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Chauhan G, Arya M, Kumar V, Verma D, Sharma M. An improved protocol for metagenomic DNA isolation from low microbial biomass alkaline hot-spring sediments and soil samples. 3 Biotech 2024; 14:34. [PMID: 38188309 PMCID: PMC10769977 DOI: 10.1007/s13205-023-03824-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Accepted: 09/25/2023] [Indexed: 01/09/2024] Open
Abstract
High-quality, humic-acid-free pure DNA is a prerequisite for functional and sequence-based approaches of metagenomics. In the present investigation, an improved extraction buffer was developed by making a combination of powdered activated charcoal (2%; w/v), polyvinyl poly pyrrolidone (2%; w/v), and CaCl2 (2%; w/v). This trio significantly improved the purity and yield of the metagenomic DNA from the hot spring's hot and alkaline soil. The quality of extracted metagenomic DNA was successfully validated by PCR amplification and restriction enzymes. Besides, the thermophilic amylase encoding genes were also retrieved from these soil DNA samples. Extreme habitats I harbour low microbial biomass and, therefore, demand in-situ lysis of the microbial cells to access their genomes. The protocol can potentially extract DNA from geothermal spring habitats where the count of microbial cells is low.
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Affiliation(s)
- Garima Chauhan
- Department of Biotechnology, School of Life Sciences, Babasaheb Bhimrao Ambedkar University, Lucknow, Uttar Pradesh 226025 India
| | - Meghna Arya
- Department of Biotechnology, School of Life Sciences, Babasaheb Bhimrao Ambedkar University, Lucknow, Uttar Pradesh 226025 India
| | - Vikas Kumar
- Department of Biotechnology, School of Life Sciences, Babasaheb Bhimrao Ambedkar University, Lucknow, Uttar Pradesh 226025 India
- Indian Institute of Toxicology Research (CSIR-IITR), Vishvigyan Bhawan 31, Mahatma Gandhi Marg, Lucknow, Uttar Pradesh India
| | - Digvijay Verma
- Department of Environmental Microbiology, School of Earth and Environmental Sciences, Babasaheb Bhimrao Ambedkar University, Lucknow, Uttar Pradesh 226025 India
| | - Monica Sharma
- Department of Biotechnology, School of Life Sciences, Babasaheb Bhimrao Ambedkar University, Lucknow, Uttar Pradesh 226025 India
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2
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Narh Mensah DL, Wingfield BD, Coetzee MP. A practical approach to genome assembly and annotation of Basidiomycota using the example of Armillaria. Biotechniques 2023; 75:115-128. [PMID: 37681497 DOI: 10.2144/btn-2023-0023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/09/2023] Open
Abstract
Technological advancements in genome sequencing, assembly and annotation platforms and algorithms that resulted in several genomic studies have created an opportunity to further our understanding of the biology of phytopathogens, including Armillaria species. Most Armillaria species are facultative necrotrophs that cause root- and stem-rot, usually on woody plants, significantly impacting agriculture and forestry worldwide. Genome sequencing, assembly and annotation in terms of samples used and methods applied in Armillaria genome projects are evaluated in this review. Infographic guidelines and a database of resources to facilitate future Armillaria genome projects were developed. Knowledge gained from genomic studies of Armillaria species is summarized and prospects for further research are provided. This guide can be applied to other diploid and dikaryotic fungal genomics.
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Affiliation(s)
- Deborah L Narh Mensah
- Department of Biochemistry, Genetics & Microbiology, Forestry & Agricultural Biotechnology Institute (FABI), Faculty of Natural & Agricultural Sciences, University of Pretoria, Pretoria, Gauteng, South Africa
- Council for Scientific and Industrial Research - Food Research Institute (CSIR-FRI), PO Box M20, Accra, Ghana
| | - Brenda D Wingfield
- Department of Biochemistry, Genetics & Microbiology, Forestry & Agricultural Biotechnology Institute (FABI), Faculty of Natural & Agricultural Sciences, University of Pretoria, Pretoria, Gauteng, South Africa
| | - Martin Pa Coetzee
- Department of Biochemistry, Genetics & Microbiology, Forestry & Agricultural Biotechnology Institute (FABI), Faculty of Natural & Agricultural Sciences, University of Pretoria, Pretoria, Gauteng, South Africa
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3
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Feng S, DeKlotz M, Taş N. Comparison of three DNA extraction methods for recovery of microbial DNA from Arctic permafrost. MICROPUBLICATION BIOLOGY 2023; 2023:10.17912/micropub.biology.000834. [PMID: 37416892 PMCID: PMC10320573 DOI: 10.17912/micropub.biology.000834] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Figures] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Revised: 05/23/2023] [Accepted: 06/19/2023] [Indexed: 07/08/2023]
Abstract
Permafrost soils, which contain one of Earth's largest terrestrial carbon stocks, are vulnerable to thaw and microbial decomposition, exacerbating climate change. Advancements in sequencing technologies have facilitated the identification and functional profiling of microbial communities in permafrost, but DNA extraction from these soils is challenging due to their high microbial diversity and low biomass. This study assessed the effectiveness of the DNeasy PowerSoil Pro kit in extracting DNA from permafrost samples and found that it produced significantly different results than the discontinued DNeasy PowerSoil kit. The study highlights the importance of consistent DNA extraction methods in permafrost studies.
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Affiliation(s)
- Sarah Feng
- Lawrence Berkeley National Laboratory, Berkeley, California, United States
| | - Marla DeKlotz
- Lawrence Berkeley National Laboratory, Berkeley, California, United States
| | - Neslihan Taş
- Lawrence Berkeley National Laboratory, Berkeley, California, United States
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Grinding Beads Influence Microbial DNA Extraction from Organic-Rich Sub-Seafloor Sediment. Microorganisms 2022; 10:microorganisms10122505. [PMID: 36557758 PMCID: PMC9784657 DOI: 10.3390/microorganisms10122505] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2022] [Revised: 12/15/2022] [Accepted: 12/16/2022] [Indexed: 12/23/2022] Open
Abstract
Sub-seafloor sediment is the largest microbial habitat on Earth. The study of microbes in sub-seafloor sediment is largely limited by the technical challenge of acquiring ambient microbial DNA because of sediment heterogeneity. Changes in the extraction method, even just by one step, can affect the extraction yields for complicated sediment samples. In this work, sub-seafloor sediment samples from the Baltic Sea with high organic carbon content were used to evaluate the influence of different grinding beads on DNA extraction. We found that the grinding beads can affect the DNA extraction from the organic-matter- and biosiliceous-clay-rich samples. A mixture of 0.5-mm and 0.1-mm grinding beads exhibited higher DNA yields and recovered more unique taxa than other bead combinations, such as Stenotrophomonas from Gammaproteobacteria and Leptotrichia from Fusobacteria; therefore, these beads are more suitable than the others for DNA extraction from the samples used in this study. This advantage might be magnified in samples with high biomass. On the contrary, the use of only small beads might lead to underestimation for certain Gram-positive strains. Overall, the discovery of abundant widespread deep biosphere clades in our samples indicated that our optimized DNA extraction method successfully recovered the in situ microbial community.
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Assessment of three DNA extraction kits for the absolute quantification of strongyle nematode eggs in faecal samples. Acta Vet Scand 2022; 64:5. [PMID: 35139862 PMCID: PMC8826664 DOI: 10.1186/s13028-022-00624-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Accepted: 01/26/2022] [Indexed: 11/10/2022] Open
Abstract
Background Haemonchus contortus is one of the most pathogenic gastrointestinal nematodes of small ruminants. The current diagnostic approach for the detection of this species relies on coproscopic methods, which both have low sensitivity and are time consuming. Methods employing detection through DNA amplification, such as droplet digital polymerase chain reaction (ddPCR), offer an advantageous approach to the diagnosis of H. contortus. However, DNA extraction protocols need to be constantly updated for the optimal retrieval of diagnostically usable template. Here, we describe the evaluation of three genomic DNA extraction kits for the detection and quantification of H. contortus ITS2 amplicon DNA from faecal samples, using droplet digital PCR. Results DNA samples, extracted from faecal material with the Nucleospin DNA Stool kit, produced the highest amounts of ITS2 amplicon copies and had the lowest coefficient of variation across different dilutions and sample types (fresh or frozen) out of the tested kits (Nucleospin DNA Stool, E.Z.N.A.® Stool DNA Kit and QIAamp Fast DNA Stool Mini Kit). Furthermore, the protocol of this kit has the fewest number of steps and the price of DNA extraction per sample is reasonable (2.77 €). Conclusions The Nucleospin DNA Stool kit is an attractive option for the detection and quantification of H. contortus DNA in faecal samples of small ruminants in a diagnostic setting.
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Peris D, Janssen K, Barthel HJ, Bierbaum G, Delclòs X, Peñalver E, Solórzano-Kraemer MM, Jordal BH, Rust J. DNA from resin-embedded organisms: Past, present and future. PLoS One 2020; 15:e0239521. [PMID: 32986737 PMCID: PMC7521698 DOI: 10.1371/journal.pone.0239521] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Accepted: 09/09/2020] [Indexed: 11/19/2022] Open
Abstract
Past claims have been made for fossil DNA recovery from various organisms (bacteria, plants, insects and mammals, including humans) dating back in time from thousands to several million years BP. However, many of these recoveries, especially those described from million-year-old amber (fossil resin), have faced criticism as being the result of modern environmental contamination and for lack of reproducibility. Using modern genomic techniques, DNA can be obtained with confidence from a variety of substrates (e.g. bones, teeth, gum, museum specimens and fossil insects) of different ages, albeit always less than one million years BP, and results can also be obtained from much older materials using palaeoproteomics. Nevertheless, new attempts to determine if ancient DNA (aDNA) is present in insects preserved in 40 000-year old sub-fossilised resin, the precursor of amber, have been unsuccessful or not well documented. Resin-embedded specimens are therefore regarded as unsuitable for genetic studies. However, we demonstrate here, for the first time, that although a labile molecule, DNA is still present in platypodine beetles (Coleoptera: Curculionidae) embedded in six-year-old and two-year-old resin pieces from Hymenaea verrucosa (Angiospermae: Fabaceae) collected in Madagascar. We describe an optimised method which meets all the requirements and precautions for aDNA experiments for our purpose: to explore the DNA preservation limits in resin. Our objective is far from starting an uncontrolled search for aDNA in amber as it was in the past, but to start resolving basic aspects from the DNA preservation in resin and search from the most modern samples to the ancient ones, step by step. We conclude that it is therefore possible to study genomics from resin-embedded organisms, although the time limits remain to be determined.
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Affiliation(s)
- David Peris
- Section Paleontology, Institute of Geosciences, University of Bonn, Bonn, Germany
| | - Kathrin Janssen
- Institute of Medical Microbiology, Immunology and Parasitology, Medical Faculty, University of Bonn, Bonn, Germany
| | - H. Jonas Barthel
- Section Paleontology, Institute of Geosciences, University of Bonn, Bonn, Germany
| | - Gabriele Bierbaum
- Institute of Medical Microbiology, Immunology and Parasitology, Medical Faculty, University of Bonn, Bonn, Germany
| | - Xavier Delclòs
- Department of Earth and Ocean Dynamics and Biodiversity Research Institute (IRBio), Faculty of Earth Sciences, Universitat de Barcelona, Barcelona, Spain
| | - Enrique Peñalver
- Geological and Mining Institute of Spain (Geominero Museum), Valencia, Spain
| | - Mónica M. Solórzano-Kraemer
- Department of Palaeontology and Historical Geology, Senckenberg Research Institute, Frankfurt am Main, Germany
| | - Bjarte H. Jordal
- Museum of Natural History, University Museum of Bergen, University of Bergen, Bergen, Norway
| | - Jes Rust
- Section Paleontology, Institute of Geosciences, University of Bonn, Bonn, Germany
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Simultaneous cell lysis and DNA extraction from whole blood using magnetic ionic liquids. Anal Bioanal Chem 2020; 412:8039-8049. [PMID: 32918171 DOI: 10.1007/s00216-020-02941-w] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Revised: 08/27/2020] [Accepted: 09/03/2020] [Indexed: 02/07/2023]
Abstract
Conventional DNA sample preparation methods involve tedious sample handling steps that require numerous inhibitors of the polymerase chain reaction (PCR) and instrumentation to implement. These disadvantages limit the applicability of conventional cell lysis and DNA extraction methods in high-throughput applications, particularly in forensics and clinical laboratories. To overcome these drawbacks, a series of nine hydrophobic magnetic ionic liquids (MILs) previously shown to preconcentrate DNA were explored as cell lysis reagents. The MILs were found to lyse white blood cells from whole blood, 2-fold diluted blood, and dry blood samples while simultaneously extracting human genomic DNA. The identity of metal ion incorporated within the MIL appears to cause hemolysis while the cationic component further reduces the cell's integrity. Over 500 pg of human genomic DNA was isolated from 50 μL of whole blood using the trioctylbenzylammonium tris(hexafluoroacetylaceto)nickelate(II) ([N8,8,8,Bz+][Ni(hfacac)3-]) MIL, and 800 pg DNA was isolated from a dry blood samples using the trihexyl(tetradecyl)phosphonium tris(phenyltrifluoroacetylaceto)nickelate(II) ([P6,6,6,14+][Ni(Phfacac)3-]) MIL following a 1-min vortex step. A rapid, one-step cell lysis and DNA extraction from blood is ideal for settings that seek high-throughput analysis while minimizing the potential for contamination.Graphical abstract.
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Abstract
DNA-based technologies have become widespread tools for soil microbiological analyses in recent years. DNA extraction from the soil is a key step for these approaches: it is a challenge for researchers as it is still both expensive and time-consuming when large surveys are planned. The aim of this study was to develop a high-throughput automated protocol for DNA extraction and purification from soil. The protocol was based on the BioSprint 96 platform and compared for validation with another automated procedure and two commercial column-based kits. To evaluate the performances of the protocols, we considered quality, quantity, and amplifiability of the isolated DNA. The material isolated by means of the four protocols showed appropriate yield and quality and positive amplification. The isolation protocol presented here provided similar results to those of the commercial kits but with two essential differences: cost and time for DNA extraction were drastically reduced. This rapid and efficient protocol is envisaged as ideal to standardize soil studies and treat large numbers of samples, representing a workable alternative to low-throughput and expensive manual extraction methods.
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Muha TP, Robinson CV, Garcia de Leaniz C, Consuegra S. An optimised eDNA protocol for detecting fish in lentic and lotic freshwaters using a small water volume. PLoS One 2019; 14:e0219218. [PMID: 31314760 PMCID: PMC6636732 DOI: 10.1371/journal.pone.0219218] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2018] [Accepted: 06/19/2019] [Indexed: 01/07/2023] Open
Abstract
Environmental DNA is increasingly being used for assessing the presence and relative abundance of fish in freshwater, but existing protocols typically rely on filtering large volumes of water which is not always practical. We compared the effects of water volume, filtration type and eDNA extraction procedures in the detection of fish in three freshwater bodies (pond, lake and river) using a short fragment of the 12s rRNA mtDNA gene. Quantification of eDNA capture efficiency after DNA extraction, as well as amplification efficiency, were evaluated by conventional PCR and quantitative PCR. No significant differences on eDNA capture yield were found among freshwater bodies, but increasing water volume had a positive effect on eDNA capture and amplification efficiency. Although highest eDNA capture rates were obtained using 2 L of filtered water, 100 mL syringe filtration in combination with ethanol- sodium acetate precipitation proved to be more practical and increased quantitative PCR amplification efficiency by 6.4%. Our results indicate that such method may be optimal to detect fish species effectively across both lotic and lentic freshwater environments.
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Affiliation(s)
- Teja Petra Muha
- Swansea University, Department of Biosciences, Singleton Park, Swansea, Wales, United Kingdom
- * E-mail:
| | - Chloe Victoria Robinson
- Swansea University, Department of Biosciences, Singleton Park, Swansea, Wales, United Kingdom
| | - Carlos Garcia de Leaniz
- Swansea University, Department of Biosciences, Singleton Park, Swansea, Wales, United Kingdom
| | - Sofia Consuegra
- Swansea University, Department of Biosciences, Singleton Park, Swansea, Wales, United Kingdom
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Majaneva M, Diserud OH, Eagle SH, Hajibabaei M, Ekrem T. Choice of DNA extraction method affects DNA metabarcoding of unsorted invertebrate bulk samples. METABARCODING AND METAGENOMICS 2018. [DOI: 10.3897/mbmg.2.26664] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Characterisation of freshwater benthic biodiversity using DNA metabarcoding may allow more cost-effective environmental assessments than the current morphological-based assessment methods. DNA metabarcoding methods where sorting or pre-sorting of samples are avoided altogether are especially interesting, since the time between sampling and taxonomic identification is reduced. Due to the presence of non-target material like plants and sediments in crude samples, DNA extraction protocols become important for maximising DNA recovery and sample replicability. We sampled freshwater invertebrates from six river and lake sites and extracted DNA from homogenised bulk samples in quadruplicate subsamples, using a published method and two commercially available kits: HotSHOT approach, Qiagen DNeasy Blood & Tissue Kit and Qiagen DNeasy PowerPlant Pro Kit. The performance of the selected extraction methods was evaluated by measuring DNA yield and applying DNA metabarcoding to see if the choice of DNA extraction method affects DNA yield and metazoan diversity results. The PowerPlant Kit extractions resulted in the highest DNA yield and a strong significant correlation between sample weight and DNA yield, while the DNA yields of the Blood & Tissue Kit and HotSHOT method did not correlate with the sample weights. Metazoan diversity measures were more repeatable in samples extracted with the PowerPlant Kit compared to those extracted with the HotSHOT method or the Blood & Tissue Kit. Subsampling using Blood & Tissue Kit and HotSHOT extraction failed to describe the same community in the lake samples. Our study exemplifies that the choice of DNA extraction protocol influences the DNA yield as well as the subsequent community analysis. Based on our results, low specimen abundance samples will likely provide more stable results if specimens are sorted prior to DNA extraction and DNA metabarcoding, but the repeatability of the DNA extraction and DNA metabarcoding results was close to ideal in high specimen abundance samples.
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Le Maréchal C, Fourour S, Ballan V, Rouxel S, Souillard R, Chemaly M. Detection of Clostridium botulinum group III in environmental samples from farms by real-time PCR using four commercial DNA extraction kits. BMC Res Notes 2018; 11:441. [PMID: 29973253 PMCID: PMC6030735 DOI: 10.1186/s13104-018-3549-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2018] [Accepted: 06/27/2018] [Indexed: 02/05/2023] Open
Abstract
Objectives Few studies have tested DNA extraction methods to optimize the detection of Clostridium botulinum in environmental samples that can be collected during animal botulism outbreaks. In this study, we evaluated four commercial DNA extraction kits for the detection of C. botulinum group III in 82 various environmental samples (9 manure, 53 swabs, 3 insects, 8 water, 1 silage and 8 soil samples) collected in a context of animal botulism outbreaks. Results The PowerSoil® kit was the most efficient for almost all matrices (83.6% of the 73 tested samples), except manure for which the NucleoSpin® Soil kit was the most efficient. The NucleoSpin® Soil kit enabled detection in 75.3%, the QIAamp® DNA Mini Kit in 68.5%, and the QIAamp® Fast DNA Stool Mini Kit in 45.2%. However, the NucleoSpin® Soil kit detected C. botulinum in 9 of the 9 manure samples tested, while the PowerSoil® kit found C. botulinum in only two samples, and the other two kits in none of the samples. This study showed that PowerSoil® can be recommended for DNA extraction from environmental samples except for manure, for which the NucleoSpin® Soil kit appeared to be far more appropriate.
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Affiliation(s)
- Caroline Le Maréchal
- ANSES, Laboratoire de Ploufragan-Plouzané, Unité Hygiène et Qualité des Produits Avicoles et Porcins, Université Bretagne-Loire, BP 53, 22440, Ploufragan, France.
| | - Sarah Fourour
- ANSES, Laboratoire de Ploufragan-Plouzané, Unité Hygiène et Qualité des Produits Avicoles et Porcins, Université Bretagne-Loire, BP 53, 22440, Ploufragan, France
| | - Valentine Ballan
- ANSES, Laboratoire de Ploufragan-Plouzané, Unité Hygiène et Qualité des Produits Avicoles et Porcins, Université Bretagne-Loire, BP 53, 22440, Ploufragan, France
| | - Sandra Rouxel
- ANSES, Laboratoire de Ploufragan-Plouzané, Unité Hygiène et Qualité des Produits Avicoles et Porcins, Université Bretagne-Loire, BP 53, 22440, Ploufragan, France
| | - Rozenn Souillard
- ANSES, Laboratoire de Ploufragan-Plouzané, Unité d'Épidémiologie et Bien-être en Aviculture et Cuniculture, Université Bretagne-Loire, BP 53, 22440, Ploufragan, France
| | - Marianne Chemaly
- ANSES, Laboratoire de Ploufragan-Plouzané, Unité Hygiène et Qualité des Produits Avicoles et Porcins, Université Bretagne-Loire, BP 53, 22440, Ploufragan, France
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12
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Pruski P, Lewis HV, Lee YS, Marchesi JR, Bennett PR, Takats Z, MacIntyre DA. Assessment of microbiota:host interactions at the vaginal mucosa interface. Methods 2018; 149:74-84. [PMID: 29705211 DOI: 10.1016/j.ymeth.2018.04.022] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2018] [Revised: 03/10/2018] [Accepted: 04/22/2018] [Indexed: 12/12/2022] Open
Abstract
There is increasing appreciation of the role that vaginal microbiota play in health and disease throughout a woman's lifespan. This has been driven partly by molecular techniques that enable detailed identification and characterisation of microbial community structures. However, these methods do not enable assessment of the biochemical and immunological interactions between host and vaginal microbiota involved in pathophysiology. This review examines our current knowledge of the relationships that exist between vaginal microbiota and the host at the level of the vaginal mucosal interface. We also consider methodological approaches to microbiomic, immunologic and metabolic profiling that permit assessment of these interactions. Integration of information derived from these platforms brings the potential for biomarker discovery, disease risk stratification and improved understanding of the mechanisms regulating vaginal microbial community dynamics in health and disease.
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Affiliation(s)
- Pamela Pruski
- Division of Computational and Systems Medicine, Department of Surgery and Cancer, Imperial College London, London SW7 2AZ, UK
| | - Holly V Lewis
- Imperial College Parturition Research Group, Institute of Reproductive and Developmental Biology, Department of Surgery and Cancer, Imperial College London, London W12 0NN, UK; Queen Charlotte's Hospital, Imperial College Healthcare National Health Service (NHS) Trust, London W12 0HS, UK
| | - Yun S Lee
- Imperial College Parturition Research Group, Institute of Reproductive and Developmental Biology, Department of Surgery and Cancer, Imperial College London, London W12 0NN, UK
| | - Julian R Marchesi
- Department of Biosciences, Cardiff University, Cardiff CF10 3AX, UK; Centre for Digestive and Gut Health, Surgery and Cancer, Imperial College London, London W2 1NY, UK
| | - Phillip R Bennett
- Division of Computational and Systems Medicine, Department of Surgery and Cancer, Imperial College London, London SW7 2AZ, UK; Imperial College Parturition Research Group, Institute of Reproductive and Developmental Biology, Department of Surgery and Cancer, Imperial College London, London W12 0NN, UK
| | - Zoltan Takats
- Division of Computational and Systems Medicine, Department of Surgery and Cancer, Imperial College London, London SW7 2AZ, UK
| | - David A MacIntyre
- Imperial College Parturition Research Group, Institute of Reproductive and Developmental Biology, Department of Surgery and Cancer, Imperial College London, London W12 0NN, UK.
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13
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Hull N, Miller J, Berry D, Laegreid W, Smith A, Klinghagen C, Schumaker B. Optimization of Brucella abortus Protocols for Downstream Molecular Applications. J Clin Microbiol 2018; 56:e01894-17. [PMID: 29436425 PMCID: PMC5869842 DOI: 10.1128/jcm.01894-17] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2017] [Accepted: 02/02/2018] [Indexed: 01/30/2023] Open
Abstract
We compared the performances of various DNA extraction kits for their ability to recover Brucella abortus strain 19 inoculated into Brucella-free bovine tissues. Tissues were homogenized in a FastPrep bead homogenizer and extracted in triplicate by using one of five kits (Qiagen DNeasy, GE Illustra, Omega Bio-tek E.Z.N.A., Quanta Extracta, and IBI Science DNA Tissue kit). Whole blood was also taken from animals prior to chemical euthanasia, aliquoted, and then fractioned into buffy coat, red blood cells, and plasma. DNA was extracted from whole blood, buffy coat, and plasma by using four kits (Qiagen DNeasy, Omega Bio-tek E.Z.N.A., IBI Science DNA Blood kit, and 5PRIME PerfectPure). Previously reported primers targeting strain 19 were used to amplify extracted DNA and identify the optimal extraction kit. Real-time PCR was performed, and kits were compared for statistical differences by using quantification cycles as an outcome measure. Omega Bio-tek E.Z.N.A. was superior (P < 0.0068) in its lower quantification cycle values across all tissue kits. The IBI Science DNA Blood kit was superior to Qiagen DNeasy, 5PRIME PerfectPure, and Quanta Extracta (P < 0.0001, P = 0.0004, and P = 0.0013, respectively) but was not different from Omega Bio-tek E.Z.N.A. (P = 1.0). In summary, the optimal extraction kit for B. abortus strain 19 for tissues is Omega Bio-tek E.Z.N.A., and that for blood and its fractions is the IBI Science Mini Genomic DNA kit. Eluted DNA was also concentrated by using the Zymo Research DNA Clean & Concentrator-25 kit. Concentrated eluted DNA with the target was superior (P = <0.0001) to unconcentrated eluted DNA.
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Affiliation(s)
- Noah Hull
- Department of Veterinary Sciences, University of Wyoming, Laramie, Wyoming, USA
| | - Jonathan Miller
- Department of Veterinary Sciences, University of Wyoming, Laramie, Wyoming, USA
| | - David Berry
- Department of Veterinary Sciences, University of Wyoming, Laramie, Wyoming, USA
| | - William Laegreid
- Department of Veterinary Sciences, University of Wyoming, Laramie, Wyoming, USA
- Wyoming State Veterinary Laboratory, University of Wyoming, Laramie, Wyoming, USA
| | - Ashley Smith
- Department of Veterinary Sciences, University of Wyoming, Laramie, Wyoming, USA
| | - Callie Klinghagen
- Department of Veterinary Sciences, University of Wyoming, Laramie, Wyoming, USA
| | - Brant Schumaker
- Department of Veterinary Sciences, University of Wyoming, Laramie, Wyoming, USA
- Wyoming State Veterinary Laboratory, University of Wyoming, Laramie, Wyoming, USA
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14
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Rafael K, Marchioro AA, Colli CM, Tiyo BT, Evangelista FF, Bezagio RC, Falavigna-Guilherme AL. Genotyping of Giardia duodenalis in vegetables cultivated with organic and chemical fertilizer from street markets and community vegetable gardens in a region of Southern Brazil. Trans R Soc Trop Med Hyg 2018. [DOI: 10.1093/trstmh/try013] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- Katyelle Rafael
- Postgraduate Program in Health Sciences, State University of Maringa (UEM). Av. Colombo, 5790, CEP: 87020-900 Maringá
| | - Ariella A Marchioro
- Postgraduate Program in Health Sciences, State University of Maringa (UEM). Av. Colombo, 5790, CEP: 87020-900 Maringá
| | | | - Bruna T Tiyo
- Postgraduate Program on Bioscience and Physiopathology, UEM, Brazil
| | - Fernanda F Evangelista
- Postgraduate Program in Health Sciences, State University of Maringa (UEM). Av. Colombo, 5790, CEP: 87020-900 Maringá
| | - Renata C Bezagio
- Postgraduate Program in Health Sciences, State University of Maringa (UEM). Av. Colombo, 5790, CEP: 87020-900 Maringá
| | - Ana L Falavigna-Guilherme
- Postgraduate Program in Health Sciences, State University of Maringa (UEM). Av. Colombo, 5790, CEP: 87020-900 Maringá
- Department of Basic Health Sciences, UEM
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15
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Mahajan R, Attri S, Sharma K, Singh N, Sharma D, Goel G. Statistical assessment of DNA extraction methodology for culture-independent analysis of microbial community associated with diverse environmental samples. Mol Biol Rep 2018; 45:297-308. [PMID: 29453765 DOI: 10.1007/s11033-018-4162-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2017] [Accepted: 02/12/2018] [Indexed: 12/20/2022]
Abstract
Cost-effectiveness, quality, time-effectiveness and ease of the methodology are the most crucial factors in isolating quality DNA from wide variety of samples. Thus, research efforts focusing on the development of an efficient DNA extraction protocol is the need of the hour. The present study therefore, focuses on development of an efficient, rapid and free of inhibitory substances based methodology for extracting metagenomic DNA from diverse environmental samples viz. anaerobic biogas digesta, ruminant stomach, human feces, soil, and microbial starter cultures used for preparation of fermented food. PCR-DGGE based analysis and quality metagenomic library preparation, using DNA extraction methodology, validates the developed protocol. The developed protocol is cost effective, capable of isolating DNA from small sample size (100-1000 µl), time efficient (1.5-2.0 h protocol) and results in significantly higher DNA yield (4-8 times increased yield) when compared to previously available DNA extraction method and a commercial DNA extraction kit. The DNA extracted from the samples using different protocols was evaluated based on its ability to identify diverse microbial species using PCR-DGGE profiles targeting variable region within the 16S rRNA gene. The results of microbial community analysis revealed comparability of the developed protocol to commercial kits, in effectively identifying dominant representatives of the microbial community in different samples. Using the DNA extracted from the presented methodology, metagenomic libraries were prepared, which were found suitable for sequencing on Illumina platform.
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Affiliation(s)
- Rishi Mahajan
- Department of Biotechnology and Bioinformatics, Jaypee University of Information Technology, Waknaghat, Solan, 173234, India
| | - Sampan Attri
- Department of Biotechnology and Bioinformatics, Jaypee University of Information Technology, Waknaghat, Solan, 173234, India
| | - Kavita Sharma
- Department of Biotechnology and Bioinformatics, Jaypee University of Information Technology, Waknaghat, Solan, 173234, India
| | - Niharika Singh
- Department of Biotechnology and Bioinformatics, Jaypee University of Information Technology, Waknaghat, Solan, 173234, India
| | - Deepika Sharma
- Department of Biotechnology and Bioinformatics, Jaypee University of Information Technology, Waknaghat, Solan, 173234, India
| | - Gunjan Goel
- Department of Biotechnology and Bioinformatics, Jaypee University of Information Technology, Waknaghat, Solan, 173234, India.
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16
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McKenney EA, Greene LK, Drea CM, Yoder AD. Down for the count: Cryptosporidium infection depletes the gut microbiome in Coquerel's sifakas. MICROBIAL ECOLOGY IN HEALTH AND DISEASE 2017; 28:1335165. [PMID: 28740461 PMCID: PMC5508644 DOI: 10.1080/16512235.2017.1335165] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/20/2017] [Accepted: 05/17/2017] [Indexed: 12/12/2022]
Abstract
Background: The gut microbiome (GMB) is the first line of defense against enteric pathogens, which are a leading cause of disease and mortality worldwide. One such pathogen, the protozoan Cryptosporidium, causes a variety of digestive disorders that can be devastating and even lethal. The Coquerel’s sifaka (Propithecus coquereli) – an endangered, folivorous primate endemic to Madagascar – is precariously susceptible to cryptosporidiosis under captive conditions. If left untreated, infection can rapidly advance to morbidity and death. Objective: To gain a richer understanding of the pathophysiology of this pathogen while also improving captive management of endangered species, we examine the impact of cryptosporidiosis on the GMB of a flagship species known to experience a debilitating disease state upon infection. Design: Using 16S sequencing of DNA extracted from sifaka fecal samples, we compared the microbial communities of healthy sifakas to those of infected individuals, across infection and recovery periods. Results: Over the course of infection, we found that the sifaka GMB responds with decreased microbial diversity and increased community dissimilarity. Compared to the GMB of unaffected individuals, as well as during pre-infection and recovery periods, the GMB during active infection was enriched for microbial taxa associated with dysbiosis and rapid transit time. Time to recovery was inversely related to age, with young animals being slowest to recover GMB diversity and full community membership. Antimicrobial treatment during infection caused a significant depletion in GMB diversity. Conclusions: Although individual sifakas show unique trajectories of microbial loss and recolonization in response to infection, recovering sifakas exhibit remarkably consistent patterns, similar to initial community assembly of the GMB in infants. This observation, in particular, provides biological insight into the rules by which the GMB recovers from the disease state. Fecal transfaunation may prove effective in restoring a healthy GMB in animals with specialized diets.
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Affiliation(s)
| | - Lydia K Greene
- University Program in Ecology, Duke University, Durham, NC, USA.,Department of Evolutionary Anthropology, Duke University, Durham, NC
| | - Christine M Drea
- Department of Biology, Duke University, Durham, NC, USA.,Department of Evolutionary Anthropology, Duke University, Durham, NC
| | - Anne D Yoder
- Department of Biology, Duke University, Durham, NC, USA.,University Program in Ecology, Duke University, Durham, NC, USA.,Duke Lemur Center, Durham, NC, USA
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17
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Pioneering particle-based strategy for isolating viable bacteria from multipart soil samples compatible with Raman spectroscopy. Anal Bioanal Chem 2017; 409:3779-3788. [PMID: 28364142 DOI: 10.1007/s00216-017-0320-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2017] [Accepted: 03/15/2017] [Indexed: 12/25/2022]
Abstract
The study of edaphic bacteria is of great interest, particularly for evaluating soil remediation and recultivation methods. Therefore, a fast and simple strategy to isolate various bacteria from complex soil samples using poly(ethyleneimine) (PEI)-modified polyethylene particles is introduced. The research focuses on the binding behavior under different conditions, such as the composition, pH value, and ionic strength, of the binding buffer, and is supported by the characterization of the surface properties of particles and bacteria. The results demonstrate that electrostatic forces and hydrophobicity are responsible for the adhesion of target bacteria to the particles. Distinct advantages of the particle-based isolation strategy include simple handling, enrichment efficiency, and the preservation of viable bacteria. The presented isolation method allows a subsequent identification of the bacteria using Raman microspectroscopy in combination with chemometrical methods. This is demonstrated with a dataset of five different bacteria (Escherichia coli, Bacillus subtilis, Pseudomonas fluorescens, Streptomyces tendae, and Streptomyces acidiscabies) which were isolated from spiked soil samples. In total 92% of the Raman spectra could be identified correctly.
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18
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High-quality metagenomic DNA from marine sediment samples for genomic studies through a preprocessing approach. 3 Biotech 2016; 6:160. [PMID: 28330232 PMCID: PMC4976055 DOI: 10.1007/s13205-016-0482-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2016] [Accepted: 08/01/2016] [Indexed: 11/20/2022] Open
Abstract
Recent advances in culture-independent studies of microbes had proved to be more reliable and efficient than the conventional ones. The isolation of good quality and quantity of total community DNA are one of the major hurdles in this endeavour. Shearing of DNA during the extraction process and the co-extraction of inhibitory compounds reduce the quality of the isolated nucleic acids making it unsuitable for the construction of large insert metagenomic libraries. In the present study, a multi-level filtration step was brought in which efficiently isolated total bacterial DNA from three different environment samples. The preprocessing method could efficiently improve the 260/230 ratio of the isolated DNA by 2.3–45 % and decreased the protein contamination by 22.5–34.5 % on saltpan and arctic sediment samples, respectively. The more significant part of the experiment was that the DNA obtained was of high quality with minimal shearing making it most suitable for the construction of large insert genomic libraries. PCR amplification of 16S rRNA gene confirmed that the filtration method was effective in the isolation of high-quality DNA.
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19
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Cappelini LTD, de Fátima Menegoci Eugênio P, Leão PAGC, Alberice JV, Urbaczek AC, Assunção NA, Juliano L, Carrilho E. Capillary electrophoresis coupled to contactless conductivity detection for analysis of amino acids of agricultural interest in composting. Electrophoresis 2016; 37:2449-2457. [DOI: 10.1002/elps.201600302] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2016] [Revised: 06/29/2016] [Accepted: 07/12/2016] [Indexed: 12/18/2022]
Affiliation(s)
- Luciana Teresa Dias Cappelini
- Universidade Federal de São Paulo - UNIFESP - Rua 3 de Maio; São Paulo Brazil
- Instituto de Química de São Carlos - IQSC - USP - Avenida Trabalhador São-carlense 400; São Carlos Brazil
| | | | | | - Juliana Vieira Alberice
- Instituto de Química de São Carlos - IQSC - USP - Avenida Trabalhador São-carlense 400; São Carlos Brazil
| | - Ana Carolina Urbaczek
- Instituto de Química de São Carlos - IQSC - USP - Avenida Trabalhador São-carlense 400; São Carlos Brazil
| | - Nilson Antonio Assunção
- Instituto de Ciências Ambientais, Químicas e Farmacêuticas; Universidade Federal de Sao Paulo - UNIFESP, Rua Prof. Artur Riedel, 275; Diadema Brazil
| | - Luiz Juliano
- Universidade Federal de São Paulo - UNIFESP - Rua 3 de Maio; São Paulo Brazil
| | - Emanuel Carrilho
- Instituto de Química de São Carlos - IQSC - USP - Avenida Trabalhador São-carlense 400; São Carlos Brazil
- Instituto Nacional de Ciência e Tecnologia de Bioanalítica - INCTBio; Campinas Brazil
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20
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An Optimized Method for Quantification of Pathogenic Leptospira in Environmental Water Samples. PLoS One 2016; 11:e0160523. [PMID: 27487084 PMCID: PMC4972417 DOI: 10.1371/journal.pone.0160523] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2016] [Accepted: 07/20/2016] [Indexed: 12/19/2022] Open
Abstract
Leptospirosis is a zoonotic disease usually acquired by contact with water contaminated with urine of infected animals. However, few molecular methods have been used to monitor or quantify pathogenic Leptospira in environmental water samples. Here we optimized a DNA extraction method for the quantification of leptospires using a previously described Taqman-based qPCR method targeting lipL32, a gene unique to and highly conserved in pathogenic Leptospira. QIAamp DNA mini, MO BIO PowerWater DNA and PowerSoil DNA Isolation kits were evaluated to extract DNA from sewage, pond, river and ultrapure water samples spiked with leptospires. Performance of each kit varied with sample type. Sample processing methods were further evaluated and optimized using the PowerSoil DNA kit due to its performance on turbid water samples and reproducibility. Centrifugation speeds, water volumes and use of Escherichia coli as a carrier were compared to improve DNA recovery. All matrices showed a strong linearity in a range of concentrations from 106 to 10° leptospires/mL and lower limits of detection ranging from <1 cell /ml for river water to 36 cells/mL for ultrapure water with E. coli as a carrier. In conclusion, we optimized a method to quantify pathogenic Leptospira in environmental waters (river, pond and sewage) which consists of the concentration of 40 mL samples by centrifugation at 15,000×g for 20 minutes at 4°C, followed by DNA extraction with the PowerSoil DNA Isolation kit. Although the method described herein needs to be validated in environmental studies, it potentially provides the opportunity for effective, timely and sensitive assessment of environmental leptospiral burden.
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21
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Mölsä M, Kalin-Mänttäri L, Tonteri E, Hemmilä H, Nikkari S. Comparison of four commercial DNA extraction kits for the recovery of Bacillus spp. spore DNA from spiked powder samples. J Microbiol Methods 2016; 128:69-73. [PMID: 27435532 DOI: 10.1016/j.mimet.2016.07.013] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2016] [Revised: 07/15/2016] [Accepted: 07/15/2016] [Indexed: 11/28/2022]
Abstract
Bacillus spp. include human pathogens such as Bacillus anthracis, the causative agent of anthrax and a biothreat agent. Bacillus spp. form spores that are physically highly resistant and may remain active over sample handling. We tested four commercial DNA extraction kits (QIAamp DNA Mini Kit, RTP Pathogen Kit, ZR Fungal/Bacterial DNA MiniPrep, and genesig Easy DNA/RNA Extraction kit) for sample inactivation and DNA recovery from two powders (icing sugar and potato flour) spiked with Bacillus thuringiensis spores. The DNA was analysed using a B. thuringiensis-specific real-time PCR assay. The detection limit was 3×10(1)CFU of spiked B. thuringiensis spores with the QIAamp DNA Mini, RTP Pathogen, and genesig Easy DNA/RNA Extraction kits, and 3×10(3)CFU with the ZR Fungal/Bacterial DNA MiniPrep kit. The results showed that manual extraction kits are effective and safe for fast and easy DNA extraction from powder samples even in field conditions. Adding a DNA filtration step to the extraction protocol ensures the removal of Bacillus spp. spores from DNA samples without affecting sensitivity.
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Affiliation(s)
- Markos Mölsä
- Centres for Military Medicine and for Biological Threat Preparedness, Helsinki, Finland.
| | | | - Elina Tonteri
- Centres for Military Medicine and for Biological Threat Preparedness, Helsinki, Finland
| | - Heidi Hemmilä
- Centres for Military Medicine and for Biological Threat Preparedness, Helsinki, Finland
| | - Simo Nikkari
- Centres for Military Medicine and for Biological Threat Preparedness, Helsinki, Finland
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22
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Lai XH, Zhao LF, Chen XM, Ren Y. Rapid Identification and Characterization of Francisella by Molecular Biology and Other Techniques. Open Microbiol J 2016; 10:64-77. [PMID: 27335619 PMCID: PMC4899538 DOI: 10.2174/1874285801610010064] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2015] [Revised: 10/20/2015] [Accepted: 10/22/2015] [Indexed: 11/22/2022] Open
Abstract
Francisella tularensis is the causative pathogen of tularemia and a
Tier 1 bioterror agent on the CDC list. Considering the fact that some
subpopulation of the F. tularensis strains is more virulent, more
significantly associated with mortality, and therefore poses more threat to
humans, rapid identification and characterization of this subpopulation strains
is of invaluable importance. This review summarizes the up-to-date developments
of assays for mainly detecting and characterizing F. tularensis and a
touch of caveats of some of the assays.
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Affiliation(s)
- Xin-He Lai
- Institute of Inflammation & Diseases, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China; Institute of Translational Medicine, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Long-Fei Zhao
- College of Life Sciences, Key Laboratory of Plant-Microbe Interactions of Henan, Shangqiu Normal University, Shangqiu, Henan, 476000, PR China
| | - Xiao-Ming Chen
- Institute of Inflammation & Diseases, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China; Institute of Translational Medicine, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China ; Department of Pediatric Surgery, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Yi Ren
- Institute of Inflammation & Diseases, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China; Department of Biomedical Sciences, Florida State University College of Medicine, Tallahassee, FL, USA
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23
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Bowman S, Roffey P, McNevin D, Gahan ME. Evaluation of commercial DNA extraction methods for biosecurity applications. AUST J FORENSIC SCI 2015. [DOI: 10.1080/00450618.2015.1106585] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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24
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Silvestri EE, Perkins SD, Rice EW, Stone H, Schaefer FW. Review of processing and analytical methods for Francisella tularensis in soil and water. ANN MICROBIOL 2015. [DOI: 10.1007/s13213-015-1144-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
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25
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Hebda LM, Foran DR. Assessing the Utility of Soil DNA Extraction Kits for Increasing DNA Yields and Eliminating PCR Inhibitors from Buried Skeletal Remains. J Forensic Sci 2015; 60:1322-30. [PMID: 26258388 DOI: 10.1111/1556-4029.12878] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2014] [Revised: 09/16/2014] [Accepted: 09/22/2014] [Indexed: 10/23/2022]
Abstract
DNA identification of human remains is often necessary when decedents are skeletonized; however, poor DNA recovery and polymerase chain reaction (PCR) inhibition are frequently encountered, a situation exacerbated by burial. In this research, the utility of integrating soil DNA isolation kits into buried skeletal DNA analysis was evaluated and compared to a standard human DNA extraction kit and organic extraction. The soil kits successfully extracted skeletal DNA at quantities similar to standard methods, although the two kits tested, which differ mechanistically, were not equivalent. Further, the PCR inhibitors calcium and humic acid were effectively removed using the soil kits, whereas collagen was less so. Finally, concordant control region sequences were obtained from human skeletal remains using all four methods. Based on these comparisons, soil DNA isolation kits, which quickened the extraction process, proved to be a viable extraction technique for skeletal remains that resulted in positive identification of a decedent.
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Affiliation(s)
- Lisa M Hebda
- Forensic Science Program, School of Criminal Justice, Michigan State University, 655 Auditorium Road, 560A Baker Hall, East Lansing, MI, 48824
| | - David R Foran
- Forensic Science Program, School of Criminal Justice, Michigan State University, 655 Auditorium Road, 560A Baker Hall, East Lansing, MI, 48824.,Department of Integrated Biology, Michigan State University, East Lansing, MI, 48824
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26
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Microbial rRNA:rDNA gene ratios may be unexpectedly low due to extracellular DNA preservation in soils. J Microbiol Methods 2015; 115:112-20. [PMID: 26055315 DOI: 10.1016/j.mimet.2015.05.027] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2015] [Revised: 05/30/2015] [Accepted: 05/30/2015] [Indexed: 01/05/2023]
Abstract
We tested a method of estimating the activity of detectable individual bacterial and archaeal OTUs within a community by calculating ratios of absolute 16S rRNA to rDNA copy numbers. We investigated phylogenetically coherent patterns of activity among soil prokaryotes in non-growing soil communities. 'Activity ratios' were calculated for bacteria and archaea in soil sampled from a tropical rainforest and temperate agricultural field and incubated for one year at two levels of moisture availability and with and without carbon additions. Prior to calculating activity ratios, we corrected the relative abundances of OTUs to account for multiple copies of the 16S gene per genome. Although necessary to ensure accurate activity ratios, this correction did not change our interpretation of differences in microbial community composition across treatments. Activity ratios in this study were lower than those previously published (0.0003-210, logarithmic mean=0.24), suggesting significant extracellular DNA preservation. After controlling for the influence of individual incubation jars, significant differences in activity ratios between all members of each phylum were observed. Planctomycetes and Firmicutes had the highest activity ratios and Crenarchaeota had the lowest activity overall. Our results suggest that greater caution should be taken in interpreting soil microbial community data derived from extracted DNA. Indirect extraction methods may be useful in ensuring that microbes identified from extracellular DNA are not erroneously interpreted as components of an active microbial community.
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27
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Brooks JP, Edwards DJ, Harwich MD, Rivera MC, Fettweis JM, Serrano MG, Reris RA, Sheth NU, Huang B, Girerd P, Strauss JF, Jefferson KK, Buck GA. The truth about metagenomics: quantifying and counteracting bias in 16S rRNA studies. BMC Microbiol 2015; 15:66. [PMID: 25880246 PMCID: PMC4433096 DOI: 10.1186/s12866-015-0351-6] [Citation(s) in RCA: 300] [Impact Index Per Article: 33.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2014] [Accepted: 01/16/2015] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Characterizing microbial communities via next-generation sequencing is subject to a number of pitfalls involving sample processing. The observed community composition can be a severe distortion of the quantities of bacteria actually present in the microbiome, hampering analysis and threatening the validity of conclusions from metagenomic studies. We introduce an experimental protocol using mock communities for quantifying and characterizing bias introduced in the sample processing pipeline. We used 80 bacterial mock communities comprised of prescribed proportions of cells from seven vaginally-relevant bacterial strains to assess the bias introduced in the sample processing pipeline. We created two additional sets of 80 mock communities by mixing prescribed quantities of DNA and PCR product to quantify the relative contribution to bias of (1) DNA extraction, (2) PCR amplification, and (3) sequencing and taxonomic classification for particular choices of protocols for each step. We developed models to predict the "true" composition of environmental samples based on the observed proportions, and applied them to a set of clinical vaginal samples from a single subject during four visits. RESULTS We observed that using different DNA extraction kits can produce dramatically different results but bias is introduced regardless of the choice of kit. We observed error rates from bias of over 85% in some samples, while technical variation was very low at less than 5% for most bacteria. The effects of DNA extraction and PCR amplification for our protocols were much larger than those due to sequencing and classification. The processing steps affected different bacteria in different ways, resulting in amplified and suppressed observed proportions of a community. When predictive models were applied to clinical samples from a subject, the predicted microbiome profiles were better reflections of the physiology and diagnosis of the subject at the visits than the observed community compositions. CONCLUSIONS Bias in 16S studies due to DNA extraction and PCR amplification will continue to require attention despite further advances in sequencing technology. Analysis of mock communities can help assess bias and facilitate the interpretation of results from environmental samples.
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Affiliation(s)
- J Paul Brooks
- Department of Statistical Sciences and Operations Research, Virginia Commonwealth University, 23284-3083, Richmond, VA, USA. .,Center for the Study of Biological Complexity, Virginia Commonwealth University, 23284, Richmond, VA, USA.
| | - David J Edwards
- Department of Statistical Sciences and Operations Research, Virginia Commonwealth University, 23284-3083, Richmond, VA, USA.
| | - Michael D Harwich
- Department of Microbiology and Immunology, Virginia Commonwealth University, 23284, Richmond, VA, USA.
| | - Maria C Rivera
- Department of Biology, Virginia Commonwealth University, 23284, Richmond, VA, USA.
| | - Jennifer M Fettweis
- Department of Microbiology and Immunology, Virginia Commonwealth University, 23284, Richmond, VA, USA.
| | - Myrna G Serrano
- Center for the Study of Biological Complexity, Virginia Commonwealth University, 23284, Richmond, VA, USA. .,Department of Microbiology and Immunology, Virginia Commonwealth University, 23284, Richmond, VA, USA.
| | - Robert A Reris
- Department of Statistical Sciences and Operations Research, Virginia Commonwealth University, 23284-3083, Richmond, VA, USA.
| | - Nihar U Sheth
- Center for the Study of Biological Complexity, Virginia Commonwealth University, 23284, Richmond, VA, USA.
| | - Bernice Huang
- Department of Microbiology and Immunology, Virginia Commonwealth University, 23284, Richmond, VA, USA.
| | - Philippe Girerd
- Department of Obstetrics and Gynecology, Virginia Commonwealth University, 23284, Richmond, VA, USA.
| | | | - Jerome F Strauss
- Department of Obstetrics and Gynecology, Virginia Commonwealth University, 23284, Richmond, VA, USA.
| | - Kimberly K Jefferson
- Center for the Study of Biological Complexity, Virginia Commonwealth University, 23284, Richmond, VA, USA. .,Department of Microbiology and Immunology, Virginia Commonwealth University, 23284, Richmond, VA, USA.
| | - Gregory A Buck
- Center for the Study of Biological Complexity, Virginia Commonwealth University, 23284, Richmond, VA, USA. .,Department of Microbiology and Immunology, Virginia Commonwealth University, 23284, Richmond, VA, USA.
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28
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Vojkovska H, Kubikova I, Kralik P. Evaluation of DNA extraction methods for PCR-based detection of Listeria monocytogenes
from vegetables. Lett Appl Microbiol 2014; 60:265-72. [DOI: 10.1111/lam.12367] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2014] [Revised: 11/06/2014] [Accepted: 11/17/2014] [Indexed: 11/30/2022]
Affiliation(s)
- H. Vojkovska
- Department of Food and Feed Safety; Veterinary Research Institute; Brno Czech Republic
| | - I. Kubikova
- Department of Food and Feed Safety; Veterinary Research Institute; Brno Czech Republic
| | - P. Kralik
- Department of Food and Feed Safety; Veterinary Research Institute; Brno Czech Republic
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29
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Hedman J, Knutsson R, Ansell R, Rådström P, Rasmusson B. Pre-PCR processing in bioterrorism preparedness: improved diagnostic capabilities for laboratory response networks. Biosecur Bioterror 2014; 11 Suppl 1:S87-101. [PMID: 23971826 DOI: 10.1089/bsp.2012.0090] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Diagnostic DNA analysis using polymerase chain reaction (PCR) has become a valuable tool for rapid detection of biothreat agents. However, analysis is often challenging because of the limited size, quality, and purity of the biological target. Pre-PCR processing is an integrated concept in which the issues of analytical limit of detection and simplicity for automation are addressed in all steps leading up to PCR amplification--that is, sampling, sample treatment, and the chemical composition of PCR. The sampling method should maximize target uptake and minimize uptake of extraneous substances that could impair the analysis--so-called PCR inhibitors. In sample treatment, there is a trade-off between yield and purity, as extensive purification leads to DNA loss. A cornerstone of pre-PCR processing is to apply DNA polymerase-buffer systems that are tolerant to specific sample impurities, thereby lowering the need for expensive purification steps and maximizing DNA recovery. Improved awareness among Laboratory Response Networks (LRNs) regarding pre-PCR processing is important, as ineffective sample processing leads to increased cost and possibly false-negative or ambiguous results, hindering the decision-making process in a bioterrorism crisis. This article covers the nature and mechanisms of PCR-inhibitory substances relevant for agroterrorism and bioterrorism preparedness, methods for quality control of PCR reactions, and applications of pre-PCR processing to optimize and simplify the analysis of various biothreat agents. Knowledge about pre-PCR processing will improve diagnostic capabilities of LRNs involved in the response to bioterrorism incidents.
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Affiliation(s)
- Johannes Hedman
- Johannes Hedman, PhD, is employed as a specialist at the Swedish National Laboratory of Forensic Science (SKL) and holds a research position at Applied Microbiology, Lund University. Rickard Knutsson, PhD, is Director of Security Department, National Veterinary Institute (SVA), Uppsala, Sweden . Ricky Ansell, PhD, is employed as forensic advisor and senior reporting officer at the Swedish National Laboratory of Forensic Science (SKL). Birgitta Rasmusson, PhD, is employed as research director at the Swedish National Laboratory of Forensic Science (SKL) and holds a position as adjunct professor at Applied Microbiology, Lund University. Peter Rådström, PhD, is employed as professor Applied Microbiology, Lund University
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30
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Recent literature review of soil processing methods for recovery of Bacillus anthracis spores. ANN MICROBIOL 2014. [DOI: 10.1007/s13213-014-0932-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022] Open
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31
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A method suitable for DNA extraction from humus-rich soil. Biotechnol Lett 2014; 36:2223-8. [DOI: 10.1007/s10529-014-1591-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2014] [Accepted: 06/12/2014] [Indexed: 11/28/2022]
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Desneux J, Pourcher AM. Comparison of DNA extraction kits and modification of DNA elution procedure for the quantitation of subdominant bacteria from piggery effluents with real-time PCR. Microbiologyopen 2014; 3:437-45. [PMID: 24838631 PMCID: PMC4287173 DOI: 10.1002/mbo3.178] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2014] [Revised: 04/01/2014] [Accepted: 04/07/2014] [Indexed: 11/11/2022] Open
Abstract
Four commercial DNA extraction kits and a minor modification in the DNA elution procedure were evaluated for the quantitation of bacteria in pig manure samples. The PowerSoil®, PowerFecal®, NucleoSpin® Soil kits and QIAamp® DNA Stool Mini kit were tested on raw manure samples and on lagoon effluents for their ability to quantify total bacteria and a subdominant bacteria specific of pig manure contamination: Lactobacillus amylovorus. The NucleoSpin® Soil kit (NS kit), and to a lesser extent the PowerFecal® kit were the most efficient methods. Regardless of the kit utilized, the modified elution procedure increased DNA yield in the lagoon effluent by a factor of 1.4 to 1.8. When tested on 10 piggery effluent samples, compared to the QIAamp kit, the NS kit combined with the modified elution step, increased by a factor up to 1.7 log10 the values of the concentration of L. amylovorus. Regardless of the type of manure, the best DNA quality and the highest concentrations of bacteria were obtained using the NS kit combined with the modification of the elution procedure. The method recommended here significantly improved quantitation of subdominant bacteria in manure.
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Affiliation(s)
- Jérémy Desneux
- Irstea-Rennes, Rennes, France; Université Européenne de Bretagne, Rennes, France
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Rafiee M, Jahangiri-rad M, Hajjaran H, Mesdaghinia A, Hajaghazadeh M. Detection and identification of Legionella species in hospital water supplies through Polymerase Chain Reaction (16S rRNA). JOURNAL OF ENVIRONMENTAL HEALTH SCIENCE & ENGINEERING 2014; 12:83. [PMID: 24860661 PMCID: PMC4032159 DOI: 10.1186/2052-336x-12-83] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/09/2013] [Accepted: 04/20/2014] [Indexed: 06/03/2023]
Abstract
Legionella spp. are important waterborne pathogens that are normally transmitted through aerosols. The present work was conducted to investigate the presence of Legionella spp. and its common species in hospital water supplies. Considering the limitations of culture method, polymerase chain reaction (PCR) assays were developed to detect the gene 16S rRNA irrespective of the bacterial serotype. Four well-established DNA extraction protocols (freeze & thaw and phenol-chloroform as two manual protocols and two commercial kits) were tested and evaluated to release DNA from bacterial cells. A total of 45 samples were collected from seven distinct hospitals' sites during a period of 10 months. The PCR assay was used to amplify a 654-bp fragment of the 16S rRNA gene. Legionella were detected in 13 samples (28.9%) by all of the methods applied for DNA extraction. Significant differences were noted in the yield of extracted nucleic acids. Legionella were not detected in any of the samples when DNA extraction by freeze & thaw was used. Excluding this method and comparing manual protocol with commercial kits, Kappa coefficient was calculated as 0.619 with p < 0.05. Although no meaningful differences were found between the kits, DNA extraction with Bioneer kit exhibited a higher sensitivity than classical Qiagen. Showerheads and cold-water taps were the most and least contaminated sources with 55.5 and 9 percent positive samples, respectively. Moreover two positive samples were identified for species by DNA sequencing and submitted to the Gene Bank database with accession Nos. FJ480932 and FJ480933. The results obtained showed that despite the advantages of molecular assays in Legionella tracing in environmental sources, the use of optimised DNA extraction methods is critical.
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Affiliation(s)
- Mohammad Rafiee
- Department of Environmental Health Engineering, School of Public Health, Alborz University of Medical Sciences, Alborz, Iran
| | - Mahsa Jahangiri-rad
- Department of Environmental Health Engineering, Islamic Azad University, Tehran Medical Sciences Branch, Tehran, Iran
| | - Homa Hajjaran
- Department of Parasitology and Mycology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - Alireza Mesdaghinia
- Department of Environmental Health Engineering, School of Public Health, Center for Water Quality Research, Institute for Environmental Research, Tehran University of Medical Sciences, Tehran, Iran
| | - Mohammad Hajaghazadeh
- Department of Occupational Health, Health Faculty, Urmia University of Medical Sciences, Urmia, Iran
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Gonçalves-de-Albuquerque SDC, Pessoa E Silva R, de Morais RCS, Trajano-Silva LAM, Régis-da-Silva CG, Brandão-Filho SP, de Paiva-Cavalcanti M. Tracking false-negative results in molecular diagnosis: proposal of a triplex-PCR based method for leishmaniasis diagnosis. J Venom Anim Toxins Incl Trop Dis 2014; 20:16. [PMID: 24808911 PMCID: PMC4012836 DOI: 10.1186/1678-9199-20-16] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2013] [Accepted: 04/07/2014] [Indexed: 11/26/2022] Open
Abstract
Background Molecular biological methods have become increasingly relevant to the diagnosis and control of infectious diseases, such as leishmaniasis. Since various factors may affect the sensitivity of PCR assays, including DNA yield and purity, an optimal extraction method is pivotal. Losses of a parasite’s DNA during extraction may significantly impair its detection by PCR and lead to false-negative results. This study proposes a triplex PCR assay targeting the parasite’s DNA, an external control (pUC18) and an internal control (G3PD) for accurate diagnosis of leishmaniasis. Results Two primer pairs were designed to detect the plasmid pUC18 and a triplex PCR assay targeting the Leishmania braziliensis kinetoplast DNA, the external control and the internal control was standardized. The triplex PCR assay was assessed for its ability to detect the three target DNA fragments simultaneously. PCR products from pUC18 DNA resulted in bands of 368 (P1) and 316 (P2) base pairs (bp). The triplex PCR optimized with the chosen external control system (P1) allowed the simultaneous detection of the internal control (G3PD – 567 bp) as well as of small quantities (10 pg) of the target parasite’s DNA, detected by amplification of a 138 bp product. Conclusions The new tool standardized herein enables a more reliable interpretation of PCR results, mainly by contributing to quality assurance of leishmaniasis diagnosis. Furthermore, after simple standardization steps, this protocol could be applied to the diagnosis of other infectious diseases in reference laboratories. This triplex PCR enables the assessment of small losses during the DNA extraction process, problems concerning DNA degradation (sample quality) and the detection of L. braziliensis kDNA.
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Affiliation(s)
| | - Rômulo Pessoa E Silva
- Departamento de Imunologia, Centro de Pesquisas Aggeu Magalhães (CPqAM), Av. Prof. Moraes Rego, s/n, Recife, Pernambuco CEP 50670-420, Brasil
| | - Rayana Carla Silva de Morais
- Departamento de Imunologia, Centro de Pesquisas Aggeu Magalhães (CPqAM), Av. Prof. Moraes Rego, s/n, Recife, Pernambuco CEP 50670-420, Brasil
| | | | - Carlos Gustavo Régis-da-Silva
- Departamento de Imunologia, Centro de Pesquisas Aggeu Magalhães (CPqAM), Av. Prof. Moraes Rego, s/n, Recife, Pernambuco CEP 50670-420, Brasil
| | - Sinval Pinto Brandão-Filho
- Departamento de Imunologia, Centro de Pesquisas Aggeu Magalhães (CPqAM), Av. Prof. Moraes Rego, s/n, Recife, Pernambuco CEP 50670-420, Brasil
| | - Milena de Paiva-Cavalcanti
- Departamento de Imunologia, Centro de Pesquisas Aggeu Magalhães (CPqAM), Av. Prof. Moraes Rego, s/n, Recife, Pernambuco CEP 50670-420, Brasil
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Hutchins AS, Astwood MJ, Saah JR, Michel PA, Newton BR, Dauphin LA. Evaluation of automated and manual DNA purification methods for detecting Ricinus communis DNA during ricin investigations. Forensic Sci Int 2014; 236:10-5. [PMID: 24529769 DOI: 10.1016/j.forsciint.2013.12.011] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2013] [Revised: 11/26/2013] [Accepted: 12/10/2013] [Indexed: 11/25/2022]
Abstract
In April of 2013, letters addressed to the President of United States and other government officials were intercepted and found to be contaminated with ricin, heightening awareness about the need to evaluate laboratory methods for detecting ricin. This study evaluated commercial DNA purification methods for isolating Ricinus communis DNA as measured by real-time polymerase chain reaction (PCR). Four commercially available DNA purification methods (two automated, MagNA Pure compact and MagNA Pure LC, and two manual, MasterPure complete DNA and RNA purification kit and QIAamp DNA blood mini kit) were evaluated. We compared their ability to purify detectable levels of R. communis DNA from four different sample types, including crude preparations of ricin that could be used for biological crimes or acts of bioterrorism. Castor beans, spiked swabs, and spiked powders were included to simulate sample types typically tested during criminal and public health investigations. Real-time PCR analysis indicated that the QIAamp kit resulted in the greatest sensitivity for ricin preparations; the MasterPure kit performed best with spiked powders. The four methods detected equivalent levels by real-time PCR when castor beans and spiked swabs were used. All four methods yielded DNA free of PCR inhibitors as determined by the use of a PCR inhibition control assay. This study demonstrated that DNA purification methods differ in their ability to purify R. communis DNA; therefore, the purification method used for a given sample type can influence the sensitivity of real-time PCR assays for R. communis.
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Affiliation(s)
- Anne S Hutchins
- Bioterrorism and Emerging Pathogens Unit, North Carolina State Laboratory of Public Health, Raleigh, NC 27607, USA
| | | | - J Royden Saah
- Bioterrorism and Emerging Pathogens Unit, North Carolina State Laboratory of Public Health, Raleigh, NC 27607, USA
| | - Pierre A Michel
- Bioterrorism Rapid Response and Advanced Technology (BRRAT) Laboratory, Laboratory Preparedness and Response Branch (LPRB), Division of Preparedness and Emerging Infections (DPEI), National Center for Emerging and Zoonotic Infectious Diseases (NCEZID), Centers for Disease Control and Prevention (CDC), Atlanta, GA 30333, USA
| | | | - Leslie A Dauphin
- Bioterrorism Rapid Response and Advanced Technology (BRRAT) Laboratory, Laboratory Preparedness and Response Branch (LPRB), Division of Preparedness and Emerging Infections (DPEI), National Center for Emerging and Zoonotic Infectious Diseases (NCEZID), Centers for Disease Control and Prevention (CDC), Atlanta, GA 30333, USA.
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Microbial diversity in fecal samples depends on DNA extraction method: easyMag DNA extraction compared to QIAamp DNA stool mini kit extraction. BMC Res Notes 2014; 7:50. [PMID: 24447346 PMCID: PMC4015497 DOI: 10.1186/1756-0500-7-50] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2013] [Accepted: 01/13/2014] [Indexed: 12/21/2022] Open
Abstract
Background There are challenges, when extracting bacterial DNA from specimens for molecular diagnostics, since fecal samples also contain DNA from human cells and many different substances derived from food, cell residues and medication that can inhibit downstream PCR. The purpose of the study was to evaluate two different DNA extraction methods in order to choose the most efficient method for studying intestinal bacterial diversity using Denaturing Gradient Gel Electrophoresis (DGGE). Findings In this study, a semi-automatic DNA extraction system (easyMag®, BioMérieux, Marcy I’Etoile, France) and a manual one (QIAamp DNA Stool Mini Kit, Qiagen, Hilden, Germany) were tested on stool samples collected from 3 patients with Inflammatory Bowel disease (IBD) and 5 healthy individuals. DNA extracts obtained by the QIAamp DNA Stool Mini Kit yield a higher amount of DNA compared to DNA extracts obtained by easyMag® from the same fecal samples. Furthermore, DNA extracts obtained using easyMag® seemed to contain inhibitory compounds, since in order to perform a successful PCR-analysis, the sample should be diluted at least 10 times. DGGE performed on PCR from DNA extracted by QIAamp DNA Stool Mini Kit DNA was very successful. Conclusion QIAamp DNA Stool Mini Kit DNA extracts are optimal for DGGE runs and this extraction method yields a higher amount of DNA compared to easyMag®.
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Recovery and identification of bacterial DNA from illicit drugs. Forensic Sci Int 2013; 235:78-85. [PMID: 24447454 DOI: 10.1016/j.forsciint.2013.12.006] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2013] [Accepted: 12/06/2013] [Indexed: 11/22/2022]
Abstract
Bacterial infections, including Bacillus anthracis (anthrax), are a common risk associated with illicit drug use, particularly among injecting drug users. There is, therefore, an urgent need to survey illicit drugs used for injection for the presence of bacteria and provide valuable information to health and forensic authorities. The objectives of this study were to develop a method for the extraction of bacterial DNA from illicit drugs and conduct a metagenomic survey of heroin and methamphetamine seized in the Australian Capital Territory during 2002-2011 for the presence of pathogens. Trends or patterns in drug contamination and their health implications for injecting drug users were also investigated. Methods based on the ChargeSwitch(®)gDNA mini kit (Invitrogen), QIAamp DNA extraction mini kit (QIAGEN) with and without bead-beating, and an organic phenol/chloroform extraction with ethanol precipitation were assessed for the recovery efficiency of both free and cellular bacterial DNA. Bacteria were identified using polymerase chain reaction and electrospray ionization-mass spectrometry (PCR/ESI-MS). An isopropanol pre-wash to remove traces of the drug and diluents, followed by a modified ChargeSwitch(®) method, was found to efficiently lyse cells and extract free and cellular DNA from Gram-positive and Gram-negative bacteria in heroin and methamphetamine which could then be identified by PCR/ESI-MS. Analysis of 12 heroin samples revealed the presence of DNA from species of Comamonas, Weissella, Bacillus, Streptococcus and Arthrobacter. No organisms were detected in the nine methamphetamine samples analysed. This study develops a method to extract and identify Gram-positive and Gram-negative bacteria from illicit drugs and demonstrates the presence of a range of bacterial pathogens in seized drug samples. These results will prove valuable for future work investigating trends or patterns in drug contamination and their health implications for injecting drug users as well as enabling forensic links between seizures to be examined.
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Griffin MJ, Goodwin AE, Merry GE, Liles MR, Williams MA, Ware C, Waldbieser GC. Rapid quantitative detection of Aeromonas hydrophila strains associated with disease outbreaks in catfish aquaculture. J Vet Diagn Invest 2013; 25:473-81. [DOI: 10.1177/1040638713494210] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
A new strain of Aeromonas hydrophila has been implicated in significant losses in farm-raised catfish. Outbreaks attributable to this new strain began in Alabama in the summer of 2009 and have spread to Arkansas and Mississippi in subsequent years. These outbreaks mostly afflicted market-sized fish and resulted in considerable losses in short periods of time. The present research was designed to develop an expeditious diagnostic procedure to detect the new strains of A. hydrophila due to the rapid onset and biosecurity concerns associated with this new disease. A discriminatory quantitative polymerase chain reaction assay was developed using gene sequences unique to the virulent strains identified in a related comparative genomic study. Using this assay, suspect colonies on a culture plate can be positively identified as the new strain within 2 hr. The assay is repeatable and reproducible with a linear dynamic range covering 8 orders of magnitude and a sensitivity of approximately 7 copies of target DNA in a 15-µl reaction. In addition, the assay is able to detect and quantify the virulent strain from catfish tissues (0.025 g), pond water (40 ml), and sediments (0.25 g) with a sensitivity limit of approximately 100 bacteria in a sample. This assay provides rapid discrimination between the new virulent strain and more common A. hydrophila and is useful for epidemiological studies involving the detection and quantification of the virulent strain in environmental samples and fish tissues.
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Affiliation(s)
- Matt J. Griffin
- Aquatic Research and Diagnostic Laboratory, College of Veterinary Medicine, Mississippi State University (Griffin, Ware)
- U.S. Department of Agriculture, Catfish Genetics Research Unit (Waldbieser)
- Thad Cochran National Warmwater Aquaculture Center, Stoneville, MS; the Aquaculture/Fisheries Center, University of Arkansas at Pine Bluff, Pine Bluff, AR (Goodwin, Merry)
- Department of Biological Sciences, Auburn University, Auburn, AL (Liles, Williams)
| | - Andrew E. Goodwin
- Aquatic Research and Diagnostic Laboratory, College of Veterinary Medicine, Mississippi State University (Griffin, Ware)
- U.S. Department of Agriculture, Catfish Genetics Research Unit (Waldbieser)
- Thad Cochran National Warmwater Aquaculture Center, Stoneville, MS; the Aquaculture/Fisheries Center, University of Arkansas at Pine Bluff, Pine Bluff, AR (Goodwin, Merry)
- Department of Biological Sciences, Auburn University, Auburn, AL (Liles, Williams)
| | - Gwenn E. Merry
- Aquatic Research and Diagnostic Laboratory, College of Veterinary Medicine, Mississippi State University (Griffin, Ware)
- U.S. Department of Agriculture, Catfish Genetics Research Unit (Waldbieser)
- Thad Cochran National Warmwater Aquaculture Center, Stoneville, MS; the Aquaculture/Fisheries Center, University of Arkansas at Pine Bluff, Pine Bluff, AR (Goodwin, Merry)
- Department of Biological Sciences, Auburn University, Auburn, AL (Liles, Williams)
| | - Mark R. Liles
- Aquatic Research and Diagnostic Laboratory, College of Veterinary Medicine, Mississippi State University (Griffin, Ware)
- U.S. Department of Agriculture, Catfish Genetics Research Unit (Waldbieser)
- Thad Cochran National Warmwater Aquaculture Center, Stoneville, MS; the Aquaculture/Fisheries Center, University of Arkansas at Pine Bluff, Pine Bluff, AR (Goodwin, Merry)
- Department of Biological Sciences, Auburn University, Auburn, AL (Liles, Williams)
| | - Malachi A. Williams
- Aquatic Research and Diagnostic Laboratory, College of Veterinary Medicine, Mississippi State University (Griffin, Ware)
- U.S. Department of Agriculture, Catfish Genetics Research Unit (Waldbieser)
- Thad Cochran National Warmwater Aquaculture Center, Stoneville, MS; the Aquaculture/Fisheries Center, University of Arkansas at Pine Bluff, Pine Bluff, AR (Goodwin, Merry)
- Department of Biological Sciences, Auburn University, Auburn, AL (Liles, Williams)
| | - Cynthia Ware
- Aquatic Research and Diagnostic Laboratory, College of Veterinary Medicine, Mississippi State University (Griffin, Ware)
- U.S. Department of Agriculture, Catfish Genetics Research Unit (Waldbieser)
- Thad Cochran National Warmwater Aquaculture Center, Stoneville, MS; the Aquaculture/Fisheries Center, University of Arkansas at Pine Bluff, Pine Bluff, AR (Goodwin, Merry)
- Department of Biological Sciences, Auburn University, Auburn, AL (Liles, Williams)
| | - Geoffrey C. Waldbieser
- Aquatic Research and Diagnostic Laboratory, College of Veterinary Medicine, Mississippi State University (Griffin, Ware)
- U.S. Department of Agriculture, Catfish Genetics Research Unit (Waldbieser)
- Thad Cochran National Warmwater Aquaculture Center, Stoneville, MS; the Aquaculture/Fisheries Center, University of Arkansas at Pine Bluff, Pine Bluff, AR (Goodwin, Merry)
- Department of Biological Sciences, Auburn University, Auburn, AL (Liles, Williams)
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Dong B, Yi J, Dai L, Dai X. Evaluation of Several DNA Extraction Methods for Obtaining Total Community DNA from Anaerobic Digestion Sludge. ACTA ACUST UNITED AC 2013. [DOI: 10.1016/j.proenv.2013.04.115] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Abstract
Background Quantitative polymerase chain reaction (qPCR) assays used in pathogen detection require rigorous methods development including characterizing DNA extraction products. A DNA extract characterization process is demonstrated using DNA extracted from five different cells types (two Gram-negatives: Escherichia coli, and Burkholderia thailandensis, spores and vegetative cells from the Gram-positive Bacillus cereus, and yeast Saccharomyces cerevisiae) with six different methods. Results DNA extract quantity (concentration and extraction efficiency) and quality (purity and intactness) varied by cell type and extraction method enabling the demonstration of different DNA characterization methods. DNA purity was measured using UV spectroscopy, where the A260/A280 and A260/A230 ratios are indicators of different contaminants. Reproducibility of UV spectroscopy measurements decreased for DNA concentrations less than 17.5 ng/μL. Forty-seven extracts had concentrations greater than 17.5 ng/μL, 25 had A260/A280 above 2.0, and 28 had A260/A230 ratios below 1.8 indicating RNA and polysaccharide contamination respectively. Based on a qPCR inhibition assay the contaminants did not inhibit PCR. Extract intactness was evaluated using microfluidic gel electrophoresis. Thirty-five samples had concentrations above the limit of quantification (LOQ, roughly 11 ng/ μL), 93.5% of the DNA was larger than 1kb and 1% was smaller than 300 bp. Extract concentrations ranged from 1502.2 ng/μL to below the LOQ when UV spectroscopy, fluorometry, and qPCR were used. LOQ for UV spectroscopic and fluorometric measurements were 3.5 ng/μL and 0.25 ng/μL respectively. The qPCR LOQ varied by cell type (5.72 × 10-3 ng/μL for E. coli, 2.66 × 10-3 ng/μL, for B. cereus, 3.78 × 10-3 ng/μL for B. thailandensis, and 7.67 × 10-4 ng/μL for S. cerevisiae). A number of samples were below the UV spectroscopy (n = 27), flurometry (n = 15), and qPCR (n = 3) LOQ. Conclusion The presented DNA extract characterization process provides measures of DNA quantity and quality applicable to microbial detection methods development and validation studies. Evaluating DNA quality and quantity results in a better understanding of process LOD and contributing factors to suboptimal assay performance. The samples used demonstrated the use of different DNA characterization methods presented but did not encompass the full range of DNA extract characteristics.
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Evaluation of six commercial DNA extraction kits for recovery of Burkholderia pseudomallei DNA. J Microbiol Methods 2012; 91:487-9. [PMID: 23022447 DOI: 10.1016/j.mimet.2012.09.019] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2012] [Revised: 09/17/2012] [Accepted: 09/17/2012] [Indexed: 11/23/2022]
Abstract
Six commercially available DNA extraction kits, as well as thermal lysis and proteinase K DNA extraction were evaluated regarding bacterial inactivation, DNA yield and purity, and their use in a Burkholderia pseudomallei real-time PCR. While all methods successfully inactivated the bacteria, by measuring DNA purity and the level of detection by real-time PCR, the proteinase K method was the most sensitive.
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Bacterial biodiversity from anthropogenic extreme environments: a hyper-alkaline and hyper-saline industrial residue contaminated by chromium and iron. Appl Microbiol Biotechnol 2012; 97:369-78. [DOI: 10.1007/s00253-012-3923-5] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2010] [Revised: 01/21/2012] [Accepted: 01/25/2012] [Indexed: 11/26/2022]
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Wielinga PR, de Heer L, de Groot A, Hamidjaja RA, Bruggeman G, Jordan K, van Rotterdam BJ. Evaluation of DNA extraction methods for Bacillus anthracis spores spiked to food and feed matrices at biosafety level 3 conditions. Int J Food Microbiol 2011; 150:122-7. [DOI: 10.1016/j.ijfoodmicro.2011.07.023] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2010] [Revised: 05/25/2011] [Accepted: 07/21/2011] [Indexed: 11/30/2022]
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44
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Rose HL, Dewey CA, Ely MS, Willoughby SL, Parsons TM, Cox V, Spencer PM, Weller SA. Comparison of eight methods for the extraction of Bacillus atrophaeus spore DNA from eleven common interferents and a common swab. PLoS One 2011; 6:e22668. [PMID: 21818364 PMCID: PMC3144239 DOI: 10.1371/journal.pone.0022668] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2011] [Accepted: 06/28/2011] [Indexed: 11/19/2022] Open
Abstract
Eight DNA extraction products or methods (Applied Biosystems PrepFiler Forensic DNA Extraction Kit; Bio-Rad Instagene Only, Bio-Rad Instagene & Spin Column Purification; EpiCentre MasterPure DNA & RNA Kit; FujiFilm QuickGene Mini80; Idaho Technologies 1-2-3 Q-Flow Kit; MoBio UltraClean Microbial DNA Isolation Kit; Sigma Extract-N-Amp Plant and Seed Kit) were adapted to facilitate extraction of DNA under BSL3 containment conditions. DNA was extracted from 12 common interferents or sample types, spiked with spores of Bacillus atropheaus. Resulting extracts were tested by real-time PCR. No one method was the best, in terms of DNA extraction, across all sample types. Statistical analysis indicated that the PrepFiler method was the best method from six dry powders (baking, biological washing, milk, plain flour, filler and talcum) and one solid (Underarm deodorant), the UltraClean method was the best from four liquids (aftershave, cola, nutrient broth, vinegar), and the MasterPure method was the best from the swab sample type. The best overall method, in terms of DNA extraction, across all sample types evaluated was the UltraClean method.
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Affiliation(s)
- Helen L. Rose
- Detection Department, Defence Science and Technology Laboratory, Porton Down, Salisbury, United Kingdom
| | - Caroline A. Dewey
- Detection Department, Defence Science and Technology Laboratory, Porton Down, Salisbury, United Kingdom
| | - Morgan S. Ely
- Detection Department, Defence Science and Technology Laboratory, Porton Down, Salisbury, United Kingdom
| | - Sarah L. Willoughby
- Detection Department, Defence Science and Technology Laboratory, Porton Down, Salisbury, United Kingdom
| | - Tanya M. Parsons
- Detection Department, Defence Science and Technology Laboratory, Porton Down, Salisbury, United Kingdom
| | - Victoria Cox
- Detection Department, Defence Science and Technology Laboratory, Porton Down, Salisbury, United Kingdom
| | - Phillippa M. Spencer
- Detection Department, Defence Science and Technology Laboratory, Porton Down, Salisbury, United Kingdom
| | - Simon A. Weller
- Detection Department, Defence Science and Technology Laboratory, Porton Down, Salisbury, United Kingdom
- * E-mail:
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Lin YT, Whitman WB, Coleman DC, Chih-Yu C. Molecular characterization of soil bacterial community in a perhumid, low mountain forest. Microbes Environ 2011; 26:325-31. [PMID: 21727759 DOI: 10.1264/jsme2.me11114] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Forest disturbance often results in changes in soil properties and microbial communities. In the present study, we characterized a soil bacterial community subjected to disturbance using 16S rRNA gene clone libraries. The community was from a disturbed broad-leaved, low mountain forest ecosystem at Huoshaoliao (HSL) located in northern Taiwan. This locality receives more than 4,000 mm annual precipitation, one of the highest precipitations in Taiwan. Based on the Shannon diversity index, Chao1 estimator, richness and rarefaction curve analysis, the bacterial community in HSL forest soils was more diverse than those previously investigated in natural and disturbed forest soils with colder or less humid weather conditions. Analysis of molecular variance also revealed that the bacterial community in disturbed soils significantly differed from natural forest soils. Most of the abundant operational taxonomic units (OTUs) in the disturbed soil community at HSL were less abundant or absent in other soils. The disturbances influenced the composition of bacterial communities in natural and disturbed forests and increased the diversity of the disturbed forest soil community. Furthermore, the warmer and humid weather conditions could also increase community diversity in HSL soils.
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Affiliation(s)
- Yu-Te Lin
- Biodiversity Research Center, Academia Sinica, Nankang, Taipei, Taiwan
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Dauphin LA, Walker RE, Petersen JM, Bowen MD. Comparative evaluation of automated and manual commercial DNA extraction methods for detection of Francisella tularensis DNA from suspensions and spiked swabs by real-time polymerase chain reaction. Diagn Microbiol Infect Dis 2011; 70:299-306. [PMID: 21546201 DOI: 10.1016/j.diagmicrobio.2011.02.010] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2010] [Revised: 12/08/2010] [Accepted: 02/28/2011] [Indexed: 01/27/2023]
Abstract
This study evaluated commercial automated and manual DNA extraction methods for the isolation of Francisella tularensis DNA suitable for real-time polymerase chain reaction (PCR) analysis from cell suspensions and spiked cotton, foam, and polyester swabs. Two automated methods, the MagNA Pure Compact and the QIAcube, were compared to 4 manual methods, the IT 1-2-3 DNA sample purification kit, the MasterPure Complete DNA and RNA purification kit, the QIAamp DNA blood mini kit, and the UltraClean Microbial DNA isolation kit. The methods were compared using 6 F. tularensis strains representing the 2 subspecies which cause the majority of reported cases of tularemia in humans. Cell viability testing of the DNA extracts showed that all 6 extraction methods efficiently inactivated F. tularensis at concentrations of ≤10⁶ CFU/mL. Real-time PCR analysis using a multitarget 5' nuclease assay for F. tularensis revealed that the PCR sensitivity was equivalent using DNA extracted by the 2 automated methods and the manual MasterPure and QIAamp methods. These 4 methods resulted in significantly better levels of detection from bacterial suspensions and performed equivalently for spiked swab samples than the remaining 2. This study identifies optimal DNA extraction methods for processing swab specimens for the subsequent detection of F. tularensis DNA using real-time PCR assays. Furthermore, the results provide diagnostic laboratories with the option to select from 2 automated DNA extraction methods as suitable alternatives to manual methods for the isolation of DNA from F. tularensis.
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Affiliation(s)
- Leslie A Dauphin
- Bioterrorism Rapid Response and Advanced Technology (BRRAT) Laboratory, Laboratory Preparedness and Response Branch (LPRB), Division of Preparedness and Emerging Infections (DPEI), Centers for Disease Control and Prevention (CDC), Atlanta, GA 30333, USA.
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Pontiroli A, Travis ER, Sweeney FP, Porter D, Gaze WH, Mason S, Hibberd V, Holden J, Courtenay O, Wellington EMH. Pathogen quantitation in complex matrices: a multi-operator comparison of DNA extraction methods with a novel assessment of PCR inhibition. PLoS One 2011; 6:e17916. [PMID: 21448453 PMCID: PMC3063169 DOI: 10.1371/journal.pone.0017916] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2010] [Accepted: 02/15/2011] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Mycobacterium bovis is the aetiological agent of bovine tuberculosis (bTB), an important recrudescent zoonosis, significantly increasing in British herds in recent years. Wildlife reservoirs have been identified for this disease but the mode of transmission to cattle remains unclear. There is evidence that viable M. bovis cells can survive in soil and faeces for over a year. METHODOLOGY/PRINCIPAL FINDINGS We report a multi-operator blinded trial for a rigorous comparison of five DNA extraction methods from a variety of soil and faecal samples to assess recovery of M. bovis via real-time PCR detection. The methods included four commercial kits: the QIAamp Stool Mini kit with a pre-treatment step, the FastDNA® Spin kit, the UltraClean™ and PowerSoil™ soil kits and a published manual method based on phenol:chloroform purification, termed Griffiths. M. bovis BCG Pasteur spiked samples were extracted by four operators and evaluated using a specific real-time PCR assay. A novel inhibition control assay was used alongside spectrophotometric ratios to monitor the level of inhibitory compounds affecting PCR, DNA yield, and purity. There were statistically significant differences in M. bovis detection between methods of extraction and types of environmental samples; no significant differences were observed between operators. Processing times and costs were also evaluated. To improve M. bovis detection further, the two best performing methods, FastDNA® Spin kit and Griffiths, were optimised and the ABI TaqMan environmental PCR Master mix was adopted, leading to improved sensitivities. CONCLUSIONS M. bovis was successfully detected in all environmental samples; DNA extraction using FastDNA® Spin kit was the most sensitive method with highest recoveries from all soil types tested. For troublesome faecal samples, we have used and recommend an improved assay based on a reduced volume, resulting in detection limits of 4.25×10(5) cells g(-1) using Griffiths and 4.25×10(6) cells g(-1) using FastDNA® Spin kit.
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Dineen SM, Aranda R, Anders DL, Robertson JM. An evaluation of commercial DNA extraction kits for the isolation of bacterial spore DNA from soil. J Appl Microbiol 2011; 109:1886-96. [PMID: 20666869 DOI: 10.1111/j.1365-2672.2010.04816.x] [Citation(s) in RCA: 92] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
AIMS To evaluate six commercial DNA extraction kits for their ability to isolate PCR-quality DNA from Bacillus spores in various soil samples. METHODS AND RESULTS Three soils were inoculated with various amounts of Bacillus cereus spores to simulate an outbreak or intentional release of the threat agent Bacillus anthracis. DNA was isolated from soil samples using six commercial DNA extraction kits. Extraction and purification efficiencies were assessed using a duplex real-time PCR assay that included an internal positive control. The FastDNA(®) SPIN kit for Soil showed the highest DNA extraction yield, while the E.Z.N.A.(®) Soil DNA and PowerSoil(®) DNA Isolation kits showed the highest efficiencies in removing PCR inhibitors from loam soil extracts. CONCLUSIONS The results of this study suggest that commercially available extraction kits can be used to extract PCR-quality DNA from bacterial spores in soil. The selection of an appropriate extraction kit should depend on the characteristics of the soil sample and the intended downstream application. SIGNIFICANCE AND IMPACT OF THE STUDY The results of this study aid in the selection of an appropriate DNA extraction kit for a given soil sample. Its application could expedite sample processing for real-time PCR detection of a pathogen in soil.
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Affiliation(s)
- S M Dineen
- Federal Bureau of Investigation Laboratory, Quantico, VA, USA
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Persson S, de Boer RF, Kooistra-Smid AM, Olsen KE. Five commercial DNA extraction systems tested and compared on a stool sample collection. Diagn Microbiol Infect Dis 2011; 69:240-4. [DOI: 10.1016/j.diagmicrobio.2010.09.023] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2010] [Revised: 09/15/2010] [Accepted: 09/29/2010] [Indexed: 10/18/2022]
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van Zanten E, Wisselink G, de Boer W, Stoll S, Alvarez R, Kooistra-Smid A. Comparison of the QIAsymphony automated nucleic acid extraction and PCR setup platforms with NucliSens easyMAG and Corbett CAS-1200 liquid handling station for the detection of enteric pathogens in fecal samples. J Microbiol Methods 2011; 84:335-40. [DOI: 10.1016/j.mimet.2010.12.024] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2010] [Revised: 12/10/2010] [Accepted: 12/21/2010] [Indexed: 10/18/2022]
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