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Zhao S, Zhang H, Zhao Z, Zhang Y, Yu J, Tang Y, Zhou C. Integrated DNA barcoding methods to identify species in the processed fish products from Chinese market. Food Res Int 2024; 182:114140. [PMID: 38519172 DOI: 10.1016/j.foodres.2024.114140] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2023] [Revised: 02/04/2024] [Accepted: 02/17/2024] [Indexed: 03/24/2024]
Abstract
DNA-based methods are reliable for a precise identification of species in processed products. In this study, we assessed five typical DNA extraction methods from multiple aspects. Full-length and mini-length DNA barcoding were performed to detect the species substitution and mislabeling of 305 processed fish products from the Chinese market covering six processed fish products. The salt extraction method that exhibited the best overall performance was applied. All samples were successfully extracted; however, only 19.3 % of samples could be amplified using the full-DNA barcode primer set, and 90.2 % of samples could be amplified using the newly designed mini-DNA barcode primer sets (401 and 320 bp). Overall, the molecular identification results revealed that 36.4 % (111/305) of the samples were inconsistent with the labels, with commercial fraud observed in all six types of processed fish products. The survey findings provide technical references for effective fish authentication monitoring, offering insights into the seafood safety in markets.
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Affiliation(s)
- Shu Zhao
- College of Life Sciences, Henan Normal University, Xinxiang 453007, Henan, China
| | - Han Zhang
- College of Life Sciences, Henan Normal University, Xinxiang 453007, Henan, China
| | - Ziyi Zhao
- College of Life Sciences, Henan Normal University, Xinxiang 453007, Henan, China
| | - Yizheng Zhang
- College of Fisheries, Henan Normal University, Xinxiang 453007, Henan, China
| | - Jinhui Yu
- College of Life Sciences, Henan Normal University, Xinxiang 453007, Henan, China
| | - Yongtao Tang
- College of Fisheries, Henan Normal University, Xinxiang 453007, Henan, China
| | - Chuanjiang Zhou
- College of Life Sciences, Henan Normal University, Xinxiang 453007, Henan, China.
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2
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Ekundayo TC, Swalaha FM, Ijabadeniyi OA. Global and regional prevalence of Helicobacter pylori in drinking waters: A sustainable, human development and socio-demographic indices based meta-regression-modelling. Sci Total Environ 2023; 861:160633. [PMID: 36481137 DOI: 10.1016/j.scitotenv.2022.160633] [Citation(s) in RCA: 1] [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] [Subscribe] [Scholar Register] [Received: 10/22/2022] [Revised: 11/27/2022] [Accepted: 11/28/2022] [Indexed: 06/17/2023]
Abstract
Helicobacter pylori (Hp) transmission dynamics via drinking water (DW) has a far much higher direct and indirect public health disease burden than previously thought. This study aimed to assess the global prevalence of Hp in DW, distributions across regions and socioeconomic indices (continent, world bank income, Human Development Index (HDI), Sustainable Development Index (SuDI), Socio-Demographic Index (SDI) quintile, and WHO regions). Hp-DW related data mined from five databases until 10/12/2022 according to PRISMA standard were quality-appraised and fitted to a generalized linear mixed-effects model. Sub-group analysis and meta-regression-modelling coupled with a 1000-permutation test (⁎) were conducted. The global prevalence of Hp in DW was 15.7% (95% confidence interval [CI]: 7.98-27.5), which varied significantly by sampling methods (Moore swabbing (61.0% [0.00-100.0]) vs. grab sampling (13.68%[6.99-25.04])) and detection technique (non-culture (21.35%[9.13-42.31]) vs. cultured-based methods (Psubgroup < 0.01)). The period 1990-99 had the highest prevalence (41.24% [0.02-99.97]). Regarding regional designations, Hp prevalence in DW was significantly different being highest in North America (61.82% [41.03-79.02]) by continents, AMR (42.66% [20.81-67.82]) by WHO group, high HDI (24.64% [10.98-46.43]) by HDI group and North America (61.90% [2.79-98.93]) by world bank region (Psubgroup < 0.01). Generally, sample preparation, SuDI grouping, and detection/confirmation techniques, have significant effects on the detection/prevalence of Hp in DW (Psubgroup < 0.01). Hp prevalence in DW was not significantly different among rural and urban DW (Psubgroup = 0.90), world bank income groups (Psubgroup = 0.15), and SDI quintiles (Psubgroup = 0.07). Among the predictors examined, only sample size (p < 0.1, R∗2(coefficient of determinant) = 15.29%), continent (p∗val = 0.04), HDI (p∗val = 0.02), HDI group (p∗val = 0.05), and microbiological methods (p < 0.1; R∗2=28.09 %) predicted Hp prevalence in DW robustly. In conclusion, Hp prevalence is still endemic in DW regardless of the regional designations/improve DW supplies.
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Affiliation(s)
- Temitope C Ekundayo
- Department of Biotechnology and Food Science, Durban University of Technology, Steve Biko Campus, 121 Steve Biko Rd, Musgrave, Berea, 4001 Durban, South Africa.
| | - Feroz M Swalaha
- Department of Biotechnology and Food Science, Durban University of Technology, Steve Biko Campus, 121 Steve Biko Rd, Musgrave, Berea, 4001 Durban, South Africa
| | - Oluwatosin A Ijabadeniyi
- Department of Biotechnology and Food Science, Durban University of Technology, Steve Biko Campus, 121 Steve Biko Rd, Musgrave, Berea, 4001 Durban, South Africa
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3
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Amin H, Marshall IPG, Bertelsen RJ, Wouters IM, Schlünssen V, Sigsgaard T, Šantl-Temkiv T. Optimization of bacterial DNA and endotoxin extraction from settled airborne dust. Sci Total Environ 2023; 857:159455. [PMID: 36252657 DOI: 10.1016/j.scitotenv.2022.159455] [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: 07/29/2022] [Revised: 10/03/2022] [Accepted: 10/11/2022] [Indexed: 06/16/2023]
Abstract
Collecting and obtaining sufficient amount of airborne particles for multiple microbial component assessments can be challenging. A passive dust sampling device, the electrostatic dust fall collector (EDC) has been established for assessing airborne exposures including endotoxin and glucans. Recently, with advances in next-generation sequencing techniques, EDCs were used to collect microbial cells for DNA sequencing analysis to promote the study of airborne bacterial and fungal communities. However, low DNA yields have been problematic when employing passive sampling with EDC. To address this challenge, we attempted to increase the efficiency of extraction. We compared DNA extraction efficiency of bacterial components from EDCs captured on filters through filtration using five extraction techniques. By measuring the abundance, diversity and structure of bacterial communities using qPCR and amplicon sequencing targeting 16S rRNA genes, we found that two techniques outperformed the rest. Furthermore, we developed protocols to simultaneously extract both DNA and endotoxin from a single EDC cloth. Our technique promotes a high quality to price ratio and may be employed in large epidemiological studies addressing airborne bacterial exposure where a large number of samples is needed.
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Affiliation(s)
- Hesham Amin
- Department of Clinical Science, University of Bergen, Bergen, Norway.
| | - Ian P G Marshall
- Section for Microbiology, Department of Biology, Aarhus University, Aarhus, Denmark
| | - Randi J Bertelsen
- Department of Clinical Science, University of Bergen, Bergen, Norway
| | - Inge M Wouters
- Institute for Risk Assessment Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, the Netherlands
| | - Vivi Schlünssen
- Department of Clinical Science, University of Bergen, Bergen, Norway
| | - Torben Sigsgaard
- Department of Public Health, Environment, Work and Health, Danish Ramazzini Centre, Aarhus University, Aarhus, Denmark
| | - Tina Šantl-Temkiv
- Section for Microbiology, Department of Biology, Aarhus University, Aarhus, Denmark
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4
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Davey ML, Kamenova S, Fossøy F, Solberg EJ, Davidson R, Mysterud A, Rolandsen CM. Faecal metabarcoding provides improved detection and taxonomic resolution for non-invasive monitoring of gastrointestinal nematode parasites in wild moose populations. Parasit Vectors 2023; 16:19. [PMID: 36653864 PMCID: PMC9847159 DOI: 10.1186/s13071-022-05644-6] [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: 07/06/2022] [Accepted: 12/28/2022] [Indexed: 01/19/2023] Open
Abstract
BACKGROUND Although wild ungulate populations are heavily monitored throughout Europe, we understand little of how parasites affect population dynamics, and there is no systematic, long-term monitoring of parasite diversity and parasite loads. Such monitoring is in part hampered by a lack of time- and cost-effective assay methodologies with high sensitivity and good taxonomic resolution. DNA metabarcoding has been successfully used to characterize the parasitic nemabiome with high taxonomic resolution in a variety of wild and domestic hosts. However, in order to implement this technique in large-scale, potentially non-invasive monitoring of gastrointestinal parasitic nematodes (GIN), protocol optimization is required to maximize biodiversity detection, whilst maintaining time- and cost-effectiveness. METHODS Faecal samples were collected from a wild moose population and GIN communities were characterized and quantified using both parasitological techniques (egg and larva counting) and DNA metabarcoding of the ITS2 region of rDNA. Three different isolation methods were compared that differed in the volume of starting material and cell lysis method. RESULTS Similar nematode faunas were recovered from all samples using both parasitological and metabarcoding methods, and the approaches were largely congruent. However, metabarcoding assays showed better taxonomic resolution and slightly higher sensitivity than egg and larvae counts. The metabarcoding was not strictly quantitative, but the proportion of target nematode sequences recovered was correlated with the parasitologically determined parasite load. Species detection rates in the metabarcoding assays were maximized using a DNA isolation method that included mechanical cell disruption and maximized the starting material volume. CONCLUSIONS DNA metabarcoding is a promising technique for the non-invasive, large-scale monitoring of parasitic GINs in wild ungulate populations, owing to its high taxonomic resolution, increased assay sensitivity, and time- and cost-effectiveness. Although metabarcoding is not a strictly quantitative method, it may nonetheless be possible to create a management- and conservation-relevant index for the host parasite load from this data. To optimize the detection rates and time- and cost-effectiveness of metabarcoding assays, we recommend choosing a DNA isolation method that involves mechanical cell disruption and maximizes the starting material volume.
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Affiliation(s)
- Marie L. Davey
- grid.420127.20000 0001 2107 519XNorwegian Institute for Nature Research (NINA), Trondheim, Norway
| | - Stefaniya Kamenova
- grid.5510.10000 0004 1936 8921University of Oslo, Oslo, Norway ,grid.19477.3c0000 0004 0607 975XNorwegian University of Life Sciences, Ås, Norway
| | - Frode Fossøy
- grid.420127.20000 0001 2107 519XNorwegian Institute for Nature Research (NINA), Trondheim, Norway
| | - Erling J. Solberg
- grid.420127.20000 0001 2107 519XNorwegian Institute for Nature Research (NINA), Trondheim, Norway
| | - Rebecca Davidson
- grid.410549.d0000 0000 9542 2193Norwegian Veterinary Institute, Tromsø, Norway
| | - Atle Mysterud
- grid.420127.20000 0001 2107 519XNorwegian Institute for Nature Research (NINA), Trondheim, Norway ,grid.5510.10000 0004 1936 8921University of Oslo, Oslo, Norway
| | - Christer M. Rolandsen
- grid.420127.20000 0001 2107 519XNorwegian Institute for Nature Research (NINA), Trondheim, Norway
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5
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Oba U, Kohashi K, Sangatsuda Y, Oda Y, Sonoda KH, Ohga S, Yoshimoto K, Arai Y, Yachida S, Shibata T, Ito T, Miura F. An efficient procedure for the recovery of DNA from formalin-fixed paraffin-embedded tissue sections. Biol Methods Protoc 2022; 7:bpac014. [PMID: 35937639 PMCID: PMC9351614 DOI: 10.1093/biomethods/bpac014] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [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: 04/25/2022] [Revised: 06/30/2022] [Indexed: 11/16/2022] Open
Abstract
With the advent of new molecular diagnostic techniques, retrieving DNA from the formalin-fixed paraffin-embedded (FFPE) tissues has become an essential yet challenging step for efficient downstream processes. Owing to low quality and quantity of DNA retrieved from the FFPE sections, the process is often impractical and needs significant improvements. Here, we established an efficient method for the purification of DNA from FFPE specimens by optimizing incubation temperature, incubation time, and the concentration of a formalin scavenger tris(hydroxymethyl)aminomethane (Tris) for reverse-crosslinking. The optimized method, named "Highly concentrated Tris-mediated DNA extraction" (HiTE), yielded three times the DNA yield per tissue slice compared with a representative DNA extraction kit. Moreover, the use of HiTE-extracted DNA increased the yield of the sequencing library three times and accordingly yielded a log higher and more reproducible sequencing library compared with that obtained using the commonly used commercial kit. The sequencing library prepared from HiTE-extracted FFPE-DNA had longer inserts and produced reads that evenly covered the reference genome. Successful application of HiTE-extracted FFPE-DNA for whole-genome and targeted gene panel sequencing indicates its practical usability.
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Affiliation(s)
- Utako Oba
- Department of Biochemistry, Kyushu University Graduate School of Medical Sciences, 3-1-1 Maidashi, Higashi-Ku, Fukuoka 812-8582, Japan
| | - Kenichi Kohashi
- Department of Anatomic Pathology, Kyushu University Graduate School of Medical Sciences, 3-1-1 Maidashi, Higashi-Ku, Fukuoka 812-8582, Japan
| | - Yuhei Sangatsuda
- Department of Neurosurgery, Kyushu University Graduate School of Medical Sciences, 3-1-1 Maidashi, Higashi-Ku, Fukuoka 812-8582, Japan
| | - Yoshinao Oda
- Department of Anatomic Pathology, Kyushu University Graduate School of Medical Sciences, 3-1-1 Maidashi, Higashi-Ku, Fukuoka 812-8582, Japan
| | - Koh-Hei Sonoda
- Department of Ophthalmology, Kyushu University Graduate School of Medical Sciences, 3-1-1 Maidashi, Higashi-Ku, Fukuoka 812-8582, Japan
| | - Shouichi Ohga
- Department of Pediatrics, Kyushu University Graduate School of Medical Sciences, 3-1-1 Maidashi, Higashi-Ku, Fukuoka 812-8582, Japan
| | - Koji Yoshimoto
- Department of Neurosurgery, Kyushu University Graduate School of Medical Sciences, 3-1-1 Maidashi, Higashi-Ku, Fukuoka 812-8582, Japan
| | - Yasuhito Arai
- Division of Cancer Genomics, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-ku, Tokyo 104-0045, Japan
| | - Shinichi Yachida
- Department of Cancer Genome Informatics, Graduate School of Medicine, Osaka University, 2-2 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Tatsuhiro Shibata
- Division of Cancer Genomics, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-ku, Tokyo 104-0045, Japan
| | - Takashi Ito
- Department of Biochemistry, Kyushu University Graduate School of Medical Sciences, 3-1-1 Maidashi, Higashi-Ku, Fukuoka 812-8582, Japan
| | - Fumihito Miura
- Department of Biochemistry, Kyushu University Graduate School of Medical Sciences, 3-1-1 Maidashi, Higashi-Ku, Fukuoka 812-8582, Japan
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6
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Chen XX, Chen W, Liu YL, Lin CX, Li M, Chen WJ, Xie SH, Lin DF, Cao SM. Development and validation of a flexible DNA extraction (PAN) method for liquid biopsy of multiple sample types. J Clin Lab Anal 2021; 35:e23962. [PMID: 34399000 PMCID: PMC8418477 DOI: 10.1002/jcla.23962] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Revised: 07/07/2021] [Accepted: 08/03/2021] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND Liquid biopsy is gaining increasing popularity in cancer screening and diagnosis. However, there is no relatively mature DNA isolation method or commercial kit available that is compatible with different LB sample types. This study developed a PAN-sample DNA isolation method (PAN method) for liquid biopsy samples. METHODS The PAN method has two key steps, including biosample-specific pretreatments for various LB sample types and high concentration guanidine thiocyanate buffer for lysis and denaturation procedure. Subsequently, the performance of PAN method was validated by a series of molecular analyses. RESULTS The PAN method was used to isolate DNA from multiple sample types related to LB, including plasma, serum, saliva, nasopharyngeal swab, and stool. All purified DNA products showed good quality and high quantity. Comparison of KRAS mutation analysis using DNA purified using PAN method versus QIAamp methods showed similar efficiency. Epstein-Barr virus DNA was detected via Q-PCR using DNA purified from serum, plasma, nasopharyngeal swab, and saliva samples collected from nasopharyngeal carcinoma patients. Similarly, methylation sequencing of swab and saliva samples revealed good coverage of target region and high methylation of HLA-DPB1 gene. Finally, 16S rDNA gene sequencing of saliva, swab, and stool samples successfully defines the relative abundance of microbial communities. CONCLUSIONS This study developed and validated a PAN-sample DNA isolation method that can be used for different LB samples, which can be applied to molecular epidemiological research and other areas.
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Affiliation(s)
- Xiao-Xia Chen
- Department of Cancer Prevention Research, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Wei Chen
- Department of Pathology, The Seventh Affiliated Hospital, Sun Yat-sen University, Shenzhen, China
| | - Yi-Long Liu
- Department of Cancer Prevention Research, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Can-Xiang Lin
- Department of Plastic Surgery, The First Affiliated Hospital of Jinan University, Guangzhou, China
| | - Mengmeng Li
- Department of Cancer Prevention Research, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Wen-Jie Chen
- Department of Cancer Prevention Research, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Shang-Hang Xie
- Department of Cancer Prevention Research, Sun Yat-sen University Cancer Center, Guangzhou, China.,State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, and Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-Sen University Cancer Center, Guangzhou, China
| | - Dong-Feng Lin
- Department of Cancer Prevention Research, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Su-Mei Cao
- Department of Cancer Prevention Research, Sun Yat-sen University Cancer Center, Guangzhou, China.,State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, and Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-Sen University Cancer Center, Guangzhou, China
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7
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Zhang M, Cao P, Dai Q, Wang Y, Feng X, Wang H, Wu H, Ko AMS, Mao X, Liu Y, Yu L, Roos C, Nadler T, Xiao W, Bennett EA, Fu Q. Comparative analysis of DNA extraction protocols for ancient soft tissue museum samples. Zool Res 2021; 42:280-286. [PMID: 33855818 PMCID: PMC8175948 DOI: 10.24272/j.issn.2095-8137.2020.377] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
Abstract
DNA studies of endangered or extinct species often rely on ancient or degraded remains. The majority of ancient DNA (aDNA) extraction protocols focus on skeletal elements, with skin and hair samples rarely explored. Similar to that found in bones and teeth, DNA extracted from historical or ancient skin and fur samples is also extremely fragmented with low endogenous content due to natural degradation processes. Thus, the development of effective DNA extraction methods is required for these materials. Here, we compared the performance of two DNA extraction protocols (commercial and custom laboratory aDNA methods) on hair and skin samples from decades-old museum specimens to Iron Age archaeological material. We found that apart from the impact sample-specific taphonomic and handling history has on the quantity and quality of DNA preservation, skin yielded more endogenous DNA than hair of the samples and protocols tested. While both methods recovered DNA from ancient soft tissue, the laboratory method performed better overall in terms of DNA yield and quality, which was primarily due to the poorer performance of the commercial binding buffer in recovering aDNA.
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Affiliation(s)
- Ming Zhang
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing 100044, China.,CAS Center for Excellence in Life and Paleoenvironment, Beijing 100044, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Peng Cao
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing 100044, China.,CAS Center for Excellence in Life and Paleoenvironment, Beijing 100044, China
| | - Qingyan Dai
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing 100044, China.,CAS Center for Excellence in Life and Paleoenvironment, Beijing 100044, China
| | - Yongqiang Wang
- Institute of cultural relics and archaeology in Xinjiang, Urumqi, Xinjiang 830011, China
| | - Xiaotian Feng
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing 100044, China.,CAS Center for Excellence in Life and Paleoenvironment, Beijing 100044, China
| | - Hongru Wang
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing 100044, China
| | - Hong Wu
- State Key Laboratory for Conservation and Utilization of Bio-resource in Yunnan, Yunnan University, Kunming, Yunnan 650091, China
| | - Albert Min-Shan Ko
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing 100044, China
| | - Xiaowei Mao
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing 100044, China.,CAS Center for Excellence in Life and Paleoenvironment, Beijing 100044, China
| | - Yichen Liu
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing 100044, China.,CAS Center for Excellence in Life and Paleoenvironment, Beijing 100044, China
| | - Li Yu
- State Key Laboratory for Conservation and Utilization of Bio-resource in Yunnan, Yunnan University, Kunming, Yunnan 650091, China
| | - Christian Roos
- Gene Bank of Primates and Primate Genetics Laboratory, German Primate Center, Leibniz Institute for Primate Research, Göttingen 37077, Germany
| | - Tilo Nadler
- Wildlife Consultant, Cuc Phuong Commune, Nho Quan, Ninh Binh 430000, Vietnam
| | - Wen Xiao
- Institute of Eastern-Himalaya Biodiversity Research, Dali University, Dali, Yunnan 671003, China
| | - E Andrew Bennett
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing 100044, China.,CAS Center for Excellence in Life and Paleoenvironment, Beijing 100044, China. E-mail:
| | - Qiaomei Fu
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing 100044, China.,CAS Center for Excellence in Life and Paleoenvironment, Beijing 100044, China.,University of Chinese Academy of Sciences, Beijing 100049, China. E-mail:
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8
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Sullivan AP, Marciniak S, O'Dea A, Wake TA, Perry GH. Modern, archaeological, and paleontological DNA analysis of a human-harvested marine gastropod (Strombus pugilis) from Caribbean Panama. Mol Ecol Resour 2021; 21:1517-1528. [PMID: 33595921 DOI: 10.1111/1755-0998.13361] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Revised: 01/26/2021] [Accepted: 02/05/2021] [Indexed: 12/17/2022]
Abstract
Although protocols exist for the recovery of ancient DNA from land snail and marine bivalve shells, marine conch shells have yet to be studied from a paleogenomic perspective. We first present reference assemblies for both a 623.7 Mbp nuclear genome and a 15.4 kbp mitochondrial genome for Strombus pugilis, the West Indian fighting conch. We next detail a method to extract and sequence DNA from conch shells and apply it to conch from Bocas del Toro, Panama across three time periods: recently-eaten and discarded (n = 3), Late Holocene (984-1258 before present [BP]) archaeological midden (n = 5), and mid-Holocene (5711-7187 BP) paleontological fossil coral reef (n = 5). These results are compared to control DNA extracted from live-caught tissue and fresh shells (n = 5). Using high-throughput sequencing, we were able to obtain S. pugilis nuclear sequence reads from shells across all age periods: up to 92.5 thousand filtered reads per sample in live-caught shell material, 4.57 thousand for modern discarded shells, 12.1 thousand reads for archaeological shells, and 114 reads in paleontological shells. We confirmed authenticity of the ancient DNA recovered from the archaeological and paleontological shells based on 5.7× higher average frequency of deamination-driven misincorporations and 15% shorter average read lengths compared to the modern shells. Reads also mapped to the S. pugilis mitochondrial genome for all but the paleontological shells, with consistent ratios of mitochondrial to nuclear mapped reads across sample types. Our methods can be applied to diverse archaeological sites to facilitate reconstructions of the long-term impacts of human behaviour on mollusc evolutionary biology.
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Affiliation(s)
- Alexis P Sullivan
- Department of Biology, Pennsylvania State University, University Park, PA, USA
| | - Stephanie Marciniak
- Department of Anthropology, Pennsylvania State University, University Park, PA, USA
| | - Aaron O'Dea
- Smithsonian Tropical Research Institute, Panama City, Panama.,Department of Biological, Geological, and Environmental Sciences, University of Bologna, Bologna, Italy
| | - Thomas A Wake
- Smithsonian Tropical Research Institute, Panama City, Panama.,Department of Anthropology and the Costen Institute of Archaeology, University of California, Los Angeles, CA, USA
| | - George H Perry
- Department of Biology, Pennsylvania State University, University Park, PA, USA.,Department of Anthropology, Pennsylvania State University, University Park, PA, USA.,Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA, USA
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9
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Angthong P, Uengwetwanit T, Pootakham W, Sittikankaew K, Sonthirod C, Sangsrakru D, Yoocha T, Nookaew I, Wongsurawat T, Jenjaroenpun P, Rungrassamee W, Karoonuthaisiri N. Optimization of high molecular weight DNA extraction methods in shrimp for a long-read sequencing platform. PeerJ 2020; 8:e10340. [PMID: 33240651 PMCID: PMC7668203 DOI: 10.7717/peerj.10340] [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] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Accepted: 10/20/2020] [Indexed: 12/12/2022] Open
Abstract
Marine organisms are important to global food security as they are the largest source of animal proteins feeding mankind. Genomics-assisted aquaculture can increase yield while preserving the environment to ensure sufficient and sustainable production for global food security. However, only few high-quality genome sequences of marine organisms, especially shellfish, are available to the public partly because of the difficulty in the sequence assembly due to the complex nature of their genomes. A key step for a successful genome sequencing is the preparation of high-quality high molecular weight (HMW) genomic DNA. This study evaluated the effectiveness of five DNA extraction protocols (CTAB, Genomic-tip, Mollusc DNA, TIANamp Marine Animals DNA, and Sbeadex livestock kits) in obtaining shrimp HMW DNA for a long-read sequencing platform. DNA samples were assessed for quality and quantity using a Qubit fluorometer, NanoDrop spectrophotometer and pulsed-field gel electrophoresis. Among the five extraction methods examined without further optimization, the Genomic-tip kit yielded genomic DNA with the highest quality. However, further modifications of these established protocols might yield even better DNA quality and quantity. To further investigate whether the obtained genomic DNA could be used in a long-read sequencing application, DNA samples from the top three extraction methods (CTAB method, Genomic-tip and Mollusc DNA kits) were used for Pacific Biosciences (PacBio) library construction and sequencing. Genomic DNA obtained from Genomic-tip and Mollusc DNA kits allowed successful library construction, while the DNA obtained from the CTAB method did not. Genomic DNA isolated using the Genomic-tip kit yielded a higher number of long reads (N50 of 14.57 Kb) than those obtained from Mollusc DNA kits (N50 of 9.74 Kb). Thus, this study identified an effective extraction method for high-quality HMW genomic DNA of shrimp that can be applied to other marine organisms for a long-read sequencing platform.
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Affiliation(s)
- Pacharaporn Angthong
- Microarray Research Team, National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency, Pathum Thani, Thailand
| | - Tanaporn Uengwetwanit
- Microarray Research Team, National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency, Pathum Thani, Thailand
| | - Wirulda Pootakham
- National Omics Center, National Science and Technology Development Agency, Pathum Thani, Thailand
| | - Kanchana Sittikankaew
- Microarray Research Team, National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency, Pathum Thani, Thailand
| | - Chutima Sonthirod
- National Omics Center, National Science and Technology Development Agency, Pathum Thani, Thailand
| | - Duangjai Sangsrakru
- National Omics Center, National Science and Technology Development Agency, Pathum Thani, Thailand
| | - Thippawan Yoocha
- National Omics Center, National Science and Technology Development Agency, Pathum Thani, Thailand
| | - Intawat Nookaew
- Department of Biomedical Informatics, College of Medicine, University of Arkansas for Medical Sciences, Little Rock, AR, United States of America
| | - Thidathip Wongsurawat
- Division of Bioinformatics and Data Management for Research, Department of Research and Development, Faculty of Medicine, Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Piroon Jenjaroenpun
- Division of Bioinformatics and Data Management for Research, Department of Research and Development, Faculty of Medicine, Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Wanilada Rungrassamee
- Microarray Research Team, National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency, Pathum Thani, Thailand
| | - Nitsara Karoonuthaisiri
- Microarray Research Team, National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency, Pathum Thani, Thailand
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10
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Khosravi Babadi Z, Ebrahimipour G, Wink J, Narmani A, Risdian C. Isolation and identification of Streptomyces sp. Act4Zk, a good producer of Staurosporine and some derivatives. Lett Appl Microbiol 2020; 72:206-218. [PMID: 33058293 DOI: 10.1111/lam.13415] [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] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2020] [Revised: 10/07/2020] [Accepted: 10/09/2020] [Indexed: 11/28/2022]
Abstract
In this study, strain Streptomyces sp. Act4Zk was isolated based on a method developed for the isolation of myxobacteria. Due to the low efficiency of the majority of conventional DNA extraction techniques, for molecular identification of the strain Streptomyces sp. Act4Zk, a new technique for DNA extraction of Actinobacteria was developed. In order to explore potential bioactivities of the strain, extracts of the fermented broth culture were prepared by an organic solvent (i.e. ethyl acetate) extraction method using. These ethyl acetate extracts were subjected to HPLC fractionation against standard micro-organisms, followed by LC/MS analysis. Based on morphological, physiological, biochemical and 16S rRNA gene sequence data, strain Streptomyces sp. Act4Zk is likely to be a new species of Streptomyces, close to Streptomyces genecies and Streptomyces roseolilacinus. Antimicrobial assay indicated high antifungal activity as well as antibacterial activity against Mycobacterium smegmatis and Gram-positive bacteria for the new strain. HPLC and LC/MS analyses of the extracts led to the identification of three different compounds and confirmed our hypothesis that the interesting species of the genus Streptomyces being a good producer of staurosporine and some derivatives.
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Affiliation(s)
- Z Khosravi Babadi
- Department of Microbiology & Microbial Biotechnology, Faculty of Life Sciences and Biotechnology, Shahid Beheshti University GC, Tehran, Iran.,Microbial Strain Collection, Helmholtz Centre for Infection Research GmbH (HZI), Braunschweig, Germany
| | - G Ebrahimipour
- Department of Microbiology & Microbial Biotechnology, Faculty of Life Sciences and Biotechnology, Shahid Beheshti University GC, Tehran, Iran
| | - J Wink
- Microbial Strain Collection, Helmholtz Centre for Infection Research GmbH (HZI), Braunschweig, Germany
| | - A Narmani
- Department of Plant Protection, Faculty of Agriculture, University of Tabriz, Tabriz, Iran.,Department of Microbial Drugs, Helmholtz Centre for Infection Research and German Centre for Infection Research (DZIF), Braunschweig, Germany
| | - C Risdian
- Microbial Strain Collection, Helmholtz Centre for Infection Research GmbH (HZI), Braunschweig, Germany.,Research Unit for Clean Technology, Indonesian Institute of Sciences (LIPI), Bandung, Indonesia
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11
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Sui HY, Weil AA, Nuwagira E, Qadri F, Ryan ET, Mezzari MP, Phipatanakul W, Lai PS. Impact of DNA Extraction Method on Variation in Human and Built Environment Microbial Community and Functional Profiles Assessed by Shotgun Metagenomics Sequencing. Front Microbiol 2020; 11:953. [PMID: 32528434 PMCID: PMC7262970 DOI: 10.3389/fmicb.2020.00953] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [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: 02/19/2020] [Accepted: 04/21/2020] [Indexed: 12/26/2022] Open
Abstract
Both the host microbiome and the microbiome of the built environment can have profound impacts on human health. While prior studies have suggested that the variability introduced by DNA extraction method is less than typical biologic variation, most studies have focused on 16S rRNA amplicon sequencing or on high biomass fecal samples. Shotgun metagenomic sequencing provides advantages over amplicon sequencing for surveying the microbiome, but is a challenge to perform in lower microbial biomass samples with high human DNA content such as sputum or vacuumed dust. Here we systematically evaluate the impact of four different extraction methods (phenol:choloroform, and three high-throughput kit-based approaches, the Promega Maxwell gDNA, Qiagen MagAttract PowerSoil DNA, and ZymoBIOMICS 96 MagBead). We report the variation in microbial community structure and predicted microbial function assessed by shotgun metagenomics sequencing in human stool, sputum, and vacuumed dust obtained from ongoing cohort studies or clinical trials. The same beadbeating protocol was used for all samples to focus our evaluation on the impact of kit chemistries on sequencing results. DNA yield was overall highest in the phenol:choloroform and Promega approaches. Only the phenol:choloroform approach showed evidence of contamination in negative controls. Bias was evaluated using mock community controls, and was noted across all extraction methods, although Promega exhibited the least amount of bias. The extraction method did not impact the proportion of human reads, although stool had the lowest proportion of human reads (0.1%) as compared to dust (44.1%) and sputum (80%). We calculated Bray-Curtis dissimilarity and Aitchison distances to evaluate the impact of extraction method on microbial community structure by sample type. Extraction method had the lowest impact in stool (extraction method responsible for 3.0-3.9% of the variability), the most impact in vacuumed dust (12-16% of the variability) and intermediate values for sputum (9.2-12% variability). Similar differences were noted when evaluating microbial community function. Our results will inform investigators planning microbiome studies using diverse sample types in large clinical studies. A consistent DNA extraction approach across all sample types is recommended, particularly with lower microbial biomass samples that are more heavily influenced by extraction method.
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Affiliation(s)
- Hui-yu Sui
- Division of Pulmonary and Critical Care Medicine, Massachusetts General Hospital, Boston, MA, United States
| | - Ana A. Weil
- Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA, United States,Harvard Medical School, Boston, MA, United States
| | - Edwin Nuwagira
- Mbarara University of Science and Technology, Mbarara, Uganda
| | - Firdausi Qadri
- Infectious Diseases Division, International Centre for Diarrhoeal Disease Research, Bangladesh, Dhaka, Bangladesh
| | - Edward T. Ryan
- Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA, United States,Harvard Medical School, Boston, MA, United States
| | - Melissa P. Mezzari
- Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, United States
| | - Wanda Phipatanakul
- Harvard Medical School, Boston, MA, United States,Division of Immunology, Boston Children’s Hospital, Boston, MA, United States
| | - Peggy S. Lai
- Division of Pulmonary and Critical Care Medicine, Massachusetts General Hospital, Boston, MA, United States,Harvard Medical School, Boston, MA, United States,Division of Immunology, Boston Children’s Hospital, Boston, MA, United States,*Correspondence: Peggy S. Lai, ;
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12
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Inkret J, Podovšovnik E, Zupanc T, Pajnič IZ. Nails as a primary sample type for molecular genetic identification of highly decomposed human remains. Int J Legal Med 2020; 134:1629-1638. [PMID: 32372234 DOI: 10.1007/s00414-020-02289-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Accepted: 03/30/2020] [Indexed: 11/30/2022]
Abstract
For identification of badly preserved cadavers, only a few tissues can be used as a source of DNA, mostly bones and teeth, from which sampling and DNA extraction are difficult and time-consuming. In most highly decomposed remains, the nails are preserved. The aim of this study was to evaluate nails as an alternative source of DNA instead of bones and teeth in demanding routine identification cases. An automated extraction method was optimized on nails obtained from 33 cadavers with a post-mortem interval (PMI) up to 5 years. The commercially available EZ1 Investigator Kit (Qiagen) was used for extraction, and the G2 buffer included in the kit was replaced with TNCa buffer, and DTT was added for digestion of 5 mg of nail. The DNA was purified in a Biorobot EZ1 device (Qiagen), quantified using the PowerQuant System (Promega), and STR typing was performed with the NGM kit (TFS). From 0.3 to 270 μg DNA/g of nail was obtained from the samples analyzed, with an average yield of 36 μg DNA/g of nail. Full STR profiles were obtained from all nails except one. The optimized extraction method proved to be fast and highly efficient in the removal of PCR inhibitors, and it yields high amounts of DNA for successful STR typing. Nails were implemented as the primary sample type for obtaining DNA from highly decomposed and partially skeletonized cadavers in routine forensic identification cases in our laboratory.
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Affiliation(s)
- Jezerka Inkret
- Institute of Forensic Medicine, Faculty of Medicine, University of Ljubljana, Korytkova 2, 1000, Ljubljana, Slovenia
| | - Eva Podovšovnik
- Faculty of Tourism Studies - Turistica, University of Primorska, Portorož, Slovenia
| | - Tomaž Zupanc
- Institute of Forensic Medicine, Faculty of Medicine, University of Ljubljana, Korytkova 2, 1000, Ljubljana, Slovenia
| | - Irena Zupanič Pajnič
- Institute of Forensic Medicine, Faculty of Medicine, University of Ljubljana, Korytkova 2, 1000, Ljubljana, Slovenia.
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13
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Boulesnane Y, Leloup J, Lerch TZ, Roynette A, Pensé-Lhéritier AM, Mielcarek C, Changey F. Impact of sampling and DNA extraction methods on skin microbiota assessment. J Microbiol Methods 2020; 171:105880. [PMID: 32109500 DOI: 10.1016/j.mimet.2020.105880] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [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: 12/05/2019] [Revised: 02/12/2020] [Accepted: 02/22/2020] [Indexed: 01/01/2023]
Abstract
The skin microbiota is characterized by high intra- and inter-variability among individuals, due to a multitude of intrinsic and extrinsic parameters such as genetics, lifestyles or pollution. This variability may be heightened due to sampling method as the skin is a multilayer organ and its outermost layer consists of dead cells. In order to investigate this biological variability in a reproducible way, we studied how sampling procedure and DNA extraction methods influence the qualitative and quantitative gathering of bacterial communities. Here, we tested a new sampling procedure that consists in exerting a slight abrasion (scrubbing) on the skin prior to swabbing and extracting DNA in order to remove squames and access deeper ecological niches. Scrubbed and non-scrubbed samples were collected from a panel of six volunteers, and four DNA extraction methods were performed on the samples. The abundance, diversity and structure of the bacterial communities were measured using qPCR technics and 16S rDNA gene-metabarcoding. Bacterial community abundance was significantly impacted by the DNA extraction method (in favor of a method designed for tissues) but not by sampling procedure, as scrubbing does not increase bacterial biomass gathered. Bacterial α- and β-diversities were both affected by DNA extraction methods and sampling procedure. Scrubbing reveals different microbial composition by gathering bacteria living in deeper skin layer, resulting in a lower intra-personal variability. The taxonomic analysis showed that more bacteria belonging to anaerobes groups were present in scrubbed samples. We conclude that DNA extraction methods designed for tissue are not necessarily associated with high qualitative efficiency and slight scrubbing prior DNA extraction reduces intrapersonal variability and give access to a new microbial diversity.
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Affiliation(s)
- Yanisse Boulesnane
- Laboratoire EBInnov, Ecole de Biologie Industrielle, 49 Avenue des Genottes, 95800 Cergy, France
| | - Julie Leloup
- Institute of Ecology and Environmental Sciences, UMR 7618, Sorbonne Université, IRD, CNRS, INRA, UPEC, Université de Paris Diderot, 4 place Jussieu, 75005 Paris, France
| | - Thomas Z Lerch
- Institute of Ecology and Environmental Sciences, UMR 7618, Sorbonne Université, IRD, CNRS, INRA, UPEC, Université de Paris Diderot, 4 place Jussieu, 75005 Paris, France
| | - Anne Roynette
- Laboratoire EBInnov, Ecole de Biologie Industrielle, 49 Avenue des Genottes, 95800 Cergy, France
| | | | - Christine Mielcarek
- Laboratoire EBInnov, Ecole de Biologie Industrielle, 49 Avenue des Genottes, 95800 Cergy, France
| | - Frédérique Changey
- Laboratoire EBInnov, Ecole de Biologie Industrielle, 49 Avenue des Genottes, 95800 Cergy, France.
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14
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Cafiero C, Re A, Stigliano E, Bassotti E, Moroni R, Grippaudo C. Optimization of DNA extraction from dental remains. Electrophoresis 2019; 40:1820-1823. [PMID: 31111969 PMCID: PMC6771583 DOI: 10.1002/elps.201900142] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [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: 12/18/2018] [Revised: 05/16/2019] [Accepted: 05/17/2019] [Indexed: 12/18/2022]
Abstract
Efficient DNA extraction procedures is a critical step involved in the process of successful DNA analysis of such samples. Various protocols have been devised for the genomic DNA extraction from human tissues and forensic stains, such as dental tissue that is the skeletal part that better preserves DNA over time. However DNA recovery is low and protocols require labor‐intensive and time‐consuming step prior to isolating genetic material. Herein, we describe an extremely fast procedure of DNA extraction from teeth compared to classical method. Sixteen teeth of 100‐year‐old human remains were divided into two groups of 8 teeth and we compared DNA yield, in term of quantity and quality, starting from two different sample preparation steps. Specifically, teeth of group 1 were treated with a classic technique based on several steps of pulverization and decalcification, while teeth of group 2 were processed following a new procedure to withdraw dental pulp. In the next phase, the samples of both group underwent the same procedure of extraction, quantification and DNA profile analysis. Our findings provide an alternative protocol to obtain a higher amount of good quality DNA in a fast time procedure, helpful for forensic and anthropological studies.
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Affiliation(s)
- Concetta Cafiero
- Università Cattolica del Sacro Cuore-Dental Institute, Rome, Italy
| | - Agnese Re
- Università Cattolica del Sacro Cuore-Dental Institute, Rome, Italy
| | - Egidio Stigliano
- Università Cattolica del Sacro Cuore-Institute of Pathological Anatomy, Rome, Italy
| | - Ezio Bassotti
- Università Cattolica del Sacro Cuore-Dental Institute, Rome, Italy
| | - Rossana Moroni
- Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy
| | - Cristina Grippaudo
- Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy.,Università Cattolica del Sacro Cuore, Rome, Italy
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15
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Jiang B, Sun J, Lv A, Hu X, Shi H, Sung Y, Wang Q, Wang Y. Impact of DNA extraction methods on the observed microbial communities from the intestinal flora of the penaeid shrimp Litopenaeus vannamei. FEMS Microbiol Lett 2019; 366:5487890. [PMID: 31074797 DOI: 10.1093/femsle/fnz099] [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] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Accepted: 05/09/2019] [Indexed: 12/25/2022] Open
Abstract
Two DNA extraction methods, the Zirmil-beating cell disruption method (ZBC) and the QIAamp fast DNA stool mini kit (QIA), were used to extract DNA from the intestinal flora of the penaeid shrimp Litopenaeus vannamei, and their microbial communities were analyzed using 16S rDNA high-throughput sequencing. Results were obtained in terms of the number of reads, alpha diversity indexes, beta diversity indexes and taxonomic composition. The alpha diversity indexes of the community, according to the ZBC method, were higher than those according to the QIA method. Furthermore, results from the three samples using the ZBC method were less consistent than those where the QIA method was used. Further, using the latter method led to substantive clustering. It is suggested that the QIA method is more stable and repeatable than the ZBC method. Although the two extraction methods shared the major abundant microflora based on 16S rDNA high-throughput sequencing, bias associated with diversity analysis indexes and certain species was observed.
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Affiliation(s)
- Boyun Jiang
- Tianjin Key Lab of Aqua-Ecology and Aquaculture, College of Fisheries, Tianjin Agricultural University, Tianjin 300384, China
| | - Jingfeng Sun
- Tianjin Key Lab of Aqua-Ecology and Aquaculture, College of Fisheries, Tianjin Agricultural University, Tianjin 300384, China
| | - Aijun Lv
- Tianjin Key Lab of Aqua-Ecology and Aquaculture, College of Fisheries, Tianjin Agricultural University, Tianjin 300384, China
| | - Xiucai Hu
- Tianjin Key Lab of Aqua-Ecology and Aquaculture, College of Fisheries, Tianjin Agricultural University, Tianjin 300384, China
| | - Hongyue Shi
- Tianjin Key Lab of Aqua-Ecology and Aquaculture, College of Fisheries, Tianjin Agricultural University, Tianjin 300384, China
| | - YeongYik Sung
- Tianjin Key Lab of Aqua-Ecology and Aquaculture, College of Fisheries, Tianjin Agricultural University, Tianjin 300384, China.,Institute of Marine Biotechnology, Universiti Malaysia Terengganu, Terengganu 21030, Malaysia
| | - Qingkui Wang
- Tianjin Key Lab of Aqua-Ecology and Aquaculture, College of Fisheries, Tianjin Agricultural University, Tianjin 300384, China
| | - Yang Wang
- Tianjin Key Lab of Aqua-Ecology and Aquaculture, College of Fisheries, Tianjin Agricultural University, Tianjin 300384, China
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16
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Fiedorová K, Radvanský M, Němcová E, Grombiříková H, Bosák J, Černochová M, Lexa M, Šmajs D, Freiberger T. The Impact of DNA Extraction Methods on Stool Bacterial and Fungal Microbiota Community Recovery. Front Microbiol 2019; 10:821. [PMID: 31057522 PMCID: PMC6479168 DOI: 10.3389/fmicb.2019.00821] [Citation(s) in RCA: 54] [Impact Index Per Article: 10.8] [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: 10/26/2018] [Accepted: 04/01/2019] [Indexed: 12/13/2022] Open
Abstract
Our understanding of human gut microbiota in health and disease depends on accurate and reproducible microbial data acquisition. The critical step in this process is to apply an appropriate methodology to extract microbial DNA, since biases introduced during the DNA extraction process may result in inaccurate microbial representation. In this study, we attempted to find a DNA extraction protocol which could be effectively used to analyze both the bacterial and fungal community. We evaluated the effect of five DNA extraction methods (QIAamp DNA Stool Mini Kit, PureLinkTM Microbiome DNA Purification Kit, ZR Fecal DNA MiniPrepTM Kit, NucleoSpin® DNA Stool Kit, and IHMS protocol Q) on bacterial and fungal gut microbiome recovery using (i) a defined system of germ-free mice feces spiked with bacterial or fungal strains, and (ii) non-spiked human feces. In our experimental setup, we confirmed that the examined methods significantly differed in efficiency and quality, which affected the identified stool microbiome composition. In addition, our results indicated that fungal DNA extraction might be prone to be affected by reagent/kit contamination, and thus an appropriate blank control should be included in mycobiome research. Overall, standardized IHMS protocol Q, recommended by the International Human Microbiome Consortium, performed the best when considering all the parameters analyzed, and thus could be applied not only in bacterial, but also in fungal microbiome research.
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Affiliation(s)
- Kristýna Fiedorová
- Centre for Cardiovascular Surgery and Transplantation, Brno, Czechia.,Central European Institute of Technology, Masaryk University, Brno, Czechia.,Department of Clinical Immunology and Allergology, Faculty of Medicine, Masaryk University, Brno, Czechia
| | | | - Eva Němcová
- Centre for Cardiovascular Surgery and Transplantation, Brno, Czechia
| | - Hana Grombiříková
- Centre for Cardiovascular Surgery and Transplantation, Brno, Czechia
| | - Juraj Bosák
- Department of Biology, Faculty of Medicine, Masaryk University, Brno, Czechia
| | | | - Matej Lexa
- Faculty of Informatics, Masaryk University, Brno, Czechia
| | - David Šmajs
- Department of Biology, Faculty of Medicine, Masaryk University, Brno, Czechia
| | - Tomáš Freiberger
- Centre for Cardiovascular Surgery and Transplantation, Brno, Czechia.,Central European Institute of Technology, Masaryk University, Brno, Czechia.,Department of Clinical Immunology and Allergology, Faculty of Medicine, Masaryk University, Brno, Czechia
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17
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Kim SH, Lee JY, Kim JJ. Investigation on STR profiling of maternal DNA from a degraded placenta with an abandoned newborn male baby. Leg Med (Tokyo) 2019; 37:37-40. [PMID: 30612023 DOI: 10.1016/j.legalmed.2019.01.001] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2018] [Revised: 12/10/2018] [Accepted: 01/01/2019] [Indexed: 01/06/2023]
Abstract
The placenta is a unique and complex organ composed of a mixture of fetal and maternal tissues. In this study, we aimed to detect maternal short tandem repeats (STRs) in degraded placenta from a newborn male baby found abandoned in a river. In order to deduce maternal alleles-which was not possible by sampling of different parts of the placenta-we collected samples from the maternal blood pool in the intervillous space and applied a multi-step method (named tempo-gap DNA extraction) for extracting DNA at defined time points after cell lysis (10 min, 2 h 10 min, and 4 h 10 min). The first lysis step (10 min) effectively removed severely degraded DNA; this was followed by a second lysis step (2 h 10 min) for high recovery of both fetal and maternal DNA. The third lysis step (4 h 10 min) effectively eliminated unwanted residual fetal DNA. The differential lysis of fetal and maternal cells occurred not because fetal and maternal cells exhibited different lysis behavior, but because of the difference in their numbers. Although all of the lysates showed fetal cell contamination, we were able to derive a maternal STR profile from the good-quality mixed STR profile from the second lysate of placental piece B. This study provides technical insight into concurrent issues encountered during routine forensic analysis of DNA samples, such as degradation, cell contamination (mixed DNA), and low-template DNA.
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Affiliation(s)
- Soon Hee Kim
- Seoul Institute, National Forensic Service, 139, Jiyang-ro, Yangcheon-gu, Seoul 08036, Republic of Korea.
| | - Jung Yoon Lee
- Seoul Institute, National Forensic Service, 139, Jiyang-ro, Yangcheon-gu, Seoul 08036, Republic of Korea
| | - Jong Jin Kim
- Seoul Institute, National Forensic Service, 139, Jiyang-ro, Yangcheon-gu, Seoul 08036, Republic of Korea
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18
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Paydar S, Ucar E, Yari P, Safavi SM, Kahrizi D, Nateqi M, Mirmoayedi A, Yari K. A simplified and optimized protocol for total DNA extraction from insect species: applicable for studying genetic diversity and PCR-based specimen identification via partial amplification of cytochrome oxidase I (COI) gene. Cell Mol Biol (Noisy-le-grand) 2018; 64:22-25. [PMID: 30301497] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2017] [Revised: 08/27/2018] [Accepted: 12/07/2017] [Indexed: 06/08/2023]
Abstract
The efficient DNA extraction from insects has been suggested as a critical and main step affecting molecular entomology for taxonomic identification, the establishment of DNA barcoding library and analysis of genetic diversity relationship between insect populations. For successfully apply these molecular techniques, high-quantity and high-quality of the extracted DNA are required. Several protocols for efficient genomic DNA extraction from insects have been developed. In this research, we represent a rapid, reliable and cost-effective method that it is not reliant on poisonous and enzymatic reagents for DNA extraction from insect tissues. Results showed that high quantity and high-quality of the isolated DNA by this method is suitable and can be used directly for PCR, also is enough to do hundreds of molecular reactions. In conclusion, we described a fast, cost-effective, non-toxic and enzyme-free protocol for high yield genomic DNA extraction from green Lacewings (Chrysoperla carnea) tissues in basic equipment laboratories.
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Affiliation(s)
- Samira Paydar
- Department of Agronomy and Plant Breeding, Razi University, Kermanshah, Iran
| | - Esra Ucar
- Department of Crop and Animal Production, Sivas Vocational School, Cumhuriyet University, Sivas, Turkey
| | - Peyman Yari
- Medical Biology Research Center, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Seyed Mehdi Safavi
- Department of Agronomy and Plant Breeding, Kermanshah Branch, Islamic Azad University, Kermanshah, Iran
| | - Danial Kahrizi
- Fertility and Infertility Research Center, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Masoud Nateqi
- Department of Plant Protection, Faculty of Agricultural Sciences and Engineering, University of Tehran, Karaj, Iran
| | | | - Kheirollah Yari
- Medical Biology Research Center, Kermanshah University of Medical Sciences, Kermanshah, Iran
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Cheng F, Hou L, Woeste K, Shang Z, Peng X, Zhao P, Zhang S. Soil pretreatment and fast cell lysis for direct polymerase chain reaction from forest soils for terminal restriction fragment length polymorphism analysis of fungal communities. Braz J Microbiol 2016; 47:817-27. [PMID: 27528083 DOI: 10.1016/j.bjm.2016.06.007] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2014] [Accepted: 02/11/2016] [Indexed: 11/21/2022] Open
Abstract
Humic substances in soil DNA samples can influence the assessment of microbial diversity and community composition. Using multiple steps during or after cell lysis adds expenses, is time-consuming, and causes DNA loss. A pretreatment of soil samples and a single step DNA extraction may improve experimental results. In order to optimize a protocol for obtaining high purity DNA from soil microbiota, five prewashing agents were compared in terms of their efficiency and effectiveness in removing soil contaminants. Residual contaminants were precipitated by adding 0.6 mL of 0.5 M CaCl2. Four cell lysis methods were applied to test their compatibility with the pretreatment (prewashing + Ca2+ flocculation) and to ultimately identify the optimal cell lysis method for analyzing fungal communities in forest soils. The results showed that pretreatment with TNP + Triton X-100 + skim milk (100 mM Tris, 100 mM Na4P2O7, 1% polyvinylpyrrolidone, 100 mM NaCl, 0.05% Triton X-100, 4% skim milk, pH 10.0) removed most soil humic contaminants. When the pretreatment was combined with Ca2+ flocculation, the purity of all soil DNA samples was further improved. DNA samples obtained by the fast glass bead-beating method (MethodFGB) had the highest purity. The resulting DNA was successfully used, without further purification steps, as a template for polymerase chain reaction targeting fungal internal transcribed spacer regions. The results obtained by terminal restriction fragment length polymorphism analysis indicated that the MethodFGB revealed greater fungal diversity and more distinctive community structure compared with the other methods tested. Our study provides a protocol for fungal cell lysis in soil, which is fast, convenient, and effective for analyzing fungal communities in forest soils.
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Nieratschker V, Lahtinen J, Meier S, Strohmaier J, Frank J, Heinrich A, Breuer R, Witt SH, Nöthen MM, Rietschel M, Hovatta I. Longer telomere length in patients with schizophrenia. Schizophr Res 2013; 149:116-20. [PMID: 23870621 DOI: 10.1016/j.schres.2013.06.043] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/29/2013] [Revised: 06/02/2013] [Accepted: 06/29/2013] [Indexed: 10/26/2022]
Abstract
Previous studies have reported an association between shorter leukocyte telomere length and schizophrenia (SCZ). The aim of the present study was to replicate this finding in a large sample of SCZ patients (n=539) and population-based controls (n=519). In addition, the possible influence of SCZ severity on telomere length - as measured by age of onset, mode of onset, and course of the disorder - was investigated. Telomere length was negatively associated with age in both patients and controls. This is a consistently reported phenomenon, related to the problem of DNA end-replication. However, in contrast to previous findings, SCZ patients displayed longer telomeres compared to controls (p=0.015). No association was found with any SCZ-severity subphenotype. Interestingly, recent studies have reported associations between longer leukocyte telomere length and both smaller hippocampal volume, and poorer episodic memory performance. Both phenotypes are common in patients with SCZ. Further studies are warranted to investigate whether the present association between SCZ and increased telomere length was driven by such associations, or rather by association with the clinical disease per se or other associated phenotypes, endophenotypes or lifestyle factors.
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Affiliation(s)
- Vanessa Nieratschker
- Department of Genetic Epidemiology in Psychiatry, Central Institute of Mental Health, Medical Faculty Mannheim, Heidelberg University, J 5, 68159 Mannheim, Germany.
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Smith B, Li N, Andersen AS, Slotved HC, Krogfelt KA. Optimising bacterial DNA extraction from faecal samples: comparison of three methods. Open Microbiol J 2011; 5:14-7. [PMID: 21643498 PMCID: PMC3106334 DOI: 10.2174/1874285801105010014] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.8] [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: 02/01/2011] [Revised: 02/15/2011] [Accepted: 02/17/2011] [Indexed: 02/01/2023] Open
Abstract
Culture independent methods are used widely in diagnostic laboratories for infectious disease Isolation of genomic DNA from clinical samples is the first and important step in the procedure. Several procedures for extracting DNA from faecal samples have been described, including different mechanical cell disruptors. To our knowledge, the use of TissueLyser as a mechanical disruptor on faecal samples before DNA extraction has not been previously described. The purpose of the study was to implement a method for preparing faecal samples for optimal DNA extraction. Thus, three different procedures for extracting DNA from human faeces were compared. This was done either by using the mechanical disrupter by Mini BeadBeater 8, or the TissueLyser both followed by DNA purification using QIAamp DNA stool MiniKit, in comparison with DNA extractions using QIAamp DNA stool MiniKit without any prior mechanical disruption, according to manufacturer’s instructions. The obtained DNA from the three procedures was analysed by DGGE, and the number of bands was compared between each procedure. There was no significant difference between the numbers of bacterial bands obtained from DGGE when using a TissueLyser or Mini BeadBeater 8, so the two different mechanical cell disruptors can be used comparably when isolating bacterial DNA from faecal samples. The QIAamp DNA stool MiniKit alone resulted in a reduced number of bands compared to the two mechanical disruption methods.
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Affiliation(s)
- Birgitte Smith
- Department of Microbiological Surveillance and Research, Statens Serum Institut, DK-2300 S, Copenhagen, Denmark
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Atibalentja N, Noel GR, Ciancio A. A Simple Method for the Extraction, PCR-amplification, Cloning, and Sequencing of Pasteuria 16S rDNA from Small Numbers of Endospores. J Nematol 2004; 36:100-105. [PMID: 19262793 PMCID: PMC2620735] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/27/2023] Open
Abstract
For many years the taxonomy of the genus Pasteuria has been marred with confusion because the bacterium could not be cultured in vitro and, therefore, descriptions were based solely on morphological, developmental, and pathological characteristics. The current study sought to devise a simple method for PCR-amplification, cloning, and sequencing of Pasteuria 16S rDNA from small numbers of endospores, with no need for prior DNA purification. Results show that DNA extracts from plain glass bead-beating of crude suspensions containing 10,000 endospores at 0.2 x 10 endospores ml(-1) were sufficient for PCR-amplification of Pasteuria 16S rDNA, when used in conjunction with specific primers. These results imply that for P. penetrans and P. nishizawae only one parasitized female of Meloidogyne spp. and Heterodera glycines, respectively, should be sufficient, and as few as eight cadavers of Belonolaimus longicaudatus with an average number of 1,250 endospores of "Candidatus Pasteuria usgae" are needed for PCR-amplification of Pasteuria 16S rDNA. The method described in this paper should facilitate the sequencing of the 16S rDNA of the many Pasteuria isolates that have been reported on nematodes and, consequently, expedite the classification of those isolates through comparative sequence analysis.
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