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Aizpurua O, Dunn RR, Hansen LH, Gilbert MTP, Alberdi A. Field and laboratory guidelines for reliable bioinformatic and statistical analysis of bacterial shotgun metagenomic data. Crit Rev Biotechnol 2024; 44:1164-1182. [PMID: 37731336 DOI: 10.1080/07388551.2023.2254933] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Revised: 05/22/2023] [Accepted: 06/27/2023] [Indexed: 09/22/2023]
Abstract
Shotgun metagenomics is an increasingly cost-effective approach for profiling environmental and host-associated microbial communities. However, due to the complexity of both microbiomes and the molecular techniques required to analyze them, the reliability and representativeness of the results are contingent upon the field, laboratory, and bioinformatic procedures employed. Here, we consider 15 field and laboratory issues that critically impact downstream bioinformatic and statistical data processing, as well as result interpretation, in bacterial shotgun metagenomic studies. The issues we consider encompass intrinsic properties of samples, study design, and laboratory-processing strategies. We identify the links of field and laboratory steps with downstream analytical procedures, explain the means for detecting potential pitfalls, and propose mitigation measures to overcome or minimize their impact in metagenomic studies. We anticipate that our guidelines will assist data scientists in appropriately processing and interpreting their data, while aiding field and laboratory researchers to implement strategies for improving the quality of the generated results.
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Affiliation(s)
- Ostaizka Aizpurua
- Center for Evolutionary Hologenomics, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Robert R Dunn
- Department of Applied Ecology, North Carolina State University, Raleigh, NC, USA
| | - Lars H Hansen
- Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - M T P Gilbert
- Center for Evolutionary Hologenomics, Globe Institute, University of Copenhagen, Copenhagen, Denmark
- University Museum, NTNU, Trondheim, Norway
| | - Antton Alberdi
- Center for Evolutionary Hologenomics, Globe Institute, University of Copenhagen, Copenhagen, Denmark
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2
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Wang J, Deng Z, Gao X, Long J, Wang Y, Wang W, Li C, He Y, Wu Z. Combined control of plant diseases by Bacillus subtilis SL44 and Enterobacter hormaechei Wu15. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 934:173297. [PMID: 38761953 DOI: 10.1016/j.scitotenv.2024.173297] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Revised: 04/12/2024] [Accepted: 05/14/2024] [Indexed: 05/20/2024]
Abstract
Co-incubation of plant growth promoting rhizobacteria (PGPRs) have been proposed as a potential alternative to pesticides for controlling fungal pathogens in crops, but their synergism mechanisms are not yet fully understood. In this study, combined use of Bacillus subtilis SL44 and Enterobacter hormaechei Wu15 could decrease the density of Colletotrichum gloeosporioides and Rhizoctonia solani and enhance the growth of beneficial bacteria on the mycelial surface, thereby mitigating disease severity. Meanwhile, PGPR application led to a reorganization of the rhizosphere microbial community through modulating its metabolites, such as extracellular polymeric substances and chitinase. These metabolites demonstrated positive effects on attracting and enhancing conventional periphery bacteria, inhibiting fungal pathogens and promoting soil health effectively. The improvement in the microbial community structure altered the trophic mode of soil fungal communities, effectively decreasing the proportion of saprotrophic soil and reducing fungal plant diseases. Certain combinations of PGPR have the potential to serve as precise instruments for managing plant pathogens.
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Affiliation(s)
- Jianwen Wang
- School of Chemistry and Chemical Engineering/Key Lab. for Green Processing of Chemical Engineering of Xinjiang Bingtuan, Shihezi University, Shihezi 832003, PR China; School of Environmental and Chemical Engineering, Xi'an Key Laboratory of Textile Chemical Engineering Auxiliaries, Engineering Research Center of Biological Resources Development and Pollution Control Universities of Shaanxi Province, Key Laboratory of Textile Dyeing Wastewater Treatment Universities of Shaanxi Province, Xi'an Polytechnic University, Xi'an 710048, PR China; Department of Chemical Engineering, Tsinghua University, Beijing 100084, PR China
| | - Zihe Deng
- School of Chemistry and Chemical Engineering/Key Lab. for Green Processing of Chemical Engineering of Xinjiang Bingtuan, Shihezi University, Shihezi 832003, PR China; School of Environmental and Chemical Engineering, Xi'an Key Laboratory of Textile Chemical Engineering Auxiliaries, Engineering Research Center of Biological Resources Development and Pollution Control Universities of Shaanxi Province, Key Laboratory of Textile Dyeing Wastewater Treatment Universities of Shaanxi Province, Xi'an Polytechnic University, Xi'an 710048, PR China
| | - Xizhuo Gao
- School of Environmental and Chemical Engineering, Xi'an Key Laboratory of Textile Chemical Engineering Auxiliaries, Engineering Research Center of Biological Resources Development and Pollution Control Universities of Shaanxi Province, Key Laboratory of Textile Dyeing Wastewater Treatment Universities of Shaanxi Province, Xi'an Polytechnic University, Xi'an 710048, PR China
| | - Jiajia Long
- School of Environmental and Chemical Engineering, Xi'an Key Laboratory of Textile Chemical Engineering Auxiliaries, Engineering Research Center of Biological Resources Development and Pollution Control Universities of Shaanxi Province, Key Laboratory of Textile Dyeing Wastewater Treatment Universities of Shaanxi Province, Xi'an Polytechnic University, Xi'an 710048, PR China
| | - Yiwei Wang
- School of Environmental and Chemical Engineering, Xi'an Key Laboratory of Textile Chemical Engineering Auxiliaries, Engineering Research Center of Biological Resources Development and Pollution Control Universities of Shaanxi Province, Key Laboratory of Textile Dyeing Wastewater Treatment Universities of Shaanxi Province, Xi'an Polytechnic University, Xi'an 710048, PR China
| | - Wanying Wang
- School of Environmental and Chemical Engineering, Xi'an Key Laboratory of Textile Chemical Engineering Auxiliaries, Engineering Research Center of Biological Resources Development and Pollution Control Universities of Shaanxi Province, Key Laboratory of Textile Dyeing Wastewater Treatment Universities of Shaanxi Province, Xi'an Polytechnic University, Xi'an 710048, PR China
| | - Chun Li
- School of Chemistry and Chemical Engineering/Key Lab. for Green Processing of Chemical Engineering of Xinjiang Bingtuan, Shihezi University, Shihezi 832003, PR China; Department of Chemical Engineering, Tsinghua University, Beijing 100084, PR China
| | - Yanhui He
- School of Environmental and Chemical Engineering, Xi'an Key Laboratory of Textile Chemical Engineering Auxiliaries, Engineering Research Center of Biological Resources Development and Pollution Control Universities of Shaanxi Province, Key Laboratory of Textile Dyeing Wastewater Treatment Universities of Shaanxi Province, Xi'an Polytechnic University, Xi'an 710048, PR China; Shanxi Qinfengkesheng Biotechnology Company Ltd., Xianyang 713700, PR China.
| | - Zhansheng Wu
- School of Environmental and Chemical Engineering, Xi'an Key Laboratory of Textile Chemical Engineering Auxiliaries, Engineering Research Center of Biological Resources Development and Pollution Control Universities of Shaanxi Province, Key Laboratory of Textile Dyeing Wastewater Treatment Universities of Shaanxi Province, Xi'an Polytechnic University, Xi'an 710048, PR China.
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3
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Yin J, Yan G, Qin L, Zhu C, Fan J, Li Y, Jia J, Wu Z, Jiang H, Khan MT, Wu J, Chu N, Takiff HE, Gao Q, Qin S, Liu Q, Li W. Genomic investigation of bone tuberculosis highlighted the role of subclinical pulmonary tuberculosis in transmission. Tuberculosis (Edinb) 2024; 148:102534. [PMID: 38909563 DOI: 10.1016/j.tube.2024.102534] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2024] [Revised: 06/09/2024] [Accepted: 06/13/2024] [Indexed: 06/25/2024]
Abstract
BACKGROUND Extrapulmonary tuberculosis (EPTB) without symptomatic pulmonary involvement has been thought to be non-transmissible, but EPTB with asymptomatic pulmonary tuberculosis (PTB) could transmit tuberculosis (TB). Genomic investigation of Mycobacterium tuberculosis (Mtb) isolates from EPTB may provide insight into its epidemiological role in TB transmission. METHODS Between January 2017 and May 2020, 107 Mtb isolates were obtained from surgical drainage of bone TB patients at the Beijing Chest Hospital, and 218 Mtb strains were isolated from PTB cases. These 325 Mtb isolates were whole-genome sequenced to reconstruct a phylogenetic tree, identify transmission clusters, and infer transmission links using a Bayesian approach. Possible subclinical PTB in the bone TB patients was investigated with chest imaging by two independent experts. RESULTS Among 107 bone TB patients, 10 were in genomic clusters (≤12 SNPs). Phylogenetic analysis suggested that three bone TB patients transmitted the infection to secondary cases, supported by epidemiological investigations. Pulmonary imaging of 44 bone TB patients revealed that 79.5 % (35/44) had radiological abnormalities suggestive of subclinical PTB. CONCLUSIONS This study provides genomic evidence that bone TB patients without clinically diagnosed PTB can be sources of TB transmission, underscoring the importance of screening for subclinical, transmissible PTB among EPTB cases.
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Affiliation(s)
- Jinfeng Yin
- Beijing Chest Hospital, Capital Medical University, Beijing, China; Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing, China; China National Clinical Research Center for Neurological Diseases, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Guangxuan Yan
- Beijing Chest Hospital, Capital Medical University, Beijing, China; Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing, China
| | - Liyi Qin
- Beijing Chest Hospital, Capital Medical University, Beijing, China; Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing, China
| | - Chendi Zhu
- Beijing Chest Hospital, Capital Medical University, Beijing, China; Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing, China
| | - Jun Fan
- Beijing Chest Hospital, Capital Medical University, Beijing, China; Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing, China
| | - Yuwei Li
- Beijing Chest Hospital, Capital Medical University, Beijing, China; Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing, China
| | - Junnan Jia
- Beijing Chest Hospital, Capital Medical University, Beijing, China; Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing, China
| | - Zhaojun Wu
- Beijing Chest Hospital, Capital Medical University, Beijing, China; Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing, China
| | - Hui Jiang
- Beijing Chest Hospital, Capital Medical University, Beijing, China; Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing, China
| | - Muhammad Tahir Khan
- Institute of Molecular Biology and Biotechnology (IMBB), the University of Lahore, Lahore, Pakistan
| | - Jiangdong Wu
- Key Laboratory of Xinjiang Endemic and Ethnic Diseases Cooperated by Education Ministry with Xinjiang Province, Shihezi University, Shihezi, China
| | - Naihui Chu
- Beijing Chest Hospital, Capital Medical University, Beijing, China; Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing, China
| | - Howard E Takiff
- Instituto Venezolano de Investigaciones Cientificas, Caracas, Venezuela
| | - Qian Gao
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Sciences, Shanghai Medical College, Shanghai Institute of Infectious Disease and Biosecurity, Fudan University, Shanghai, China
| | - Shibing Qin
- Beijing Chest Hospital, Capital Medical University, Beijing, China; Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing, China.
| | - Qingyun Liu
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA; Department of Microbiology and Immunology, UNC-Chapel Hill School of Medicine, Chapel Hill, NC, 27599, USA.
| | - Weimin Li
- Beijing Chest Hospital, Capital Medical University, Beijing, China; Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing, China; Beijing Key Laboratory for Drug-resistant Tuberculosis Research, Beijing Chest Hospital, Capital Medical University, Beijing, China; Beijing Municipal Key Laboratory of Clinical Epidemiology, School of Public Health, Capital Medical University, Beijing, China.
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4
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Schwaiger G, Matt M, Streich P, Bromann S, Clauß M, Elsner M, Seidel M. Standard addition method for rapid, cultivation-independent quantification of Legionella pneumophila cells by qPCR in biotrickling filters. Analyst 2024; 149:2978-2987. [PMID: 38602145 DOI: 10.1039/d3an02207b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/12/2024]
Abstract
Cultivation-independent molecular biological methods are essential to rapidly quantify pathogens like Legionella pneumophila (L. pneumophila) which is important to control aerosol-generating engineered water systems. A standard addition method was established to quantify L. pneumophila in the very complex matrix of process water and air of exhaust air purification systems in animal husbandry. Therefore, cryopreserved standards of viable L. pneumophila were spiked in air and water samples to calibrate the total bioanalytical process which includes cell lysis, DNA extraction, and qPCR. A standard addition algorithm was employed for qPCR to determine the initial concentration of L. pneumophila. In mineral water, the recovery rate of this approach (73%-134% within the concentration range of 100-5000 Legionella per mL) was in good agreement with numbers obtained from conventional genomic unit (GU) calibration with DNA standards. In air samples of biotrickling filters, in contrast, the conventional DNA standard approach resulted in a significant overestimation of up to 729%, whereas our standard addition gave a more realistic recovery of 131%. With this proof-of-principle study, we were able to show that the molecular biology-based standard addition approach is a suitable method to determine realistic concentrations of L. pneumophila in air and process water samples of biotrickling filter systems. Moreover, this quantification strategy is generally a promising method to quantify pathogens in challenging samples containing a complex microbiota and the classical GU approach used for qPCR leads to unreliable results.
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Affiliation(s)
- Gerhard Schwaiger
- Institute of Water Chemistry, Chair of Analytical Chemistry and Water Chemistry, Technical University of Munich, Lichtenbergstraße 4, 85748 Garching, Germany.
| | - Marco Matt
- Institute of Water Chemistry, Chair of Analytical Chemistry and Water Chemistry, Technical University of Munich, Lichtenbergstraße 4, 85748 Garching, Germany.
| | - Philipp Streich
- Institute of Water Chemistry, Chair of Analytical Chemistry and Water Chemistry, Technical University of Munich, Lichtenbergstraße 4, 85748 Garching, Germany.
| | - Sarah Bromann
- Thuenen-Institute for Agricultural Technology, Bundesallee 47, D-38116 Braunschweig, Germany
| | - Marcus Clauß
- Thuenen-Institute for Agricultural Technology, Bundesallee 47, D-38116 Braunschweig, Germany
| | - Martin Elsner
- Institute of Water Chemistry, Chair of Analytical Chemistry and Water Chemistry, Technical University of Munich, Lichtenbergstraße 4, 85748 Garching, Germany.
| | - Michael Seidel
- Institute of Water Chemistry, Chair of Analytical Chemistry and Water Chemistry, Technical University of Munich, Lichtenbergstraße 4, 85748 Garching, Germany.
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5
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Galla G, Praeg N, Rzehak T, Sprecher E, Colla F, Seeber J, Illmer P, Hauffe HC. Comparison of DNA extraction methods on different sample matrices within the same terrestrial ecosystem. Sci Rep 2024; 14:8715. [PMID: 38622248 PMCID: PMC11018758 DOI: 10.1038/s41598-024-59086-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Accepted: 04/07/2024] [Indexed: 04/17/2024] Open
Abstract
Metataxonomic studies of ecosystem microbiotas require the simultaneous processing of samples with contrasting physical and biochemical traits. However, there are no published studies of comparisons of different DNA extraction kits to characterize the microbiotas of the main components of terrestrial ecosystems. Here, and to our knowledge for the first time, five DNA extraction kits were used to investigate the composition and diversity of the microbiota of a subset of samples typically studied in terrestrial ecosystems such as bulk soil, rhizosphere soil, invertebrate taxa and mammalian feces. DNA extraction kit was associated with changes in the relative abundance of hundreds of ASVs, in the same samples, resulting in significant differences in alpha and beta diversity estimates of their microbiotas. Importantly, the impact of DNA extraction kit on sample diversity varies according to sample type, with mammalian feces and soil samples showing the most and least consistent diversity estimates across DNA extraction kits, respectively. We show that the MACHEREY-NAGEL NucleoSpin® Soil kit was associated with the highest alpha diversity estimates, providing the highest contribution to the overall sample diversity, as indicated by comparisons with computationally assembled reference communities, and is recommended to be used for any large-scale microbiota study of terrestrial ecosystems.
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Affiliation(s)
- Giulio Galla
- Conservation Genomics Research Unit, Research and Innovation Centre, Fondazione Edmund Mach, S. Michele all'Adige, Italy.
| | - Nadine Praeg
- Department of Microbiology, Universität Innsbruck, Innsbruck, Austria
| | - Theresa Rzehak
- Department of Microbiology, Universität Innsbruck, Innsbruck, Austria
| | - Else Sprecher
- Conservation Genomics Research Unit, Research and Innovation Centre, Fondazione Edmund Mach, S. Michele all'Adige, Italy
| | - Filippo Colla
- Institute for Alpine Environment, EURAC Research, Bolzano, Italy
- Department of Ecology, Universität Innsbruck, Innsbruck, Austria
| | - Julia Seeber
- Institute for Alpine Environment, EURAC Research, Bolzano, Italy
- Department of Ecology, Universität Innsbruck, Innsbruck, Austria
| | - Paul Illmer
- Department of Microbiology, Universität Innsbruck, Innsbruck, Austria
| | - Heidi C Hauffe
- Conservation Genomics Research Unit, Research and Innovation Centre, Fondazione Edmund Mach, S. Michele all'Adige, Italy
- National Biodiversity Future Center (NBFC), S.c.a.r.l., Palermo, Italy
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Cunningham SW, Tessler M, Johnson-Rosemond J, Whittaker IS, Brugler MR. Environmental DNA Isolation, Validation, and Preservation Methods. Methods Mol Biol 2024; 2744:171-180. [PMID: 38683318 DOI: 10.1007/978-1-0716-3581-0_10] [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: 05/01/2024]
Abstract
Environmental DNA (eDNA) workflows contain many familiar molecular-lab techniques, but also employ several unique methodologies. When working with eDNA, it is essential to avoid contamination from the point of collection through preservation and select a meaningful negative control. As eDNA can be obtained from a variety of samples and habitats (e.g., soil, water, air, or tissue), protocols will vary depending on usage. Samples may require additional steps to dilute, block, or remove inhibitors or physically break up samples or filters. Thereafter, standard DNA isolation techniques (kit-based or phenol:chloroform:isoamyl [PCI]) are employed. Once DNA is extracted, it is typically quantified using a fluorometer. Yields vary greatly, but are important to know prior to amplification of the gene(s) of interest. Long-term storage of both the sampled material and the extracted DNA is encouraged, as it provides a backup for spilled/contaminated samples, lost data, reanalysis, and future studies using newer technology. Storage in a freezer is often ideal; however, some storage buffers (e.g., Longmires) require that filters or swabs are kept at room temperature to prevent precipitation of buffer-related solutes. These baseline methods for eDNA isolation, validation, and preservation are detailed in this protocol chapter. In addition, we outline a cost-effective, homebrew extraction protocol optimized to extract eDNA.
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Affiliation(s)
- Seth W Cunningham
- Department of Biological Sciences, Fordham University, Bronx, NY, USA.
- Institute for Comparative Genomics, American Museum of Natural History, New York, NY, USA.
| | - Michael Tessler
- Institute for Comparative Genomics, American Museum of Natural History, New York, NY, USA
- Division of Invertebrate Zoology, American Museum of Natural History, New York, NY, USA
- Department of Biology, St. Francis College, Brooklyn, NY, USA
| | | | - Iesha S Whittaker
- Department of Natural Sciences, University of South Carolina Beaufort, Beaufort, SC, USA
| | - Mercer R Brugler
- Division of Invertebrate Zoology, American Museum of Natural History, New York, NY, USA
- Department of Natural Sciences, University of South Carolina Beaufort, Beaufort, SC, USA
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Chen Y, Wang Y, Ma C, Li Y, Zuo D, Huang X, Tian X, Wang W. Advances in the authentication of collagen products based on DNA technology. Crit Rev Food Sci Nutr 2023:1-12. [PMID: 37983141 DOI: 10.1080/10408398.2023.2283278] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2023]
Abstract
Collagenous products are making their way into consumer markets such as foods, nutraceuticals, cosmetics and pharmaceuticals increasingly. Collagen in a large family of proteins is ubiquitous in metazoan. The most effective way to identify biological samples including collagen is DNA technology indisputably. However, the DNA content of collagen mostly derived from connective tissue is relatively less, and commercial collagen products are usually subjected to some harsh treatments in the production process, which makes DNA damage more serious, thus tracing their origin becomes a huge challenge. At present, DNA enrichment mainly relies on silica based centrifugal columns after extraction by classical phenol chloroform method. For improving the amplification of DNA fragments, small amplicons are designed based on more stable mitochondrial genes, such as cytochrome b gene (cytb). In addition to conventional PCR for DNA amplification, some new PCR techniques have also been developed, such as DNA barcoding techniques, PCR-Southern hybridization and fluorescent PCR. These PCR techniques have their pros and cons, and are mainly used in the identification of gelatin at present. The development of a complete set of DNA authentication is of great significance for the control of collagen products quality and will contribute to sustainable development of collagen industry.
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Affiliation(s)
- Yuan Chen
- College of Food Science and Engineering, Tianjin University of Science and Technology, Tianjin, China
| | - Yang Wang
- College of Food Science and Engineering, Tianjin University of Science and Technology, Tianjin, China
| | - Chenwei Ma
- College of Food Science and Engineering, Tianjin University of Science and Technology, Tianjin, China
| | - Yangshuai Li
- College of Food Science and Engineering, Tianjin University of Science and Technology, Tianjin, China
| | - Doudou Zuo
- College of Food Science and Engineering, Tianjin University of Science and Technology, Tianjin, China
| | - Xiaoli Huang
- College of Food Science and Engineering, Tianjin University of Science and Technology, Tianjin, China
| | - Xiaojing Tian
- College of Food Science and Engineering, Tianjin University of Science and Technology, Tianjin, China
| | - Wenhang Wang
- College of Food Science and Engineering, Tianjin University of Science and Technology, Tianjin, China
- RandD Centre of Collagen Products, Xingjia Biotechnology Co. LTD, Tianjin, China
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Ambra R, Marcelli M, D’Orso F. Development of a Sensitive, Easy and High-Throughput Compliant Protocol for Maize and Soybean DNA Extraction and Quantitation Using a Plant-Specific Universal Taqman Minor Groove Binder Probe. Genes (Basel) 2023; 14:1797. [PMID: 37761937 PMCID: PMC10530873 DOI: 10.3390/genes14091797] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Revised: 09/05/2023] [Accepted: 09/13/2023] [Indexed: 09/29/2023] Open
Abstract
We report the optimization of a high-throughput, compliant DNA extraction method that uses standard format 96-well plates and a commercial automated DNA purification system (ABI PRISM® 6100 Nucleic Acid PrepStation). The procedure was set up for maize and soybean, the most common GMO crops and the main ingredients of several foodstuffs, and compared with an EU-validated CTAB-based method. Optimization of the DNA extraction was achieved by applying self-prepared buffers (for DNA extraction, binding, and washing) on the PrepStation loaded with proprietary glass-fiber-coated purification plates. Quantification of extracted DNA was performed by real-time PCR using previously reported endogenous soybean lectin and maize starch synthase genes and a novel plant-specific universal TaqMan MGB probe that targets the 18S rRNA multiple copy gene. Using serial dilutions of both maize and soybean genomic DNAs, we show low PCR sensitivity and efficiency for the official TransPrep DNA extraction protocol compared to the CTAB-based one. On the other hand, using serial dilutions of a standard reference plasmid containing a 137 bp sequence cloned from the 18S rRNA plant-specific ribosomal gene, we demonstrate the high PCR sensitivity and efficiency of the optimized DNA extraction protocol setup with self-prepared buffers. The limits of detection and quantification of the 18S rDNA reiteration were consistent with the calculated values, supporting the suitability of the DNA extraction procedure for high-throughput analyses of large populations and small amounts of tissue.
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Affiliation(s)
- Roberto Ambra
- Council for Agricultural Research and Economics, Research Centre for Food and Nutrition (CREA-AN), 00178 Rome, Italy
| | - Marco Marcelli
- Volta Institute, MIUR (Italian Ministry of Education, University and Research), 09036 Guspini, Italy;
| | - Fabio D’Orso
- Council for Agricultural Research and Economics, Research Centre for Genomics and Bioinformatics (CREA-GB), 00178 Rome, Italy;
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9
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Li M, Qiu Y, Guo M, Qu R, Tian F, Wang G, Wang Y, Ma J, Liu S, Takiff H, Tang YW, Gao Q. Comparison of Xpert MTB/RIF Ultra with Xpert MTB/RIF for the detection of Mycobacterium tuberculosis and rifampicin resistance in a primary-level clinic in rural China. Tuberculosis (Edinb) 2023; 142:102397. [PMID: 37597313 DOI: 10.1016/j.tube.2023.102397] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Revised: 08/11/2023] [Accepted: 08/14/2023] [Indexed: 08/21/2023]
Abstract
The Xpert MTB/RIF Ultra (Ultra) is not yet used for the diagnosis of tuberculosis (TB) in China. We compared the performance of the Xpert and Ultra for detecting Mycobacterium tuberculosis and rifampicin resistance in a primary-level clinic in rural China. Sputum samples from suspected pulmonary TB patients were collected and subjected to smear microscopy, liquid culture, Xpert and Ultra tests. We then compared the sensitivity and specificity of Xpert and Ultra for diagnosing TB against liquid culture. Whole-genome sequencing was performed to predict rifampicin resistance and the results were compared with the Xpert and Ultra tests. The sensitivities of Xpert and Ultra were 88.1% and 95.1%, and the specificities were 91.9% and 84.4%, respectively. Among the 61 smear-negative culture-positive patients, the sensitivities of Xpert and Ultra were 80.3% and 91.8%. All Xpert-positive patients were Ultra-positive. Among culture-negative Xpert or Ultra-positive patients, 69.6% were taking anti-TB drugs or had a previous history of TB. Of the samples that Ultra classified as trace, nearly 25% were probably false-positives. Both Xpert and Ultra accurately detected all rifampicin-resistant patients. In conclusion, Ultra was more sensitive than Xpert, especially for smear-negative patients but had decreased specificity with more false-positives, especially with Ultra trace results.
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Affiliation(s)
- Meng Li
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Science, Shanghai Medical College, Shanghai Institute of Infectious Disease and Biosecurity, Fudan University, Shanghai, China
| | - Yong Qiu
- Wusheng County Center for Disease Control and Prevention, Guang'an, China
| | - Mingcheng Guo
- Wusheng County Center for Disease Control and Prevention, Guang'an, China
| | - Rong Qu
- Wusheng County Center for Disease Control and Prevention, Guang'an, China
| | - Fajun Tian
- Wusheng County Center for Disease Control and Prevention, Guang'an, China
| | - Gengsheng Wang
- Wusheng County Center for Disease Control and Prevention, Guang'an, China
| | - Ya Wang
- Wusheng County Center for Disease Control and Prevention, Guang'an, China
| | - Jian Ma
- Medical Affairs, Danaher Diagnostic Platform/Cepheid, Shanghai, China
| | - Siyuan Liu
- Medical Affairs, Danaher Diagnostic Platform/Cepheid, Shanghai, China
| | - Howard Takiff
- Laboratorio de Genética Molecular, CMBC, Instituto Venezolano de Investigaciones Científicas, IVIC, Caracas, Venezuela
| | - Yi-Wei Tang
- Medical Affairs, Danaher Diagnostic Platform/Cepheid, Shanghai, China
| | - Qian Gao
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Science, Shanghai Medical College, Shanghai Institute of Infectious Disease and Biosecurity, Fudan University, Shanghai, China.
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10
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Tao B, Li Z, Wang Y, Wu J, Shi X, Shi J, Liu Q, Wang J. Environment pollutants exposure affects the endogenous activation of within-host Mycobacterium tuberculosis. ENVIRONMENTAL RESEARCH 2023; 227:115695. [PMID: 36958381 DOI: 10.1016/j.envres.2023.115695] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Revised: 03/01/2023] [Accepted: 03/14/2023] [Indexed: 05/08/2023]
Abstract
OBJECTIVE Epidemiological studies have linked ambient pollutants with tuberculosis (TB) risk, but the association has not been fully understood. Here, for the first time, we applied whole-genome sequencing (WGS) to assess the reproductive state of Mycobacterium tuberculosis (MTB) by profiling the mutation rate of MTB (MTBMR) during within-host endogenous reactivated progression, intending to dissect the actual effects of ambient pollutants on the endogenous reactivation. METHODS We conducted a retrospective cohort study on bacteriologically confirmed TB patients and followed them for relapse in Jiangsu and Sichuan Province, China. Endogenous and exogenous activation were distinguished by WGS of the pathogen. The average concentration of air pollution was estimated by considering a lag of 0-1 to 0-12 months. We applied a generalized additive model with a Poisson function to evaluate the relationships between ambient pollutants exposure and MTBMR. RESULTS In the single-pollutant adjusted models, the maximum effect for PM10 (MTBMR increase: 81.87%, 95% CI: 38.38, 139.03) and PM2.5 (MTBMR increase: 73.91%, 95% CI: 22.17, 147.55) was observed at a lag of 0-12 months for every 10 μg/m³ increase. For SO2, the maximum effect was observed at lag 0-8 months, with MTBMR increasing by 128.06% (95% CI: 45.92, 256.44); and for NO2, the maximum effect was observed at lag 0-9 months, with MTBMR increasing by 124.02% (95% CI: 34.5, 273.14). In contrast, the O3 concentration was inversely associated with MTBMR, and the maximum reduction of MTBMR was 6.18% (95% CI: -9.24, -3.02) at a lag of 0-9 months. Similar results were observed for multi-pollutant models. CONCLUSIONS Increased exposure to ambient pollutants (PM10, PM2.5, SO2, and NO2) contributed to a faster MTBMR, indicating that MTB exhibits increased reproductive activity, thus accelerating within-host endogenous reactivation. O3 exposure could decrease the MTBMR, suggesting that MTB exerts low reproductive activity by inhibiting within-host endogenous activation.
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Affiliation(s)
- Bilin Tao
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China; Department of Epidemiology, The Third People's Hospital of Changzhou, Changzhou, China; Department of Epidemiology, Gusu School, Nanjing Medical University, Nanjing, China
| | - Zhongqi Li
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Yuting Wang
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Jizhou Wu
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Xinling Shi
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Jinyan Shi
- Department of Clinical Laboratory, The Fourth People's Hospital of Lianyungang, Lianyungang, China
| | - Qiao Liu
- Department of Chronic Communicable Disease, Center for Disease Control and Prevention of Jiangsu Province, Nanjing, China.
| | - Jianming Wang
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China; Department of Epidemiology, The Third People's Hospital of Changzhou, Changzhou, China; Department of Epidemiology, Gusu School, Nanjing Medical University, Nanjing, China.
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11
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Novotny A, Serandour B, Kortsch S, Gauzens B, Jan KMG, Winder M. DNA metabarcoding highlights cyanobacteria as the main source of primary production in a pelagic food web model. SCIENCE ADVANCES 2023; 9:eadg1096. [PMID: 37126549 PMCID: PMC10132751 DOI: 10.1126/sciadv.adg1096] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Models that estimate rates of energy flow in complex food webs often fail to account for species-specific prey selectivity of diverse consumer guilds. While DNA metabarcoding is increasingly used for dietary studies, methodological biases have limited its application for food web modeling. Here, we used data from dietary metabarcoding studies of zooplankton to calculate prey selectivity indices and assess energy fluxes in a pelagic resource-consumer network. We show that food web dynamics are influenced by prey selectivity and temporal match-mismatch in growth cycles and that cyanobacteria are the main source of primary production in the investigated coastal pelagic food web. The latter challenges the common assumption that cyanobacteria are not supporting food web productivity, a result that is increasingly relevant as global warming promotes cyanobacteria dominance. While this study provides a method for how DNA metabarcoding can be used to quantify energy fluxes in a marine food web, the approach presented here can easily be extended to other ecosystems.
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Affiliation(s)
- Andreas Novotny
- Department of Ecology, Environment and Plant Sciences, Stockholm University, Stockholm, Sweden
| | - Baptiste Serandour
- Department of Ecology, Environment and Plant Sciences, Stockholm University, Stockholm, Sweden
| | - Susanne Kortsch
- Spatial Foodweb Ecology Group, Department of Agricultural Sciences, University of Helsinki, Helsinki, Finland
- Environmental and Marine Biology, Åbo Akademi University, Turku 20500, Finland
| | - Benoit Gauzens
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
- Institute of Biodiversity, Friedrich Schiller University, Jena, Germany
| | - Kinlan M G Jan
- Department of Ecology, Environment and Plant Sciences, Stockholm University, Stockholm, Sweden
| | - Monika Winder
- Department of Ecology, Environment and Plant Sciences, Stockholm University, Stockholm, Sweden
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12
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Jiang Q, Liu HC, Liu QY, Phelan JE, Tao FX, Zhao XQ, Wang J, Glynn JR, Takiff HE, Clark TG, Wan KL, Gao Q. The Evolution and Transmission Dynamics of Multidrug-Resistant Tuberculosis in an Isolated High-Plateau Population of Tibet, China. Microbiol Spectr 2023; 11:e0399122. [PMID: 36912683 PMCID: PMC10101056 DOI: 10.1128/spectrum.03991-22] [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: 10/06/2022] [Accepted: 02/15/2023] [Indexed: 03/14/2023] Open
Abstract
On the Tibetan Plateau, most tuberculosis is caused by indigenous Mycobacterium tuberculosis strains with a monophyletic structure and high-level drug resistance. This study investigated the emergence, evolution, and transmission dynamics of multidrug-resistant tuberculosis (MDR-TB) in Tibet. The whole-genome sequences of 576 clinical strains from Tibet were analyzed with the TB-profiler tool to identify drug-resistance mutations. The evolution of the drug resistance was then inferred based on maximum-likelihood phylogeny and dated trees that traced the serial acquisition of mutations conferring resistance to different drugs. Among the 576 clinical M. tuberculosis strains, 346 (60.1%) carried at least 1 resistance-conferring mutation and 231 (40.1%) were MDR-TB. Using a pairwise distance of 50 single nucleotide polymorphisms (SNPs), most strains (89.9%, 518/576) were phylogenetically separated into 50 long-term transmission clusters. Eleven large drug-resistant clusters contained 76.1% (176/231) of the local multidrug-resistant strains. A total of 85.2% of the isoniazid-resistant strains were highly transmitted with an average of 6.6 cases per cluster, of which most shared the mutation KatG Ser315Thr. A lower proportion (71.6%) of multidrug-resistant strains were transmitted, with an average cluster size of 2.9 cases. The isoniazid-resistant clusters appear to have undergone substantial bacterial population growth in the 1970s to 1990s and then subsequently accumulated multiple rifampicin-resistance mutations and caused the current local MDR-TB burden. These findings highlight the importance of detecting and curing isoniazid-resistant strains to prevent the emergence of endemic MDR-TB. IMPORTANCE Emerging isoniazid resistance in the 1970s allowed M. tuberculosis strains to spread and form into large multidrug-resistant tuberculosis clusters in the isolated plateau of Tibet, China. The epidemic was driven by the high risk of transmission as well as the potential of acquiring further drug resistance from isoniazid-resistant strains. Eleven large drug-resistant clusters consisted of the majority of local multidrug-resistant cases. Among the clusters, isoniazid resistance overwhelmingly evolved before all the other resistance types. A large bacterial population growth of isoniazid-resistant clusters occurred between 1970s and 1990s, which subsequently accumulated rifampicin-resistance-conferring mutations in parallel and accounted for the local multidrug-resistant tuberculosis burden. The results of our study indicate that it may be possible to restrict MDR-TB evolution and dissemination by prioritizing screening for isoniazid (INH)-resistant TB strains before they become MDR-TB and by adopting measures that can limit their transmission.
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Affiliation(s)
- Qi Jiang
- Department of Epidemiology and Biostatistics, School of Public Health, Wuhan University, Wuhan, China
| | - Hai-Can Liu
- State Key Laboratory for Infectious Disease Prevention and Control and National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Qing-Yun Liu
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, Massachusetts, USA
| | - Jody E. Phelan
- Department of Infection Biology, London School of Hygiene & Tropical Medicine, London, United Kingdom
| | - Feng-Xi Tao
- Department of Epidemiology and Biostatistics, School of Public Health, Wuhan University, Wuhan, China
| | - Xiu-Qin Zhao
- State Key Laboratory for Infectious Disease Prevention and Control and National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Jian Wang
- Tibet Center for Disease Control and Prevention, Lhasa, Tibet Autonomous Region, China
| | - Judith R. Glynn
- Department of Infectious Disease Epidemiology, London School of Hygiene & Tropical Medicine, London, United Kingdom
| | - Howard E. Takiff
- Laboratorio de Genética Molecular, CMBC, IVIC, Caracas, Venezuela
| | - Taane G. Clark
- Department of Infection Biology, London School of Hygiene & Tropical Medicine, London, United Kingdom
- Department of Infectious Disease Epidemiology, London School of Hygiene & Tropical Medicine, London, United Kingdom
| | - Kang-Lin Wan
- State Key Laboratory for Infectious Disease Prevention and Control and National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Qian Gao
- National Clinical Research Center for Infectious Diseases, The Third People’s Hospital of Shenzhen, Shenzhen, Guangdong, China
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13
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Lutz Í, Miranda J, Santana P, Martins T, Ferreira C, Sampaio I, Vallinoto M, Gomes GE. Quality analysis of genomic DNA and authentication of fisheries products based on distinct methods of DNA extraction. PLoS One 2023; 18:e0282369. [PMID: 36854012 PMCID: PMC9974130 DOI: 10.1371/journal.pone.0282369] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Accepted: 02/14/2023] [Indexed: 03/02/2023] Open
Abstract
Molecular genetic techniques are an effective monitoring tool, but high-quality DNA samples are usually required. In this study, we compared three different protocols of DNA extraction: NaCl (saline); phenol-chloroform and commercial kit (Promega)-from three biological tissues of five individuals of Lutjanus purpureus under two methods of storage. The evaluated items included DNA concentration and purity, processing time and cost, as well as the obtaining of functional sequences. The highest average values of DNA concentration were obtained using the saline procedure and the commercial kit. Pure DNA was only obtained using the saline protocol, evaluated by the ratio of 260/280. The saline and phenol-chloroform protocols were the least expensive methods. The commercial kit costs are counterbalanced by the short time required. The procedure based on phenol-chloroform presented the worst results regarding DNA yield and the time required to perform all steps. The saline and commercial kit protocols showed similar results concerning the amount and quality of extracted DNA. Therefore, the final choice should be based on the available financial resources and the available time for carrying out each procedure of DNA extraction.
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Affiliation(s)
- Ítalo Lutz
- Laboratório de Genética Aplicada, Instituto de Estudos Costeiros, Universidade Federal do Pará, Bragança, Pará, Brazil
| | - Josy Miranda
- Laboratório de Genética Aplicada, Instituto de Estudos Costeiros, Universidade Federal do Pará, Bragança, Pará, Brazil
| | - Paula Santana
- Laboratório de Genética Aplicada, Instituto de Estudos Costeiros, Universidade Federal do Pará, Bragança, Pará, Brazil
| | - Thais Martins
- Laboratório de Genética Aplicada, Instituto de Estudos Costeiros, Universidade Federal do Pará, Bragança, Pará, Brazil
| | - Charles Ferreira
- Laboratório de Genética Aplicada, Instituto de Estudos Costeiros, Universidade Federal do Pará, Bragança, Pará, Brazil
| | - Iracilda Sampaio
- Laboratório de Genética e Biologia Molecular, Instituto de Estudos Costeiros, Universidade Federal do Pará, Bragança, Pará, Brazil
| | - Marcelo Vallinoto
- Laboratório de Evolução, Instituto de Estudos Costeiros, Universidade Federal do Pará, Bragança, Pará, Brazil
| | - Grazielle Evangelista Gomes
- Laboratório de Genética Aplicada, Instituto de Estudos Costeiros, Universidade Federal do Pará, Bragança, Pará, Brazil
- * E-mail:
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14
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Sanabria GE, Sequera G, Aguirre S, Méndez J, Dos Santos PCP, Gustafson NW, Godoy M, Ortiz A, Cespedes C, Martínez G, García-Basteiro AL, Andrews JR, Croda J, Walter KS. Phylogeography and transmission of Mycobacterium tuberculosis spanning prisons and surrounding communities in Paraguay. Nat Commun 2023; 14:303. [PMID: 36658111 PMCID: PMC9849832 DOI: 10.1038/s41467-023-35813-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2022] [Accepted: 01/04/2023] [Indexed: 01/20/2023] Open
Abstract
Recent rises in incident tuberculosis (TB) cases in Paraguay and the increasing concentration of TB within prisons highlight the urgency of targeting strategies to interrupt transmission and prevent new infections. However, whether specific cities or carceral institutions play a disproportionate role in transmission remains unknown. We conducted prospective genomic surveillance, sequencing 471 Mycobacterium tuberculosis complex genomes, from inside and outside prisons in Paraguay's two largest urban areas, Asunción and Ciudad del Este, from 2016 to 2021. We found genomic evidence of frequent recent transmission within prisons and transmission linkages spanning prisons and surrounding populations. We identified a signal of frequent M. tuberculosis spread between urban areas and marked recent population size expansion of the three largest genomic transmission clusters. Together, our findings highlight the urgency of strengthening TB control programs to reduce transmission risk within prisons in Paraguay, where incidence was 70 times that outside prisons in 2021.
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Affiliation(s)
| | - Guillermo Sequera
- Instituto de Salud Global de Barcelona (ISGLOBAL), Barcelona, Spain
- Programa Nacional de Control de la Tuberculosis, Ministerio de Salud Pública y Bienestar Social (MSPyBS), Asunción, Paraguay
| | - Sarita Aguirre
- Programa Nacional de Control de la Tuberculosis, Ministerio de Salud Pública y Bienestar Social (MSPyBS), Asunción, Paraguay
| | - Julieta Méndez
- Instituto Regional de Investigación en Salud, Caaguazú, Paraguay
| | - Paulo César Pereira Dos Santos
- Postgraduate Program in Infectious and Parasitic Diseases, Federal University of Mato Grosso do Sul, Mato Grosso do Sul, Brazil
| | - Natalie Weiler Gustafson
- Laboratorio Central de Salud Pública (LCSP), Ministerio de Salud Publica y Bienestar Social (MSPyBS), Asunción, Paraguay
| | - Margarita Godoy
- Laboratorio Central de Salud Pública (LCSP), Ministerio de Salud Publica y Bienestar Social (MSPyBS), Asunción, Paraguay
| | - Analía Ortiz
- Instituto Regional de Investigación en Salud, Caaguazú, Paraguay
| | - Cynthia Cespedes
- Programa Nacional de Control de la Tuberculosis, Ministerio de Salud Pública y Bienestar Social (MSPyBS), Asunción, Paraguay
| | - Gloria Martínez
- Instituto Regional de Investigación en Salud, Caaguazú, Paraguay
| | - Alberto L García-Basteiro
- Instituto de Salud Global de Barcelona (ISGLOBAL), Barcelona, Spain
- Centro de Investigação em Saude de Manhiça (CISM), Maputo, Mozambique
- Centro de Investigación Biomédica en Red de Enfermedades Infecciosas (CIBERINFEC), Barcelona, Spain
| | - Jason R Andrews
- Division of Infectious Diseases and Geographic Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Julio Croda
- Federal University of Mato Grosso do Sul - UFMS, Campo Grande, MS, Brazil
- Oswaldo Cruz Foundation Mato Grosso do Sul, Mato Grosso do Sul, Brazil
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, USA
| | - Katharine S Walter
- Division of Epidemiology, University of Utah, Salt Lake City, UT, 84105, USA.
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15
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Patin NV, Goodwin KD. Capturing marine microbiomes and environmental DNA: A field sampling guide. Front Microbiol 2023; 13:1026596. [PMID: 36713215 PMCID: PMC9877356 DOI: 10.3389/fmicb.2022.1026596] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Accepted: 11/22/2022] [Indexed: 01/15/2023] Open
Abstract
The expanding interest in marine microbiome and eDNA sequence data has led to a demand for sample collection and preservation standard practices to enable comparative assessments of results across studies and facilitate meta-analyses. We support this effort by providing guidelines based on a review of published methods and field sampling experiences. The major components considered here are environmental and resource considerations, sample processing strategies, sample storage options, and eDNA extraction protocols. It is impossible to provide universal recommendations considering the wide range of eDNA applications; rather, we provide information to design fit-for-purpose protocols. To manage scope, the focus here is on sampling collection and preservation of prokaryotic and microeukaryotic eDNA. Even with a focused view, the practical utility of any approach depends on multiple factors, including habitat type, available resources, and experimental goals. We broadly recommend enacting rigorous decontamination protocols, pilot studies to guide the filtration volume needed to characterize the target(s) of interest and minimize PCR inhibitor collection, and prioritizing sample freezing over (only) the addition of preservation buffer. An annotated list of studies that test these parameters is included for more detailed investigation on specific steps. To illustrate an approach that demonstrates fit-for-purpose methodologies, we provide a protocol for eDNA sampling aboard an oceanographic vessel. These guidelines can aid the decision-making process for scientists interested in sampling and sequencing marine microbiomes and/or eDNA.
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Affiliation(s)
- Nastassia Virginia Patin
- Atlantic Oceanographic and Meteorological Laboratory, Ocean Chemistry and Ecosystems Division, National Oceanic and Atmospheric Administration, Miami, FL, United States,Cooperative Institute for Marine and Atmospheric Studies, Rosenstiel School of Marine, Atmospheric, and Earth Science, University of Miami, Miami, FL, United States,Stationed at Southwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, La Jolla, CA, United States,*Correspondence: Nastassia Virginia Patin,
| | - Kelly D. Goodwin
- Atlantic Oceanographic and Meteorological Laboratory, Ocean Chemistry and Ecosystems Division, National Oceanic and Atmospheric Administration, Miami, FL, United States,Stationed at Southwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, La Jolla, CA, United States
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16
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Lima Â, Sousa LGV, Macedo F, Muzny CA, Cerca N. Assessing recovery rates of distinct exogenous controls for gDNA extraction efficiency using phenol-chloroform or silica-column based extractions. J Microbiol Methods 2022; 203:106607. [PMID: 36343770 PMCID: PMC10804838 DOI: 10.1016/j.mimet.2022.106607] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Revised: 11/02/2022] [Accepted: 11/02/2022] [Indexed: 11/06/2022]
Abstract
Assessment of genomic DNA (gDNA) extraction efficiency is required for accurate bacterial quantification by qPCR. Exogenous DNA molecules are often added after bacterial cultures are lysed, but before DNA purification steps, to determine extraction efficiency. Herein we found that different exogenous DNA controls have different recovery rates, suggesting distinct DNA extraction efficiencies. Recovery rates are also affected by the gDNA extraction method being more affected in silica-based columns than in phenol-chloroform extraction. Overall, we determined that the use of long DNA fragments, such as gDNA, as exogenous controls have a higher recovery rate than use of smaller size DNA molecules.
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Affiliation(s)
- Ângela Lima
- Laboratório of Research in Biofilms Rosário Oliveira (LIBRO), Centre of Biological Engineering (CEB), University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal; LABBELS -Associate Laboratory, Braga & Guimarães, Portugal
| | - Lúcia G V Sousa
- Laboratório of Research in Biofilms Rosário Oliveira (LIBRO), Centre of Biological Engineering (CEB), University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal; LABBELS -Associate Laboratory, Braga & Guimarães, Portugal
| | - Filipa Macedo
- Laboratório of Research in Biofilms Rosário Oliveira (LIBRO), Centre of Biological Engineering (CEB), University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal; LABBELS -Associate Laboratory, Braga & Guimarães, Portugal
| | - Christina A Muzny
- Division of Infectious Diseases, University of Alabama at Birmingham, Birmingham, AL, United States
| | - Nuno Cerca
- Laboratório of Research in Biofilms Rosário Oliveira (LIBRO), Centre of Biological Engineering (CEB), University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal; LABBELS -Associate Laboratory, Braga & Guimarães, Portugal.
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17
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Yin J, Zhang H, Gao Z, Jiang H, Qin L, Zhu C, Gao Q, He X, Li W. Transmission of multidrug-resistant tuberculosis in Beijing, China: An epidemiological and genomic analysis. Front Public Health 2022; 10:1019198. [PMID: 36408017 PMCID: PMC9672842 DOI: 10.3389/fpubh.2022.1019198] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2022] [Accepted: 10/13/2022] [Indexed: 11/06/2022] Open
Abstract
Background Understanding multidrug-resistant tuberculosis (MDR-TB) transmission patterns is crucial for controlling the disease. We aimed to identify high-risk populations and geographic settings of MDR-TB transmission. Methods We conducted a population-based retrospective study of MDR-TB patients in Beijing from 2018 to 2020, and assessed MDR-TB recent transmission using whole-genome sequencing of isolates. Geospatial analysis was conducted with kernel density estimation. We combined TransPhylo software with epidemiological investigation data to construct transmission networks. Logistic regression analysis was utilized to identify risk factors for recent transmission. Results We included 241 MDR-TB patients, of which 146 (60.58%) were available for genomic analysis. Drug resistance prediction showed that resistance to fluoroquinolones (FQs) was as high as 39.74% among new cases. 36 (24.66%) of the 146 MDR strains were grouped into 12 genome clusters, suggesting recent transmission of MDR strains. 44.82% (13/29) of the clustered patients lived in the same residential community, adjacent residential community or the same street as other cases. The inferred transmission chain found a total of 6 transmission events in 3 clusters; of these, 4 transmission events occurred in residential areas and nearby public places. Logistic regression analysis revealed that being aged 25-34 years-old was a risk factor for recent transmission. Conclusions The recent transmission of MDR-TB in Beijing is severe, and residential areas are common sites of transmission; high levels of FQs drug resistance suggest that FQs should be used with caution unless resistance can be ruled out by laboratory testing.
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Affiliation(s)
- Jinfeng Yin
- Beijing Chest Hospital, Capital Medical University, Beijing, China,National Tuberculosis Clinical Laboratory, Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing, China
| | - Hongwei Zhang
- Tuberculosis Prevention and Control Institute, Beijing Center for Disease Prevention and Control, Beijing, China
| | - Zhidong Gao
- Tuberculosis Prevention and Control Institute, Beijing Center for Disease Prevention and Control, Beijing, China
| | - Hui Jiang
- Beijing Chest Hospital, Capital Medical University, Beijing, China,National Tuberculosis Clinical Laboratory, Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing, China
| | - Liyi Qin
- Beijing Chest Hospital, Capital Medical University, Beijing, China,National Tuberculosis Clinical Laboratory, Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing, China
| | - Chendi Zhu
- Beijing Chest Hospital, Capital Medical University, Beijing, China,National Tuberculosis Clinical Laboratory, Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing, China
| | - Qian Gao
- Key Laboratory of Medical Molecular Virology, School of Basic Medical Sciences, Fudan University, Shanghai, China
| | - Xiaoxin He
- Tuberculosis Prevention and Control Institute, Beijing Center for Disease Prevention and Control, Beijing, China
| | - Weimin Li
- Beijing Chest Hospital, Capital Medical University, Beijing, China,National Tuberculosis Clinical Laboratory, Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing, China,*Correspondence: Weimin Li
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18
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Díaz T, Ortega-Pinazo J, Martínez B, Jiménez A, Gómez-Zumaquero JM, Caracuel Z, Hortas ML, Ferro P. Measurement of yield and quality of DNA in human buffy coat is extraction method dependent. Prep Biochem Biotechnol 2022:1-8. [PMID: 36121058 DOI: 10.1080/10826068.2022.2119574] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
Abstract
During the last few years, an important element in the improvement of the molecular biology techniques has been the necessity for availability of high quality and functionality DNA. Several DNA extraction procedures with different results in both performance and quality, have been proposed. In this study our objective was to determine the most reliable extraction method that balances DNA quantity, and to assess the sample quantification of the fluorometric DNA quantification methods. For this, blood extracted by venopunction from 20 healthy volunteers was used to obtain DNA from buffy coat, and 4 commercial DNA extraction kits were assessed as well as two fluorometric DNA quantification methods with protocols of different complexity. Results suggest that manual methods achieve higher quality and larger yields of DNA. DNA purity obtained with the 4 extraction kits evaluated through the 260/280 and 260/230 ratio showed that the Qiacube kit fulfilled the criteria established in this work, followed very close by the Flexigene kit. On the other hand, the fluorometric DNA methods used in the samples quantification showed a higher variability when using QuantiFlour method, obtaining better results probably due to the simplicity of this protocol.
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Affiliation(s)
- T Díaz
- Andalusian Public Health System Biobank, Instituto de Investigación Biomédica de Málaga-IBIMA, Malaga, Spain
| | - J Ortega-Pinazo
- Neuroimmunology and Neuroinflammation Group, Instituto de Investigación Biomédica de Málaga-IBIMA, UGC Neurociencias, Hospital Regional Universitario de Málaga, Malaga, Spain
| | - B Martínez
- Andalusian Public Health System Biobank, Instituto de Investigación Biomédica de Málaga-IBIMA, Malaga, Spain
| | - A Jiménez
- Andalusian Public Health System Biobank, Instituto de Investigación Biomédica de Málaga-IBIMA, Malaga, Spain
| | - J M Gómez-Zumaquero
- Genomic ECAI, Instituto de Investigación Biomédica de Málaga-IBIMA, Malaga, Spain
| | - Z Caracuel
- Costa del Sol Sanitary Agency, Sanitary District of Málaga, Malaga, Spain
| | - M L Hortas
- Costa del Sol Sanitary Agency, Sanitary District of Málaga, Malaga, Spain
| | - P Ferro
- Andalusian Public Health System Biobank, Instituto de Investigación Biomédica de Málaga-IBIMA, Malaga, Spain.,Unidad Clínica de Endocrinología y Nutrición, Hospital Universitario Virgen de la Victoria, Málaga, Spain
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19
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Motamedi M, Amini A, Yazdanpanah S, Mahmoodi M, Khodadadi H, Zalpoor H. Evaluation of different DNA extraction methods based on steel-bullet beating for molecular diagnosis of onychomycosis. J Clin Lab Anal 2022; 36:e24657. [PMID: 35989493 PMCID: PMC9550968 DOI: 10.1002/jcla.24657] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Revised: 07/29/2022] [Accepted: 08/01/2022] [Indexed: 11/06/2022] Open
Abstract
BACKGROUND Considering increased trends toward molecular methods for detection/identification of fungi causing onychomycosis, the aim of this study is comparison three DNA extraction methods based on steel-bullet beating to extract DNA from nail. METHODS Ex -vivo onychomycosis model was developed using bovine hoof with Candida albicans and Aspergillus flavus. For two models, total DNA was extracted using the three different methods. In method 1, the extraction and purification were performed by steel-bullet beating and phenol chloroform protocol, respectively. In method 2, a freezing step were applied before beating. The purification step in method 3 was carried out using a commercial kit, although DNA extraction was done similarly to method 1 in that approach. To evaluate the efficacy of each method, the extracted genomic DNA was amplified with Polymerase Chain Reaction (PCR) using Internal Transcribed Spacer (ITS) regions. Moreover, 50 nail samples were evaluated for onychomycosis using direct microscopy examination as well as PCR in order to evaluate the diagnostic efficiency of the optimal DNA extraction method. RESULTS Regarding the desirable quality of the extracted DNA, cost effectiveness, and simplicity, method 1 could be used to extract DNA effectively. Additionally, the obtained data showed that PCR had a higher detection rate of fungal agents in the nail samples than direct microscopic examination. CONCLUSIONS This study demonstrated that the mechanical disruption of the cell wall by steel-bullet beating is a useful and practical method to improve the quantity and quality of fungal DNA thorough the extraction process.
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Affiliation(s)
- Marjan Motamedi
- Department of Parasitology and Mycology, School of Medicine, Shiraz University of Medical
- Science, Shiraz, Iran
| | - Abdulbaqi Amini
- Department of Parasitology and Mycology, School of Medicine, Shiraz University of Medical
- Science, Shiraz, Iran
| | - Somayeh Yazdanpanah
- Department of Parasitology and Mycology, School of Medicine, Shiraz University of Medical
- Science, Shiraz, Iran
| | - Mozhgan Mahmoodi
- Department of Parasitology and Mycology, School of Medicine, Shiraz University of Medical
- Science, Shiraz, Iran
| | - Hossein Khodadadi
- Department of Parasitology and Mycology, School of Medicine, Shiraz University of Medical
- Science, Shiraz, Iran
| | - Hamidreza Zalpoor
- Neuroscience Research Center, Shiraz University of Medical Siences, Shiraz, Iran
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20
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Schmidt A, Schneider C, Decker P, Hohberg K, Römbke J, Lehmitz R, Bálint M. Shotgun metagenomics of soil invertebrate communities reflects taxonomy, biomass, and reference genome properties. Ecol Evol 2022; 12:e8991. [PMID: 35784064 PMCID: PMC9170594 DOI: 10.1002/ece3.8991] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2021] [Revised: 05/11/2022] [Accepted: 05/17/2022] [Indexed: 12/03/2022] Open
Abstract
Metagenomics - shotgun sequencing of all DNA fragments from a community DNA extract - is routinely used to describe the composition, structure, and function of microorganism communities. Advances in DNA sequencing and the availability of genome databases increasingly allow the use of shotgun metagenomics on eukaryotic communities. Metagenomics offers major advances in the recovery of biomass relationships in a sample, in comparison to taxonomic marker gene-based approaches (metabarcoding). However, little is known about the factors which influence metagenomics data from eukaryotic communities, such as differences among organism groups, the properties of reference genomes, and genome assemblies.We evaluated how shotgun metagenomics records composition and biomass in artificial soil invertebrate communities at different sequencing efforts. We generated mock communities of controlled biomass ratios from 28 species from all major soil mesofauna groups: mites, springtails, nematodes, tardigrades, and potworms. We shotgun sequenced these communities and taxonomically assigned them with a database of over 270 soil invertebrate genomes.We recovered over 95% of the species, and observed relatively high false-positive detection rates. We found strong differences in reads assigned to different taxa, with some groups (e.g., springtails) consistently attracting more hits than others (e.g., enchytraeids). Original biomass could be predicted from read counts after considering these taxon-specific differences. Species with larger genomes, and with more complete assemblies, consistently attracted more reads than species with smaller genomes. The GC content of the genome assemblies had no effect on the biomass-read relationships. Results were similar among different sequencing efforts.The results show considerable differences in taxon recovery and taxon specificity of biomass recovery from metagenomic sequence data. The properties of reference genomes and genome assemblies also influence biomass recovery, and they should be considered in metagenomic studies of eukaryotes. We show that low- and high-sequencing efforts yield similar results, suggesting high cost-efficiency of metagenomics for eukaryotic communities. We provide a brief roadmap for investigating factors which influence metagenomics-based eukaryotic community reconstructions. Understanding these factors is timely as accessibility of DNA sequencing and momentum for reference genomes projects show a future where the taxonomic assignment of DNA from any community sample becomes a reality.
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Affiliation(s)
- Alexandra Schmidt
- Senckenberg Biodiversity Climate Research CenterFrankfurt am MainGermany
- Biology DepartmentJ.W. Goethe UniversityFrankfurt am MainGermany
- Loewe Center for Translational Biodiversity Genomics (LOEWE‐TBG)Frankfurt am MainGermany
- Limnological Institute (Environmental Genomics)University of KonstanzKonstanzGermany
| | - Clément Schneider
- Loewe Center for Translational Biodiversity Genomics (LOEWE‐TBG)Frankfurt am MainGermany
- Soil Zoology DepartmentSenckenberg Museum of Natural History GörlitzGörlitzGermany
| | - Peter Decker
- Loewe Center for Translational Biodiversity Genomics (LOEWE‐TBG)Frankfurt am MainGermany
- Blumenstr. 5GörlitzGermany
| | - Karin Hohberg
- Loewe Center for Translational Biodiversity Genomics (LOEWE‐TBG)Frankfurt am MainGermany
- Soil Zoology DepartmentSenckenberg Museum of Natural History GörlitzGörlitzGermany
| | - Jörg Römbke
- ECT Oekotoxikologie GmbHFlörsheim am MainGermany
| | - Ricarda Lehmitz
- Loewe Center for Translational Biodiversity Genomics (LOEWE‐TBG)Frankfurt am MainGermany
- Soil Zoology DepartmentSenckenberg Museum of Natural History GörlitzGörlitzGermany
| | - Miklós Bálint
- Senckenberg Biodiversity Climate Research CenterFrankfurt am MainGermany
- Loewe Center for Translational Biodiversity Genomics (LOEWE‐TBG)Frankfurt am MainGermany
- Institute for Insect BiotechnologyJustus Liebig UniversityGießenGermany
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21
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Yuan Q, Liang Z, Wang S, Zuo P, Wang Y, Luo Y. Size-controlled mesoporous magnetic silica beads effectively extract extracellular DNA in the absence of chaotropic solutions. Colloids Surf A Physicochem Eng Asp 2022. [DOI: 10.1016/j.colsurfa.2022.128831] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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22
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Shen C, Huang YY, Xin JL, He CT, Yang ZY. A novel microRNA IamiR-4-3p from water spinach (Ipomoea aquatica Forsk.) increased Cd uptake and translocation in Arabidopsis thaliana. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2022; 29:41375-41385. [PMID: 35089521 DOI: 10.1007/s11356-022-18875-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2021] [Accepted: 01/21/2022] [Indexed: 06/14/2023]
Abstract
MicroRNAs (miRNAs) play important roles in plant response to Cd stress. In our previous study, we observed significant differences in the expression levels of IamiR-4-3p between high-Cd and low-Cd cultivars of water spinach. The function of IamiR-4-3p was investigated by using wild type Arabidopsis (WT), Arabidopsis transfected with empty vector pCambia1302 (CK), and Arabidopsis transfected with IamiR-4-3p + vector pCambia1302 (p35S::miR-4-3p) in this study. In p35S::miR-4-3p Arabidopsis, the expression levels of GST3 and AWPM19-like were reduced by 20% and 24%. Under Cd treatment, higher root and shoot Cd concentrations were detected in the transgenic p35S::miR-4-3p Arabidopsis. MDA and H2O2 concentrations were positively correlated with the Cd concentrations in all Arabidopsis. The elevated GSH pool in p35S::miR-4-3p Arabidopsis should compensate for its restricted GST3 expression in response to Cd-induced oxidative stress. Lower F1 (cell wall) and higher F2 (organelle) and F3 (soluble fraction) Cd concentrations were observed along with the reduced ABA level in p35S::miR-4-3p Arabidopsis, which could induce a weakened apoplastic barrier and higher Cd accumulation and translocation in roots. It is suggested that IamiR-4-3p is able to reduce the expression levels of GST3 and AWPM19-like, resulting in higher Cd uptake and translocation in Arabidopsis.
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Affiliation(s)
- Chuang Shen
- Research Center for Environmental Pollution Control Technology, School of Safety and Environmental Engineering, Hunan Institute of Technology, Hengyang, 421002, China
| | - Ying-Ying Huang
- Research Center for Environmental Pollution Control Technology, School of Safety and Environmental Engineering, Hunan Institute of Technology, Hengyang, 421002, China
| | - Jun-Liang Xin
- Research Center for Environmental Pollution Control Technology, School of Safety and Environmental Engineering, Hunan Institute of Technology, Hengyang, 421002, China
| | - Chun-Tao He
- State Key Laboratory for Biocontrol, School of Life Sciences, Sun Yat-Sen University, Xingang Xi Road 135, Guangzhou, 510275, China.
| | - Zhong-Yi Yang
- State Key Laboratory for Biocontrol, School of Life Sciences, Sun Yat-Sen University, Xingang Xi Road 135, Guangzhou, 510275, China.
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23
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Jang M, Kim S, Song J, Kim S. Rapid and simple detection of influenza virus via isothermal amplification lateral flow assay. Anal Bioanal Chem 2022; 414:4685-4696. [PMID: 35501506 PMCID: PMC9060413 DOI: 10.1007/s00216-022-04090-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Revised: 04/12/2022] [Accepted: 04/19/2022] [Indexed: 12/03/2022]
Abstract
Respiratory illness caused by influenza virus is a serious public health problem worldwide. As the symptoms of influenza virus infection are similar to those of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection, it is essential to distinguish these two viruses. Therefore, to properly respond to a pathogen, a detection method that is capable of rapid and accurate diagnosis in a hospital or at home is required. To satisfy this need, we applied loop-mediated isothermal amplification (LAMP) and an isothermal nucleic acid amplification technique, along with a system to analyze the results without specialized equipment, a lateral flow assay (LFA). Using the platform developed in this study, all processes, from sample preparation to detection, can be performed without special equipment. Unlike existing PCR methods, the nucleic acid amplification can be performed in the field because hot packs do not require electricity. Thus, the designed platform can provide rapid results without the need to transport the samples to a laboratory or hospital. These advantages are not limited to operations in developing countries with poor access to medical systems. In conclusion, the developed technology is a promising tool for infectious disease management that allows for rapid identification of infectious diseases and appropriate treatment of patients.
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Affiliation(s)
- Minju Jang
- Department of Bionanotechnology, Gachon University, Seongnam, 13120, Republic of Korea
| | - SeJin Kim
- 33, Sagimakgol-ro 62beon-gil, Jungwon-gu, Seongnam, 13211, Republic of Korea
| | - Junkyu Song
- 33, Sagimakgol-ro 62beon-gil, Jungwon-gu, Seongnam, 13211, Republic of Korea
| | - Sanghyo Kim
- Department of Bionanotechnology, Gachon University, Seongnam, 13120, Republic of Korea. .,33, Sagimakgol-ro 62beon-gil, Jungwon-gu, Seongnam, 13211, Republic of Korea.
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24
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Yang C, Sobkowiak B, Naidu V, Codreanu A, Ciobanu N, Gunasekera KS, Chitwood MH, Alexandru S, Bivol S, Russi M, Havumaki J, Cudahy P, Fosburgh H, Allender CJ, Centner H, Engelthaler DM, Menzies NA, Warren JL, Crudu V, Colijn C, Cohen T. Phylogeography and transmission of M. tuberculosis in Moldova: A prospective genomic analysis. PLoS Med 2022; 19:e1003933. [PMID: 35192619 PMCID: PMC8903246 DOI: 10.1371/journal.pmed.1003933] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/17/2021] [Revised: 03/08/2022] [Accepted: 01/31/2022] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND The incidence of multidrug-resistant tuberculosis (MDR-TB) remains critically high in countries of the former Soviet Union, where >20% of new cases and >50% of previously treated cases have resistance to rifampin and isoniazid. Transmission of resistant strains, as opposed to resistance selected through inadequate treatment of drug-susceptible tuberculosis (TB), is the main driver of incident MDR-TB in these countries. METHODS AND FINDINGS We conducted a prospective, genomic analysis of all culture-positive TB cases diagnosed in 2018 and 2019 in the Republic of Moldova. We used phylogenetic methods to identify putative transmission clusters; spatial and demographic data were analyzed to further describe local transmission of Mycobacterium tuberculosis. Of 2,236 participants, 779 (36%) had MDR-TB, of whom 386 (50%) had never been treated previously for TB. Moreover, 92% of multidrug-resistant M. tuberculosis strains belonged to putative transmission clusters. Phylogenetic reconstruction identified 3 large clades that were comprised nearly uniformly of MDR-TB: 2 of these clades were of Beijing lineage, and 1 of Ural lineage, and each had additional distinct clade-specific second-line drug resistance mutations and geographic distributions. Spatial and temporal proximity between pairs of cases within a cluster was associated with greater genomic similarity. Our study lasted for only 2 years, a relatively short duration compared with the natural history of TB, and, thus, the ability to infer the full extent of transmission is limited. CONCLUSIONS The MDR-TB epidemic in Moldova is associated with the local transmission of multiple M. tuberculosis strains, including distinct clades of highly drug-resistant M. tuberculosis with varying geographic distributions and drug resistance profiles. This study demonstrates the role of comprehensive genomic surveillance for understanding the transmission of M. tuberculosis and highlights the urgency of interventions to interrupt transmission of highly drug-resistant M. tuberculosis.
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Affiliation(s)
- Chongguang Yang
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen, China
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, United States of America
| | | | - Vijay Naidu
- Department of Mathematics, Simon Fraser University, Burnaby, Canada
| | | | - Nelly Ciobanu
- Phthisiopneumology Institute, Chisinau, Republic of Moldova
| | - Kenneth S. Gunasekera
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, United States of America
| | - Melanie H. Chitwood
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, United States of America
| | | | - Stela Bivol
- Center for Health Policies and Studies, Chisinau, Republic of Moldova
| | - Marcus Russi
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, United States of America
| | - Joshua Havumaki
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, United States of America
| | - Patrick Cudahy
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, United States of America
| | - Heather Fosburgh
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, United States of America
| | | | - Heather Centner
- Translational Genomics Research Institute, Flagstaff, Arizona, United States of America
| | - David M. Engelthaler
- Translational Genomics Research Institute, Flagstaff, Arizona, United States of America
| | - Nicolas A. Menzies
- Department of Global Health and Population, and Center for Health Decision Science, Harvard TH Chan School of Public Health, Boston, Massachusetts, United States of America
| | - Joshua L. Warren
- Department of Biostatistics, Yale School of Public Health, New Haven, Connecticut, United States of America
| | - Valeriu Crudu
- Phthisiopneumology Institute, Chisinau, Republic of Moldova
| | - Caroline Colijn
- Department of Mathematics, Simon Fraser University, Burnaby, Canada
| | - Ted Cohen
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, United States of America
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25
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Investigation on the cause of recurrent tuberculosis in a rural area in China using whole-genome sequencing: A retrospective cohort study. Tuberculosis (Edinb) 2022; 133:102174. [DOI: 10.1016/j.tube.2022.102174] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Revised: 01/25/2022] [Accepted: 01/30/2022] [Indexed: 11/17/2022]
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26
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Lau HC, Hsueh CY, Gong H, Sun J, Huang HY, Zhang M, Zhou L. Oropharynx microbiota transitions in hypopharyngeal carcinoma treatment of induced chemotherapy followed by surgery. BMC Microbiol 2021; 21:310. [PMID: 34753420 PMCID: PMC8577011 DOI: 10.1186/s12866-021-02362-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2021] [Accepted: 10/14/2021] [Indexed: 12/29/2022] Open
Abstract
AIMS To analyze changes in oropharynx microbiota composition after receiving induced chemotherapy followed by surgery for hypopharyngeal squamous cell carcinoma (HPSCC) patients. METHODS Clinical data and swab samples of 38 HPSCC patients (HPSCC group) and 30 patients with benign disease (control group, CG) were enrolled in the study. HPSCC group was stratified into two groups: induced chemotherapy group (IC) of 10 patients and non-induced chemotherapy group (nIC) of 28 patients. The microbiota from oropharyngeal membrane was analyzed through 16S rRNA sequencing. RESULTS Alpha-diversity (Shannon and Ace indexes) and weighted UniFrac based beta-diversity severely decreased in the HPSCC group when compared with CG. In pre-operative comparisons, PCoA and NMDS analyses showed microbial structures in the IC group were more similar to CG than nIC. Both IC group and nIC group yielded significantly diverse post-operative communities in contrast to their pre-operative counterparts, evident by the decrease in genera Veillonella and Fusobacterium and increase in genera Streptococcus and Gemella. Given that post-operative oropharynx microbiota showed no difference between IC and nIC groups, the IC group showed less accumulation in anaerobic communities. The abundance of genera Fusobacterium, Parvimonas, Actinomyces were enhanced in the advanced stages (III/IV). CONCLUSIONS Oropharynx microbiota in the HPSCC group presents dysbiosis with low diversity and abundance. Induced chemotherapy is beneficial in adjusting the oropharynx microbial environment leading to fewer amounts of anaerobe accumulation after operation. Higher amounts of Fusobacterium in advanced stages (III/IV) may influence the progression of HPSCC.
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Affiliation(s)
- Hui-Ching Lau
- Department of Otorhinolaryngology, Eye & ENT Hospital, Fudan University, Shanghai, China.,Shanghai Key Clinical Disciplines of Otorhinolaryngology, Shanghai, People's Republic of China
| | - Chi-Yao Hsueh
- Department of Otorhinolaryngology, Eye & ENT Hospital, Fudan University, Shanghai, China.,Shanghai Key Clinical Disciplines of Otorhinolaryngology, Shanghai, People's Republic of China
| | - Hongli Gong
- Department of Otorhinolaryngology, Eye & ENT Hospital, Fudan University, Shanghai, China. .,Shanghai Key Clinical Disciplines of Otorhinolaryngology, Shanghai, People's Republic of China. .,Department of Otolaryngology, Head and Neck Surgery, Eye & ENT Hospital, Fudan University, 83 Fen Yang Road, Shanghai, 200031, People's Republic of China.
| | - Ji Sun
- Department of Pathology, Eye & ENT Hospital, Fudan University, Shanghai, China
| | - Hui-Ying Huang
- Department of Otorhinolaryngology, Eye & ENT Hospital, Fudan University, Shanghai, China.,Shanghai Key Clinical Disciplines of Otorhinolaryngology, Shanghai, People's Republic of China
| | - Ming Zhang
- Department of Otorhinolaryngology, Eye & ENT Hospital, Fudan University, Shanghai, China.,Shanghai Key Clinical Disciplines of Otorhinolaryngology, Shanghai, People's Republic of China
| | - Liang Zhou
- Department of Otorhinolaryngology, Eye & ENT Hospital, Fudan University, Shanghai, China. .,Shanghai Key Clinical Disciplines of Otorhinolaryngology, Shanghai, People's Republic of China. .,Department of Otolaryngology, Head and Neck Surgery, Eye & ENT Hospital, Fudan University, 83 Fen Yang Road, Shanghai, 200031, People's Republic of China.
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27
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Quaresma A, Brodschneider R, Gratzer K, Gray A, Keller A, Kilpinen O, Rufino J, van der Steen J, Vejsnæs F, Pinto MA. Preservation methods of honey bee-collected pollen are not a source of bias in ITS2 metabarcoding. ENVIRONMENTAL MONITORING AND ASSESSMENT 2021; 193:785. [PMID: 34755261 DOI: 10.1007/s10661-021-09563-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Accepted: 10/26/2021] [Indexed: 06/13/2023]
Abstract
Pollen metabarcoding is emerging as a powerful tool for ecological research and offers unprecedented scale in citizen science projects for environmental monitoring via honey bees. Biases in metabarcoding can be introduced at any stage of sample processing and preservation is at the forefront of the pipeline. While in metabarcoding studies pollen has been preserved at - 20 °C (FRZ), this is not the best method for citizen scientists. Herein, we compared this method with ethanol (EtOH), silica gel (SG) and room temperature (RT) for preservation of pollen collected from hives in Austria and Denmark. After ~ 4 months of storage, DNAs were extracted with a food kit, and their quality and concentration measured. Most DNA extracts exhibited 260/280 absorbance ratios close to the optimal 1.8, with RT samples from Austria performing slightly worse than FRZ and SG samples (P < 0.027). Statistical differences were also detected for DNA concentration, with EtOH samples producing lower yields than RT and FRZ samples in both countries and SG in Austria (P < 0.042). Yet, qualitative and quantitative assessments of floral composition obtained using high-throughput sequencing with the ITS2 barcode gave non-significant effects of preservation methods on richness, relative abundance and Shannon diversity, in both countries. While freezing and ethanol are commonly employed for archiving tissue for molecular applications, desiccation is cheaper and easier to use regarding both storage and transportation. Since SG is less dependent on ambient humidity and less prone to contamination than RT, we recommend SG for preserving pollen for metabarcoding. SG is straightforward for laymen to use and hence robust for widespread application in citizen science studies.
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Affiliation(s)
- Andreia Quaresma
- Centro de Investigação de Montanha, Instituto Politécnico de Bragança, Campus de Santa Apolónia, 5300-253, Bragança, Portugal
| | - Robert Brodschneider
- Institute of Biology, University of Graz, Universitätsplatz 2, 8010, Graz, Austria
| | - Kristina Gratzer
- Institute of Biology, University of Graz, Universitätsplatz 2, 8010, Graz, Austria
| | - Alison Gray
- Department of Mathematics and Statistics, University of Strathclyde, Glasgow, UK
| | - Alexander Keller
- Center for Computational and Theoretical Biology, Hubland Nord, Würzburg, Germany
- Department of Bioinformatics, University of Würzburg, Am Hubland, BiocenterWürzburg, Germany
| | | | - José Rufino
- Research Centre in Digitalization and Intelligent Robotics (CeDRI), Instituto Politécnico de Bragança, Bragança, Portugal
| | | | | | - M Alice Pinto
- Centro de Investigação de Montanha, Instituto Politécnico de Bragança, Campus de Santa Apolónia, 5300-253, Bragança, Portugal.
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Roshka NM, Cherevatov OV, Volkov RA. Molecular Organization and Polymorphism of 5S rDNA in Carpathian Bees. CYTOL GENET+ 2021. [DOI: 10.3103/s0095452721050108] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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29
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Shu HY, Zhang W, Zheng CC, Gao MY, Li YC, Wang YG. Identification and Functional Characterization of a Low-Density Lipoprotein Receptor Gene Pathogenic Variant in Familial Hypercholesterolemia. Front Genet 2021; 12:650077. [PMID: 34497632 PMCID: PMC8419346 DOI: 10.3389/fgene.2021.650077] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Accepted: 06/01/2021] [Indexed: 11/13/2022] Open
Abstract
We report a single-point variant of low-density lipoprotein receptor (LDLR) in a Chinese proband with a clinical diagnosis of familial hypercholesterolemia (FH) with a comprehensive functional analysis. Target exome capture-based next-generation sequencing was used for sequencing and identification of genomic variants in the LDLR gene. The expression, cellular location, and function of the mutant LDLR were analyzed. Sequencing of LDLR in FH patients indicated a point variant of single-base substitution (G < A) at a position of 2389 in the 16th exon, which led to a loss of the 16th exon in the LDLR messenger RNA. This genomic variant was found to cause exon 16 deletion in the mutant LDLR protein. Subsequent functional analyses showed that the mutant LDLR was retained in the Golgi apparatus and rarely expressed in the cellular membranes of HepG2 cells. Accordingly, the intake ability of HepG2 cells with the mutant LDLR was significantly reduced (P < 0.05). In conclusion, our results suggest that a mutant with a single-base substitution (c. 2389G > A) in the 16th exon of the LDLR gene was associated with miscleavage of messenger RNA and the retention of mutant LDLR in the Golgi apparatus, which revealed a pathogenic variant in LDLR underlying the pathogenesis of FH.
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Affiliation(s)
- Hong-Yan Shu
- Department of Endocrinology and Metabolic Diseases, Zibo Municipal Hospital, Zibo, China
| | - Wei Zhang
- Department of Endocrinology and Metabolic Diseases, Zibo Municipal Hospital, Zibo, China
| | - Cong-Cong Zheng
- Department of Endocrinology and Metabolic Diseases, Zibo Municipal Hospital, Zibo, China
| | - Man-Yun Gao
- Department of Endocrinology and Metabolic Diseases, Zibo Municipal Hospital, Zibo, China
| | - Yong-Cun Li
- Department of Endocrinology and Metabolic Diseases, Zibo Municipal Hospital, Zibo, China
| | - Yan-Gang Wang
- Department of Endocrinology and Metabolic Diseases, The Affiliated Hospital of Qingdao University, Qingdao, China
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30
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Lal MM, Macahig DAS, Brown KT, Juinio-Meñez MA, Southgate PC, Ravago-Gotanco R. Preliminary population genomic study on the sandfish Holothuria (Metriatyla) scabra. Anim Genet 2021; 52:775-776. [PMID: 34219251 DOI: 10.1111/age.13116] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/25/2021] [Indexed: 11/29/2022]
Affiliation(s)
- Monal M Lal
- Australian Centre for Pacific Islands Research and School of Science, Technology and Engineering, University of the Sunshine Coast, 90 Sippy Downs Drive, Maroochydore, QLD, 4558, Australia.,Discipline of Marine Studies, School of Agriculture, Geography, Environment, Ocean and Natural Sciences, University of the South Pacific, Lower Laucala Campus, Laucala Bay Road, Suva, Fiji Islands
| | - Deo A S Macahig
- The Marine Science Institute, University of the Philippines Diliman, Quezon City, Philippines
| | - Kelly T Brown
- Discipline of Marine Studies, School of Agriculture, Geography, Environment, Ocean and Natural Sciences, University of the South Pacific, Lower Laucala Campus, Laucala Bay Road, Suva, Fiji Islands
| | - Marie A Juinio-Meñez
- The Marine Science Institute, University of the Philippines Diliman, Quezon City, Philippines
| | - Paul C Southgate
- Australian Centre for Pacific Islands Research and School of Science, Technology and Engineering, University of the Sunshine Coast, 90 Sippy Downs Drive, Maroochydore, QLD, 4558, Australia
| | - Rachel Ravago-Gotanco
- The Marine Science Institute, University of the Philippines Diliman, Quezon City, Philippines
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van der Loos LM, Nijland R. Biases in bulk: DNA metabarcoding of marine communities and the methodology involved. Mol Ecol 2021; 30:3270-3288. [PMID: 32779312 PMCID: PMC8359149 DOI: 10.1111/mec.15592] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2020] [Accepted: 07/28/2020] [Indexed: 12/22/2022]
Abstract
With the growing anthropogenic pressure on marine ecosystems, the need for efficient monitoring of biodiversity grows stronger. DNA metabarcoding of bulk samples is increasingly being implemented in ecosystem assessments and is more cost-efficient and less time-consuming than monitoring based on morphology. However, before raw sequences are obtained from bulk samples, a profound number of methodological choices must be made. Here, we critically review the recent methods used for metabarcoding of marine bulk samples (including benthic, plankton and diet samples) and indicate how potential biases can be introduced throughout sampling, preprocessing, DNA extraction, marker and primer selection, PCR amplification and sequencing. From a total of 64 studies evaluated, our recommendations for best practices include to (a) consider DESS as a fixative instead of ethanol, (b) use the DNeasy PowerSoil kit for any samples containing traces of sediment, (c) not limit the marker selection to COI only, but preferably include multiple markers for higher taxonomic resolution, (d) avoid touchdown PCR profiles, (e) use a fixed annealing temperature for each primer pair when comparing across studies or institutes, (f) use a minimum of three PCR replicates, and (g) include both negative and positive controls. Although the implementation of DNA metabarcoding still faces several technical complexities, we foresee wide-ranging advances in the near future, including improved bioinformatics for taxonomic assignment, sequencing of longer fragments and the use of whole-genome information. Despite the bulk of biases involved in metabarcoding of bulk samples, if appropriate controls are included along the data generation process, it is clear that DNA metabarcoding provides a valuable tool in ecosystem assessments.
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Affiliation(s)
- Luna M. van der Loos
- Marine Animal Ecology GroupWageningen UniversityWageningenThe Netherlands
- Present address:
Department of BiologyPhycology Research GroupGhent UniversityGhentBelgium
| | - Reindert Nijland
- Marine Animal Ecology GroupWageningen UniversityWageningenThe Netherlands
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Sloan S, Jenvey CJ, Piedrafita D, Preston S, Stear MJ. Comparative evaluation of different molecular methods for DNA extraction from individual Teladorsagia circumcincta nematodes. BMC Biotechnol 2021; 21:35. [PMID: 34001079 PMCID: PMC8130168 DOI: 10.1186/s12896-021-00695-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Accepted: 05/09/2021] [Indexed: 11/10/2022] Open
Abstract
Background The purpose of this study was to develop a reliable DNA extraction protocol to use on individual Teladorsagia circumcincta nematode specimens to produce high quality DNA for genome sequencing and phylogenetic analysis. Pooled samples have been critical in providing the groundwork for T. circumcincta genome construction, but there is currently no standard method for extracting high-quality DNA from individual nematodes. 11 extraction kits were compared based on DNA quality, yield, and processing time. Results 11 extraction protocols were compared, and the concentration and purity of the extracted DNA was quantified. Median DNA concentration among all methods measured on NanoDrop 2000™ ranged between 0.45–11.5 ng/μL, and on Qubit™ ranged between undetectable – 0.962 ng/μL. Median A260/280 ranged between 0.505–3.925, and median A260/230 ranged − 0.005 – 1.545. Larval exsheathment to remove the nematode cuticle negatively impacted DNA concentration and purity. Conclusions A Schistosoma sp. DNA extraction method was determined as most suitable for individual T. circumcincta nematode specimens due to its resulting DNA concentration, purity, and relatively fast processing time. Supplementary Information The online version contains supplementary material available at 10.1186/s12896-021-00695-6.
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Affiliation(s)
- S Sloan
- AgriBio Centre for AgriBioscience, Department of Animal, Plant and Soil Sciences, School of Life Sciences, La Trobe University, 5 Ring Road, Bundoora, Victoria, 3086, Australia.
| | - C J Jenvey
- AgriBio Centre for AgriBioscience, Department of Animal, Plant and Soil Sciences, School of Life Sciences, La Trobe University, 5 Ring Road, Bundoora, Victoria, 3086, Australia
| | - D Piedrafita
- School of Science, Psychology and Sport, Federation University, Churchill, Victoria, Australia
| | - S Preston
- School of Science, Psychology and Sport, Federation University, Churchill, Victoria, Australia
| | - M J Stear
- AgriBio Centre for AgriBioscience, Department of Animal, Plant and Soil Sciences, School of Life Sciences, La Trobe University, 5 Ring Road, Bundoora, Victoria, 3086, Australia
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PCR-Based Direct Detection of Streptococcus uberis from Subclinical and Clinical Dairy Cattle Milk Samples. Vet Med Int 2020; 2020:8828624. [PMID: 33376590 PMCID: PMC7746883 DOI: 10.1155/2020/8828624] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Revised: 11/20/2020] [Accepted: 11/25/2020] [Indexed: 11/30/2022] Open
Abstract
Streptococcus uberis is one of the leading causes worldwide of mastitis in the dairy industry, with the most likely sources of infection attributed to environmental reservoirs such as contaminated bedding materials. Early detection of those cases most likely to progress to clinical disease would lead to improved animal welfare, a critical component of overall health and productivity. A multiplex PCR-based diagnostic test was developed for detection of S. uberis directly from milk and targeting two genes previously identified as important for intramammary colonisation and persistence in dairy cattle. Results indicated the threshold for detection directly from milk was 20,000 CFU/ml and this was achieved without the need for preenrichment. In addition, S. uberis could be identified from milk samples collected during intramammary challenge studies, prior to clinical signs of infection and at much lower detection limits. The PCR test developed for confirmation of the presence of S. uberis directly from infected milk has potential value as a diagnostic test to identify early infection and/or to confirm that antibiotic therapy has been successful.
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Wang K, Liu X, Qi T, Hui Y, Yan H, Qu L, Lan X, Pan C. Whole-genome sequencing to identify candidate genes for litter size and to uncover the variant function in goats (Capra hircus). Genomics 2020; 113:142-150. [PMID: 33276007 DOI: 10.1016/j.ygeno.2020.11.024] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Revised: 10/28/2020] [Accepted: 11/26/2020] [Indexed: 01/23/2023]
Abstract
To select candidate genes for goat prolificacy, we managed six multi- and six single-kid female goats at the same feeding level and in the same management mode over a 4-year period. These goats showed stable differences in litter size over five continuous parturition records. Whole-genome re-sequencing was used in all 12 to select candidate genes, namely, AURKA, ENDOG, SOX2, RORA, GJA10, RXFP2, CDC25C, and NANOS3, by the strength of their differentiation signals. Most of the selected genes were enriched in the coiled coil process and ovarian development, which suggests that the coiled coil process has a potential regulatory effect on fecundity. Detection of the distribution of variants and association analyses with litter size in 400 goats showed that NANOS3 exon mutations may lead to a transformation of the protein structure. The variation in CDC25C, ENDOG, and NANOS3 showed a significant association with litter size. These results can contribute to the improvement of reproduction traits in the artificial breeding of goats.
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Affiliation(s)
- Ke Wang
- College of Animal Science and Technology, Northwest A&F University, Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, Key Laboratory of Animal Biotechnology, Ministry of Agriculture, Yangling 712100, PR China
| | - Xinfeng Liu
- College of Animal Science and Technology, Northwest A&F University, Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, Key Laboratory of Animal Biotechnology, Ministry of Agriculture, Yangling 712100, PR China
| | - Tang Qi
- College of Animal Science and Technology, Northwest A&F University, Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, Key Laboratory of Animal Biotechnology, Ministry of Agriculture, Yangling 712100, PR China
| | - Yiqing Hui
- College of Animal Science and Technology, Northwest A&F University, Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, Key Laboratory of Animal Biotechnology, Ministry of Agriculture, Yangling 712100, PR China
| | - Hailong Yan
- Department of Neurology, Institute of Brain Science, Medical School, Shanxi Datong University, Datong 037000, China
| | - Lei Qu
- Life Science Research Center, Yulin University, Shaanxi Provincial Engineering and Technology Research Center of Cashmere Goats, Yulin 719000, China
| | - Xianyong Lan
- College of Animal Science and Technology, Northwest A&F University, Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, Key Laboratory of Animal Biotechnology, Ministry of Agriculture, Yangling 712100, PR China.
| | - Chuanying Pan
- College of Animal Science and Technology, Northwest A&F University, Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, Key Laboratory of Animal Biotechnology, Ministry of Agriculture, Yangling 712100, PR China.
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Jung H, Ventura T, Chung JS, Kim WJ, Nam BH, Kong HJ, Kim YO, Jeon MS, Eyun SI. Twelve quick steps for genome assembly and annotation in the classroom. PLoS Comput Biol 2020; 16:e1008325. [PMID: 33180771 PMCID: PMC7660529 DOI: 10.1371/journal.pcbi.1008325] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Eukaryotic genome sequencing and de novo assembly, once the exclusive domain of well-funded international consortia, have become increasingly affordable, thus fitting the budgets of individual research groups. Third-generation long-read DNA sequencing technologies are increasingly used, providing extensive genomic toolkits that were once reserved for a few select model organisms. Generating high-quality genome assemblies and annotations for many aquatic species still presents significant challenges due to their large genome sizes, complexity, and high chromosome numbers. Indeed, selecting the most appropriate sequencing and software platforms and annotation pipelines for a new genome project can be daunting because tools often only work in limited contexts. In genomics, generating a high-quality genome assembly/annotation has become an indispensable tool for better understanding the biology of any species. Herein, we state 12 steps to help researchers get started in genome projects by presenting guidelines that are broadly applicable (to any species), sustainable over time, and cover all aspects of genome assembly and annotation projects from start to finish. We review some commonly used approaches, including practical methods to extract high-quality DNA and choices for the best sequencing platforms and library preparations. In addition, we discuss the range of potential bioinformatics pipelines, including structural and functional annotations (e.g., transposable elements and repetitive sequences). This paper also includes information on how to build a wide community for a genome project, the importance of data management, and how to make the data and results Findable, Accessible, Interoperable, and Reusable (FAIR) by submitting them to a public repository and sharing them with the research community.
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Affiliation(s)
- Hyungtaek Jung
- School of Biological Sciences, The University of Queensland, St Lucia, Queensland, Australia
- Centre for Agriculture and Bioeconomy, Queensland University of Technology, Brisbane, Queensland, Australia
| | - Tomer Ventura
- Genecology Research Centre, School of Science and Engineering, University of the Sunshine Coast, Sippy Downs, Queensland, Australia
| | - J. Sook Chung
- Institute of Marine and Environmental Technology, University of Maryland Center for Environmental Science, Baltimore, Maryland, United States of America
| | - Woo-Jin Kim
- Genetics and Breeding Research Center, National Institute of Fisheries Science, Geoje, Korea
| | - Bo-Hye Nam
- Biotechnology Research Division, National Institute of Fisheries Science, Busan, Korea
| | - Hee Jeong Kong
- Biotechnology Research Division, National Institute of Fisheries Science, Busan, Korea
| | - Young-Ok Kim
- Biotechnology Research Division, National Institute of Fisheries Science, Busan, Korea
| | - Min-Seung Jeon
- Department of Life Science, Chung-Ang University, Seoul, Korea
| | - Seong-il Eyun
- Department of Life Science, Chung-Ang University, Seoul, Korea
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36
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Jiang Q, Liu Q, Ji L, Li J, Zeng Y, Meng L, Luo G, Yang C, Takiff HE, Yang Z, Tan W, Yu W, Gao Q. Citywide Transmission of Multidrug-resistant Tuberculosis Under China's Rapid Urbanization: A Retrospective Population-based Genomic Spatial Epidemiological Study. Clin Infect Dis 2020; 71:142-151. [PMID: 31504306 PMCID: PMC8127054 DOI: 10.1093/cid/ciz790] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Accepted: 08/26/2019] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Population movement could extend multidrug-resistant tuberculosis (MDR-TB) transmission and complicate its global prevalence. We sought to identify the high-risk populations and geographic sites of MDR-TB transmission in Shenzhen, the most common destination for internal migrants in China. METHODS We performed a population-based, retrospective study in patients diagnosed with MDR-TB in Shenzhen during 2013-2017. By defining genomic clusters with a threshold of 12-single-nucleotide polymorphism distance based on whole-genome sequencing of their clinical strains, the clustering rate was calculated to evaluate the level of recent transmission. Risk factors were identified by multivariable logistic regression. To further delineate the epidemiological links, we invited the genomic-clustered patients to an in-depth social network investigation. RESULTS In total, 105 (25.2%) of the 417 enrolled patients with MDR-TB were grouped into 40 genome clusters, suggesting recent transmission of MDR strains. The adjusted risk for student to have a clustered strain was 4.05 (95% confidence interval, 1.06-17.0) times greater than other patients. The majority (70%, 28/40) of the genomic clusters involved patients who lived in different districts, with residences separated by an average of 8.76 kilometers. Other than household members, confirmed epidemiological links were also identified among classmates and workplace colleagues. CONCLUSIONS These findings demonstrate that local transmission of MDR-TB is a serious problem in Shenzhen. While most transmission occurred between people who lived distant from each other, there was clear evidence that transmission occurred in schools and workplaces, which should be included as targeted sites for active case finding.The average residential distance between genomic-clustered cases was more than 8 kilometers, while schools and workplaces, identified as sites of transmission in this study, deserve increased vigilance for targeted case finding of multidrug-resistant tuberculosis.
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Affiliation(s)
- Qi Jiang
- Shenzhen Center for Chronic Disease Control, Shenzhen, China
- Key Laboratory of Medical Molecular Virology (Ministry of Education,National Health Commission, Chinese Academy of Medical Sciences), School of Basic Medical Sciences, Shanghai Medical College and Shanghai Public Health Clinical Center, Fudan University, Shenzhen, China
| | - Qingyun Liu
- Shenzhen Center for Chronic Disease Control, Shenzhen, China
- Key Laboratory of Medical Molecular Virology (Ministry of Education,National Health Commission, Chinese Academy of Medical Sciences), School of Basic Medical Sciences, Shanghai Medical College and Shanghai Public Health Clinical Center, Fudan University, Shenzhen, China
| | - Lecai Ji
- Shenzhen Center for Chronic Disease Control, Shenzhen, China
| | - Jinli Li
- Shenzhen Center for Chronic Disease Control, Shenzhen, China
| | - Yaling Zeng
- Shenzhen Center for Chronic Disease Control, Shenzhen, China
| | - Liangguang Meng
- Shenzhen Center for Chronic Disease Control, Shenzhen, China
| | - Geyang Luo
- Key Laboratory of Medical Molecular Virology (Ministry of Education,National Health Commission, Chinese Academy of Medical Sciences), School of Basic Medical Sciences, Shanghai Medical College and Shanghai Public Health Clinical Center, Fudan University, Shenzhen, China
| | - Chongguang Yang
- School of Public Health, Yale University, New Haven, Connecticut, USA
| | - Howard E Takiff
- Integrated Mycobacterial Pathogenomics Unit, Institut Pasteur, Paris, France
- Nanshan Center for Chronic Disease Control, Shenzhen, China
| | - Zheng Yang
- Shenzhen Center for Chronic Disease Control, Shenzhen, China
| | - Weiguo Tan
- Shenzhen Center for Chronic Disease Control, Shenzhen, China
| | - Weiye Yu
- Shenzhen Center for Chronic Disease Control, Shenzhen, China
| | - Qian Gao
- Shenzhen Center for Chronic Disease Control, Shenzhen, China
- Key Laboratory of Medical Molecular Virology (Ministry of Education,National Health Commission, Chinese Academy of Medical Sciences), School of Basic Medical Sciences, Shanghai Medical College and Shanghai Public Health Clinical Center, Fudan University, Shenzhen, China
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37
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Huggins LG, Koehler AV, Schunack B, Inpankaew T, Traub RJ. A Host-Specific Blocking Primer Combined with Optimal DNA Extraction Improves the Detection Capability of a Metabarcoding Protocol for Canine Vector-Borne Bacteria. Pathogens 2020; 9:E258. [PMID: 32244645 PMCID: PMC7238069 DOI: 10.3390/pathogens9040258] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Revised: 03/31/2020] [Accepted: 03/31/2020] [Indexed: 12/20/2022] Open
Abstract
Bacterial canine vector-borne diseases are responsible for some of the most life-threatening conditions of dogs in the tropics and are typically poorly researched with some presenting a zoonotic risk to cohabiting people. Next-generation sequencing based methodologies have been demonstrated to accurately characterise a diverse range of vector-borne bacteria in dogs, whilst also proving to be more sensitive than conventional PCR techniques. We report two improvements to a previously developed metabarcoding tool that increased the sensitivity and diversity of vector-borne bacteria detected from canine blood. Firstly, we developed and tested a canine-specific blocking primer that prevents cross-reactivity of bacterial primer amplification on abundant canine mitochondrial sequences. Use of our blocking primer increased the number of canine vector-borne infections detected (five more Ehrlichia canis and three more Anaplasma platys infections) and increased the diversity of bacterial sequences found. Secondly, the DNA extraction kit employed can have a significant effect on the bacterial community characterised. Therefore, we compared four different DNA extraction kits finding the Qiagen DNeasy Blood and Tissue Kit to be superior for detection of blood-borne bacteria, identifying nine more A. platys, two more E. canis, one more Mycoplasma haemocanis infection and more putative bacterial pathogens than the lowest performing kit.
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Affiliation(s)
- Lucas G. Huggins
- Faculty of Veterinary and Agricultural Sciences, University of Melbourne, Parkville, Victoria 3050, Australia; (A.V.K.); (R.J.T.)
| | - Anson V. Koehler
- Faculty of Veterinary and Agricultural Sciences, University of Melbourne, Parkville, Victoria 3050, Australia; (A.V.K.); (R.J.T.)
| | | | - Tawin Inpankaew
- Faculty of Veterinary Medicine, Kasetsart University, Bangkok 10900, Thailand;
| | - Rebecca J. Traub
- Faculty of Veterinary and Agricultural Sciences, University of Melbourne, Parkville, Victoria 3050, Australia; (A.V.K.); (R.J.T.)
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Andermann T, Torres Jiménez MF, Matos-Maraví P, Batista R, Blanco-Pastor JL, Gustafsson ALS, Kistler L, Liberal IM, Oxelman B, Bacon CD, Antonelli A. A Guide to Carrying Out a Phylogenomic Target Sequence Capture Project. Front Genet 2020; 10:1407. [PMID: 32153629 PMCID: PMC7047930 DOI: 10.3389/fgene.2019.01407] [Citation(s) in RCA: 52] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Accepted: 12/24/2019] [Indexed: 12/17/2022] Open
Abstract
High-throughput DNA sequencing techniques enable time- and cost-effective sequencing of large portions of the genome. Instead of sequencing and annotating whole genomes, many phylogenetic studies focus sequencing effort on large sets of pre-selected loci, which further reduces costs and bioinformatic challenges while increasing coverage. One common approach that enriches loci before sequencing is often referred to as target sequence capture. This technique has been shown to be applicable to phylogenetic studies of greatly varying evolutionary depth. Moreover, it has proven to produce powerful, large multi-locus DNA sequence datasets suitable for phylogenetic analyses. However, target capture requires careful considerations, which may greatly affect the success of experiments. Here we provide a simple flowchart for designing phylogenomic target capture experiments. We discuss necessary decisions from the identification of target loci to the final bioinformatic processing of sequence data. We outline challenges and solutions related to the taxonomic scope, sample quality, and available genomic resources of target capture projects. We hope this review will serve as a useful roadmap for designing and carrying out successful phylogenetic target capture studies.
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Affiliation(s)
- Tobias Andermann
- Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden
- Gothenburg Global Biodiversity Centre, Gothenburg, Sweden
| | - Maria Fernanda Torres Jiménez
- Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden
- Gothenburg Global Biodiversity Centre, Gothenburg, Sweden
| | - Pável Matos-Maraví
- Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden
- Gothenburg Global Biodiversity Centre, Gothenburg, Sweden
- Institute of Entomology, Biology Centre of the Czech Academy of Sciences, České Budějovice, Czechia
| | - Romina Batista
- Gothenburg Global Biodiversity Centre, Gothenburg, Sweden
- Programa de Pós-Graduação em Genética, Conservação e Biologia Evolutiva, PPG GCBEv–Instituto Nacional de Pesquisas da Amazônia—INPA Campus II, Manaus, Brazil
- Coordenação de Zoologia, Museu Paraense Emílio Goeldi, Belém, Brazil
| | - José L. Blanco-Pastor
- Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden
- INRAE, Centre Nouvelle-Aquitaine-Poitiers, Lusignan, France
| | | | - Logan Kistler
- Department of Anthropology, National Museum of Natural History, Smithsonian Institution, Washington, DC, United States
| | - Isabel M. Liberal
- Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden
| | - Bengt Oxelman
- Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden
- Gothenburg Global Biodiversity Centre, Gothenburg, Sweden
| | - Christine D. Bacon
- Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden
- Gothenburg Global Biodiversity Centre, Gothenburg, Sweden
| | - Alexandre Antonelli
- Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden
- Gothenburg Global Biodiversity Centre, Gothenburg, Sweden
- Royal Botanic Gardens, Kew, Richmond-Surrey, United Kingdom
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Tuschhoff EJ, Hutter CR, Glor RE. Improving sustainable use of genetic resources in biodiversity archives. PeerJ 2020; 8:e8369. [PMID: 32095317 PMCID: PMC7024571 DOI: 10.7717/peerj.8369] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2019] [Accepted: 12/09/2019] [Indexed: 11/20/2022] Open
Abstract
Tissue sample databases housed in biodiversity archives represent a vast trove of genetic resources, and these tissues are often destructively subsampled and provided to researchers for DNA extractions and subsequent sequencing. While obtaining a sufficient quantity of DNA for downstream applications is vital for these researchers, it is also important to preserve tissue resources for future use given that the original material is destructively and consumptively sampled with each use. It is therefore necessary to develop standardized tissue subsampling and loaning procedures to ensure that tissues are being used efficiently. In this study, we specifically focus on the efficiency of DNA extraction methods by using anuran liver and muscle tissues maintained at a biodiversity archive. We conducted a series of experiments to test whether current practices involving coarse visual assessments of tissue size are effective, how tissue mass correlates with DNA yield and concentration, and whether the amount of DNA recovered is correlated with sample age. We found that tissue samples between 2 and 8 mg resulted in the most efficient extractions, with tissues at the lower end of this range providing more DNA per unit mass and tissues at the higher end of this range providing more total DNA. Additionally, we found no correlation between tissue age and DNA yield. Because we find that even very small tissue subsamples tend to yield far more DNA than is required by researchers for modern sequencing applications (including whole genome shotgun sequencing), we recommend that biodiversity archives consider dramatically improving sustainable use of their archived material by providing researchers with set quantities of extracted DNA rather than with the subsampled tissues themselves.
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Affiliation(s)
- E. J. Tuschhoff
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, USA
- Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, KS, USA
- University of Kansas Biodiversity Institute, Lawrence, KS, USA
| | - Carl R. Hutter
- Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, KS, USA
- University of Kansas Biodiversity Institute, Lawrence, KS, USA
| | - Richard E. Glor
- Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, KS, USA
- University of Kansas Biodiversity Institute, Lawrence, KS, USA
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40
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Zhang C, Sun G, Senapati S, Chang HC. A bifurcated continuous field-flow fractionation (BCFFF) chip for high-yield and high-throughput nucleic acid extraction and purification. LAB ON A CHIP 2019; 19:3853-3861. [PMID: 31621762 PMCID: PMC6982425 DOI: 10.1039/c9lc00818g] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
We report a bifurcated continuous field-flow fractionation (BCFFF) chip for high-yield and high-throughput (20 min) extraction of nucleic acids from physiological samples. The design uses a membrane ionic transistor to sustain low-ionic strength in a localized region at a junction, such that the resulting high field can selectively isolate high-charge density nucleic acids from the main flow channel and insert them into a standardized buffer in a side channel that bifurcates from the junction. The high local electric field and the bifurcated field-flow design facilitate concentration reduction of both divalent cation (Ca2+) and molecular PCR inhibitors by more than two orders of magnitude, even with high-throughput continuous loading. The unique design with a large (>20 mM mm-1) on-chip ionic-strength gradient allows miniaturization into a high-throughput field-flow fractionation chip that can be integrated with upstream lysing and downstream PCR/sensor modules for various nucleic acid detection/quantification applications. A concentration-independent 85% yield for extraction and an overall post-PCR yield exceeding 60% are demonstrated for a 111 bp dsDNA in 10 μL of human plasma, compared to no amplification with the raw sample. A net yield four times larger than a commercial extraction kit is demonstrated for miR-39 in human plasma.
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Affiliation(s)
- Chenguang Zhang
- Department of Chemical and Biomolecular Engineering, University of Notre Dame, Notre Dame, IN 46556, USA. and Center for Microfluidics and Medical Diagnostics, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Gongchen Sun
- School of Chemical & Biomolecular Engineering, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Satyajyoti Senapati
- Department of Chemical and Biomolecular Engineering, University of Notre Dame, Notre Dame, IN 46556, USA. and Center for Microfluidics and Medical Diagnostics, University of Notre Dame, Notre Dame, IN 46556, USA and Harper Cancer Research Institute, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Hsueh-Chia Chang
- Department of Chemical and Biomolecular Engineering, University of Notre Dame, Notre Dame, IN 46556, USA. and Center for Microfluidics and Medical Diagnostics, University of Notre Dame, Notre Dame, IN 46556, USA and Harper Cancer Research Institute, University of Notre Dame, Notre Dame, IN 46556, USA and Department of Aerospace and Mechanical Engineering, University of Notre Dame, Notre Dame, IN 46556, USA
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Lienhard A, Schäffer S. Extracting the invisible: obtaining high quality DNA is a challenging task in small arthropods. PeerJ 2019; 7:e6753. [PMID: 30997294 PMCID: PMC6463856 DOI: 10.7717/peerj.6753] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2018] [Accepted: 03/09/2019] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND The application of an appropriate extraction method is a relevant factor for the success of all molecular studies. METHODS Seven different DNA extraction methods suitable for high-throughput DNA sequencing with very small arthropods were compared by applying nine different protocols: three silica gel based spin methods, two cetyltrimethyl ammonium bromide (CTAB) based ones (one with an additional silica membrane), a protein precipitation method and a method based on a chelating resin (applying different protocols). The quantity (concentration) and quality (degradation, contamination, polymerase chain reaction (PCR) and sequencing success) of the extracted DNA as well as the costs, preparation times, user friendliness, and required supplies were compared across these methods. To assess the DNA quantity, two different DNA concentration measurements were applied. Additionally, the effect of varying amounts of starting material (different body sizes), variable lysis temperatures and mixing during DNA extraction was evaluated. RESULTS Although low DNA concentrations were measured for all methods, the results showed that-with the exception of two methods-the PCR success was 100%. However, other parameters show vast differences. The time taken to perform DNA extraction varied from 20 min to 2.5 h (Chelex vs. CTAB) and the costs from 0.02 to 3.46 € (Chelex vs. QIAamp kit) per sample. High quality genomic DNA was only gained from four methods. Results of DNA quantity measurements further indicated that some devices cannot deal with small amounts of DNA and show variant results. DISCUSSION In conclusion, using Chelex (chelating resin) turned out as a rapid, low-cost method which can provide high quality DNA for different kinds of molecular investigations.
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Mayday MY, Khan LM, Chow ED, Zinter MS, DeRisi JL. Miniaturization and optimization of 384-well compatible RNA sequencing library preparation. PLoS One 2019; 14:e0206194. [PMID: 30629604 PMCID: PMC6328170 DOI: 10.1371/journal.pone.0206194] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2018] [Accepted: 12/12/2018] [Indexed: 01/15/2023] Open
Abstract
Preparation of high-quality sequencing libraries is a costly and time-consuming component of metagenomic next generation sequencing (mNGS). While the overall cost of sequencing has dropped significantly over recent years, the reagents needed to prepare sequencing samples are likely to become the dominant expense in the process. Furthermore, libraries prepared by hand are subject to human variability and needless waste due to limitations of manual pipetting volumes. Reduction of reaction volumes, combined with sub-microliter automated dispensing of reagents without consumable pipette tips, has the potential to provide significant advantages. Here, we describe the integration of several instruments, including the Labcyte Echo 525 acoustic liquid handler and the iSeq and NovaSeq Illumina sequencing platforms, to miniaturize and automate mNGS library preparation, significantly reducing the cost and the time required to prepare samples. Through the use of External RNA Controls Consortium (ERCC) spike-in RNAs, we demonstrated the fidelity of the miniaturized preparation to be equivalent to full volume reactions. Furthermore, detection of viral and microbial species from cell culture and patient samples was also maintained in the miniaturized libraries. For 384-well mNGS library preparations, we achieved cost savings of over 80% in materials and reagents alone, and reduced preparation time by 90% compared to manual approaches, without compromising quality or representation within the library.
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Affiliation(s)
- Madeline Y. Mayday
- UCSF School of Medicine, Benioff Children’s Hospital, Department of Pediatrics, Division of Critical Care, San Francisco, California, United States of America
| | - Lillian M. Khan
- UCSF School of Medicine, Department of Biochemistry & Biophysics, San Francisco, California, United States of America
| | - Eric D. Chow
- UCSF School of Medicine, Department of Biochemistry & Biophysics, San Francisco, California, United States of America
| | - Matt S. Zinter
- UCSF School of Medicine, Benioff Children’s Hospital, Department of Pediatrics, Division of Critical Care, San Francisco, California, United States of America
| | - Joseph L. DeRisi
- UCSF School of Medicine, Department of Biochemistry & Biophysics, San Francisco, California, United States of America
- Chan Zuckerberg Biohub, San Francisco, California, United States of America
- * E-mail:
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Evans JS, López-Legentil S, Erwin PM. Comparing Two Common DNA Extraction Kits for the Characterization of Symbiotic Microbial Communities from Ascidian Tissue. Microbes Environ 2018; 33:435-439. [PMID: 30487350 PMCID: PMC6308000 DOI: 10.1264/jsme2.me18031] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2018] [Accepted: 08/01/2018] [Indexed: 11/30/2022] Open
Abstract
Various DNA extraction methods are often used interchangeably for the characterization of microbial communities despite indications that different techniques produce disparate results. The microbiomes of two ascidian species were herein characterized using two common DNA extraction kits, the DNeasy Blood and Tissue Kit (Qiagen) and the PowerSoil DNA Isolation Kit (Mo Bio Laboratories), followed by next-generation (Illumina) sequencing of partial 16S rRNA genes. Significant differences were detected in microbial community diversity and structure between ascidian species, but not between kits, suggesting similar recovery of biological variation and low technical variation between the two extraction methods for ascidian microbiome characterization.
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Affiliation(s)
- James S. Evans
- Department of Biology & Marine Biology, and Center for Marine Science, University of North Carolina Wilmington5600 Marvin K. Moss Lane, Wilmington NC 28409United States of America
| | - Susanna López-Legentil
- Department of Biology & Marine Biology, and Center for Marine Science, University of North Carolina Wilmington5600 Marvin K. Moss Lane, Wilmington NC 28409United States of America
| | - Patrick M. Erwin
- Department of Biology & Marine Biology, and Center for Marine Science, University of North Carolina Wilmington5600 Marvin K. Moss Lane, Wilmington NC 28409United States of America
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Koziol A, Stat M, Simpson T, Jarman S, DiBattista JD, Harvey ES, Marnane M, McDonald J, Bunce M. Environmental DNA metabarcoding studies are critically affected by substrate selection. Mol Ecol Resour 2018; 19:366-376. [DOI: 10.1111/1755-0998.12971] [Citation(s) in RCA: 78] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Revised: 11/08/2018] [Accepted: 11/14/2018] [Indexed: 01/24/2023]
Affiliation(s)
- Adam Koziol
- Trace and Environmental DNA (TrEnD) Laboratory, School Molecular and Life Sciences Curtin University Bentley Western Australia Australia
| | - Michael Stat
- Trace and Environmental DNA (TrEnD) Laboratory, School Molecular and Life Sciences Curtin University Bentley Western Australia Australia
- School of Biological Sciences Macquarie University North Ryde New South Wales Australia
| | - Tiffany Simpson
- Trace and Environmental DNA (TrEnD) Laboratory, School Molecular and Life Sciences Curtin University Bentley Western Australia Australia
| | - Simon Jarman
- Trace and Environmental DNA (TrEnD) Laboratory, School Molecular and Life Sciences Curtin University Bentley Western Australia Australia
- CSIRO Environomics Future Science Platform Indian Ocean Marine Research Centre The University of Western Australia Perth Western Australia Australia
| | - Joseph D. DiBattista
- Trace and Environmental DNA (TrEnD) Laboratory, School Molecular and Life Sciences Curtin University Bentley Western Australia Australia
- Australian Museum Research Institute, Australian Museum Sydney New South Wales Australia
| | - Euan S. Harvey
- Fish Ecology Laboratory, School Molecular and Life Sciences Curtin University Bentley Western Australia Australia
| | - Michael Marnane
- Chevron Energy Technology Company Perth Western Australia Australia
| | - Justin McDonald
- Sustainability and Biosecurity, Department of Primary Industries and Regional Development (DPIRD) Hillarys Western Australia Australia
| | - Michael Bunce
- Trace and Environmental DNA (TrEnD) Laboratory, School Molecular and Life Sciences Curtin University Bentley Western Australia Australia
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Lamb PD, Hunter E, Pinnegar JK, Creer S, Davies RG, Taylor MI. How quantitative is metabarcoding: A meta-analytical approach. Mol Ecol 2018; 28:420-430. [PMID: 30408260 PMCID: PMC7379500 DOI: 10.1111/mec.14920] [Citation(s) in RCA: 142] [Impact Index Per Article: 23.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2018] [Revised: 10/25/2018] [Accepted: 10/26/2018] [Indexed: 12/12/2022]
Abstract
Metabarcoding has been used in a range of ecological applications such as taxonomic assignment, dietary analysis and the analysis of environmental DNA. However, after a decade of use in these applications there is little consensus on the extent to which proportions of reads generated corresponds to the original proportions of species in a community. To quantify our current understanding, we conducted a structured review and meta‐analysis. The analysis suggests that a weak quantitative relationship may exist between the biomass and sequences produced (slope = 0.52 ± 0.34, p < 0.01), albeit with a large degree of uncertainty. None of the tested moderators, sequencing platform type, the number of species used in a trial or the source of DNA, were able to explain the variance. Our current understanding of the factors affecting the quantitative performance of metabarcoding is still limited: additional research is required before metabarcoding can be confidently utilized for quantitative applications. Until then, we advocate the inclusion of mock communities when metabarcoding as this facilitates direct assessment of the quantitative ability of any given study.
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Affiliation(s)
- Philip D Lamb
- School of Biological Sciences, University of East Anglia, Norwich, UK
| | - Ewan Hunter
- School of Environmental Sciences, University of East Anglia, Norwich, UK.,Cefas, Lowestoft, UK
| | - John K Pinnegar
- School of Environmental Sciences, University of East Anglia, Norwich, UK.,Cefas, Lowestoft, UK
| | - Simon Creer
- School of Biological Sciences, Bangor University, Bangor, UK
| | - Richard G Davies
- School of Biological Sciences, University of East Anglia, Norwich, UK
| | - Martin I Taylor
- School of Biological Sciences, University of East Anglia, Norwich, UK
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A simple, rapid and economic manual method for human sperm DNA extraction in genetic and epigenetic studies. MIDDLE EAST FERTILITY SOCIETY JOURNAL 2018. [DOI: 10.1016/j.mefs.2017.12.005] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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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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Prosser C, Meyer W, Ellis J, Lee R. Evolutionary ARMS Race: Antimalarial Resistance Molecular Surveillance. Trends Parasitol 2018; 34:322-334. [PMID: 29396203 DOI: 10.1016/j.pt.2018.01.001] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2017] [Revised: 01/02/2018] [Accepted: 01/03/2018] [Indexed: 01/13/2023]
Abstract
Molecular surveillance of antimalarial drug resistance markers has become an important part of resistance detection and containment. In the current climate of multidrug resistance, including resistance to the global front-line drug artemisinin, there is a consensus to upscale molecular surveillance. The most salient limitation to current surveillance efforts is that skill and infrastructure requirements preclude many regions. This includes sub-Saharan Africa, where Plasmodium falciparum is responsible for most of the global malaria disease burden. New molecular and data technologies have emerged with an emphasis on accessibility. These may allow surveillance to be conducted in broad settings where it is most needed, including at the primary healthcare level in endemic countries, and extending to the village health worker.
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Affiliation(s)
- Christiane Prosser
- Molecular Mycology Research Laboratory, Centre for Infectious Diseases and Microbiology, Westmead Clinical School-Sydney Medical School, Marie Bashir Institute for Infectious Diseases and Biosecurity, University of Sydney, Sydney, NSW, Australia; Westmead Institute for Medical Research, Westmead, NSW, Australia.
| | - Wieland Meyer
- Molecular Mycology Research Laboratory, Centre for Infectious Diseases and Microbiology, Westmead Clinical School-Sydney Medical School, Marie Bashir Institute for Infectious Diseases and Biosecurity, University of Sydney, Sydney, NSW, Australia; Westmead Institute for Medical Research, Westmead, NSW, Australia
| | - John Ellis
- School of Life Sciences, University of Technology Sydney, NSW, Australia
| | - Rogan Lee
- Centre for Infectious Diseases and Microbiology Laboratory Services, Institute of Clinical Pathology & Medical Research, Westmead Hospital, Westmead, NSW, Australia
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49
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Biomonitoring for the 21st Century: Integrating Next-Generation Sequencing Into Ecological Network Analysis. ADV ECOL RES 2018. [DOI: 10.1016/bs.aecr.2017.12.001] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]
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50
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Wallinger C, Staudacher K, Sint D, Thalinger B, Oehm J, Juen A, Traugott M. Evaluation of an automated protocol for efficient and reliable DNA extraction of dietary samples. Ecol Evol 2017; 7:6382-6389. [PMID: 28861241 PMCID: PMC5574753 DOI: 10.1002/ece3.3197] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2017] [Accepted: 05/26/2017] [Indexed: 02/01/2023] Open
Abstract
Molecular techniques have become an important tool to empirically assess feeding interactions. The increased usage of next‐generation sequencing approaches has stressed the need of fast DNA extraction that does not compromise DNA quality. Dietary samples here pose a particular challenge, as these demand high‐quality DNA extraction procedures for obtaining the minute quantities of short‐fragmented food DNA. Automatic high‐throughput procedures significantly decrease time and costs and allow for standardization of extracting total DNA. However, these approaches have not yet been evaluated for dietary samples. We tested the efficiency of an automatic DNA extraction platform and a traditional CTAB protocol, employing a variety of dietary samples including invertebrate whole‐body extracts as well as invertebrate and vertebrate gut content samples and feces. Extraction efficacy was quantified using the proportions of successful PCR amplifications of both total and prey DNA, and cost was estimated in terms of time and material expense. For extraction of total DNA, the automated platform performed better for both invertebrate and vertebrate samples. This was also true for prey detection in vertebrate samples. For the dietary analysis in invertebrates, there is still room for improvement when using the high‐throughput system for optimal DNA yields. Overall, the automated DNA extraction system turned out as a promising alternative to labor‐intensive, low‐throughput manual extraction methods such as CTAB. It is opening up the opportunity for an extensive use of this cost‐efficient and innovative methodology at low contamination risk also in trophic ecology.
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Affiliation(s)
- Corinna Wallinger
- Mountain Agriculture Research Unit Institute of Ecology University of Innsbruck Innsbruck Austria
| | - Karin Staudacher
- Mountain Agriculture Research Unit Institute of Ecology University of Innsbruck Innsbruck Austria
| | - Daniela Sint
- Mountain Agriculture Research Unit Institute of Ecology University of Innsbruck Innsbruck Austria
| | - Bettina Thalinger
- Mountain Agriculture Research Unit Institute of Ecology University of Innsbruck Innsbruck Austria
| | - Johannes Oehm
- Mountain Agriculture Research Unit Institute of Ecology University of Innsbruck Innsbruck Austria
| | - Anita Juen
- Mountain Agriculture Research Unit Institute of Ecology University of Innsbruck Innsbruck Austria
| | - Michael Traugott
- Mountain Agriculture Research Unit Institute of Ecology University of Innsbruck Innsbruck Austria
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