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Du S, Feng J, Bi L, Hu HW, Hao X, Huang Q, Liu YR. Tracking soil resistance and virulence genes in rice-crayfish co-culture systems across China. ENVIRONMENT INTERNATIONAL 2023; 172:107789. [PMID: 36736026 DOI: 10.1016/j.envint.2023.107789] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Revised: 01/03/2023] [Accepted: 01/26/2023] [Indexed: 06/18/2023]
Abstract
Rice-crayfish co-culture (RC) has been widely and rapidly promoted as a sustainable agricultural system in many countries. The accumulation of crayfish residues could enhance soil organic matters; however, impacts of this integrated farming model on the dissemination and pathogenicity of resistance and virulence genes remain poorly understood. Here, we characterized antibiotic resistance genes (ARGs), biocide resistance genes (BRGs), metal resistance genes (MRGs) and virulence factor genes (VFGs) using metagenomic methods in paired RC and rice monoculture (RM) systems across China. The RC model did not increase the abundance of soil ARGs, BRGs, MRGs, or VFGs in comparison to the RM model, but selectively enriched 35 subtypes of these potential resistance and virulence genes. Network analysis revealed that resistance and virulence genes had a higher number of connections with mobile genetic elements (MGEs) in the RC system than that in the RM system, suggesting a higher horizontal transfer potential of these genes. Moreover, the RC model had a higher abundance of human opportunistic pathogens such as Salmonella enterica, Vibrio cholerae, and Shigella dysenteriae which were potential hosts of VFGs such as phoP, fleS, and gspE, suggesting a potential threat to human health. We further unraveled that stochastic process was the main driver of the assembly of resistance and virulence genes in the RC system. The abundance of ARGs and VFGs were primarily associated with microbial community compositions, while the abundance of BRGs and MRGs were mainly associated with that of MGEs. Taken together, our results suggest that the RC model has potential to cause the dissemination and pathogenicity of resistance and virulence genes, which has important implications for the control of soil-borne biological risks and the strategic management of sustainable agriculture.
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Affiliation(s)
- Shuai Du
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China; College of Resources and Environment, Huazhong Agricultural University, Wuhan 430070, China
| | - Jiao Feng
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China; College of Resources and Environment, Huazhong Agricultural University, Wuhan 430070, China
| | - Li Bi
- School of Agriculture and Food, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Hang-Wei Hu
- School of Agriculture and Food, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Xiuli Hao
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China; College of Resources and Environment, Huazhong Agricultural University, Wuhan 430070, China
| | - Qiaoyun Huang
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China; College of Resources and Environment, Huazhong Agricultural University, Wuhan 430070, China
| | - Yu-Rong Liu
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China; College of Resources and Environment, Huazhong Agricultural University, Wuhan 430070, China.
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Jin J, Duan L, Fu J, Chai F, Zhou Q, Wang Y, Shao X, Wang L, Yan M, Su X, Zhang Y, Pan J, Chen J. A real-time LAMP-based dual-sample microfluidic chip for rapid and simultaneous detection of multiple waterborne pathogenic bacteria from coastal waters. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2021; 13:2710-2721. [PMID: 34041513 DOI: 10.1039/d1ay00492a] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Waterborne pathogens are becoming a serious worldwide health hazard; thus, the regular monitoring of epidemic pathogens is urgently required for public safety. In the present study, we developed a microfluidic chip integrated loop-mediated isothermal amplification technique (on-chip LAMP) to simultaneously detect 10 waterborne pathogenic bacteria, Campylobacter jejuni, Listeria monocytogenes, Salmonella enterica, Shigella flexneri, Staphylococcus aureus, Vibrio alginolyticus, V. cholerae, V. parahemolyticus, V. vulnificus, and Yersinia enterocolitica. This method was capable of simultaneously completing 22 genetic analyses of two specimens and achieved limits of detection ranging from 7.92 × 10-3 to 9.54 × 10-1 pg of genomic DNA of pure bacteria per reaction. The processes from sample loading to microfluidic operation were in a highly automated format, and the LAMP reaction ran to completion within 35 minutes, with a minimal volume of 22 μl per each half of a single chip. The coefficient of variation for the time-to-positive value was less than 0.1, indicating an excellent reproducibility of the dual-sample on-chip LAMP assay. The clinical sensitivity and specificity in analyses of coastal water samples were 93.1% and 98.0%, respectively, in comparison with traditional microbiological methods. Our established dual-sample on-chip LAMP assay provides an effective multiple-pathogen analysis of waterborne bacterial pathogens. This indicates that the method is applicable for on-site detection and routine monitoring of waterborne bacteria in aquatic environments.
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Affiliation(s)
- Jinglei Jin
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo University, Ningbo, 315211, China and School of Marine Sciences, Ningbo University, Ningbo 315832, China.
| | - Lijun Duan
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo University, Ningbo, 315211, China and School of Marine Sciences, Ningbo University, Ningbo 315832, China. and Ningbo Haishu District Animal Husbandry and Veterinary Medicine Technical Management Service Station, Ningbo 315153, China
| | - Jiali Fu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo University, Ningbo, 315211, China and School of Marine Sciences, Ningbo University, Ningbo 315832, China.
| | - Fangchao Chai
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo University, Ningbo, 315211, China and School of Marine Sciences, Ningbo University, Ningbo 315832, China.
| | - Qianjin Zhou
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo University, Ningbo, 315211, China and School of Marine Sciences, Ningbo University, Ningbo 315832, China.
| | - Yaohua Wang
- Zhejiang Key Laboratory of Exploitation and Preservation of Coastal Bio-resource, Zhejiang Mariculture Research Institute, Wenzhou 325005, China
| | - Xinbin Shao
- Zhejiang Key Laboratory of Exploitation and Preservation of Coastal Bio-resource, Zhejiang Mariculture Research Institute, Wenzhou 325005, China
| | - Lei Wang
- CapitalBio Corporation, 18 Life Science Parkway, Changping District, Beijing 102206, China
| | - Maocang Yan
- Zhejiang Key Laboratory of Exploitation and Preservation of Coastal Bio-resource, Zhejiang Mariculture Research Institute, Wenzhou 325005, China
| | - Xiurong Su
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo University, Ningbo, 315211, China and School of Marine Sciences, Ningbo University, Ningbo 315832, China.
| | - Yanjun Zhang
- Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou 310009, China
| | - Junhang Pan
- Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou 310009, China
| | - Jiong Chen
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo University, Ningbo, 315211, China and School of Marine Sciences, Ningbo University, Ningbo 315832, China. and Key Laboratory of Applied Marine Biotechnology of Ministry of Education, Ningbo University, Ningbo 315211, China
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Anas A, Sukumaran V, Nampullipurackal Devarajan D, Maniyath S, Chekidhenkuzhiyil J, Mary A, Parakkaparambil Kuttan S, Tharakan B. Probiotics inspired from natural ecosystem to inhibit the growth of Vibrio spp. causing white gut syndrome in Litopenaeus vannamei. 3 Biotech 2021; 11:66. [PMID: 33489684 PMCID: PMC7803865 DOI: 10.1007/s13205-020-02618-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Accepted: 12/26/2020] [Indexed: 12/19/2022] Open
Abstract
Probiotics inspired by host-microbe interactions in the natural ecosystem are propitious in controlling bacterial infections in aquaculture and veterinary systems. Here we report the isolation and characterization of pathogenic Vibrio spp. and lactic acid bacteria from an intensive culture system of Litopenaeus vannamei and natural ecosystem, respectively. The pathogen isolated from the gut of L. vannamei showing the symptoms of white gut disease were identified as V. parahaemolyticus and V. campbelli. Both the pathogens expressed the virulence genes, rtxA, and tcpA and were showing multiple antibiotic resistance (MAR) index of more than 0.5. The lactic acid bacteria isolated from the sediment and gut of benthic organisms (shrimp and polychaetes) collected from a tropical estuary were classified as member of 9 OTUs such as Pediococcus stilessi, Lactobacillus fermentum, L. rhamnosus, Weissella cibaria, Enterococcus durans, E. fecalis, Streptococcus gallolyticus and L. garvieae. Majority of these isolates were facultative in nature and were able to tolerate gastric juice and bile salt. Out of 83 bacteria isolated from sediment and gut, 36 showed abilities to reduce the pH of culture medium to less than five. Many of these isolates (34 Nos.) showed production of hydrolytic enzymes and secondary metabolites with antagonistic activity against both the pathogens (1 No.) or separately toward V. parahaemolyticus (9 Nos.) and V. campbelli (11 Nos.). Overall, the current study proposes a natural ecosystem as a potential source of lactic acid bacteria with probiotic potentials to prevent the vibriosis disease outbreaks in shrimp aquaculture systems. Further studies are required to understand the abilities of lactic acid bacteria to colonize shrimp intestine, stimulate immune system and manipulate microbiome. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s13205-020-02618-2.
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Affiliation(s)
- Abdulaziz Anas
- CSIR-National Institute of Oceanography, Regional Centre Cochin, Kochi, India
| | - Vrinda Sukumaran
- CSIR-National Institute of Oceanography, Regional Centre Cochin, Kochi, India
| | | | - Shijina Maniyath
- CSIR-National Institute of Oceanography, Regional Centre Cochin, Kochi, India
| | | | - Ann Mary
- CSIR-National Institute of Oceanography, Regional Centre Cochin, Kochi, India
| | | | - Balu Tharakan
- CSIR-National Institute of Oceanography, Regional Centre Cochin, Kochi, India
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Munir A, Waseem H, Williams MR, Stedtfeld RD, Gulari E, Tiedje JM, Hashsham SA. Modeling Hybridization Kinetics of Gene Probes in a DNA Biochip Using FEMLAB. MICROARRAYS 2017; 6:microarrays6020009. [PMID: 28555058 PMCID: PMC5487956 DOI: 10.3390/microarrays6020009] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/15/2017] [Revised: 05/22/2017] [Accepted: 05/26/2017] [Indexed: 11/29/2022]
Abstract
Microfluidic DNA biochips capable of detecting specific DNA sequences are useful in medical diagnostics, drug discovery, food safety monitoring and agriculture. They are used as miniaturized platforms for analysis of nucleic acids-based biomarkers. Binding kinetics between immobilized single stranded DNA on the surface and its complementary strand present in the sample are of interest. To achieve optimal sensitivity with minimum sample size and rapid hybridization, ability to predict the kinetics of hybridization based on the thermodynamic characteristics of the probe is crucial. In this study, a computer aided numerical model for the design and optimization of a flow-through biochip was developed using a finite element technique packaged software tool (FEMLAB; package included in COMSOL Multiphysics) to simulate the transport of DNA through a microfluidic chamber to the reaction surface. The model accounts for fluid flow, convection and diffusion in the channel and on the reaction surface. Concentration, association rate constant, dissociation rate constant, recirculation flow rate, and temperature were key parameters affecting the rate of hybridization. The model predicted the kinetic profile and signal intensities of eighteen 20-mer probes targeting vancomycin resistance genes (VRGs). Predicted signal intensities and hybridization kinetics strongly correlated with experimental data in the biochip (R2 = 0.8131).
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Affiliation(s)
- Ahsan Munir
- Department of Civil and Environmental Engineering, Michigan State University, East Lansing, MI 48823,USA.
| | - Hassan Waseem
- Department of Civil and Environmental Engineering, Michigan State University, East Lansing, MI 48823,USA.
| | - Maggie R Williams
- Department of Civil and Environmental Engineering, Michigan State University, East Lansing, MI 48823,USA.
| | - Robert D Stedtfeld
- Department of Civil and Environmental Engineering, Michigan State University, East Lansing, MI 48823,USA.
| | - Erdogan Gulari
- Department of Chemical Engineering, University of Michigan, Ann Arbor, MI 48109, USA.
| | - James M Tiedje
- Center for Microbial Ecology, Michigan State University, East Lansing, MI 48823, USA.
- Department of Plant, Soil, and Microbial Sciences, Michigan State University, East Lansing, MI 48823, USA.
| | - Syed A Hashsham
- Department of Civil and Environmental Engineering, Michigan State University, East Lansing, MI 48823,USA.
- Center for Microbial Ecology, Michigan State University, East Lansing, MI 48823, USA.
- Department of Plant, Soil, and Microbial Sciences, Michigan State University, East Lansing, MI 48823, USA.
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5
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Srinivasan V, Stedtfeld RD, Tourlousse DM, Baushke SW, Xin Y, Miller SM, Pham T, Rouillard JM, Gulari E, Tiedje JM, Hashsham SA. Diagnostic microarray for 14 water and foodborne pathogens using a flatbed scanner. J Microbiol Methods 2017; 139:15-21. [PMID: 28438642 DOI: 10.1016/j.mimet.2017.04.009] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2017] [Revised: 04/20/2017] [Accepted: 04/20/2017] [Indexed: 02/06/2023]
Abstract
Parallel detection approaches are of interest to many researchers interested in identifying multiple water and foodborne pathogens simultaneously. Availability and cost-effectiveness are two key factors determining the usefulness of such approaches for laboratories with limited resources. In this study, we developed and validated a high-density microarray for simultaneous screening of 14 bacterial pathogens using an approach that employs gold labeling with silver enhancement (GLS) protocol. In total, 8887 probes (50-mer) were designed using an in-house database of virulence and marker genes (VMGs), and synthesized in quadruplicate on glass slides using an in-situ synthesis technology. Target VMG amplicons were obtained using multiplex polymerase chain reaction (PCR), labeled with biotin, and hybridized to the microarray. The signals generated after gold deposition and silver enhancement, were quantified using a flatbed scanner having 2-μm resolution. Data analysis indicated that reliable presence/absence calls could be made, if: i) over four probes were used per gene, ii) the signal-to-noise ratio (SNR) cutoff was greater than or equal to two, and iii) the positive fraction (PF), i.e., number of probes with SNR≥2 for a given VMG was greater than 0.75. Hybridization of the array with blind samples resulted in 100% correct calls, and no false positive. Because amplicons were obtained by multiplex PCR, sensitivity of this method is similar to PCR. This assay is an inexpensive and reliable technique for high throughput screening of multiple pathogens.
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Affiliation(s)
- Vidya Srinivasan
- Department of Civil and Environmental Engineering, Michigan State University, East Lansing, MI 48824, United States
| | - Robert D Stedtfeld
- Department of Civil and Environmental Engineering, Michigan State University, East Lansing, MI 48824, United States
| | - Dieter M Tourlousse
- Department of Civil and Environmental Engineering, Michigan State University, East Lansing, MI 48824, United States
| | - Samuel W Baushke
- Department of Civil and Environmental Engineering, Michigan State University, East Lansing, MI 48824, United States
| | - Yu Xin
- Department of Environmental Engineering, Nanjing University, China
| | - Sarah M Miller
- Department of Civil and Environmental Engineering, Michigan State University, East Lansing, MI 48824, United States
| | - Trinh Pham
- Department of Chemical Engineering, University of Michigan, Ann Arbor, MI 48109, United States
| | - Jean-Marie Rouillard
- Department of Chemical Engineering, University of Michigan, Ann Arbor, MI 48109, United States
| | - Erdogan Gulari
- Department of Chemical Engineering, University of Michigan, Ann Arbor, MI 48109, United States
| | - James M Tiedje
- Department of Civil and Environmental Engineering, Michigan State University, East Lansing, MI 48824, United States
| | - Syed A Hashsham
- Department of Civil and Environmental Engineering, Michigan State University, East Lansing, MI 48824, United States.
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6
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The Composition and Spatial Patterns of Bacterial Virulence Factors and Antibiotic Resistance Genes in 19 Wastewater Treatment Plants. PLoS One 2016; 11:e0167422. [PMID: 27907117 PMCID: PMC5132249 DOI: 10.1371/journal.pone.0167422] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2016] [Accepted: 11/14/2016] [Indexed: 11/19/2022] Open
Abstract
Bacterial pathogenicity and antibiotic resistance are of concern for environmental safety and public health. Accumulating evidence suggests that wastewater treatment plants (WWTPs) are as an important sink and source of pathogens and antibiotic resistance genes (ARGs). Virulence genes (encoding virulence factors) are good indicators for bacterial pathogenic potentials. To achieve a comprehensive understanding of bacterial pathogenic potentials and antibiotic resistance in WWTPs, bacterial virulence genes and ARGs in 19 WWTPs covering a majority of latitudinal zones of China were surveyed by using GeoChip 4.2. A total of 1610 genes covering 13 virulence factors and 1903 genes belonging to 11 ARG families were detected respectively. The bacterial virulence genes exhibited significant spatial distribution patterns of a latitudinal biodiversity gradient and a distance-decay relationship across China. Moreover, virulence genes tended to coexist with ARGs as shown by their strongly positive associations. In addition, key environmental factors shaping the overall virulence gene structure were identified. This study profiles the occurrence, composition and distribution of virulence genes and ARGs in current WWTPs in China, and uncovers spatial patterns and important environmental variables shaping their structure, which may provide the basis for further studies of bacterial virulence factors and antibiotic resistance in WWTPs.
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Liao DS, Raveendran J, Golchi S, Docoslis A. Fast and sensitive detection of bacteria from a water droplet by means of electric field effects and micro-Raman spectroscopy. SENSING AND BIO-SENSING RESEARCH 2015. [DOI: 10.1016/j.sbsr.2015.09.005] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
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Gomes M, Vieira H, Vale FF. Characterization, validation and application of a DNA microarray for the detection of mandatory and other waterborne pathogens. J Biochem 2015; 158:393-401. [PMID: 25998249 DOI: 10.1093/jb/mvv052] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2015] [Accepted: 04/13/2015] [Indexed: 11/15/2022] Open
Abstract
Culture methods for the detection of indicator bacteria are currently used for detection of waterborne bacteria. The need for an increased range of analyzed bacteria coupled with the obtainment of rapid and early results justify the development of a DNA microarray for the identification of waterborne pathogens. This DNA microarray has 16 implanted probes with a median size of 147 bases, targeting 12 different parameters, including all mandatory indicator microorganisms, such as Escherichia coli, Clostridium perfringens, Pseudomonas aeruginosa, Staphylococcus aureus, total and fecal coliforms and enterococci. The validation performed with DNA extracted from pure microbial cultures showed the suitability of the probes for detection of the target microorganism. To overcome the high dilution of water samples it was included either a prior culture step of bacterial contaminants retained after filtering 100 ml of water, or a 10-fold increase in the volume of filtered water, that resulted in the increase of the detected bacteria. The analysis of complex environmental water samples using culture methods and the DNA microarray revealed that the latter detected the same parameters plus other bacteria tested only in the DNA microarray. The results show that this DNA microarray may be a useful tool for water microbiological surveillance.
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Affiliation(s)
- Maria Gomes
- Faculdade de Engenharia, Universidade Católica Portuguesa, 2635-631 Rio de Mouro, Portugal
| | - Helena Vieira
- University of Lisboa, Faculty of Sciences, BioISI-Biosystems & Integrative Sciences Institute, Campo Grande, 1749-106 Lisboa, Portugal
| | - Filipa F Vale
- Host-Pathogen Interactions Unit, Research Institute for Medicines (iMed-ULisboa), Instituto de Medicina Molecular, Faculdade de Farmácia da Universidade de Lisboa, Lisboa, Portugal
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9
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Egan SP, Grey E, Olds B, Feder JL, Ruggiero ST, Tanner CE, Lodge DM. Rapid molecular detection of invasive species in ballast and harbor water by integrating environmental DNA and light transmission spectroscopy. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2015; 49:4113-4121. [PMID: 25686279 DOI: 10.1021/es5058659] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Invasive species introduced via the ballast water of commercial ships cause enormous environmental and economic damage worldwide. Accurate monitoring for these often microscopic and morphologically indistinguishable species is challenging but critical for mitigating damages. We apply eDNA sampling, which involves the filtering and subsequent DNA extraction of microscopic bits of tissue suspended in water, to ballast and harbor water sampled during a commercial ship's 1400 km voyage through the North American Great Lakes. Using a lab-based gel electrophoresis assay and a rapid, field-ready light transmission spectroscopy (LTS) assay, we test for the presence of two invasive species: quagga (Dreissena bugensis) and zebra (D. polymorpha) mussels. Furthermore, we spiked a set of uninfested ballast and harbor samples with zebra mussel tissue to further test each assay's detection capabilities. In unmanipulated samples, zebra mussel was not detected, while quagga mussel was detected in all samples at a rate of 85% for the gel assay and 100% for the LTS assay. In the spiked experimental samples, both assays detected zebra mussel in 94% of spiked samples and 0% of negative controls. Overall, these results demonstrate that eDNA sampling is effective for monitoring ballast-mediated invasions and that LTS has the potential for rapid, field-based detection.
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Affiliation(s)
- Scott P Egan
- †Department of BioSciences, Rice University, Houston, Texas 77005, United States
- ‡Department of Biological Sciences, University of Notre Dame, Notre Dame, Indiana 46556, United States
- §Environmental Change Initiative, University of Notre Dame, Notre Dame, Indiana 46556, United States
| | - Erin Grey
- §Environmental Change Initiative, University of Notre Dame, Notre Dame, Indiana 46556, United States
- ∥College of Science, Governors State University, University Park, Illinois 60484, United States
| | - Brett Olds
- §Environmental Change Initiative, University of Notre Dame, Notre Dame, Indiana 46556, United States
| | - Jeffery L Feder
- ‡Department of Biological Sciences, University of Notre Dame, Notre Dame, Indiana 46556, United States
- §Environmental Change Initiative, University of Notre Dame, Notre Dame, Indiana 46556, United States
| | - Steven T Ruggiero
- §Environmental Change Initiative, University of Notre Dame, Notre Dame, Indiana 46556, United States
- ⊥Department of Physics, University of Notre Dame, Notre Dame, Indiana 46556, United States
| | - Carol E Tanner
- §Environmental Change Initiative, University of Notre Dame, Notre Dame, Indiana 46556, United States
- ⊥Department of Physics, University of Notre Dame, Notre Dame, Indiana 46556, United States
| | - David M Lodge
- ‡Department of Biological Sciences, University of Notre Dame, Notre Dame, Indiana 46556, United States
- §Environmental Change Initiative, University of Notre Dame, Notre Dame, Indiana 46556, United States
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10
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High-throughput metagenomic technologies for complex microbial community analysis: open and closed formats. mBio 2015; 6:mBio.02288-14. [PMID: 25626903 PMCID: PMC4324309 DOI: 10.1128/mbio.02288-14] [Citation(s) in RCA: 225] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Understanding the structure, functions, activities and dynamics of microbial communities in natural environments is one of the grand challenges of 21st century science. To address this challenge, over the past decade, numerous technologies have been developed for interrogating microbial communities, of which some are amenable to exploratory work (e.g., high-throughput sequencing and phenotypic screening) and others depend on reference genes or genomes (e.g., phylogenetic and functional gene arrays). Here, we provide a critical review and synthesis of the most commonly applied “open-format” and “closed-format” detection technologies. We discuss their characteristics, advantages, and disadvantages within the context of environmental applications and focus on analysis of complex microbial systems, such as those in soils, in which diversity is high and reference genomes are few. In addition, we discuss crucial issues and considerations associated with applying complementary high-throughput molecular technologies to address important ecological questions.
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11
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Catarino SO, Miranda JM, Lanceros-Mendez S, Minas G. Numerical prediction of acoustic streaming in a microcuvette. CAN J CHEM ENG 2014. [DOI: 10.1002/cjce.22057] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Susana O. Catarino
- Centro Algoritmi; University of Minho; Campus de Azurém; 4800-058 Guimarães Portugal
| | - Joao M. Miranda
- CEFT; Department of Chemical Engineering; FEUP; University of Porto; Portugal
| | | | - Graca Minas
- Centro Algoritmi; University of Minho; Campus de Azurém; 4800-058 Guimarães Portugal
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12
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Lee YJ, van Nostrand JD, Tu Q, Lu Z, Cheng L, Yuan T, Deng Y, Carter MQ, He Z, Wu L, Yang F, Xu J, Zhou J. The PathoChip, a functional gene array for assessing pathogenic properties of diverse microbial communities. ISME JOURNAL 2013; 7:1974-84. [PMID: 23765101 DOI: 10.1038/ismej.2013.88] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2013] [Revised: 04/10/2013] [Accepted: 04/20/2013] [Indexed: 12/21/2022]
Abstract
Pathogens present in the environment pose a serious threat to human, plant and animal health as evidenced by recent outbreaks. As many pathogens can survive and proliferate in the environment, it is important to understand their population dynamics and pathogenic potential in the environment. To assess pathogenic potential in diverse habitats, we developed a functional gene array, the PathoChip, constructed with key virulence genes related to major virulence factors, such as adherence, colonization, motility, invasion, toxin, immune evasion and iron uptake. A total of 3715 best probes were selected from 13 virulence factors, covering 7417 coding sequences from 1397 microbial species (2336 strains). The specificity of the PathoChip was computationally verified, and approximately 98% of the probes provided specificity at or below the species level, proving its excellent capability for the detection of target sequences with high discrimination power. We applied this array to community samples from soil, seawater and human saliva to assess the occurrence of virulence genes in natural environments. Both the abundance and diversity of virulence genes increased in stressed conditions compared with their corresponding controls, indicating a possible increase in abundance of pathogenic bacteria under environmental perturbations such as warming or oil spills. Statistical analyses showed that microbial communities harboring virulence genes were responsive to environmental perturbations, which drove changes in abundance and distribution of virulence genes. The PathoChip provides a useful tool to identify virulence genes in microbial populations, examine the dynamics of virulence genes in response to environmental perturbations and determine the pathogenic potential of microbial communities.
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Affiliation(s)
- Yong-Jin Lee
- Institute for Environmental Genomics and Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, USA
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13
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Nostrand JDV, He Z, Zhou J. Use of functional gene arrays for elucidating in situ biodegradation. Front Microbiol 2012; 3:339. [PMID: 23049526 PMCID: PMC3448134 DOI: 10.3389/fmicb.2012.00339] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2012] [Accepted: 09/03/2012] [Indexed: 12/18/2022] Open
Abstract
Microarrays have revolutionized the study of microbiology by providing a high-throughput method for examining thousands of genes with a single test and overcome the limitations of many culture-independent approaches. Functional gene arrays (FGA) probe a wide range of genes involved in a variety of functions of interest to microbial ecology (e.g., carbon degradation, N fixation, metal resistance) from many different microorganisms, cultured and uncultured. The most comprehensive FGA to date is the GeoChip array, which targets tens of thousands of genes involved in the geochemical cycling of carbon, nitrogen, phosphorus, and sulfur, metal resistance and reduction, energy processing, antibiotic resistance and contaminant degradation as well as phylogenetic information (gyrB). Since the development of GeoChips, many studies have been performed using this FGA and have shown it to be a powerful tool for rapid, sensitive, and specific examination of microbial communities in a high-throughput manner. As such, the GeoChip is well-suited for linking geochemical processes with microbial community function and structure. This technology has been used successfully to examine microbial communities before, during, and after in situ bioremediation at a variety of contaminated sites. These studies have expanded our understanding of biodegradation and bioremediation processes and the associated microorganisms and environmental conditions responsible. This review provides an overview of FGA development with a focus on the GeoChip and highlights specific GeoChip studies involving in situ bioremediation.
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Affiliation(s)
- Joy D Van Nostrand
- Institute for Environmental Genomics, University of Oklahoma Norman, OK, USA ; Department of Microbiology and Plant Biology, University of Oklahoma Norman, OK, USA
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CHEN SZ, CAI Q, PENG FY, HUANG XX, JIA YL. Screen-Printed Electrochemical Biosensor for Detection of DNA Hybridization. CHINESE JOURNAL OF ANALYTICAL CHEMISTRY 2012. [DOI: 10.1016/s1872-2040(11)60565-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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15
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A polymer microfluidic chip for quantitative detection of multiple water- and foodborne pathogens using real-time fluorogenic loop-mediated isothermal amplification. Biomed Microdevices 2012; 14:769-78. [DOI: 10.1007/s10544-012-9658-3] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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16
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Identification of non-specific hybridization using an empirical equation fitted to non-equilibrium dissociation curves. J Microbiol Methods 2012; 90:29-35. [PMID: 22537822 DOI: 10.1016/j.mimet.2012.04.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2011] [Revised: 04/04/2012] [Accepted: 04/06/2012] [Indexed: 11/22/2022]
Abstract
Non-equilibrium dissociation curves (NEDCs) have the potential to identify non-specific hybridizations on high throughput, diagnostic microarrays. We report a simple method for the identification of non-specific signals by using a new parameter that does not rely on comparison of perfect match and mismatch dissociations. The parameter is the ratio of specific dissociation temperature (T(d-w)) to theoretical melting temperature (T(m)) and can be obtained by automated fitting of a four-parameter, sigmoid, empirical equation to the thousands of curves generated in a typical experiment. The curves fit perfect match NEDCs from an initial experiment with an R(2) of 0.998±0.006 and root mean square of 108±91 fluorescent units. Receiver operating characteristic curve analysis showed low temperature hybridization signals (20-48°C) to be as effective as area under the curve as primary data filters. Evaluation of three datasets that target 16S rRNA and functional genes with varying degrees of target sequence similarity showed that filtering out hybridizations with T(d-w)/T(m)<0.78 greatly reduced false positive results. In conclusion, T(d-w)/T(m) successfully screened many non-specific hybridizations that could not be identified using single temperature signal intensities alone, while the empirical modeling allowed a simplified approach to the high throughput analysis of thousands of NEDCs.
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He Z, Van Nostrand JD, Zhou J. Applications of functional gene microarrays for profiling microbial communities. Curr Opin Biotechnol 2012; 23:460-6. [PMID: 22226464 DOI: 10.1016/j.copbio.2011.12.021] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2011] [Revised: 11/23/2011] [Accepted: 12/19/2011] [Indexed: 10/14/2022]
Abstract
Functional gene arrays (FGAs) have been considered as a specific, sensitive, quantitative, and high throughput metagenomic tool to detect, monitor and characterize microbial communities. Especially GeoChips, the most comprehensive FGAs have been applied to analyze the functional diversity, composition, structure, and metabolic potential or activity of a variety of microbial communities from different habitats, such as aquatic ecosystems, soils, contaminated sites, extreme environments, and bioreactors. FGAs are able to address fundamental questions related to global change, bioremediation, land use, human health, and ecological theories, and link the microbial community structure to environmental properties and ecosystem functioning. This review focuses on applications of FGA technology for profiling microbial communities, including target preparation, hybridization and data processing, and data analysis. We also discuss challenges and future directions of FGA applications.
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Affiliation(s)
- Zhili He
- Institute for Environmental Genomics, Department of Botany and Microbiology, University of Oklahoma, Norman, OK 73019, USA
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18
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He Z, Deng Y, Zhou J. Development of functional gene microarrays for microbial community analysis. Curr Opin Biotechnol 2011; 23:49-55. [PMID: 22100036 DOI: 10.1016/j.copbio.2011.11.001] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2011] [Revised: 10/31/2011] [Accepted: 11/01/2011] [Indexed: 01/21/2023]
Abstract
Functional gene arrays (FGAs) are a special type of microarrays containing probes for key genes involved in microbial functional processes, such as biogeochemical cycling of carbon, nitrogen, sulfur, phosphorus and metals, virulence and antibiotic resistance, biodegradation of environmental contaminants, and stress responses. FGAs have been demonstrated to be a specific, sensitive, and quantitative tool for rapid analysis of microbial communities from different habitats, such as waters, soils, extreme environments, bioreactors, and human microbiomes. In this review, we first summarize currently reported FGAs, and then focus on the FGA development. We will also discuss several key issues of FGA technology as well as challenges and directions in future FGA development.
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Affiliation(s)
- Zhili He
- Institute for Environmental Genomics, Department of Botany and Microbiology, University of Oklahoma, Norman, OK 73019, USA.
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Kostić T, Sessitsch A. Microbial Diagnostic Microarrays for the Detection and Typing of Food- and Water-Borne (Bacterial) Pathogens. ACTA ACUST UNITED AC 2011; 1:3-24. [PMID: 27605332 PMCID: PMC5007712 DOI: 10.3390/microarrays1010003] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2011] [Revised: 10/05/2011] [Accepted: 10/07/2011] [Indexed: 01/02/2023]
Abstract
Reliable and sensitive pathogen detection in clinical and environmental (including food and water) samples is of greatest importance for public health. Standard microbiological methods have several limitations and improved alternatives are needed. Most important requirements for reliable analysis include: (i) specificity; (ii) sensitivity; (iii) multiplexing potential; (iv) robustness; (v) speed; (vi) automation potential; and (vii) low cost. Microarray technology can, through its very nature, fulfill many of these requirements directly and the remaining challenges have been tackled. In this review, we attempt to compare performance characteristics of the microbial diagnostic microarrays developed for the detection and typing of food and water pathogens, and discuss limitations, points still to be addressed and issues specific for the analysis of food, water and environmental samples.
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Affiliation(s)
- Tanja Kostić
- AIT Austrian Institute of Technology GmbH, Health & Environment Department, Bioresources Unit, Konrad Lorenz Strasse 24, A-3430 Tulln an der Donau, Austria.
- Christian Doppler Laboratory for Molecular Food Analytics, University of Veterinary Medicine, Veterinärplatz 1, A-1210 Vienna, Austria.
| | - Angela Sessitsch
- AIT Austrian Institute of Technology GmbH, Health & Environment Department, Bioresources Unit, Konrad Lorenz Strasse 24, A-3430 Tulln an der Donau, Austria
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Marshall IPG, Berggren DRV, Azizian MF, Burow LC, Semprini L, Spormann AM. The Hydrogenase Chip: a tiling oligonucleotide DNA microarray technique for characterizing hydrogen-producing and -consuming microbes in microbial communities. ISME JOURNAL 2011; 6:814-26. [PMID: 21993396 DOI: 10.1038/ismej.2011.136] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
We developed a broad-ranging method for identifying key hydrogen-producing and consuming microorganisms through analysis of hydrogenase gene content and expression in complex anaerobic microbial communities. The method is based on a tiling hydrogenase gene oligonucleotide DNA microarray (Hydrogenase Chip), which implements a high number of probes per gene by tiling probe sequences across genes of interest at 1.67 × -2 × coverage. This design favors the avoidance of false positive gene identification in samples of DNA or RNA extracted from complex microbial communities. We applied this technique to interrogate interspecies hydrogen transfer in complex communities in (i) lab-scale reductive dehalogenating microcosms enabling us to delineate key H(2)-consuming microorganisms, and (ii) hydrogen-generating microbial mats where we found evidence for significant H(2) production by cyanobacteria. Independent quantitative PCR analysis on selected hydrogenase genes showed that this Hydrogenase Chip technique is semiquantitative. We also determined that as microbial community complexity increases, specificity must be traded for sensitivity in analyzing data from tiling DNA microarrays.
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Affiliation(s)
- Ian P G Marshall
- Department of Civil and Environmental Engineering, Stanford University, Stanford, CA 94305, USA
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Tebbs RS, Brzoska PM, Furtado MR, Petrauskene OV. Design and validation of a novel multiplex real-time PCR assay for Vibrio pathogen detection. J Food Prot 2011; 74:939-48. [PMID: 21669071 DOI: 10.4315/0362-028x.jfp-10-511] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Three species--Vibrio cholerae, Vibrio parahaemolyticus, and Vibrio vulnificus--account for the majority of vibrio infections in humans. Rapid and accurate identification of Vibrio species has been problematic because phenotypic characteristics are variable within species. Additionally, biochemical identification and confirmation require 2 or more days to complete. Rapid and sensitive molecular techniques for the detection of vibrio pathogens would be useful for the surveillance and management of outbreaks. To facilitate the identification of human-pathogenic species, we designed and validated a highly sensitive, specific, and robust multiplex real-time PCR assay to identify V. cholerae, V. parahaemolyticus, and V. vulnificus using a four-dye configuration in a convenient lyophilized format. Multiple Vibrio strains were sequenced to verify candidate target TaqMan sites. Several individual assays within the multiplex contain multiple primers or probes to ensure detection of polymorphic variants. V. cholerae, V. parahaemolyticus, and V. vulnificus were detected either individually or in mixtures at ≤30 genomic copies. V. cholerae was specifically detected in the presence or absence of Vibrio mimicus. The Vibrio multiplex assay showed 100% specificity to all targets analyzed and no detection of nearest neighbor strains. Each assay exhibited 100% ± 10% efficiency. Multiplex real-time PCR can simplify pathogen detection and reduce costs per test since three species can be analyzed in a single reaction tube. Rapid and accurate detection of pathogenic vibrios in shellfish or seawater samples will improve the microbiological safety of seafood for consumers.
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Affiliation(s)
- Robert S Tebbs
- Life Technologies Corporation, Foster City, California 94404, USA
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Yu CP, Chu KH. Molecular quantification of virulence gene-containing Aeromonas in water samples collected from different drinking water treatment processes. ENVIRONMENTAL MONITORING AND ASSESSMENT 2011; 176:225-238. [PMID: 20632090 DOI: 10.1007/s10661-010-1578-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2009] [Accepted: 06/15/2010] [Indexed: 05/29/2023]
Abstract
Pathogenic species of Aeromonas produce a range of virulence factors, including aerolysin, cytotonic enterotoxins, and serine protease, to cause acute gastroenteritis and wound infections in humans and animals. Recognizing that not all Aeromonas strains are pathogenic, in this study, we proposed to evaluate Aeromonas removal effectiveness based on the presence of virulence gene-containing Aeromonas as a proper means to assess microbial risk of Aeromonas. We developed and applied real-time PCR assays to quantify serine protease (ser) gene- and heat-labile cytotonic enterotoxin (alt) gene-containing Aeromonas in water samples. Among 18 Aeromonas isolates from the source water, only three isolates possessed all three genes (aer, ser, and alt). A higher percent of isolates has either ser gene (89%) or alt gene (72%) compared to the percent of isolates containing aer gene (44%). Results of this study suggested that several different conventional and unconventional drinking water treatment processes could effectively remove Aeromonas from source water. As the comprehensive knowledge of the distribution of virulence factors in different Aeromonas species is currently not available, using real-time PCR to quantify various virulence factor genes in water samples and/or isolates can be a practical means for better assessment of microbial risks in water.
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Affiliation(s)
- Chang-Ping Yu
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, 361021, China
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He Z, Van Nostrand JD, Deng Y, Zhou J. Development and applications of functional gene microarrays in the analysis of the functional diversity, composition, and structure of microbial communities. ACTA ACUST UNITED AC 2011. [DOI: 10.1007/s11783-011-0301-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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24
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Cupples AM, Xagoraraki I, Rose JB. New Molecular Methods for Detection of Waterborne Pathogens. Environ Microbiol 2010. [DOI: 10.1002/9780470495117.ch3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/06/2023]
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Robust detection and identification of multiple oomycetes and fungi in environmental samples by using a novel cleavable padlock probe-based ligation detection assay. Appl Environ Microbiol 2009; 75:4185-93. [PMID: 19395562 DOI: 10.1128/aem.00071-09] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Simultaneous detection and identification of multiple pathogenic microorganisms in complex environmental samples are required in numerous diagnostic fields. Here, we describe the development of a novel, background-free ligation detection (LD) system using a single compound detector probe per target. The detector probes used, referred to as padlock probes (PLPs), are long oligonucleotides containing asymmetric target complementary regions at both their 5' and 3' ends which confer extremely specific target detection. Probes also incorporate a desthiobiotin moiety and an internal endonuclease IV cleavage site. DNA samples are PCR amplified, and the resulting products serve as potential targets for PLP ligation. Upon perfect target hybridization, the PLPs are circularized via enzymatic ligation, captured, and cleaved, allowing only the originally ligated PLPs to be visualized on a universal microarray. Unlike previous procedures, the probes themselves are not amplified, thereby allowing a simple PLP cleavage to yield a background-free assay. We designed and tested nine PLPs targeting several oomycetes and fungi. All of the probes specifically detected their corresponding targets and provided perfect discrimination against closely related nontarget organisms, yielding an assay sensitivity of 1 pg genomic DNA and a dynamic detection range of 10(4). A practical demonstration with samples collected from horticultural water circulation systems was performed to test the robustness of the newly developed multiplex assay. This novel LD system enables highly specific detection and identification of multiple pathogens over a wide range of target concentrations and should be easily adaptable to a variety of applications in environmental microbiology.
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Henry O, Acero Sanchez J, Latta D, O'Sullivan C. Electrochemical quantification of DNA amplicons via the detection of non-hybridised guanine bases on low-density electrode arrays. Biosens Bioelectron 2009; 24:2064-70. [DOI: 10.1016/j.bios.2008.10.021] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2008] [Revised: 10/08/2008] [Accepted: 10/23/2008] [Indexed: 10/21/2022]
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Brettar I, Höfle MG. Molecular assessment of bacterial pathogens—a contribution to drinking water safety. Curr Opin Biotechnol 2008; 19:274-80. [DOI: 10.1016/j.copbio.2008.04.004] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2008] [Revised: 04/16/2008] [Accepted: 04/21/2008] [Indexed: 10/22/2022]
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Pozhitkov AE, Nies G, Kleinhenz B, Tautz D, Noble PA. Simultaneous quantification of multiple nucleic acid targets in complex rRNA mixtures using high density microarrays and nonspecific hybridization as a source of information. J Microbiol Methods 2008; 75:92-102. [PMID: 18579240 DOI: 10.1016/j.mimet.2008.05.013] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2008] [Revised: 05/01/2008] [Accepted: 05/07/2008] [Indexed: 11/26/2022]
Abstract
To date, it has been problematic to accurately quantify multiple nucleic acid sequences, representing microbial targets, in multi-target mixtures using oligonucleotide microarrays, primarily due to nonspecific target binding (i.e., cross-hybridization). While some studies ignore the effects of nonspecific binding, other studies have developed approaches to minimize nonspecific binding, such as physical modeling to design highly specific probes, subtracting nonspecific signal using mismatch probes, and/or removing nonspecific duplexes by scanning through a range of wash stringencies. We have developed an alternative approach that, in contrast to previous approaches, uses nonspecific target binding as a source of information. Specifically, the new approach uses hybridization patterns (fingerprints) to quantify specific nucleic acid targets in complex target mixtures. We evaluated the approach by mixing together in vitro transcribed 28S rRNA targets at varying concentrations (up to 1.0 nM), and hybridizing the 24 mixtures to microarrays (n=3160 probes, in duplicate). Three independent Latin-square-designed experiments revealed accurate quantification of the targets. The regression between actual concentration of targets and those determined by the approach were highly positively correlated with high R(2) values (e.g., R(2)=0.90, n=6 targets; R(2)=0.84, n=8 targets; R(2)=0.82, n=10 targets).
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Affiliation(s)
- Alex E Pozhitkov
- College of Marine Sciences, P.O. Box 7000, University of Southern Mississippi, Ocean Springs, MS 39566, USA.
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Development and experimental validation of a predictive threshold cycle equation for quantification of virulence and marker genes by high-throughput nanoliter-volume PCR on the OpenArray platform. Appl Environ Microbiol 2008; 74:3831-8. [PMID: 18424532 DOI: 10.1128/aem.02743-07] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Development of quantitative PCR (QPCR) assays typically requires extensive screening within and across a given species to ensure specific detection and lucid identification among various pathogenic and nonpathogenic strains and to generate standard curves. To minimize screening requirements, multiple virulence and marker genes (VMGs) were targeted simultaneously to enhance reliability, and a predictive threshold cycle (C(T)) equation was developed to calculate the number of starting copies based on an experimental C(T). The empirical equation was developed with Sybr green detection in nanoliter-volume QPCR chambers (OpenArray) and tested with 220 previously unvalidated primer pairs targeting 200 VMGs from 30 pathogens. A high correlation (R(2) = 0.816) was observed between the predicted and experimental C(T)s based on the organism's genome size, guanine and cytosine (GC) content, amplicon length, and stability of the primer's 3' end. The performance of the predictive C(T) equation was tested using 36 validation samples consisting of pathogenic organisms spiked into genomic DNA extracted from three environmental waters. In addition, the primer success rate was dependent on the GC content of the target organisms and primer sequences. Targeting multiple assays per organism and using the predictive C(T) equation are expected to reduce the extent of the validation necessary when developing QPCR arrays for a large number of pathogens or other targets.
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