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| The New Development of the Research Method for Molecular Microbial Ecology |
| LV Chang-yong, CHEN Chao-yin, GE Feng, LIU Di-qiu, KONG Xiang-jun |
| Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming 650500, China |
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Abstract Microbial community structure and functional metabolism are the research hotspots of microbial ecology. However, the research method of microbial community structure and functional metabolism has been limited by technique for a long time. With the development of new techniques, the research approaches for molecular microbial ecology have being changed. High-throughput sequencing technology has ameliorated the research method of microbial diversity, metagenomics and metatranscriptomics. Meanwhile GeoChip which covered large amount of known functional oligonucleotide probes in single chip could determine the presence or absence of microbes and functional genes quickly. The newest research approaches for molecular microbial ecology study were reviewed and compared, and the applicability, advantages and disadvantages of those approaches were discussed.
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Received: 13 March 2012
Published: 25 August 2012
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[1] Vaz-Moreira I, Egas C, Nunes O C, et al. Culture-dependent and culture-independent diversity surveys target different bacteria: a case study in a freshwater sample. Antonie Van Leeuwenhoek, 2011, 100(2): 245-257.
[2] Lewis K, Epstein S, D’Onofrio A, et al. Uncultured microorganisms as a source of secondary metabolites. J Antibiot (Tokyo), 2010, 63(8): 468-476.
[3] 李慧,何晶晶,张颖,等. 宏基因组技术在开发未培养环境微生物基因资源中的应用. 生态学报, 2008, 28(4): 1762-1773. Li H, He J J, Zhang Y et al. Application of metagenomic technique in the exploring of uncultured environmental microbial gene resource. Acta Ecologica Sinica, 2008, 28(4): 1762-1773.
[4] Schuster S C. Next-generation sequencing transforms today’s biology. Nature, 2008, 5(1): 16-18.
[5] Metzker M L. Sequencing technologies -the next generation. Nat Rev Genet, 2010, 11(1): 31-46.
[6] Mardis E R. The impact of next-generation sequencing technology on genetics. Trends Genet, 2008, 24(3): 133-141.
[7] Ansorge W J. Next-generation DNA sequencing techniques. New Biotechnology, 2009, 25(4): 195-203.
[8] Mardis E R. Next-generation DNA sequencing methods. Annu Rev Genomics Hum Genet, 2008, 9: 387-402.
[9] 李晓然. 基于核糖体RNA高通量测序分析微生物群落结构. 上海: 复旦大学, 2011. Li X R. Using ribosomal RNA pyrosequencing to explore the microbial community structure. Shanghai:College of Life Science, Fudan University, 2011.
[10] 段曌,肖炜,王永霞,等. 454测序技术在微生物生态学研究中的应用. 微生物学杂志, 2011, 31(5): 76-81. Duan Z, Xiao W, Wang Y X, et al. Application of 454 sequencing technique in microbial ecology. Journal of Microbiology, 2011, 31(5): 76-81.
[11] Thompson J R, Marcelino L A, Polz M F. Heteroduplexes in mixed-template amplifications: formation, consequence and elimination by ’reconditioning PCR’. Nucleic Acids Res, 2002, 30(9): 2083-2088.
[12] Parameswaran P, Jalili R, Tao L, et al. A pyrosequencing-tailored nucleotide barcode design unveils opportunities for large-scale sample multiplexing. Nucleic Acids Res, 2007, 35(19): e130.
[13] 徐晓宇,刘和. 454测序法在环境微生物生态研究中的应用. 生物技术通报, 2010,1: 73-76. Xu X Y, Liu H. Application of 454 sequencing in environmental microbial ecology. Biotechnology Bulletin, 2010,1: 73-76.
[14] Sogin M L, Morrison H G, Huber J A, et al. Microbial diversity in the deep sea and the underexplored "rare biosphere". Proc Natl Acad Sci U S A, 2006, 103(32): 12115-12120.
[15] Jaenicke S, Ander C, Bekel T, et al. Comparative and joint analysis of two metagenomic datasets from a biogas fermenter obtained by 454-pyrosequencing. PLoS One, 2011, 6(1): e14519.
[16] Zhang X, Yue S, Zhong H, et al. A diverse bacterial community in an anoxic quinoline-degrading bioreactor determined by using pyrosequencing and clone library analysis. Appl Microbiol Biotechnol, 2011, 91(2): 425-434.
[17] Turnbaugh P J, Hamady M, Yatsunenko T, et al. A core gut microbiome in obese and lean twins. Nature, 2009, 457(7228): 480-484.
[18] Alegria A, Szczesny P, Mayo B, et al. Biodiversity in oscypek, a traditional polish cheese, determined by culture-dependent and -independent approaches. Appl Environ Microbiol, 2012, 78(6): 1890-1898.
[19] Chen C P, Tseng C H, Chen C A, et al. The dynamics of microbial partnerships in the coral Isopora palifera. ISME J, 2011, 5(4): 728-740.
[20] Wei H, Dong L, Wang T, et al. Structural shifts of gut microbiota as surrogate endpoints for monitoring host health changes induced by carcinogen exposure. FEMS Microbiol Ecol, 2010, 73(3): 577-586.
[21] Zhang C, Zhang M, Wang S, et al. Interactions between gut microbiota, host genetics and diet relevant to development of metabolic syndromes in mice. ISME J, 2010, 4(2): 232-241.
[22] Wang T, Cai G, Qiu Y, et al. Structural segregation of gut microbiota between colorectal cancer patients and healthy volunteers. ISME J, 2012, 6(2): 320-329.
[23] Zhang C, Zhang M, Pang X, et al. Structural resilience of the gut microbiota in adult mice under high-fat dietary perturbations. ISME J, 2012.
[24] Baker G C, Smith J J, Cowan D A. Review and re-analysis of domain-specific 16S primers. J Microbiol Methods, 2003, 55(3): 541-555.
[25] Polz M F, Cavanaugh C M. Bias in template-to-product ratios in multitemplate PCR. Appl Environ Microbiol, 1998, 64(10): 3724-3730.
[26] Handelsman J, Rondon M R, Brady S F, et al. Molecular biological access to the chemistry of unknown soil microbes: a new frontier for natural products. Chem Biol, 1998, 5(10): 245-249.
[27] 周丹燕,戴世鲲,王广华,等. 宏基因组学技术与挑战. 微生物学通报, 2011, 38(4): 591-600. Zhou D Y, Dai S K, Wang G H, et al. The research innovation and challenges in metagenomics. Microbiology China, 2011, 38(4): 591-600.
[28] 蒋云霞,艾春香. 环境宏基因组学技术的主要瓶颈及发展. 环境科学, 2007, 28(12): 2861-2866. Jiang Y X, Ai C X. Main bottleneck and developments of metagenomic technology. Environmental Science, 2007, 28(12): 2861-2866.
[29] Jung J Y, Lee S H, Kim J M, et al. Metagenomic analysis of kimchi, a traditional Korean fermented food. Appl Environ Microbiol, 2011, 77(7): 2264-2274.
[30] Qin J, Li R, Raes J, et al. A human gut microbial gene catalogue established by metagenomic sequencing. Nature, 2010, 464(7285): 59-65.
[31] Durso L M, Harhay G P, Bono J L, et al. Virulence-associated and antibiotic resistance genes of microbial populations in cattle feces analyzed using a metagenomic approach. J Microbiol Methods, 2011, 84(2): 278-282.
[32] 李晓晖,李鑫鑫,张维,等. 宏转录组学在微生物生态学研究中的应用. 中国农业科技导报, 2011, 13(4): 58-65. Li X H, Li X X, Zhang W, et al. Application of metatranscriptomics in microbial ecology. Journal of Agricultural Science and Technology, 2011, 13(4): 58-65.
[33] Poretsky R S, Bano N, Buchan A, et al. Analysis of microbial gene transcripts in environmental samples. Appl Environ Microbiol, 2005, 71(7): 4121-4126.
[34] Sorek R, Cossart P. Prokaryotic transcriptomics: a new view on regulation, physiology and pathogenicity. Nat Rev Genet, 2010, 11(1): 9-16.
[35] Stewart F J, Ulloa O, Delong E F. Microbial metatranscriptomics in a permanent marine oxygen minimum zone. Environ Microbiol, 2012, 14(1): 23-40.
[36] Baldrian P, Kolarik M, Stursova M, et al. Active and total microbial communities in forest soil are largely different and highly stratified during decomposition. ISME J, 2012, 6(2): 248-258.
[37] Bomar L, Maltz M, Colston S, et al. Directed culturing of microorganisms using metatranscriptomics. MBio, 2011, 2(2): e11-e12.
[38] Gosalbes M J, Durban A, Pignatelli M, et al. Metatranscriptomic approach to analyze the functional human gut microbiota. PLoS One, 2011, 6(3): e17447.
[39] Zakrzewski M, Goesmann A, Jaenicke S, et al. Profiling of the metabolically active community from a production-scale biogas plant by means of high-throughput metatranscriptome sequencing. J Biotechnol, 2012, 158(4):248-258.
[40] Ledford H. The death of microarrays? Nature, 2008, 455(7215): 847.
[41] Roh S W, Abell G C, Kim K H, et al. Comparing microarrays and next-generation sequencing technologies for microbial ecology research. Trends Biotechnol, 2010, 28(6): 291-299.
[42] Chou L S, Liu C S, Boese B, et al. DNA sequence capture and enrichment by microarray followed by next-generation sequencing for targeted resequencing: neurofibromatosis type 1 gene as a model. Clin Chem, 2010, 56(1): 62-72.
[43] He Z, Gentry T J, Schadt C W, et al. GeoChip: a comprehensive microarray for investigating biogeochemical, ecological and environmental processes. ISME J, 2007, 1(1): 67-77.
[44] He Z, Deng Y, Van Nostrand J D, et al. GeoChip 3.0 as a high-throughput tool for analyzing microbial community composition, structure and functional activity. ISME J, 2010, 4(9): 1167-1179.
[45] Lomax C, Liu W J, Wu L, et al. Methylated arsenic species in plants originate from soil microorganisms. New Phytol, 2012, 193(3): 665-672.
[46] Van Nostrand J D, Wu W M, Wu L, et al. GeoChip-based analysis of functional microbial communities during the reoxidation of a bioreduced uranium-contaminated aquifer. Environ Microbiol, 2009, 11(10): 2611-2626.
[47] Liang Y, Van Nostrand J D, N’Guessan L A, et al. Microbial functional gene diversity with a shift of subsurface redox condition during in situ uranium reduction. Appl Environ Microbiol, 2012,78(8):2966-2972.
[48] Liu W, Wang A, Sun D, et al. Characterization of microbial communities during anode biofilm reformation in a two-chambered microbial electrolysis cell (MEC). J Biotechnol, 2011,157(4):628-632
[49] Xie J, He Z, Liu X, et al. GeoChip-based analysis of the functional gene diversity and metabolic potential of microbial communities in acid mine drainage. Appl Environ Microbiol, 2011, 77(3): 991-999.
[50] Shen P, Wang W, Krishnakumar S, et al. High-quality DNA sequence capture of 524 disease candidate genes. Proc Natl Acad Sci U S A, 2011, 108(16): 6549-6554.
[51] Kent B N, Salichos L, Gibbons J G, et al. Complete bacteriophage transfer in a bacterial endosymbiont (Wolbachia) determined by targeted genome capture. Genome Biol Evol, 2011, 3: 209-218.
[52] Isenbarger T A, Finney M, Rios-Velazquez C, et al. Miniprimer PCR, a new lens for viewing the microbial world. Appl Environ Microbiol, 2008, 74(3): 840-849.
[53] Xu R, Chen Q, Robleh Djama Z, et al. Miniprimer PCR assay targeting multiple genes: a new rapid and reliable tool for genotyping Pantoea stewartii subsp. stewartii. Lett Appl Microbiol, 2010, 50(2): 216-222.
[54] Goh K M, Chua Y S, Abudall R N, et al. A comparison of conventional and miniprimer PCR to elucidate bacteria diversity in Malaysia Ulu Slim hot spring using 16S rDNA clone library. Romanian Biotechnological Letters, 2011, 16(3): 8. |
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