高通量技术在微生物培养中的应用进展及分子测序对比分析Application Progress of High-throughput Technology in Microbial Culture and Comparative Analysis of Molecular Sequencing
刘莹;韩锰;王文磊;马成玉;张沛;
摘要(Abstract):
高通量技术是以微型生物反应器为操作平台,实现对生物细胞的分离培养和分子测序。通过着重分析几种实用型高通量技术在微生物分离培养及分子测序中的应用进展,发现微包埋技术在高通量试验中的研究及应用较为深入;而对不同环境菌样的分离培养中,海洋微生物方面的应用最为突出。另外,通过对比高通量分子测序技术可以发现,Illumina测序法的平均测序速度最快;单分子测序法所得数据的精确度最高,测序读长最长,周期相对最短。最后,对高通量技术在微生物学应用中的一些不足进行总结,并提出假设性解决方法。
关键词(KeyWords): 微生物;高通量技术;分离培养;分子测序
基金项目(Foundation): 国家自然基金青年项目(31701121);; 河南省科技公关项目(182102310667);; 河南省高等学校重点科研项目计划(18A180022)
作者(Author): 刘莹;韩锰;王文磊;马成玉;张沛;
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DOI:
参考文献(References):
- [1] 孙杨,聂简琪,白仲虎,等.高通量培养技术在生物过程研发中的应用进展[J].生物产业技术,2015(1):24-31.
- [2] QUAIL M A,KOZAREWA I,SMITH F,et al.A large genome center’s improvements to the Illumina sequencing system[J].Nature methods,2008,5:1005-1010.
- [3] 冀世奇.海洋微生物高通量培养和分选技术的建立及应用[D].青岛:中国海洋大学,2011.
- [4] RAPPé M S,GIOVANNONI S J.The uncultured microbial majority[J].Annual review of microbiology,2003,57:369-394.
- [5] BRUNS A,CYPIONKA H,OVERMANN J.Cyclic AMP and acyl homoserine lactones increase the cultivation efficiency of heterotrophic bacteria from the central baltic sea[J].Applied and environmental microbiology,2002,68(8):3978-3987.
- [6] AKSELBAND Y,CABRAL C,CASTOR T P,et al.Enrichment of slow-growing marine microorganisms from mixed cultures using gel microdrop(GMD)growth assay and fluorescence-activated cell sorting[J].Journal of experimental marine biology and ecology,2006,329(2):196-205.
- [7] 袁东芳,于乐军,刘晨光.海洋微生物高通量培养方法和分选技术的研究进展[J].微生物学通报,2014,41(6):1180-1187.
- [8] CONNON S A,GIOVANNONI S J.High-throughput methods for culturing microorganisms in very-low-nutrient media yield diverse new marine isolates[J].Applied and environmental microbiology,2002,68(8):3878-3885.
- [9] BUTTON D K,SCHUT F,QUANG P,et al.Viability and isolation of marine bacteria by dilution culture:Theory,procedures,and initial results[J].Applied and environmental microbiology,1993,59(3):881-891.
- [10] RAPPé M S,CONNON S A,VERGIN K L,et al.Cultivation of the ubiquitous sar11 marine bacterioplankton clade[J].Nature,2002,418(6898):630-633.
- [11] BENITA S.Microencapsulation:Methods and industrial applications[M].Boca Raton,FL,USA:Taylor and Francis,2005.
- [12] WEAVER J C,WILLIAMS G B,KLIBANOV A,et al.Gel microdroplets:Rapid detection and enumeration of individual microorganisms by their metabolic activity[J].Bio/Technology,1988,6(6):1084-1089.
- [13] GIFT E A,PARK H J,PARADIS G A,et al.FACS-based isolation of slowly growing cells:Double encapsulation of yeast in gel microdrops[J].Nature biotechnology,1996,14(7):884-887.
- [14] KATSURAGI T,TANAKA S,NAGAHIRO S,et al.Gel microdroplet technique leaving microorganisms alive for sorting by flow cytometry[J].Journal of microbiological methods,2000,42(1):81-86.
- [15] BHATIA S R,KHATTAK S F,ROBERTS S C.Polyelectrolytes for cell encapsulation[J].Current opinion in colloid & interface science,2005,10(1):45-51.
- [16] WEI W H,DONG X M,LIU C G.In vitro investigation of self-assembled nanoparticles based on hyaluronic acid-deoxycholic acid conjugates for controlled release doxorubicin:Effect of degree of substitution of deoxycholic acid[J].Int J Mol Sci,2015,16(4):7195-7209.
- [17] 凌海鹰.微流控芯片中制备单分散性的海藻酸钙凝胶微球[J].大众科技,2006(8):42-43.
- [18] CHOI C H,JUNG J H,RHEE Y W,et al.Generation of monodisperse alginate microbeads and in situ encapsulation of cell in microfluidic device[J].Biomedical microdevices,2007,9(6):855-862.
- [19] 张秀明.海洋微生物高通量分离培养技术的建立及青岛近海微生物多样性研究[D].青岛:中国海洋大学,2009.
- [20] 张晓华.海洋微生物学[M].青岛:中国海洋大学出版社,2007.
- [21] KAEBERLEIN T,LEWIS K,EPSTEIN S S.Isolating "uncultivable" microorganisms in pure culture in a simulated natural environment[J].Science,2002,296(5570):1127-1129.
- [22] NICHOLS D,LEWIS K,ORJALA J,et al.Short peptide induces an "uncultivable" microorganism to grow in vitro[J].Applied and environmental microbiology,2008,74:4889-4897.
- [23] AOI Y,KINOSHITA T,HATA T,et al.Hollow-fiber membrane chamber as a device for in situ environmental cultivation[J].Applied and environmental microbiology,2009,75(11):3826-3833.
- [24] NICHOLS D,CAHOON N,TRAKHTENBERG E M,et al.Use of ichip for high-throughput in situ cultivation of "uncultivable" microbial species[J].Applied and environmental microbiology,2010,76(8):2445-2450.
- [25] YASUMOTO-HIROSE M,NISHIJIMA M,NGIRCHECHOL M K,et al.Isolation of marine bacteria by in situ culture on media-supplemented polyurethane foam[J].Marine biotechnology,2006,8(3):227-237.
- [26] GAVRISH E,BOLLMANN A,EPSTEIN S,et al.A trap for in situ cultivation of filamentous actinobacteria[J].Journal of microbiological methods,2008,72(3):257-262.
- [27] FERRARI B C,BINNERUP S J,GILLINGS M.Microcolony cultivation on a soil substrate membrane system selects for previously uncultured soil bacteria[J].Applied and environmental microbiology,2005,71(12):8714-8720.
- [28] MOON H S,NAM Y W,PARK J C,et al.Dielectrophoretic separation of airborne microbes and dust particles using a microfluidic channel for real-time bioaerosol monitoring[J].Environmental science & technology,2009,43(15):5857-5863.
- [29] SANGER F,NICKLEN S,COULSON A R.DNA sequencing with chain-terminating inhibitors[J].Proceedings of the national academy of sciences,1977,74(12):5463-5467.
- [30] CLARKE J,WU H C,JAYASINGHE L,et al.Continuous base identification for single-molecule nanopore DNA sequencing[J].Nature nanotechnology,2009,4(4):265-270.
- [31] EID J,FEHR A,GRAY J,et al.Real-time DNA sequencing from single polymerase molecules[J].Science,2009,323(5910):133-138.
- [32] OZSOLAK F,PLATT A R,JONES D R,et al.Direct RNA sequencing[J].Nature,2009,461(7265):814-818.
- [33] MARDIS E R.The impact of next-generation sequencing technology on genetics[J].Trends in genetics,2008,24(3):133-141.
- [34] QUAIL M A,KOZAREWA I,SMITH F,et al.A large genome center’s improvements to the Illumina sequencing system[J].Nature methods,2008,5(12):1005-1010.
- [35] 秦楠,栗东芳,杨瑞馥.高通量测序技术及其在微生物学研究中的应用[J].微生物学报,2011,51(4):445-457.