| Orginal Article |
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| The Feasibility Analysis That Nanopore Sequencing Technology Is Applied to Food Microbiological Detection |
CAO Bi-pu1,MIAO Li-hua1,GUO Bao-yan1,HE Li-ping2,**( ) |
1 Guangzhou Guangjian Quality Testing and Research Institute Co.Ltd.,Guangzhou 510000,China
2 Testing Center of South China Agricultural University,Guangzhou 510642,China |
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Abstract DNA sequencing technology has developed rapidly in recent years and has evolved from the first generation of biochemical sequencing to the third generation of single molecule sequencing. As one of the third-generation sequencing technologies, nanopore sequencing is a physical method that based on electrical signals,different from other current popular sequencing technologies. Many researchers usually apply high-throughput sequencing techniques to the study of food microorganisms, but there are few reports of the application of nanopore sequencing technology to the detection of microorganisms in food. Oxford Nanopore Technologies successfully developed DNA sequencing instrument of MinION, the world’s first commercial instrument for the nanopore sequencing. After continuous improvement in recent years, MinION has been widely used in the DNA sequencing. The amount of DNA required for the sequencing of MinION is about 1μg DNA. The standard recognition speed of one second for 250 bases, the average reading length of 13kb to 20kb and sequencing accuracy to 98%. Its high recognition speed and high accuracy meet the requirements of rapid detection, feasible to be applied to microbiological detection in food.
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Received: 04 May 2018
Published: 10 January 2019
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Corresponding Authors:
Li-ping HE
E-mail: 582262409@qq.com
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| [1] |
刘仲敏,郑鸣,王永芬,等.食源性沙门氏菌实时定量PCR检测研究.食品工业科技,2007,28(8):233-236.
|
|
|
| [1] |
Liu Z M,Zheng M,Wang Y F,et al.The detection of salmonella in food by real-time quantitative PCR.Science and Technology of Food Industry,2007,28(8):233-236.
|
|
|
| [2] |
蔡亦红,姚余有.3种食源性致病菌的多重PCR 快速检测方法的建立.中国卫生检验杂志,2007,17(11):1959-1962.
|
|
|
| [2] |
Cai Y H,Yao Y Y.Establishment and application of multiple PCR for diagnosing three food-borne bacterial pathogens.Chinese Journal of Health Laboratory Technology,2007,17(11):1959-1962.
|
|
|
| [3] |
王敏雅,徐明汉,潘宏伟,等.沙门菌invA基因LAMP快速检测法的建立和初步应用.中国卫生检验杂志,2008,18(10):1971-1981.
|
|
|
| [3] |
Wang M Y,Xu M H,Pan H W,et al.Establishment and preliminary application of LAMP invA gene assay for rapid detection of Salmonella.Chinese Journal of Health Laboratory Technology,2008,18(10):1971-1981.
|
|
|
| [4] |
李永刚,王德国,吴建刚,等.环介导恒温扩增法(LAMP)检测金黄色葡萄球菌.食品工业科技,2010,31(1):388-391.
|
|
|
| [4] |
Li Y G,Wang D G,WU Jian-gang,et al.Detecting of Staphylococcus aureus by loop-mediated isotherma lamp lification (LAMP) method.Science and Technology of Food Industry,2010,31(1):388-391.
|
|
|
| [5] |
姜侃,吕沁风,汪新,等.三重LAMP法检测食品中沙门氏菌、单增李斯特菌和金黄色葡萄球菌.食品科学,2013,34(24):182-187.
|
|
|
| [5] |
Jiang K,Lv Q F,Wang X,et al.Development of multiplex LAMP method for the detection of Salmonella spp,Staphylococcus aureus and Listeria monocytogenes in foods.Food Science,2013,34(24):182-187.
|
|
|
| [6] |
Rudi K,Flateland S L,Hanssen J F,et al.Development and evaluation of a 16S ribosomal DNA array based approach for describing complex microbial communities in ready-to-eat vegetable salads packed in a modified atmosphere.Appl Environ Microbiol,2002,68:1146-1156.
doi: 10.1128/AEM.68.3.1146-1156.2002
pmid: 11872462
|
|
|
| [7] |
周凤丽,简纪常,吴灶和.地高辛标记的DNA探针制备及其应用于溶藻弧菌的检测.华中农业大学学报,2009,28(4):459-462.
|
|
|
| [7] |
Zhou F L,Jian J C,Wu Z H.Preparation and application of digoxigenin labeled DNA probe for detection of Vibrio alginoly ticus.Journal of Huazhong Agricultural University,2009,28(4):459-462.
|
|
|
| [8] |
何冬梅,王洪敏,柯昌文,等.单增李斯特菌检测基因芯片的研制与评价.中华微生物学和免疫学杂志,2011,31(10):916-921.
|
|
|
| [8] |
He D M,Wang H M,Ke C W,et al.Development and evaluation of a DNA microarray for Listeria monocyiogenes detection.Chinese Journal of Microbiology and Immunology,2011, 31(10):916-921.
|
|
|
| [9] |
徐保红,李秀娟,杨芳,等.PCR-焦磷酸测序法快速鉴定副溶血性弧菌.预防医学情报杂志,2011,27(01):78-80.
|
|
|
| [9] |
Xu B H,Li X J,Yang F,et al.Detection of Vibrio parahaemolyticus by PCR and Pyrosequencing.Journal of Preventive Medicine Information,2011,27(01):78-80.
|
|
|
| [10] |
朱珠,王永,兰青阔,等.应用焦磷酸测序技术快速检测食品中沙门氏菌.食品科学,2013,34(2):182-186.
|
|
|
| [10] |
Zhu Z,Wang Y,Lan Q K,et al.Application of pyrosequencing technology for rapid detection of Sallmonella spp.in foods.Food Science,2013,34(2):182-186.
|
|
|
| [11] |
曹冬梅,倪长鹏,刘宇,等.PCR-焦磷酸测序法快速鉴定食品中肠炎沙门菌.大连工业大学学报,2015,34(01):29-33.
|
|
|
| [11] |
Cao D M,Ni C P,Liu Y,et al.Rapid detection of Salmonella enteritidis in food by PCR-pyrosequencing.Journal of Dalian Polytechnic University,2015,34(01):29-33.
|
|
|
| [12] |
Liang F,Zhang P M.Nanopore DNA sequencing:Are we there yet?Science Bulletin.2015,60(3):296-303.
doi: 10.1007/s11434-014-0629-3
|
|
|
| [13] |
Avery O T,MacLeod C M, McCarty M. Studies on the chemical nature of the substance inducing transformation of pneumococcal types.Journal of Experimental Medicine,1944,79(2):137-158.
|
|
|
| [14] |
Watson J D,Crick F H.Molecular structure of nucleic acids:a structure for deoxyribose nucleic acid.Nature. 1953,171(4356):737-738.
|
|
|
| [15] |
Whitfeld P R.A method for the determination of nucleotide sequence in polyribonucleotides. Biochem J,1954,58(3):390-396.
doi: 10.1042/bj0580390
pmid: 13208627
|
|
|
| [16] |
Sanger F,Nicklen S.Coulson A R.DNA sequencing with chain-terminating inhibitors. Proc Natl Acad Sci USA,1977,74(12):5463-5467.
|
|
|
| [17] |
Maxam A M,Gilbert W.A new method for sequencing DNA.Proc Natl Acad Sci USA, 1977,74(2):560-564.
doi: 10.1073/pnas.74.2.560
pmid: 265521
|
|
|
| [18] |
Collins F S,Lander E S,Rogers R,et al.International human genome sequencing consortium.Finishing the euchromatic sequence of the human genome.Nature,2004,431(7011):931-945.
|
|
|
| [19] |
Schuster S C.Next-generation sequencing transforms today’s biology.Nature Methods,2008,5(1):16-18.
|
|
|
| [20] |
Mardis E R.The impact of next-generation sequencing technology on genetics . Trends in Genetics,2008,24(3):133-141.
doi: 10.1016/j.tig.2007.12.007
pmid: 18262675
|
|
|
| [21] |
Braslavsky I,Hebert B,Kartalov E,et al.Sequence information can be obtained from single DNA molecules . Proc Natl Acad Sci USA,2003,100(7):3960-3964.
doi: 10.1073/pnas.0230489100
pmid: 12651960
|
|
|
| [22] |
Harris T D,Buzby P R,Babcock H,et al.Single-molecule DNA sequencing of a viral genome.Science,2008,320(5872):106-109.
|
|
|
| [23] |
Clarke J,Wu H C,Jayasinghe L,et al.Continuous base identification for single-molecule nanopore DNA sequencing.Nat Nanotechnol,2009,4(4):265-270.
doi: 10.1038/nnano.2009.12
pmid: 19350039
|
|
|
| [24] |
Stoddart D,Heron A J,Klingelhoefer J,et al.Nucleobase recognition in ssDNA at the Central constriction of the α-hemolysin pore.Nano Letters,2010,10(9):3633-3637.
doi: 10.1021/nl101955a
pmid: 2935931
|
|
|
| [25] |
Oxford Nanopore Technologies.About us: Biblogy for anyone, anynhere. [2018-04-20]..
|
|
|
| [26] |
Eid J,Fehr A,Gray J,et al.Real-time DNA sequencing from single polymerase molecules.Science,2009,323(5910):133-138.
|
|
|
| [27] |
王凯歌,窦硕星,王鹏业,等.利用纳米孔研究DNA.物理,2004,33(08):579-586.
|
|
|
| [27] |
Wang K G,Dou S X,Wang P Y,et al.Study DNA with a nanopore.Physics,2004,33(08):579-586.
|
|
|
| [28] |
刘振波. DNA测序技术比较.生物学通报,2012,47(07):14-17.
|
|
|
| [28] |
Liu Z B.DNA sequencing technology comparison.Bulletin of Biology,2012,47(07):14-17.
|
|
|
| [29] |
谢浩,赵明,胡志迪,等.DNA测序技术方法研究及其进展.生命的化学,2015,35(06):811-816.
|
|
|
| [29] |
Xie H,Zhao M,Hu Z D,et al.Research of the methods for DNA sequencing technology and its progress.Chemistry of Life,2015,35(06):811-816.
|
|
|
| [30] |
Branton D,Deamer D W,Marziali A,et al.The potential and challenges of nanopore sequencing.Nature Biotechnology,2008,26(10):1146-1153.
|
|
|
| [31] |
Ying Y L,Cao C,Long Y T.Single molecule analysis by biological nanopore sensors.Analyst,2014,139(16):3826-3835.
doi: 10.1039/c4an00706a
pmid: 24991734
|
|
|
| [32] |
张春萍. α溶血素纳米孔的研究进展和应用.基因组学与应用生物学,2014,33(05):1114-1118.
|
|
|
| [32] |
Zhang C P.The research progress and application of α-hemolysin nanopore.Genomics and Applied Biology,2014,33(05):1114-1118.
|
|
|
| [33] |
Venkatesan B M,Bashir R.Nanopore sensors for nucleic acid analysis.Nature Nanotechnology,2011,6(10):615-624.
doi: 10.1038/nnano.2011.129
pmid: 21926981
|
|
|
| [34] |
Song L,Hobaugh M R,Shustak C,et al.Structure of staphylococcal alpha-hemolysin,a heptameric transmembrane pore.Science,1996,274(5294):1859-1866.
|
|
|
| [35] |
Kasianowicz J J,Brandin E,Branton D,et al.Characterization of individual polynucleotide molecules using a membrane channel.Proceedings of the National Academy of Sciences of the United States of America,1996,93(24):13770-13773.
doi: 10.1073/pnas.93.24.13770
pmid: 8943010
|
|
|
| [36] |
Cherf G M,Lieberman K R,Rashid H,et al.Automated forward and reverse ratcheting of DNA in a nanopore at five angstrom precision1.Nature Biotechnology,2012,30(4):344-348.
doi: 10.1038/nbt.2147
pmid: 978
|
|
|
| [37] |
Derrington I M,Butler T Z,Collins M D,et al.Nanopore DNA sequencing with MspA.Proceedings of the National Academy of Sciences of the United States of America,2010, 107(37):16060-16065.
|
|
|
| [38] |
Butler T Z,Pavlenok M,Derrington I M,et al.Single-molecule DNA detection with an engineered MspA protein nanopore.Proceedings of the National Academy of Sciences of the United States of America,2008,105(52):20647-20652.
|
|
|
| [39] |
Manrao E A,Derrington I M,Laszlo A H,et al.Reading DNA at single-nucleotide resolution with a mutant MspA nanopore and phi29 DNA polymerase.Nature Biotechnology,2012,30(4):349-53.
doi: 10.1038/nbt.2171
pmid: 22446694
|
|
|
| [40] |
陈文辉,罗军,赵超.固态纳米孔:下一代DNA测序技术--原理、工艺与挑战.中国科学:生命科学,2014,44(07):649-662.
|
|
|
| [40] |
Chen W H,Luo J,Zhao C.Solid-state nanopore:the next-generation sequencing technology-principles,fabrication and challenges. Scientia Sinica(Vitae),2014,44(07):649-662.
|
|
|
| [41] |
Hall A R,Scott A,Rotem D,et al.Hybrid pore formation by directed insertion of α-haemolysin into solid-state nanopores.Nature Nanotechnology,2010,5(12):874-877.
doi: 10.1038/nnano.2010.237
pmid: 21113160
|
|
|
| [42] |
Garaj S,Hubbard W,Reina A,et al.Graphene as a subnanometre trans-electrode membrane.Nature,2010,467(7312):190-3.
doi: 10.1038/nature09379
pmid: 20720538
|
|
|
| [43] |
O’Flaherty S,Klaenhammer T R.The impact of omic technologies on the study of food microbes.Annual Review of Food Science and Technology,2011,2:353-371.
doi: 10.1146/annurev-food-030810-110338
pmid: 22129387
|
|
|
| [44] |
Solieri L,Dakal T C,Giudici P.Next-generation sequencing and its potential impact on food microbial genomics.Annals of Microbiology,2013,63(1):21-37.
doi: 10.1007/s13213-012-0478-8
|
|
|
| [45] |
娄恺,班睿,赵学明.食品微生物基因组学的研究进展.食品科学,2002,23(09):138-140.
|
|
|
| [45] |
Lou K,Ban R,Zhao X M.Advances in food microbiology genomics.Food Science,2002,23(09):138-140.
|
|
|
| [46] |
Deschamps S,Mudge J,Cameron C, et al.Characterization, correction and de novo assembly of an Oxford Nanopore genomic dataset from Agrobacterium tumefaciens.Scientific Reports.2016,6(1):28625.
doi: 10.1038/srep28625
pmid: 4923883
|
|
|
| [47] |
NASA press release, “First DNA Sequencing in Space a Game Changer,” (29 August 2016)
|
|
|
| [48] |
Quick J,et al,Real-time,portable genome sequencing for Ebola surveillance.Nature,2016,530:228-232.
doi: 10.1038/nature16996
pmid: 26840485
|
|
|
| [49] |
Menegon M,Cantaloni C,Rodriguez-Prieto A,et al.On site DNA barcoding by nanopore sequencing.PLoS ONE.2017,12(10):e0184741.
doi: 10.1371/journal.pone.0184741
pmid: 5627904
|
|
|
| [50] |
石铁流. 新技术能使DNA测序的成本降低多少?科学通报,2017,62(19):2042-2046.
|
|
|
| [50] |
Shi T L.How much will new technologies lower the cost of DNA sequencing?Chinese Science Bulletin,2017,62(19):2042-2046.
|
|
|
| [51] |
Wheeler D A,Srinivasan M,Egholm M,et al.The complete genome of an individual by massively parallel DNA sequencing.Nature,2008,452(7189):872-876.
doi: 10.1038/nature06884
pmid: 18421352
|
|
|
| [52] |
王兴春,杨致荣,王敏,等.高通量测序技术及其应用.中国生物工程杂志,2012,32(01):109-114.
|
|
|
| [52] |
Wang X C,Yang Z R,Wang M,et al.High-throughput sequencing technology and its application.China Biotechnology,2012,32(01):109-114.
|
|
|
| [53] |
Jain M,Olsen H E,Paten B,et al.The oxford nanopore MinION:delivery of nanopore sequencing to the genomics community.Genome Biol.2016,17(1):239.
doi: 10.1186/s13059-016-1103-0
pmid: 5124260
|
|
|
| [54] |
Oxford Nanopore Technologies.Product specifications comparison.[2018-04-20].
|
|
|
| [55] |
吴坤,陈红歌,刘娜,等.小麦表面微生物总DNA提取方法的比较与改进.中国粮油学报,2003,18(06):34-38.
|
|
|
| [55] |
Wu K,Chen H G,Liu N,et al.Comparation and improvement of methods to extract total DNA from microbe on the surface of wheat kernels. Chinese Cereals and Oils Association,2003,18(06):34-38.
|
|
|
| [56] |
Qin D,Yang Y,Zhou X P,et al.Comparison of methods for total microbial DNA extraction from fermented meat//Proceedings of 2010 First International Conference on Cellular,Molecular Biology, Biophysics and Bioengineering(Volume 5). IITA,2010.
|
|
|
| [57] |
Tyson J R,O’Neil N J, Jain M,,et al.MinION-based long-read sequencing and assembly extends the Caenorhabditis elegans reference genome.Genome Research,2018,28:266-274.
doi: 10.1101/gr.221184.117
pmid: 29273626
|
|
|
| [58] |
Batovska J,Lynch S E,Rodoni B C,et al.Metagenomic arbovirus detection using MinION nanopore sequencing.J Virol Methods,2017,249:79-84.
doi: 10.1016/j.jviromet.2017.08.019
pmid: 28855093
|
|
|
| [59] |
Giordano F,Aigrain L,Quail M A,et al.De novo yeast genome assemblies from MinION,PacBio and MiSeq platforms.Scientific Reports,2017,7(1):3935.
doi: 10.1038/s41598-017-03996-z
pmid: 5479803
|
|
|
| [60] |
Haque F,Li J,Wu H C,et al.Solid-State and biological nanopore for real-time sensing of single chemical and sequencing of DNA.Nano Today,2013,8(1):56-74.
doi: 10.1016/j.nantod.2012.12.008
pmid: 3596169
|
|
|
| [61] |
Liu S,Zhao Q,Li Q,et al.Controlled deformation of Si3 N4 nanopores using focused electron beam in a transmission electron microscope.Nanotechnology,2011,22(11):115302.
doi: 10.1088/0957-4484/22/11/115302
pmid: 21301076
|
|
|
| [62] |
Kim M J,Wanunu M,Bell D C,et al.Rapid fabrication of uniformly sized nanopores and nanopore arrays for parallel DNA analysis.Adv Mater,2006,18(23):3149-3153.
doi: 10.1002/adma.200601191
|
|
|
|
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