of Biological Sciences, University of Guelph, 50 Stone Road East, Guelph, ON, N1G 2W1, Canada
| | - Thomas A Henry
- NHP Research Alliance, College of Biological Sciences, University of Guelph, 50 Stone Road East, Guelph, ON, N1G 2W1, Canada
| | - Steven G Newmaster
- NHP Research Alliance, College of Biological Sciences, University of Guelph, 50 Stone Road East, Guelph, ON, N1G 2W1, Canada
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13
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Shehata HR, Newmaster SG. A Validated Real-Time PCR Method for the Specific Identification of Probiotic Strain Lactobacillus rhamnosus GG (ATCC 53103). J AOAC Int 2020; 103:1604-1609. [PMID: 33247747 DOI: 10.1093/jaoacint/qsaa063] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Revised: 04/08/2020] [Accepted: 04/28/2020] [Indexed: 12/28/2022]
Abstract
BACKGROUND Strain Lactobacillus rhamnosus GG is one of the best-studied and most widely used probiotic strains, with various health benefits. Because probiotic health benefits and safety are strain specific, the availability of a reliable assay for specific identification of Lactobacillus rhamnosus GG is vital to ensure probiotic efficacy. OBJECTIVE To design and validate a probe-based real-time PCR assay for specific identification of strain Lactobacillus rhamnosus GG. METHOD Rapid Annotation using Subsystem Technology (RAST) was used to find a unique sequence region in the genome of Lactobacillus rhamnosus GG. A probe-based assay was designed and evaluated for specificity, sensitivity, efficiency, repeatability, and reproducibility. RESULTS RAST identified a unique gene coding for a hypothetical protein in the genome of Lactobacillus rhamnosus GG. The assay successfully amplified all 22 target samples and did not amplify any of the 28 non-target strains, achieving 100% true positive and 0% false positive results. The Limit of Detection (LOD) was determined to be 0.001 ng. Reaction efficiency values, from three dilution series, were 96.4%, 93.3%, and 96.8% with R square values of 0.9974, 0.9981, and 0.9998, respectively. Relative standard deviation (RSD, %) of repeatability was below 1% and RSD of reproducibility was below 4%. CONCLUSIONS This Lactobacillus rhamnosus GG specific assay proved to be specific, sensitive, efficient, and reproducible. Since the assay was evaluated on two real-time PCR platforms, including a portable one, the assay can be used for onsite testing throughout the supply chain. HIGHLIGHTS The availability of validated and reliable assays for strain-specific identification plays a vital role in achieving compliance in probiotic products.
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Affiliation(s)
- Hanan R Shehata
- NHP Research Alliance, College of Biological Sciences, University of Guelph, Guelph, Ontario N1G 2W1, Canada.,Department of Microbiology, Faculty of Pharmacy, Mansoura University, Mansoura, Egypt
| | - Steven G Newmaster
- NHP Research Alliance, College of Biological Sciences, University of Guelph, Guelph, Ontario N1G 2W1, Canada
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14
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Shehata HR, Ragupathy S, Allen S, Leyer G, Newmaster SG. Real-Time PCR Assays for the Specific Identification of Probiotic Strains Lactobacillus gasseri BNR17 and Lactobacillus reuteri LRC (NCIMB 30242). Probiotics Antimicrob Proteins 2020; 13:837-846. [PMID: 32780278 DOI: 10.1007/s12602-020-09695-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
The broad spectrum of health benefits attributed to probiotics has contributed to a rapid increase in the value of the probiotic market. Probiotic health benefits can be strain specific. Thus, strain-level identification of probiotic strains is of paramount importance to ensure probiotic efficacy. Both Lactobacillus gasseri BNR17 and Lactobacillus reuteri LRC (NCIMB 30242) strains have clinically proven health benefits; however, no assays were developed to enable strain-level identification of either of these strains. The objective of this study is to develop strain-specific PCR-based methods for Lactobacillus gasseri BNR17 and Lactobacillus reuteri LRC strains, and to validate these assays according to the guidelines for validating qualitative real-time PCR assays. Using RAST (Rapid Annotation using Subsystem Technology), unique sequence regions were identified in the genome sequences of both strains. Probe-based assays were designed and validated for specificity, sensitivity, efficiency, repeatability, and reproducibility. Both assays were specific to target strain with 100% true positive and 0% false positive rates. Reaction efficiency for both assays was in the range of 90 to 108% with R square values > 0.99. Repeatability and reproducibility were evaluated using five samples at three DNA concentrations each and relative standard deviation was < 4% for repeatability and < 8% for reproducibility. Both of the assays developed and validated in this study for the specific identification of Lactobacillus gasseri BNR17 and Lactobacillus reuteri LRC strains are specific, sensitive, and precise. These assays can be applied to evaluate and ensure compliance in probiotic products.
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Affiliation(s)
- Hanan R Shehata
- NHP Research Alliance, College of Biological Sciences, University of Guelph, Guelph, Ontario, N1G 2W1, Canada.
- Department of Microbiology, Faculty of Pharmacy, Mansoura University, Mansoura, Egypt.
| | - Subramanyam Ragupathy
- NHP Research Alliance, College of Biological Sciences, University of Guelph, Guelph, Ontario, N1G 2W1, Canada
| | - Shara Allen
- UAS Laboratories, 555 N. 72nd Ave, Wausau, WI, 54401, USA
| | - Gregory Leyer
- UAS Laboratories, 555 N. 72nd Ave, Wausau, WI, 54401, USA
| | - Steven G Newmaster
- NHP Research Alliance, College of Biological Sciences, University of Guelph, Guelph, Ontario, N1G 2W1, Canada
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15
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Shehata HR, Newmaster SG. Combined Targeted and Non-targeted PCR Based Methods Reveal High Levels of Compliance in Probiotic Products Sold as Dietary Supplements in United States and Canada. Front Microbiol 2020; 11:1095. [PMID: 32582075 PMCID: PMC7295986 DOI: 10.3389/fmicb.2020.01095] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Accepted: 05/01/2020] [Indexed: 12/28/2022] Open
Abstract
Probiotics are defined as "live microorganisms that, when administered in adequate amounts, confer a health benefit on the host." The diverse health benefits have contributed to rapid increase in probiotic consumption and in the value of probiotic market, valued at USD 46 billion in 2019. For probiotics to be effective, the correct species/strains should be delivered viable in an adequate dose. The most commonly used methods for species/strain identification are DNA based methods including targeted and non-targeted methods (e.g., high-throughput sequencing, HTS). Using different DNA based methods, previous studies reported several cases of non-compliance in probiotic products. The objectives of this study are to evaluate levels of compliance in probiotic products (presence of all declared species/strains, absence of any contaminants or undeclared species, and meeting the declared minimum viable cell count) and to compare the performance of targeted and non-targeted methods in probiotic authentication. To the best of our knowledge, this is the largest study of its kind, testing 182 probiotic products, containing a total of 520 strains, collected from United States and Canada. Using species-specific assays, 11 species could not be detected in ten products. Missing species were Lactobacillus casei in seven products, Bifidobacterium longum and Bifidobacterium bifidum in one product, B. longum in one product while B. longum subsp. longum was mislabeled as B. longum subsp. infantis in another. Additionally, undeclared Bifidobacterium animalis subsp. lactis was detected in one product. Viable count was determined for 72 samples and was found to be lower than declared in five samples, including one product showing no viable cells. Overall, non-compliance was observed in 15 out of 182 products (8%). Additionally, undeclared species at relative abundance of ∼1-2% were found in 14 products using HTS, however, their presence could not be confirmed using species-specific assays. The results show that targeted PCR based methods enable species and strain level identification. The results also highlight the need to continue to develop strain-specific assays appropriate for use with multi-strain products. True strain-specific assays will enable strain authentication in both single-strain products and multi-strain products to ensure probiotic products meet the label claims and ensure probiotic efficacy.
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Affiliation(s)
- Hanan R Shehata
- NHP Research Alliance, College of Biological Sciences, University of Guelph, Guelph, ON, Canada.,Department of Microbiology, Faculty of Pharmacy, Mansoura University, Mansoura, Egypt
| | - Steven G Newmaster
- NHP Research Alliance, College of Biological Sciences, University of Guelph, Guelph, ON, Canada
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16
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Park HS, Jayakodi M, Lee SH, Jeon JH, Lee HO, Park JY, Moon BC, Kim CK, Wing RA, Newmaster SG, Kim JY, Yang TJ. Mitochondrial plastid DNA can cause DNA barcoding paradox in plants. Sci Rep 2020; 10:6112. [PMID: 32273595 PMCID: PMC7145815 DOI: 10.1038/s41598-020-63233-y] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2019] [Accepted: 03/24/2020] [Indexed: 01/18/2023] Open
Abstract
The transfer of ancestral plastid genomes into mitochondrial genomes to generate mitochondrial plastid DNA (MTPT) is known to occur in plants, but its impacts on mitochondrial genome complexity and the potential for causing a false-positive DNA barcoding paradox have been underestimated. Here, we assembled the organelle genomes of Cynanchum wilfordii and C. auriculatum, which are indigenous medicinal herbs in Korea and China, respectively. In both species, it is estimated that 35% of the ancestral plastid genomes were transferred to mitochondrial genomes over the past 10 million years and remain conserved in these genomes. Some plastid barcoding markers co-amplified the conserved MTPTs and caused a barcoding paradox, resulting in mis-authentication of botanical ingredients and/or taxonomic mis-positioning. We identified dynamic and lineage-specific MTPTs that have contributed to mitochondrial genome complexity and might cause a putative barcoding paradox across 81 plant species. We suggest that a DNA barcoding guidelines should be developed involving the use of multiple markers to help regulate economically motivated adulteration.
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Affiliation(s)
- Hyun-Seung Park
- Department of Plant Science, Plant Genomics and Breeding Institute, and Research Institute of Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul, 08826, Republic of Korea
| | - Murukarthick Jayakodi
- Department of Plant Science, Plant Genomics and Breeding Institute, and Research Institute of Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul, 08826, Republic of Korea
| | - Sae Hyun Lee
- Department of Plant Science, Plant Genomics and Breeding Institute, and Research Institute of Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul, 08826, Republic of Korea
| | - Jae-Hyeon Jeon
- Department of Plant Science, Plant Genomics and Breeding Institute, and Research Institute of Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul, 08826, Republic of Korea
| | - Hyun-Oh Lee
- Phyzen Genomics Institute, Seongnam, 13558, Korea
| | - Jee Young Park
- Department of Plant Science, Plant Genomics and Breeding Institute, and Research Institute of Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul, 08826, Republic of Korea
| | - Byeong Cheol Moon
- Herbal Medicine Research Division, Korea Institute of Oriental Medicine, 1672 Yuseong-daero, Yuseong-gu, Daejeon, 34054, Republic of Korea
| | - Chang-Kug Kim
- Genomics Division, National Institute of Agricultural Sciences, Jeonju, 54874, Republic of Korea
| | - Rod A Wing
- Arizona Genomics Institute, School of Plant Sciences, The University of Arizona, Tucson, AZ, USA
| | - Steven G Newmaster
- NHP Research Alliance, College of Biological Sciences, University of Guelph, Guelph, Ontario, Canada
| | - Ji Yeon Kim
- Department of Food Science and Technology, Seoul National University of Science and Technology, Seoul, 01811, Korea
| | - Tae-Jin Yang
- Department of Plant Science, Plant Genomics and Breeding Institute, and Research Institute of Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul, 08826, Republic of Korea.
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17
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Bainard JD, Newmaster SG, Budke JM. Genome size and endopolyploidy evolution across the moss phylogeny. Ann Bot 2020; 125:543-555. [PMID: 31777923 PMCID: PMC7102977 DOI: 10.1093/aob/mcz194] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2019] [Accepted: 11/27/2019] [Indexed: 05/18/2023]
Abstract
BACKGROUND AND AIMS Compared with other plant lineages, bryophytes have very small genomes with little variation across species, and high levels of endopolyploid nuclei. This study is the first analysis of moss genome evolution over a broad taxonomic sampling using phylogenetic comparative methods. We aim to determine whether genome size evolution is unidirectional as well as examine whether genome size and endopolyploidy are correlated in mosses. METHODS Genome size and endoreduplication index (EI) estimates were newly generated using flow cytometry from moss samples collected in Canada. Phylogenetic relationships between moss species were reconstructed using GenBank sequence data and maximum likelihood methods. Additional 1C-values were compiled from the literature and genome size and EI were mapped onto the phylogeny to reconstruct ancestral character states, test for phylogenetic signal and perform phylogenetic independent contrasts. KEY RESULTS Genome size and EI were obtained for over 50 moss taxa. New genome size estimates are reported for 33 moss species and new EIs are reported for 20 species. In combination with data from the literature, genome sizes were mapped onto a phylogeny for 173 moss species with this analysis, indicating that genome size evolution in mosses does not appear to be unidirectional. Significant phylogenetic signal was detected for genome size when evaluated across the phylogeny, whereas phylogenetic signal was not detected for EI. Genome size and EI were not found to be significantly correlated when using phylogenetically corrected values. CONCLUSIONS Significant phylogenetic signal indicates closely related mosses have more similar genome sizes and EI values. This study supports that DNA content in mosses is defined by small genomes that are highly endopolyploid, suggesting strong selective pressure to maintain these features. Further research is needed to understand the functional significance of DNA content evolution in mosses.
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Affiliation(s)
- Jillian D Bainard
- Swift Current Research and Development Centre, Agriculture and Agri-food Canada, Swift Current, SK, Canada
- Department of Integrative Biology, University of Guelph, 50 Stone Road East, Guelph, ON, Canada
| | - Steven G Newmaster
- Department of Integrative Biology, University of Guelph, 50 Stone Road East, Guelph, ON, Canada
| | - Jessica M Budke
- Department of Ecology and Evolutionary Biology, University of Tennessee, Knoxville, TN, USA
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18
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Fryxell JM, Avgar T, Liu B, Baker JA, Rodgers AR, Shuter J, Thompson ID, Reid DEB, Kittle AM, Mosser A, Newmaster SG, Nudds TD, Street GM, Brown GS, Patterson B. Anthropogenic Disturbance and Population Viability of Woodland Caribou in Ontario. J Wildl Manage 2020. [DOI: 10.1002/jwmg.21829] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- John M. Fryxell
- Department of Integrative BiologyUniversity of Guelph 50 Stone Road E., Guelph Ontario N1G 2W1 Canada
| | - Tal Avgar
- Department of Integrative BiologyUniversity of Guelph 50 Stone Road E., Guelph Ontario N1G 2W1 Canada
| | - Boyan Liu
- Department of Integrative BiologyUniversity of Guelph 50 Stone Road E., Guelph Ontario N1G 2W1 Canada
| | - James A. Baker
- Ontario Ministry of Natural Resources and ForestryWildlife Research and Monitoring Section 300 Water Street, Peterborough Ontario K9J 8M5 Canada
| | - Arthur R. Rodgers
- Ontario Ministry of Natural Resources and ForestryCentre for Northern Forest Ecosystem Research 435 James Street Thunder‐Bay Ontario P7E 2VE Canada
| | - Jennifer Shuter
- Ontario Ministry of Natural Resources and ForestryCentre for Northern Forest Ecosystem Research 435 James Street Thunder‐Bay Ontario P7E 2VE Canada
| | - Ian D. Thompson
- Canadian Forest Service 1219 Queen Street East, Sault Ste. Marie Ontario P6A 2E5 Canada
| | - Douglas E. B. Reid
- Ontario Ministry of Natural Resources and ForestryCentre for Northern Forest Ecosystem Research 435 James Street Thunder‐Bay Ontario P7E 2VE Canada
| | - Andrew M. Kittle
- Department of Integrative BiologyUniversity of Guelph 50 Stone Road E., Guelph Ontario N1G 2W1 Canada
| | - Anna Mosser
- Department of Integrative BiologyUniversity of Guelph 50 Stone Road E., Guelph Ontario N1G 2W1 Canada
| | - Steven G. Newmaster
- Department of Integrative BiologyUniversity of Guelph 50 Stone Road E., Guelph Ontario N1G 2W1 Canada
| | - Tom D. Nudds
- Department of Integrative BiologyUniversity of Guelph 50 Stone Road E., Guelph Ontario N1G 2W1 Canada
| | - Garrett M. Street
- Department of Integrative BiologyUniversity of Guelph 50 Stone Road E., Guelph Ontario N1G 2W1 Canada
| | - Glen S. Brown
- Ontario Ministry of Natural Resources and ForestryWildlife Research and Monitoring Section 300 Water Street, Peterborough Ontario K9J 8M5 Canada
| | - Brent Patterson
- Ontario Ministry of Natural Resources and ForestryWildlife Research and Monitoring Section 300 Water Street, Peterborough Ontario K9J 8M5 Canada
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19
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Newmaster SG, Shanmughanandhan D, Kesanakurti P, Shehata H, Faller A, Noce ID, Lee JY, Rudzinski P, Lu Z, Zhang Y, Swanson G, Hanner R, Ragupathy S. Recommendations for Validation of Real-Time PCR Methods for Molecular Diagnostic Identification of Botanicals. J AOAC Int 2019. [DOI: 10.1093/jaoac/102.6.1767] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Abstract
Background: PCR methods are the most commonly used DNA-based identity tool in the commercial food, beverage, and natural health product markets. These methods are routinely used to identify foodborne pathogens and allergens in food. Proper validation methods for some sectors have been established, while there are none in other markets, such as botanicals. Results: A survey of the literature indicates that some validation criteria are not addressed when developing PCR tests for botanicals. Objective: We provide recommendations for qualitative real-time PCR methods for validating identity tests for botanical ingredients. Methods: These include common criteria that underpin the development and validation of rigorous tests, including (1) the aim of the validation test, (2) the applicability of different matrix variants, (3) specificity in identifying the target species ingredient, (4) sensitivity in detecting the smallest amount of the target material, (5) repeatability of methods, (6) reproducibility in detecting the target species in both raw and processed materials, (7) practicability of the test in a commercial laboratory, and (8) comparison with alternative methods. In addition, we recommend additional criteria, according to which the practicability of the test method is evaluated by transferring the method to a second laboratory and by comparison with alternative methods. Conclusions and Highlights: We hope that these recommendations encourage further publication on the validation of PCR methods for many botanical ingredients. These properly validated PCR methods can be developed on small, real-time biotechnology that can be placed directly into the supply chain ledger in support of highly transparent data systems that support QC from the farm to the fork of the consumer.
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Affiliation(s)
- Steven G Newmaster
- University of Guelph, College of Biological Sciences, NHP Research Alliance, Guelph, ON, Canada N1G 2W1
| | - Dhivya Shanmughanandhan
- University of Guelph, College of Biological Sciences, NHP Research Alliance, Guelph, ON, Canada N1G 2W1
| | - Prasad Kesanakurti
- University of Guelph, College of Biological Sciences, NHP Research Alliance, Guelph, ON, Canada N1G 2W1
| | - Hanan Shehata
- University of Guelph, College of Biological Sciences, NHP Research Alliance, Guelph, ON, Canada N1G 2W1
| | - Adam Faller
- University of Guelph, College of Biological Sciences, NHP Research Alliance, Guelph, ON, Canada N1G 2W1
| | - Isabella Della Noce
- Hyris Biotech R&D, Lower Ground Floor, One George Yard, EC3V 9DF London, United Kingdom
| | - Jung Yeop Lee
- NBTY, Global Analytical and Quality Control, 105 Orville Dr, Bohemia, NY 11716
| | - Pawel Rudzinski
- NBTY, Global Analytical and Quality Control, 105 Orville Dr, Bohemia, NY 11716
| | - Zhengfei Lu
- Herbalife International, 990 190th St, Torrance, CA 90502
| | - Yanjun Zhang
- Herbalife International, 990 190th St, Torrance, CA 90502
| | - Gary Swanson
- Herbalife International, 990 190th St, Torrance, CA 90502
| | - Robert Hanner
- University of Guelph, Department of Integrative Biology, Guelph, ON, Canada N1G 2W1
| | - Subramanyam Ragupathy
- University of Guelph, College of Biological Sciences, NHP Research Alliance, Guelph, ON, Canada N1G 2W1
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20
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Shehata HR, Ragupathy S, Shanmughanandhan D, Kesanakurti P, Ehlinger TM, Newmaster SG. Guidelines for Validation of Qualitative Real-Time PCR Methods for Molecular Diagnostic Identification of Probiotics. J AOAC Int 2019. [DOI: 10.1093/jaoac/102.6.1774] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
Abstract
Backgroud: Probiotics have been shown to benefit human health through several mechanisms, including their role in improving the health of our gastrointestinal tracts. The health benefits of probiotics are strain specific, and therefore it is critical to include the correct strains in probiotic products when claiming specific health benefits. Several studies have reported issues concerning the accuracy of labeling of commercial probiotic products, including inaccurate taxonomy, missing species, or undeclared species. Consequently, there is a growing need to develop and validate assays to reliably verify strain identity in commercial probiotic products. PCR-based methods are the most commonly used methods for food species ingredient diagnostics because they are simple, fast, sensitive, and can be validated. Objective: The aim of this paper is to set the guidelines for validating targeted qualitative real-time PCR assays to verify the presence of specific strains in a probiotic supplement. Methods and Results: Qualitative real-time PCR assays are validated to evaluate the assay performance in terms of specificity, sensitivity, repeatability, and reproducibility in detecting target strains. Conclusions and Highlights: Setting these guidelines will facilitate and streamline the validation process for qualitative real-time PCR-based assays for probiotic identity authentication in support of quality assurance systems.
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Affiliation(s)
- Hanan R Shehata
- University of Guelph, College of Biological Sciences, NHP Research Alliance, Guelph, ON, Canada N1G 2W1
- Mansoura University, Faculty of Pharmacy, Department of Microbiology, Mansoura, Egypt
| | - Subramanyam Ragupathy
- University of Guelph, College of Biological Sciences, NHP Research Alliance, Guelph, ON, Canada N1G 2W1
| | - Dhivya Shanmughanandhan
- University of Guelph, College of Biological Sciences, NHP Research Alliance, Guelph, ON, Canada N1G 2W1
| | - Prasad Kesanakurti
- University of Guelph, College of Biological Sciences, NHP Research Alliance, Guelph, ON, Canada N1G 2W1
| | | | - Steven G Newmaster
- University of Guelph, College of Biological Sciences, NHP Research Alliance, Guelph, ON, Canada N1G 2W1
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21
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Faller AC, Ragupathy S, Shanmughanandhan D, Zhang Y, Lu Z, Chang P, Swanson G, Newmaster SG. DNA Quality and Quantity Analysis of Camellia sinensis Through Processing from Fresh Leaves to a Green Tea Extract. J AOAC Int 2019. [DOI: 10.1093/jaoac/102.6.1798] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
Abstract
Background: Although there has been some success using DNA barcoding to authenticate raw natural health product (NHP) botanical ingredients, there are many gaps in our understanding of DNA degradation, which may explain low PCR and sequencing success in processed NHPs. Objective: In this study, we measured multiple DNA variables after each step in the processing of a green tea extract in order to document DNA quality and quantity. Methods: We sampled plant material after each step of green tea extract processing: five steps at a Chinese tea farm (n = 10) and five at an NHP processing facility (n = 3). We hypothesized that processing treatments degrade and remove DNA from NHPs, reflected by decreasing quantities of extractable genomic DNA (gDNA), an increasing proportion of small DNA fragments in genomic extracts, and decreasing quantitative PCR (QPCR) efficiency [higher cycle threshold (Ct) values]. DNA from end-production green tea extract was sequenced in order to try to validate material as the botanical of interest. Results: We saw a 41.1% decrease in mean extractable gDNA through farm processing (P < 0.01) and a 99.7% decrease through facility processing (P < 0.05). There was a 26.3% decrease in mean DNA fragment size through farm processing (P < 0.001) and an 82.0% decrease through facility processing (P < 0.05). QPCR efficiency was reduced through processing, marked by significant increases in Ct values with 100 base pair (bp) and 200 bp PCR targets (P < 0.05), and an inability to amplify 300 bp targets when using DNA template from end-production green tea extract. Conclusions: Although there was significant degradation and removal of DNA through processing, sufficiently intact DNA was able to be recovered from highly processed green tea extract for further sequencing and identification. Highlights: This work addresses a key gap in the understanding of DNA degradation through processing and provides useful information to consider when designing molecular diagnostic techniques for NHP identification.
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Affiliation(s)
- Adam C Faller
- University of Guelph, College of Biological Sciences, Natural Health Product Research Alliance, 50 Stone Rd E., Guelph, ON N1G 2W1, Canada
| | - Subramanyam Ragupathy
- University of Guelph, College of Biological Sciences, Natural Health Product Research Alliance, 50 Stone Rd E., Guelph, ON N1G 2W1, Canada
| | - Dhivya Shanmughanandhan
- University of Guelph, College of Biological Sciences, Natural Health Product Research Alliance, 50 Stone Rd E., Guelph, ON N1G 2W1, Canada
| | - Yanjun Zhang
- Herbalife International, 990 190th St, Torrance, CA 90502
| | - Zhengfei Lu
- Herbalife International, 990 190th St, Torrance, CA 90502
| | - Peter Chang
- Herbalife International, 990 190th St, Torrance, CA 90502
| | - Gary Swanson
- Herbalife International, 990 190th St, Torrance, CA 90502
| | - Steven G Newmaster
- University of Guelph, College of Biological Sciences, Natural Health Product Research Alliance, 50 Stone Rd E., Guelph, ON N1G 2W1, Canada
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22
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Dhivya S, Ragupathy S, Kesanakurti P, Jeevitha S, Noce ID, Newmaster SG. Validated Identity Test Method for Ginkgo biloba NHPs Using DNA-Based Species-Specific Hydrolysis PCR Probe. J AOAC Int 2019. [DOI: 10.1093/jaoac/102.6.1779] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Abstract
Background: There is considerable risk of adulteration of Ginkgo biloba herbal products in the natural health product (NHP) industry. Authentication of G. biloba products is challenging because of the standard, complex, analytical chemistry methods that may be too costly and not appropriate for both raw and finished products. Objective: We sought to develop and validate an alternative method to authenticate G. biloba herbal dietary supplements, based on the use of a species-specific hydrolysis PCR probe assay. Methods: A species-specific hydrolysis probe assay was developed, validated, and evaluated for the performance of the assay in accurately identifying the species of interest using the following analytical validation criteria: (1) specificity (accuracy) in identifying the target species ingredient, while not identifying other nontarget species, (2) sensitivity in detecting the smallest amount of the target material, and (3) reliability (repeatability and reproducibility) in detecting the target species in raw materials on a real-time PCR platform. Results: The species-specific hydrolysis probe assay was successfully developed for raw materials of G. biloba. The specificity of the assay was 100% to the target species. Efficiency of the assay was observed to be 99%, and the reliability of the assay was 100% for the raw/starting materials. Conclusions and Highlights: The method developed in this study is simple, rapid, and easy for supplement manufacturers to perform in their laboratories to ensure that their G. biloba supplements are authentic.
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Affiliation(s)
- Shanmughanandhan Dhivya
- University of Guelph, College of Biological Sciences, NHP Research Alliance, Guelph, ON N1G 2W1, Canada
| | - Subramanyam Ragupathy
- University of Guelph, College of Biological Sciences, NHP Research Alliance, Guelph, ON N1G 2W1, Canada
| | - Prasad Kesanakurti
- University of Guelph, College of Biological Sciences, NHP Research Alliance, Guelph, ON N1G 2W1, Canada
| | - Shanmughanandhan Jeevitha
- University of Guelph, College of Biological Sciences, NHP Research Alliance, Guelph, ON N1G 2W1, Canada
| | - Isabella Della Noce
- Hyris Ltd, Lower Ground Floor, One George Yard, EC3V 9DF London, United Kingdom
| | - Steven G Newmaster
- University of Guelph, College of Biological Sciences, NHP Research Alliance, Guelph, ON N1G 2W1, Canada
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23
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Faller AC, Arunachalam T, Shanmughanandhan D, Kesanakurti P, Shehata HR, Ragupathy S, Newmaster SG. Investigating appropriate molecular and chemical methods for ingredient identity testing of plant-based protein powder dietary supplements. Sci Rep 2019; 9:12130. [PMID: 31431646 PMCID: PMC6702227 DOI: 10.1038/s41598-019-48467-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2019] [Accepted: 08/06/2019] [Indexed: 11/09/2022] Open
Abstract
Plant-based protein powders are rapidly growing in popularity, and outdated quality assurance tools expose vulnerabilities to adulteration via different methods of "protein spiking". Adequate diagnostic tools are urgently needed to be able to authenticate protein source ingredients and screen for potential adulterants. We explored the application of three diagnostic tools for ingredient identification: targeted PCR with Sanger sequencing, NGS, and LC-MS/MS. We collected 33 samples of common commercial products from the plant-based protein powder market and sought to identify botanical components using the three technologies. We found success in detection with all approaches, with at least one main protein source being identified by at least one approach in all samples. The investigation uncovered challenges to data collection or result interpretation with each technology including but not limited to amplification biases with PCR technologies, potential influence of DNA degradation, and issues with protein solubility during isolation. Ultimately, each platform demonstrated utility along with certain caveats, which epitomized the importance of orthogonality of testing.
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Affiliation(s)
- Adam C Faller
- NHP Research Alliance, College of Biological Sciences, University of Guelph, 50 Stone Rd E, Guelph, Ontario, N1G 2W1, Canada.
| | - Thirugnanasambandam Arunachalam
- NHP Research Alliance, College of Biological Sciences, University of Guelph, 50 Stone Rd E, Guelph, Ontario, N1G 2W1, Canada
| | - Dhivya Shanmughanandhan
- NHP Research Alliance, College of Biological Sciences, University of Guelph, 50 Stone Rd E, Guelph, Ontario, N1G 2W1, Canada
| | - Prasad Kesanakurti
- NHP Research Alliance, College of Biological Sciences, University of Guelph, 50 Stone Rd E, Guelph, Ontario, N1G 2W1, Canada
| | - Hanan R Shehata
- NHP Research Alliance, College of Biological Sciences, University of Guelph, 50 Stone Rd E, Guelph, Ontario, N1G 2W1, Canada
| | - Subramanyam Ragupathy
- NHP Research Alliance, College of Biological Sciences, University of Guelph, 50 Stone Rd E, Guelph, Ontario, N1G 2W1, Canada
| | - Steven G Newmaster
- NHP Research Alliance, College of Biological Sciences, University of Guelph, 50 Stone Rd E, Guelph, Ontario, N1G 2W1, Canada
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24
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Shehata HR, Ragupathy S, Shanmughanandhan D, Kesanakurti P, Ehlinger TM, Newmaster SG. Guidelines for Validation of Qualitative Real-Time PCR Methods for Molecular Diagnostic Identification of Probiotics. J AOAC Int 2019; 102:1774-1778. [PMID: 30940283 DOI: 10.5740/jaoacint.18-0320] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Backgroud: Probiotics have been shown to benefit human health through several mechanisms, including their role in improving the health of our gastrointestinal tracts. The health benefits of probiotics are strain specific, and therefore it is critical to include the correct strains in probiotic products when claiming specific health benefits. Several studies have reported issues concerning the accuracy of labeling of commercial probiotic products, including inaccurate taxonomy, missing species, or undeclared species. Consequently, there is a growing need to develop and validate assays to reliably verify strain identity in commercial probiotic products. PCR-based methods are the most commonly used methods for food species ingredient diagnostics because they are simple, fast, sensitive, and can be validated. Objective: The aim of this paper is to set the guidelines for validating targeted qualitative real-time PCR assays to verify the presence of specific strains in a probiotic supplement. Methods and Results: Qualitative real-time PCR assays are validated to evaluate the assay performance in terms of specificity, sensitivity, repeatability, and reproducibility in detecting target strains. Conclusions and Highlights: Setting these guidelines will facilitate and streamline the validation process for qualitative real-time PCR-based assays for probiotic identity authentication in support of quality assurance systems.
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Affiliation(s)
- Hanan R Shehata
- University of Guelph, College of Biological Sciences, NHP Research Alliance, Guelph, ON, Canada N1G 2W1
| | - Subramanyam Ragupathy
- University of Guelph, College of Biological Sciences, NHP Research Alliance, Guelph, ON, Canada N1G 2W1
| | - Dhivya Shanmughanandhan
- University of Guelph, College of Biological Sciences, NHP Research Alliance, Guelph, ON, Canada N1G 2W1
| | - Prasad Kesanakurti
- University of Guelph, College of Biological Sciences, NHP Research Alliance, Guelph, ON, Canada N1G 2W1
| | | | - Steven G Newmaster
- University of Guelph, College of Biological Sciences, NHP Research Alliance, Guelph, ON, Canada N1G 2W1
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25
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Newmaster SG, Shanmughanandhan D, Kesanakurti P, Shehata H, Faller A, Noce ID, Lee JY, Rudzinski P, Lu Z, Zhang Y, Swanson G, Hanner R, Ragupathy S. Recommendations for Validation of Real-Time PCR Methods for Molecular Diagnostic Identification of Botanicals. J AOAC Int 2019; 102:1767-1773. [PMID: 30871654 DOI: 10.5740/jaoacint.18-0321] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Background: PCR methods are the most commonly used DNA-based identity tool in the commercial food, beverage, and natural health product markets. These methods are routinely used to identify foodborne pathogens and allergens in food. Proper validation methods for some sectors have been established, while there are none in other markets, such as botanicals. Results: A survey of the literature indicates that some validation criteria are not addressed when developing PCR tests for botanicals. Objective: We provide recommendations for qualitative real-time PCR methods for validating identity tests for botanical ingredients. Methods: These include common criteria that underpin the development and validation of rigorous tests, including (1) the aim of the validation test, (2) the applicability of different matrix variants, (3) specificity in identifying the target species ingredient, (4) sensitivity in detecting the smallest amount of the target material, (5) repeatability of methods, (6) reproducibility in detecting the target species in both raw and processed materials, (7) practicability of the test in a commercial laboratory, and (8) comparison with alternative methods. In addition, we recommend additional criteria, according to which the practicability of the test method is evaluated by transferring the method to a second laboratory and by comparison with alternative methods. Conclusions and Highlights: We hope that these recommendations encourage further publication on the validation of PCR methods for many botanical ingredients. These properly validated PCR methods can be developed on small, real-time biotechnology that can be placed directly into the supply chain ledger in support of highly transparent data systems that support QC from the farm to the fork of the consumer.
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Affiliation(s)
- Steven G Newmaster
- University of Guelph, College of Biological Sciences, NHP Research Alliance, Guelph, ON, Canada N1G 2W1
| | - Dhivya Shanmughanandhan
- University of Guelph, College of Biological Sciences, NHP Research Alliance, Guelph, ON, Canada N1G 2W1
| | - Prasad Kesanakurti
- University of Guelph, College of Biological Sciences, NHP Research Alliance, Guelph, ON, Canada N1G 2W1
| | - Hanan Shehata
- University of Guelph, College of Biological Sciences, NHP Research Alliance, Guelph, ON, Canada N1G 2W1
| | - Adam Faller
- University of Guelph, College of Biological Sciences, NHP Research Alliance, Guelph, ON, Canada N1G 2W1
| | - Isabella Della Noce
- Hyris Biotech R&D, Lower Ground Floor, One George Yard, EC3V 9DF London, United Kingdom
| | - Jung Yeop Lee
- NBTY, Global Analytical and Quality Control, 105 Orville Dr, Bohemia, NY 11716
| | - Pawel Rudzinski
- NBTY, Global Analytical and Quality Control, 105 Orville Dr, Bohemia, NY 11716
| | - Zhengfei Lu
- Herbalife International, 990 190th St, Torrance, CA 90502
| | - Yanjun Zhang
- Herbalife International, 990 190th St, Torrance, CA 90502
| | - Gary Swanson
- Herbalife International, 990 190th St, Torrance, CA 90502
| | - Robert Hanner
- University of Guelph, Department of Integrative Biology, Guelph, ON, Canada N1G 2W1
| | - Subramanyam Ragupathy
- University of Guelph, College of Biological Sciences, NHP Research Alliance, Guelph, ON, Canada N1G 2W1
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26
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Clare EL, Fazekas AJ, Ivanova NV, Floyd RM, Hebert PDN, Adams AM, Nagel J, Girton R, Newmaster SG, Fenton MB. Approaches to integrating genetic data into ecological networks. Mol Ecol 2018; 28:503-519. [PMID: 30427082 DOI: 10.1111/mec.14941] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Accepted: 10/25/2018] [Indexed: 01/03/2023]
Abstract
As molecular tools for assessing trophic interactions become common, research is increasingly focused on the construction of interaction networks. Here, we demonstrate three key methods for incorporating DNA data into network ecology and discuss analytical considerations using a model consisting of plants, insects, bats and their parasites from the Costa Rica dry forest. The simplest method involves the use of Sanger sequencing to acquire long sequences to validate or refine field identifications, for example of bats and their parasites, where one specimen yields one sequence and one identification. This method can be fully quantified and resolved and these data resemble traditional ecological networks. For more complex taxonomic identifications, we target multiple DNA loci, for example from a seed or fruit pulp sample in faeces. These networks are also well resolved but gene targets vary in resolution and quantification is difficult. Finally, for mixed templates such as faecal contents of insectivorous bats, we use DNA metabarcoding targeting two sequence lengths (157 and 407 bp) of one gene region and a MOTU, BLAST and BIN association approach to resolve nodes. This network type is complex to generate and analyse, and we discuss the implications of this type of resolution on network analysis. Using these data, we construct the first molecular-based network of networks containing 3,304 interactions between 762 nodes of eight trophic functions and involving parasitic, mutualistic and predatory interactions. We provide a comparison of the relative strengths and weaknesses of these data types in network ecology.
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Affiliation(s)
- Elizabeth L Clare
- School of Biological and Chemical Sciences, Queen Mary University of London, London, UK.,Centre for Biodiversity Genomics, University of Guelph, Guelph, Ontario, Canada
| | - Aron J Fazekas
- The Arboretum, University of Guelph, Guelph, Ontario, Canada
| | - Natalia V Ivanova
- Centre for Biodiversity Genomics, University of Guelph, Guelph, Ontario, Canada
| | - Robin M Floyd
- Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
| | - Paul D N Hebert
- Centre for Biodiversity Genomics, University of Guelph, Guelph, Ontario, Canada
| | - Amanda M Adams
- Department of Biology, Texas A&M University, College Station, Texas
| | - Juliet Nagel
- Center for Environmental Science, University of Maryland, Frostburg, Maryland
| | - Rebecca Girton
- School of Biological and Chemical Sciences, Queen Mary University of London, London, UK
| | - Steven G Newmaster
- Department of Integrative Biology, University of Guelph, Guelph, Ontario, Canada
| | - M Brock Fenton
- Department of Biology, University of Western Ontario, London, Ontario, Canada
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27
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Rapai SB, McMullin RT, Maloles JR, Turgeon MH, Newmaster SG. An Ecological Restoration Approach to Biological Inventories: A Case Study in the Collection of a Vegetation Biolayer That Will Inform Restoration Planning. ECOL RESTOR 2018. [DOI: 10.3368/er.36.2.116] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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28
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Faller A, Newmaster SG. DNA Quality and Quantity Analysis of Camellia sinensis Through Processing from Raw Tea Leaves to a Green Tea Extract Product. Am J Transl Res 2018. [DOI: 10.1055/s-0038-1644954] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Affiliation(s)
- A Faller
- Department of Integrative Biology, Biodiversity Institute of Ontario (BIO), University of Guelph, Guelph, Ontario, Canada
| | - SG Newmaster
- Department of Integrative Biology, Biodiversity Institute of Ontario (BIO), University of Guelph, Guelph, Ontario, Canada
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29
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Xin T, Xu Z, Jia J, Leon C, Hu S, Lin Y, Ragupathy S, Song J, Newmaster SG. Biomonitoring for traditional herbal medicinal products using DNA metabarcoding and single molecule, real-time sequencing. Acta Pharm Sin B 2018; 8:488-497. [PMID: 29881688 PMCID: PMC5990340 DOI: 10.1016/j.apsb.2017.10.001] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2017] [Revised: 09/05/2017] [Accepted: 09/13/2017] [Indexed: 11/12/2022] Open
Abstract
Global concerns have been paid to the potential hazard of traditional herbal medicinal products (THMPs). Substandard and counterfeit THMPs, including traditional Chinese patent medicine, health foods, dietary supplements, etc. are potential threats to public health. Recent marketplace studies using DNA barcoding have determined that the current quality control methods are not sufficient for ensuring the presence of authentic herbal ingredients and detection of contaminants/adulterants. An efficient biomonitoring method for THMPs is of great needed. Herein, metabarcoding and single-molecule, real-time (SMRT) sequencing were used to detect the multiple ingredients in Jiuwei Qianghuo Wan (JWQHW), a classical herbal prescription widely used in China for the last 800 years. Reference experimental mixtures and commercial JWQHW products from the marketplace were used to confirm the method. Successful SMRT sequencing results recovered 5416 and 4342 circular-consensus sequencing (CCS) reads belonging to the ITS2 and psbA-trnH regions. The results suggest that with the combination of metabarcoding and SMRT sequencing, it is repeatable, reliable, and sensitive enough to detect species in the THMPs, and the error in SMRT sequencing did not affect the ability to identify multiple prescribed species and several adulterants/contaminants. It has the potential for becoming a valuable tool for the biomonitoring of multi-ingredient THMPs.
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Affiliation(s)
- Tianyi Xin
- Key Lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People's Republic of China, Institute of Medicinal Plant Development, Peking Union Medical College & Chinese Academy of Medical Sciences, Beijing 100193, China
| | - Zhichao Xu
- Key Lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People's Republic of China, Institute of Medicinal Plant Development, Peking Union Medical College & Chinese Academy of Medical Sciences, Beijing 100193, China
| | - Jing Jia
- Key Lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People's Republic of China, Institute of Medicinal Plant Development, Peking Union Medical College & Chinese Academy of Medical Sciences, Beijing 100193, China
| | - Christine Leon
- Royal Botanic Gardens, Kew, Richmond, Surrey TW9 3AB, UK
| | - Songnian Hu
- Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
| | - Yulin Lin
- Key Lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People's Republic of China, Institute of Medicinal Plant Development, Peking Union Medical College & Chinese Academy of Medical Sciences, Beijing 100193, China
| | - Subramanyam Ragupathy
- NHP Research Alliance, Biodiversity Institute of Ontario (BIO), University of Guelph, Guelph N1G 2W1, Ontario, Canada
| | - Jingyuan Song
- Key Lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People's Republic of China, Institute of Medicinal Plant Development, Peking Union Medical College & Chinese Academy of Medical Sciences, Beijing 100193, China
| | - Steven G. Newmaster
- NHP Research Alliance, Biodiversity Institute of Ontario (BIO), University of Guelph, Guelph N1G 2W1, Ontario, Canada
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30
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Srirama R, Santhosh Kumar JU, Seethapathy GS, Newmaster SG, Ragupathy S, Ganeshaiah KN, Uma Shaanker R, Ravikanth G. Species Adulteration in the Herbal Trade: Causes, Consequences and Mitigation. Drug Saf 2018; 40:651-661. [PMID: 28389979 DOI: 10.1007/s40264-017-0527-0] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
The global economy of the international trade of herbal products has been increasing by 15% annually, with the raw material for most herbal products being sourced from South and Southeast Asian countries. In India, of the 8000 species of medicinal plants harvested from the wild, approximately 960 are in the active trade. With increasing international trade in herbal medicinal products, there is also increasing concern about the widespread adulteration and species admixtures in the raw herbal trade. The adverse consequences of such species adulteration on the health and safety of consumers have only recently begun to be recognised and documented. We provide a comprehensive review of the nature and magnitude of species adulteration in the raw herbal trade, and identify the underlying drivers that might lead to such adulteration. We also discuss the possible biological and chemical equivalence of species that are used as adulterants and substitutes, and the consequences thereof to consumer health and safety, and propose a framework for the development of a herbal trade authentication service that can help regulate the herbal trade market.
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Affiliation(s)
- Ramanujam Srirama
- Ashoka Trust for Research in Ecology and the Environment, Royal Enclave, Srirampura, Jakkur Post, Bangalore, 560064, India
| | - J U Santhosh Kumar
- School of Ecology and Conservation, University of Agricultural Sciences, GKVK, Bangalore, 560065, India
- Department of Crop Physiology, University of Agricultural Sciences, GKVK, Bangalore, 560065, India
| | - G S Seethapathy
- Ashoka Trust for Research in Ecology and the Environment, Royal Enclave, Srirampura, Jakkur Post, Bangalore, 560064, India
| | - Steven G Newmaster
- Department of Integrative Biology, Centre for Biodiversity Genomics (CBG), College of Biological Sciences, University of Guelph, Toronto, ON, N1G 2W1, Canada
| | - S Ragupathy
- Department of Integrative Biology, Centre for Biodiversity Genomics (CBG), College of Biological Sciences, University of Guelph, Toronto, ON, N1G 2W1, Canada
| | - K N Ganeshaiah
- Ashoka Trust for Research in Ecology and the Environment, Royal Enclave, Srirampura, Jakkur Post, Bangalore, 560064, India
- School of Ecology and Conservation, University of Agricultural Sciences, GKVK, Bangalore, 560065, India
| | - R Uma Shaanker
- Ashoka Trust for Research in Ecology and the Environment, Royal Enclave, Srirampura, Jakkur Post, Bangalore, 560064, India
- School of Ecology and Conservation, University of Agricultural Sciences, GKVK, Bangalore, 560065, India
- Department of Crop Physiology, University of Agricultural Sciences, GKVK, Bangalore, 560065, India
| | - Gudasalamani Ravikanth
- Ashoka Trust for Research in Ecology and the Environment, Royal Enclave, Srirampura, Jakkur Post, Bangalore, 560064, India.
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31
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Kuzmina ML, Braukmann TWA, Fazekas AJ, Graham SW, Dewaard SL, Rodrigues A, Bennett BA, Dickinson TA, Saarela JM, Catling PM, Newmaster SG, Percy DM, Fenneman E, Lauron-Moreau A, Ford B, Gillespie L, Subramanyam R, Whitton J, Jennings L, Metsger D, Warne CP, Brown A, Sears E, Dewaard JR, Zakharov EV, Hebert PDN. Using herbarium-derived DNAs to assemble a large-scale DNA barcode library for the vascular plants of Canada. Appl Plant Sci 2017; 5:apps.1700079. [PMID: 29299394 PMCID: PMC5749818 DOI: 10.3732/apps.1700079] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Accepted: 10/26/2017] [Indexed: 05/20/2023]
Abstract
PREMISE OF THE STUDY Constructing complete, accurate plant DNA barcode reference libraries can be logistically challenging for large-scale floras. Here we demonstrate the promise and challenges of using herbarium collections for building a DNA barcode reference library for the vascular plant flora of Canada. METHODS Our study examined 20,816 specimens representing 5076 of 5190 vascular plant species in Canada (98%). For 98% of the specimens, at least one of the DNA barcode regions was recovered from the plastid loci rbcL and matK and from the nuclear ITS2 region. We used beta regression to quantify the effects of age, type of preservation, and taxonomic affiliation (family) on DNA sequence recovery. RESULTS Specimen age and method of preservation had significant effects on sequence recovery for all markers, but influenced some families more (e.g., Boraginaceae) than others (e.g., Asteraceae). DISCUSSION Our DNA barcode library represents an unparalleled resource for metagenomic and ecological genetic research working on temperate and arctic biomes. An observed decline in sequence recovery with specimen age may be associated with poor primer matches, intragenomic variation (for ITS2), or inhibitory secondary compounds in some taxa.
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Affiliation(s)
- Maria L. Kuzmina
- Centre for Biodiversity Genomics, University of Guelph, 50 Stone Road East, Guelph, Ontario N1G 2W1, Canada
| | - Thomas W. A. Braukmann
- Centre for Biodiversity Genomics, University of Guelph, 50 Stone Road East, Guelph, Ontario N1G 2W1, Canada
| | - Aron J. Fazekas
- The Arboretum, University of Guelph, 50 Stone Road East, Ontario N1G 2W1, Canada
| | - Sean W. Graham
- Department of Botany, University of British Columbia, 3200-6270 University Boulevard, Vancouver, British Columbia V6T 1Z4, Canada
| | - Stephanie L. Dewaard
- Centre for Biodiversity Genomics, University of Guelph, 50 Stone Road East, Guelph, Ontario N1G 2W1, Canada
| | - Anuar Rodrigues
- Office of the Vice-Principal Academic and Dean, University of Toronto, 3359 Mississauga Road, Mississauga, Ontario L5L 1C6, Canada
| | - Bruce A. Bennett
- Yukon Conservation Data Centre (CDC), Whitehorse, Yukon Territory Y1A 2C6, Canada
| | - Timothy A. Dickinson
- Green Plant Herbarium (TRT), Department of Natural History, Royal Ontario Museum (ROM), 100 Queens Park, Toronto, Ontario M5S2C6, Canada
- Department of Ecology and Evolutionary Biology, University of Toronto, 27 King's College Circle, Toronto, Ontario M5S, Canada
| | - Jeffery M. Saarela
- Beaty Centre for Species Discovery and National Herbarium of Canada (CAN), Botany Section, Research and Collections, National Heritage Campus of the Canadian Museum of Nature, Gatineau, Québec J9J 3N7, Canada
| | - Paul M. Catling
- The Agriculture and Agri-Food Canada Collection of Vascular Plants (DAO), 960 Carling Avenue, Ottawa, Ontario K1A 0C6, Canada
| | - Steven G. Newmaster
- BIO Herbarium (OAC), University of Guelph, 50 Stone Road East, Guelph, Ontario N1G2W1, Canada
| | - Diana M. Percy
- Natural History Museum, Cromwell Road, Kensington, London SW75BD, United Kingdom
| | - Erin Fenneman
- Department of Botany, University of British Columbia, 3200-6270 University Boulevard, Vancouver, British Columbia V6T 1Z4, Canada
| | - Aurélien Lauron-Moreau
- Institut de recherche en biologie végétale, Université de Montréal, 2900 Edouard Montpetit Boulevard, Montréal, Québec H3T 1J4, Canada
| | - Bruce Ford
- University of Manitoba Vascular Plant Herbarium (WIN), Department of Biological Sciences, University of Manitoba, 66 Chancellors Circle, Winnipeg, Manitoba R3T 2N2, Canada
| | - Lynn Gillespie
- Beaty Centre for Species Discovery and National Herbarium of Canada (CAN), Botany Section, Research and Collections, National Heritage Campus of the Canadian Museum of Nature, Gatineau, Québec J9J 3N7, Canada
| | - Ragupathy Subramanyam
- BIO Herbarium (OAC), University of Guelph, 50 Stone Road East, Guelph, Ontario N1G2W1, Canada
| | - Jeannette Whitton
- Department of Botany, University of British Columbia, 3200-6270 University Boulevard, Vancouver, British Columbia V6T 1Z4, Canada
| | - Linda Jennings
- Department of Botany, University of British Columbia, 3200-6270 University Boulevard, Vancouver, British Columbia V6T 1Z4, Canada
| | - Deborah Metsger
- Green Plant Herbarium (TRT), Department of Natural History, Royal Ontario Museum (ROM), 100 Queens Park, Toronto, Ontario M5S2C6, Canada
| | - Connor P. Warne
- Centre for Biodiversity Genomics, University of Guelph, 50 Stone Road East, Guelph, Ontario N1G 2W1, Canada
| | - Allison Brown
- Centre for Biodiversity Genomics, University of Guelph, 50 Stone Road East, Guelph, Ontario N1G 2W1, Canada
| | - Elizabeth Sears
- Centre for Biodiversity Genomics, University of Guelph, 50 Stone Road East, Guelph, Ontario N1G 2W1, Canada
| | - Jeremy R. Dewaard
- Centre for Biodiversity Genomics, University of Guelph, 50 Stone Road East, Guelph, Ontario N1G 2W1, Canada
| | - Evgeny V. Zakharov
- Centre for Biodiversity Genomics, University of Guelph, 50 Stone Road East, Guelph, Ontario N1G 2W1, Canada
| | - Paul D. N. Hebert
- Centre for Biodiversity Genomics, University of Guelph, 50 Stone Road East, Guelph, Ontario N1G 2W1, Canada
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Berg KJ, Icyeh L, Lin YR, Janz A, Newmaster SG. Multiple-factor classification of a human-modified forest landscape in the Hsuehshan Mountain Range, Taiwan. Ambio 2016; 45:919-932. [PMID: 27255230 PMCID: PMC5102968 DOI: 10.1007/s13280-016-0794-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2015] [Revised: 03/06/2016] [Accepted: 05/13/2016] [Indexed: 06/05/2023]
Abstract
Human actions drive landscape heterogeneity, yet most ecosystem classifications omit the role of human influence. This study explores land use history to inform a classification of forestland of the Tayal Mrqwang indigenous people of Taiwan. Our objectives were to determine the extent to which human action drives landscape heterogeneity. We used interviews, field sampling, and multivariate analysis to relate vegetation patterns to environmental gradients and human modification across 76 sites. We identified eleven forest classes. In total, around 70 % of plots were at lower elevations and had a history of shifting cultivation, terrace farming, and settlement that resulted in alder, laurel, oak, pine, and bamboo stands. Higher elevation mixed conifer forests were least disturbed. Arboriculture and selective harvesting were drivers of other conspicuous forest patterns. The findings show that past land uses play a key role in shaping forests, which is important to consider when setting targets to guide forest management.
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Affiliation(s)
- Kevan J. Berg
- Integral Ecology Group, Ltd., #201 - 330, Duncan Street, Duncan, BC V9L 3W4 Canada
| | - Lahuy Icyeh
- Smangus Community, Yufeng Village, Jianshi, Hsinchu Taiwan
| | - Yih-Ren Lin
- Graduate Institute of Humanities in Medicine (GIHM), Taipei Medical University, No. 250, Wuxing St, Xinyi District, Taipei, 110 Taiwan
| | - Arnold Janz
- Alberta Environmental Monitoring, Evaluation and Reporting Agency (AEMERA), Edmonton, AB Canada
| | - Steven G. Newmaster
- Centre for Biodiversity Genomics, University of Guelph, Guelph, ON N1G 2W1 Canada
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Urumarudappa SKJ, Gogna N, Newmaster SG, Venkatarangaiah K, Subramanyam R, Saroja SG, Gudasalamani R, Dorai K, Ramanan US. DNA barcoding and NMR spectroscopy-based assessment of species adulteration in the raw herbal trade of Saraca asoca (Roxb.) Willd, an important medicinal plant. Int J Legal Med 2016; 130:1457-1470. [PMID: 27627901 DOI: 10.1007/s00414-016-1436-y] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2016] [Accepted: 08/09/2016] [Indexed: 11/24/2022]
Abstract
Saraca asoca (Roxb.) Willd, commonly known as "Asoka" or "Ashoka," is one of the most important medicinal plants used in raw herbal trade in India. The bark extracts of the tree are used in the treatment of leucorrhea and other uterine disorders besides also having anti-inflammatory, anti-bacterial, anti-pyretic, anti-helminthic, and analgesic activity. The indiscriminate and rampant extraction of the wood to meet the ever-increasing market demand has led to a sharp decline in naturally occurring populations of the species in the country. Consequently, the species has recently been classified as "vulnerable" by the International Union for Conservation of Nature (IUCN). Increasing deforestation and increasing demand for this medicinal plant have resulted in a limited supply and suspected widespread adulteration of the species in the raw herbal trade market. Adulteration is a serious concern due to: (i) reduction in the efficacy of this traditional medicine, (ii) considerable health risk to consumers, and (iii) fraudulent product substitution that impacts the economy for the Natural Health Product (NHP) Industry and consumers. In this paper, we provide the first attempt to assess the extent of adulteration in the raw herbal trade of S. asoca using DNA barcoding validated by NMR spectroscopic techniques. Analyzing market samples drawn from 25 shops, mostly from peninsular India, we show that more than 80 % of the samples were spurious, representing plant material from at least 7 different families. This is the first comprehensive and large-scale study to demonstrate the widespread adulteration of market samples of S. asoca in India. These results pose grave implications for the use of raw herbal drugs, such as that of S. asoca, on consumer health and safety. Based on these findings, we argue for a strong and robust regulatory framework to be put in place, which would ensure the quality of raw herbal trade products and reassure consumer confidence in indigenous medicinal systems. Graphical Abstract DNA barcoding and NMR spectroscopy-based assessment of adulteration in Saraca asoca.
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Affiliation(s)
- Santhosh Kumar Jayanthinagar Urumarudappa
- School of Ecology and Conservation, University of Agricultural Sciences, GKVK, Bangalore, 560065, India.,Department of Crop Physiology, University of Agricultural Sciences, GKVK, Bangalore, 560065, India.,Department of Post Graduate Studies and Research in Biotechnology, Jnanasahyadri, Kuvempu University, Shankaraghatta, Shimoga, 577451, India
| | - Navdeep Gogna
- Indian Institute of Science Education and Research (IISER) Mohali, Knowledge City Sector 81, PO Manauli, Mohali, 140306, Punjab, India
| | - Steven G Newmaster
- Centre for Biodiversity Genomics (CBG), College of Biological Sciences, Department of Integrative Biology, University of Guelph, Toronto, N1G 2W1, Canada
| | - Krishna Venkatarangaiah
- Department of Post Graduate Studies and Research in Biotechnology, Jnanasahyadri, Kuvempu University, Shankaraghatta, Shimoga, 577451, India
| | - Ragupathy Subramanyam
- Centre for Biodiversity Genomics (CBG), College of Biological Sciences, Department of Integrative Biology, University of Guelph, Toronto, N1G 2W1, Canada
| | | | - Ravikanth Gudasalamani
- Ashoka Trust for Research in Ecology and the Environment, Royal Enclave, Srirampura, Jakkur Post, Bangalore, 560064, India
| | - Kavita Dorai
- Indian Institute of Science Education and Research (IISER) Mohali, Knowledge City Sector 81, PO Manauli, Mohali, 140306, Punjab, India
| | - Uma Shaanker Ramanan
- School of Ecology and Conservation, University of Agricultural Sciences, GKVK, Bangalore, 560065, India. .,Department of Crop Physiology, University of Agricultural Sciences, GKVK, Bangalore, 560065, India. .,Ashoka Trust for Research in Ecology and the Environment, Royal Enclave, Srirampura, Jakkur Post, Bangalore, 560064, India.
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Rapai SB, Hunt S, Bainard LD, Turgeon MH, Newmaster SG. Soil Inoculation with Arbuscular Mycorrhizal Fungi Promotes the Growth of Boreal Plant Communities in Gold Mine Overburden. ECOL RESTOR 2016. [DOI: 10.3368/er.34.3.216] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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Bell FW, Hunt S, Dacosta J, Sharma M, Larocque GR, Winters JA, Newmaster SG. Effects of silviculture intensity on plant diversity response patterns in young managed northern temperate and boreal forests. Écoscience 2015. [DOI: 10.2980/21-(3-4)-3710] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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McGreer MT, Mallon EE, Vander Vennen LM, Wiebe PA, Baker JA, Brown GS, Avgar T, Hagens J, Kittle AM, Mosser A, Street GM, Reid DEB, Rodgers AR, Shuter J, Thompson ID, Turetsky MJ, Newmaster SG, Patterson BR, Fryxell JM. Selection for forage and avoidance of risk by woodland caribou (Rangifer tarandus caribou) at coarse and local scales. Ecosphere 2015. [DOI: 10.1890/es15-00174.1] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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Santhosh Kumar J, Krishna V, Seethapathy G, Senthilkumar U, Ragupathy S, Ganeshaiah K, Ganesan R, Newmaster SG, Ravikanth G, Uma Shaanker R. DNA barcoding to assess species adulteration in raw drug trade of “Bala” (genus: Sida L.) herbal products in South India. BIOCHEM SYST ECOL 2015. [DOI: 10.1016/j.bse.2015.07.024] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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Henry TA, Bainard JD, Newmaster SG. Genome size evolution in Ontario ferns (Polypodiidae): evolutionary correlations with cell size, spore size, and habitat type and an absence of genome downsizing. Genome 2015; 57:555-66. [PMID: 25727714 DOI: 10.1139/gen-2014-0090] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Genome size is known to correlate with a number of traits in angiosperms, but less is known about the phenotypic correlates of genome size in ferns. We explored genome size variation in relation to a suite of morphological and ecological traits in ferns. Thirty-six fern taxa were collected from wild populations in Ontario, Canada. 2C DNA content was measured using flow cytometry. We tested for genome downsizing following polyploidy using a phylogenetic comparative analysis to explore the correlation between 1Cx DNA content and ploidy. There was no compelling evidence for the occurrence of widespread genome downsizing during the evolution of Ontario ferns. The relationship between genome size and 11 morphological and ecological traits was explored using a phylogenetic principal component regression analysis. Genome size was found to be significantly associated with cell size, spore size, spore type, and habitat type. These results are timely as past and recent studies have found conflicting support for the association between ploidy/genome size and spore size in fern polyploid complexes; this study represents the first comparative analysis of the trend across a broad taxonomic group of ferns.
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Affiliation(s)
- Thomas A Henry
- Centre for Biodiversity Genomics, Department of Integrative Biology, University of Guelph, Guelph, ON N1G 2W1, Canada
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Seethapathy GS, Ganesh D, Santhosh Kumar JU, Senthilkumar U, Newmaster SG, Ragupathy S, Uma Shaanker R, Ravikanth G. Assessing product adulteration in natural health products for laxative yielding plants, Cassia, Senna, and Chamaecrista, in Southern India using DNA barcoding. Int J Legal Med 2014; 129:693-700. [DOI: 10.1007/s00414-014-1120-z] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2014] [Accepted: 11/10/2014] [Indexed: 12/19/2022]
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Liu J, Yan HF, Newmaster SG, Pei N, Ragupathy S, Ge XJ. The use of DNA barcoding as a tool for the conservation biogeography of subtropical forests in China. DIVERS DISTRIB 2014. [DOI: 10.1111/ddi.12276] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Affiliation(s)
- Juan Liu
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden; The Chinese Academy of Sciences; Guangzhou 510650 China
- University of Chinese Academy of Sciences; Beijing 100049 China
| | - Hai-Fei Yan
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden; The Chinese Academy of Sciences; Guangzhou 510650 China
| | - Steven G. Newmaster
- Centre for Biodiversity Genomics; Biodiversity Institute of Ontario (BIO); University of Guelph; Guelph ON N1G 2W1 Canada
| | - Nancai Pei
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden; The Chinese Academy of Sciences; Guangzhou 510650 China
| | - Subramanyam Ragupathy
- Centre for Biodiversity Genomics; Biodiversity Institute of Ontario (BIO); University of Guelph; Guelph ON N1G 2W1 Canada
| | - Xue-Jun Ge
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden; The Chinese Academy of Sciences; Guangzhou 510650 China
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Nithaniyal S, Newmaster SG, Ragupathy S, Krishnamoorthy D, Vassou SL, Parani M. DNA barcode authentication of wood samples of threatened and commercial timber trees within the tropical dry evergreen forest of India. PLoS One 2014; 9:e107669. [PMID: 25259794 PMCID: PMC4178033 DOI: 10.1371/journal.pone.0107669] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2014] [Accepted: 08/22/2014] [Indexed: 11/28/2022] Open
Abstract
BACKGROUND India is rich with biodiversity, which includes a large number of endemic, rare and threatened plant species. Previous studies have used DNA barcoding to inventory species for applications in biodiversity monitoring, conservation impact assessment, monitoring of illegal trading, authentication of traded medicinal plants etc. This is the first tropical dry evergreen forest (TDEF) barcode study in the World and the first attempt to assemble a reference barcode library for the trees of India as part of a larger project initiated by this research group. METHODOLOGY/PRINCIPAL FINDINGS We sampled 429 trees representing 143 tropical dry evergreen forest (TDEF) species, which included 16 threatened species. DNA barcoding was completed using rbcL and matK markers. The tiered approach (1st tier rbcL; 2nd tier matK) correctly identified 136 out of 143 species (95%). This high level of species resolution was largely due to the fact that the tree species were taxonomically diverse in the TDEF. Ability to resolve taxonomically diverse tree species of TDEF was comparable among the best match method, the phylogenetic method, and the characteristic attribute organization system method. CONCLUSIONS We demonstrated the utility of the TDEF reference barcode library to authenticate wood samples from timber operations in the TDEF. This pilot research study will enable more comprehensive surveys of the illegal timber trade of threatened species in the TDEF. This TDEF reference barcode library also contains trees that have medicinal properties, which could be used to monitor unsustainable and indiscriminate collection of plants from the wild for their medicinal value.
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Affiliation(s)
- Stalin Nithaniyal
- Department of Genetic Engineering, Center for DNA Barcoding, SRM University, Chennai, India
- Interdisciplinary School of Indian System of Medicine, SRM University, Chennai, India
| | - Steven G. Newmaster
- Centre for Biodiversity Genomics, University of Guelph, Guelph, Ontario, Canada
| | | | | | - Sophie Lorraine Vassou
- Department of Genetic Engineering, Center for DNA Barcoding, SRM University, Chennai, India
| | - Madasamy Parani
- Department of Genetic Engineering, Center for DNA Barcoding, SRM University, Chennai, India
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Percy DM, Argus GW, Cronk QC, Fazekas AJ, Kesanakurti PR, Burgess KS, Husband BC, Newmaster SG, Barrett SC, Graham SW. Understanding the spectacular failure of DNA barcoding in willows (Salix): Does this result from a trans-specific selective sweep? Mol Ecol 2014; 23:4737-56. [DOI: 10.1111/mec.12837] [Citation(s) in RCA: 85] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2012] [Revised: 05/29/2014] [Accepted: 06/04/2014] [Indexed: 02/04/2023]
Affiliation(s)
- Diana M. Percy
- Department of Botany; University of British Columbia; Vancouver BC Canada V6T 1Z4
- Biodiversity Research Centre; University of British Columbia; Vancouver BC Canada V6T 1Z4
| | - George W. Argus
- Canadian Museum of Nature; PO Box 3443 Stn “D” Ottawa ON Canada K1P 6P4
| | - Quentin C. Cronk
- Department of Botany; University of British Columbia; Vancouver BC Canada V6T 1Z4
- Biodiversity Research Centre; University of British Columbia; Vancouver BC Canada V6T 1Z4
| | - Aron J. Fazekas
- Department of Integrative Biology; University of Guelph; Guelph ON Canada N1G 2W1
| | | | - Kevin S. Burgess
- Department of Biology; Columbus State University; Columbus GA 31907-5645 USA
| | - Brian C. Husband
- Department of Integrative Biology; University of Guelph; Guelph ON Canada N1G 2W1
| | - Steven G. Newmaster
- Department of Integrative Biology; University of Guelph; Guelph ON Canada N1G 2W1
| | - Spencer C.H. Barrett
- Department of Ecology & Evolutionary Biology; University of Toronto; 25 Willcocks Street Toronto ON Canada M5S 3B2
| | - Sean W. Graham
- Department of Botany; University of British Columbia; Vancouver BC Canada V6T 1Z4
- Biodiversity Research Centre; University of British Columbia; Vancouver BC Canada V6T 1Z4
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Purushothaman N, Newmaster SG, Ragupathy S, Stalin N, Suresh D, Arunraj DR, Gnanasekaran G, Vassou SL, Narasimhan D, Parani M. A tiered barcode authentication tool to differentiate medicinal Cassia species in India. Genet Mol Res 2014; 13:2959-68. [PMID: 24782130 DOI: 10.4238/2014.april.16.4] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
DNA barcoding is a desirable tool for medicinal product authentication. DNA barcoding is a method for species identification using short DNA sequences that are conserved within species, but variable between species. Unlike animals, there is no single universal DNA barcode locus for plants. Coding markers, matK and rbcL, and noncoding markers, trnH-psbA (chloroplast) and ITS2 (nuclear), have been reported to be suitable for the DNA barcoding of plants with varying degree of success. Sixty-four accessions from 20 species of the medicinal plant Cassia were collected, and analyzed for these 4 DNA barcoding markers. PCR amplification was 100% successful for all 4 markers, while intra-species divergence was 0 for all 4 Cassia species in which multiple accessions were studied. Assuming 1.0% divergence as the minimum requirement for discriminating 2 species, the 4 markers could only differentiate 15 to 65% of the species studied when used separately. Adding indels to the divergence increased the percentage of species discrimination by trnH-psbA to 90%. In 2-locus barcoding, while matK+rbcL (which is recommended by Consortium for the Barcoding of Life) discriminated 90% of the species, the other combinations of matK+ITS and rbcL+trnH-psbA showed 100% species discrimination. However, matK is plagued with primer issues. The combination of rbcL+trnH-psbA provided the most accurate (100% species ID) and efficient tiered DNA barcoding tool for the authentication of Cassia medicinal products.
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Affiliation(s)
- N Purushothaman
- Genomics Laboratory, Department of Genetic Engineering, SRM University, Chennai, India
| | - S G Newmaster
- Centre for Biodiversity Genomics, University of Guelph, Guelph, Ontario, Canada
| | - S Ragupathy
- Centre for Biodiversity Genomics, University of Guelph, Guelph, Ontario, Canada
| | - N Stalin
- Genomics Laboratory, Department of Genetic Engineering, SRM University, Chennai, India
| | - D Suresh
- Genomics Laboratory, Department of Genetic Engineering, SRM University, Chennai, India
| | - D R Arunraj
- Genomics Laboratory, Department of Genetic Engineering, SRM University, Chennai, India
| | - G Gnanasekaran
- Genomics Laboratory, Department of Genetic Engineering, SRM University, Chennai, India
| | - S L Vassou
- Genomics Laboratory, Department of Genetic Engineering, SRM University, Chennai, India
| | - D Narasimhan
- Centre for Floristic Research, Department of Plant Biology and Plant Biotechnology, Madras Christian College, Chennai, India
| | - M Parani
- Genomics Laboratory, Department of Genetic Engineering, SRM University, Chennai, India
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Newmaster SG, Grguric M, Shanmughanandhan D, Ramalingam S, Ragupathy S. DNA barcoding detects contamination and substitution in North American herbal products. BMC Med 2013; 11:222. [PMID: 24120035 PMCID: PMC3851815 DOI: 10.1186/1741-7015-11-222] [Citation(s) in RCA: 275] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/02/2013] [Accepted: 09/12/2013] [Indexed: 11/26/2022] Open
Abstract
BACKGROUND Herbal products available to consumers in the marketplace may be contaminated or substituted with alternative plant species and fillers that are not listed on the labels. According to the World Health Organization, the adulteration of herbal products is a threat to consumer safety. Our research aimed to investigate herbal product integrity and authenticity with the goal of protecting consumers from health risks associated with product substitution and contamination. METHODS We used DNA barcoding to conduct a blind test of the authenticity for (i) 44 herbal products representing 12 companies and 30 different species of herbs, and (ii) 50 leaf samples collected from 42 herbal species. Our laboratory also assembled the first standard reference material (SRM) herbal barcode library from 100 herbal species of known provenance that were used to identify the unknown herbal products and leaf samples. RESULTS We recovered DNA barcodes from most herbal products (91%) and all leaf samples (100%), with 95% species resolution using a tiered approach (rbcL + ITS2). Most (59%) of the products tested contained DNA barcodes from plant species not listed on the labels. Although we were able to authenticate almost half (48%) of the products, one-third of these also contained contaminants and or fillers not listed on the label. Product substitution occurred in 30/44 of the products tested and only 2/12 companies had products without any substitution, contamination or fillers. Some of the contaminants we found pose serious health risks to consumers. CONCLUSIONS Most of the herbal products tested were of poor quality, including considerable product substitution, contamination and use of fillers. These activities dilute the effectiveness of otherwise useful remedies, lowering the perceived value of all related products because of a lack of consumer confidence in them. We suggest that the herbal industry should embrace DNA barcoding for authenticating herbal products through testing of raw materials used in manufacturing products. The use of an SRM DNA herbal barcode library for testing bulk materials could provide a method for 'best practices? in the manufacturing of herbal products. This would provide consumers with safe, high quality herbal products.
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Affiliation(s)
- Steven G Newmaster
- Centre for Biodiversity Genomics, Biodiversity Institute of Ontario (BIO), University of Guelph, Guelph, Ontario N1G 2W1, Canada
| | - Meghan Grguric
- Bachelor of Arts and Science Program, University of Guelph, Guelph, Ontario N1G 2W1, Canada
| | - Dhivya Shanmughanandhan
- Plant Genetic Engineering Laboratory, Department of Biotechnology, Bharathiar University, Coimbatore 641 046, Tamil Nadu, India
| | - Sathishkumar Ramalingam
- Plant Genetic Engineering Laboratory, Department of Biotechnology, Bharathiar University, Coimbatore 641 046, Tamil Nadu, India
| | - Subramanyam Ragupathy
- Centre for Biodiversity Genomics, Biodiversity Institute of Ontario (BIO), University of Guelph, Guelph, Ontario N1G 2W1, Canada
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McMullin RT, Thompson ID, Newmaster SG. Lichen conservation in heavily managed boreal forests. Conserv Biol 2013; 27:1020-1030. [PMID: 23869621 DOI: 10.1111/cobi.12094] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2012] [Accepted: 01/31/2013] [Indexed: 06/02/2023]
Abstract
Lichens are an important component of the boreal forest, where they are long lived, tend to accumulate in older stands, and are a major food source for the threatened woodland caribou (Rangifer tarandus caribou). To be fully sustainable, silvicultural practices in the boreal forest must include the conservation of ecological integrity. Dominant forest management practices, however, have short-term negative effects on lichen diversity, particularly the application of herbicides. To better understand the long-term effects of forest management, we examined lichen regeneration in 35 mixed black spruce (Picea mariana) and jack pine (Pinus banksiana) forest stands across northern Ontario to determine recovery following logging and postharvest silvicultural practices. Our forest stands were 25-40 years old and had undergone 3 common sivilcultural treatments that included harvested and planted; harvested, planted, and treated with N-[phosphonomethyl] glycine (glyphosate); and harvested, planted, and treated with 2,4-dichlorophenoxyacetic acid (2,4-D). Forest stands with herbicide treatments had lower lichen biomass and higher beta and gamma diversity than planted stands that were not treated chemically or control stands. In northwestern Ontario, planted stands that were not treated chemically had significantly greater (p < 0.05) alpha diversity than stands treated with herbicides or control stands. Our results show that common silvicultural practices do not emulate natural disturbances caused by wildfires in the boreal forest for the lichen community. We suggest a reduction in the amount of chemical application be considered in areas where lichen biomass is likely to be high and where the recovery of woodland caribou is an objective.
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Affiliation(s)
- Richard Troy McMullin
- Department of Integrative Biology, University of Guelph, Guelph, Ontario N1G 2W1, Canada.
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Ragupathy S, Newmaster SG, Murugesan M, Balasubramaniam V. DNA barcoding discriminates a new cryptic grass species revealed in an ethnobotany study by the hill tribes of the Western Ghats in southern India. Mol Ecol Resour 2013; 9 Suppl s1:164-71. [PMID: 21564975 DOI: 10.1111/j.1755-0998.2009.02641.x] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Our research brought together traditional aboriginal knowledge (TK) and scientific knowledge (SK) to explore the relationship between scientific and aboriginal systems of botanical classification and the corresponding valorization(s) of biological diversity in the Western Ghats of southern India. We worked with two aboriginal cultures namely 'Irulas' and 'Malasars' of the Nilgiri Biosphere Reserve with an objective of evaluating the ability of different knowledge systems (SK and TK) to distinguish grass species belonging to the genus Tripogon, and assess the ability of DNA barcoding to discriminate a new cryptic species 'Tripogon cope' as deciphered by the hill tribes. We discovered that the aboriginal informants identified a common ethnotaxa 'Sunai pul', which is a cryptic species of grass not recognized by the SK classification.'sunai pul' is very important to both aboriginal cultures with ritualistic and economic utility. Morphometric analysis confirms the cryptic nature of this new species, which was validated using DNA barcoding. DNA barcode regions matK and trnH-psbA showed distinct sequence variations among the closely related ethnotaxa. Given the cryptic nature of ethnotaxa, we propose that a DNA barcode may be a reliable tool to identify ethnotaxa. We have initiated further studies in other cultures to develop theoretically sophisticated insights concerning the encounter between 'local' and 'scientific' approaches to the use of biodiversity knowledge. Furthermore, the research will add to a unifying global effort to speed up the documentation and understanding of the planet's natural diversity, while simultaneously respecting the cultural heterogeneity as a vital component of biological diversity.
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Affiliation(s)
- Subramanyam Ragupathy
- Floristic Diversity Research Group, Biodiversity Institute of Ontario Herbarium (OAC), University of Guelph, Guelph, Ontario, Canada N1G 2W1 P.G. and Research Department of Botany, Kongunad Arts and Science College, Bharathiar University, Coimbatore, Tamil Nadu 641046, India
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Abstract
The concept and practice of DNA barcoding have been designed as a system to facilitate species identification and recognition. The primary challenge for barcoding plants has been to identify a suitable region on which to focus the effort. The slow relative nucleotide substitution rates of plant mitochondria and the technical issues with the use of nuclear regions have focused attention on several proposed regions in the plastid genome. One of the challenges for barcoding is to discriminate closely related or recently evolved species. The Myristicaceae, or nutmeg family, is an older group within the angiosperms that contains some recently evolved species providing a challenging test for barcoding plants. The goal of this study is to determine the relative utility of six coding (Universal Plastid Amplicon - UPA, rpoB, rpoc1, accD, rbcL, matK) and one noncoding (trnH-psbA) chloroplast loci for barcoding in the genus Compsoneura using both single region and multiregion approaches. Five of the regions we tested were predominantly invariant across species (UPA, rpoB, rpoC1, accD, rbcL). Two of the regions (matK and trnH-psbA) had significant variation and show promise for barcoding in nutmegs. We demonstrate that a two-gene approach utilizing a moderately variable region (matK) and a more variable region (trnH-psbA) provides resolution among all the Compsonuera species we sampled including the recently evolved C. sprucei and C. mexicana. Our classification analyses based on nonmetric multidimensional scaling ordination, suggest that the use of two regions results in a decreased range of intraspecific variation relative to the distribution of interspecific divergence with 95% of the samples correctly identified in a sequence identification analysis.
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Affiliation(s)
- S G Newmaster
- Floristic Diversity Research Group, Biodiversity Institute of Ontario, Department of Integrative Biology, University of Guelph, Guelph, Ontario, Canada. N1G 2W1 Botanical Research Institute of Texas (BRIT), 509 Pecan Street, Suite 101, Fort Worth, Texas 76102-4060, USA
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Bainard JD, Forrest LL, Goffinet B, Newmaster SG. Nuclear DNA content variation and evolution in liverworts. Mol Phylogenet Evol 2013; 68:619-27. [PMID: 23624193 DOI: 10.1016/j.ympev.2013.04.008] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2012] [Revised: 02/05/2013] [Accepted: 04/11/2013] [Indexed: 10/26/2022]
Abstract
Across embryophytes there is a significant range in DNA content, both in regards to genome size (total DNA in an unreduced chromosome complement) and degree of endoreduplication (when DNA replication not followed by division resulting in various ploidy levels within the same individual). However, there is little information available on DNA content evolution in liverworts, the likely sister group to all other living plants. This study seeks to detect a phylogenetic structure in the variation in genome size and degree of endopolyploidy within liverworts. Furthermore, we test the hypothesis that shifts in breeding systems and genome size are correlated, as polyploidy is suggested to be a possible mechanism for the evolution of monoecy in liverworts and could therefore be associated with larger genome sizes. Genome size was determined for 67 liverwort species from 33 families using flow cytometry. Estimates for 48 species and 16 families are new to science. A phylogeny was reconstructed using the plastid gene rbcL. Over all taxa analyzed, there was a considerable range in genome size estimates with 1C-values from 0.27 pg (Jungermannia rubra) to 20.46 pg (Phyllothallia fuegiana). Large genome sizes were also found in the Haplomitriopsida. None of the liverwort species showed evidence of endopolyploidy. Although some taxa may be polyploids, a correlation between shifts in genome size and breeding system is lacking. Importantly, genome size variation in liverworts exhibits strong phylogenetic signal (Pagel's λ=0.99955).
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Affiliation(s)
- Jillian D Bainard
- Department of Integrative Biology, University of Guelph, 50 Stone Road E., Guelph, Ontario, Canada N1G 2W1.
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Newmaster SG, Ragupathy S, Dhivya S, Jijo CJ, Sathishkumar R, Patel K. Genomic valorization of the fine scale classification of small millet landraces in southern India. Genome 2013; 56:123-7. [PMID: 23517322 DOI: 10.1139/gen-2012-0183] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Our research seeks to investigate genomic diversity of landraces of millet, addressing a key uncertainty that will provide a framework for (i) a DNA barcode method that could be used for fast, sensitive, and accurate identification of millet landraces, and (ii) millet landrace conservation including biocultural diversity. We found considerable intraspecific variation among 15 landraces representing six species of small millets using nuclear regions (ITS, ITS1, and ITS2); there was no variation in plastid regions (rbcL, matK, and trnH-psbA). An efficacious ITS2 DNA barcode was used to make 100% accurate landrace assignments for 150 blind samples representing 15 landraces. Our research revealed that genomic variation is aligned with a fine-scale classification of landraces using traditional knowledge (TK) of local farmers. The landrace classification was highly correlated with traits (morphological, agricultural, and cultural utility) associated with considerable factors such as yield, drought tolerance, growing season, medicinal properties, and nutrition. This could provide a DNA-based model for conservation of genetic diversity and the associated bicultural diversity (TK) of millet landraces, which has sustained marginal farming communities in harsh environments for many generations.
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Affiliation(s)
- Steven G Newmaster
- Centre for Biodiversity Genomics, University of Guelph, Guelph, ON N1G 2W1, Canada.
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Bainard JD, Bainard LD, Henry TA, Fazekas AJ, Newmaster SG. A multivariate analysis of variation in genome size and endoreduplication in angiosperms reveals strong phylogenetic signal and association with phenotypic traits. New Phytol 2012; 196:1240-1250. [PMID: 23078229 DOI: 10.1111/j.1469-8137.2012.04370.x] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2012] [Accepted: 08/30/2012] [Indexed: 05/03/2023]
Abstract
Genome size (C-value) and endopolyploidy (endoreduplication index, EI) are known to correlate with various morphological and ecological traits, in addition to phylogenetic placement. A phylogenetically controlled multivariate analysis was used to explore the relationships between DNA content and phenotype in angiosperms. Seeds from 41 angiosperm species (17 families) were grown in a common glasshouse experiment. Genome size (2C-value and 1Cx-value) and EI (in four tissues: leaf, stem, root, petal) were determined using flow cytometry. The phylogenetic signal was calculated for each measure of DNA content, and phylogenetic canonical correlation analysis (PCCA) explored how the variation in genome size and EI was correlated with 18 morphological and ecological traits. Phylogenetic signal (λ) was strongest for EI in all tissues, and λ was stronger for the 2C-value than the 1Cx-value. PCCA revealed that EI was correlated with pollen length, stem height, seed mass, dispersal mechanism, arbuscular mycorrhizal association, life history and flowering time, and EI and genome size were both correlated with stem height and life history. PCCA provided an effective way to explore multiple factors of DNA content variation and phenotypic traits in a phylogenetic context. Traits that were correlated significantly with DNA content were linked to plant competitive ability.
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Affiliation(s)
- Jillian D Bainard
- Department of Integrative Biology, University of Guelph, 50 Stone Road East, Guelph, ON, Canada, N1G 2W1
| | - Luke D Bainard
- Department of Integrative Biology, University of Guelph, 50 Stone Road East, Guelph, ON, Canada, N1G 2W1
| | - Thomas A Henry
- Department of Integrative Biology, University of Guelph, 50 Stone Road East, Guelph, ON, Canada, N1G 2W1
| | - Aron J Fazekas
- Department of Integrative Biology, University of Guelph, 50 Stone Road East, Guelph, ON, Canada, N1G 2W1
| | - Steven G Newmaster
- Department of Integrative Biology, University of Guelph, 50 Stone Road East, Guelph, ON, Canada, N1G 2W1
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