生物多样性 ›› 2013, Vol. 21 ›› Issue (4): 393-400.doi: 10.3724/SP.J.1003.2013.08050

所属专题: 微生物多样性专辑

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环境微生物的宏基因组学研究新进展

孙欣, 高莹, 杨云锋*()   

  1. 清华大学环境学院, 环境模拟与污染控制国家重点联合实验室, 北京 100084
  • 收稿日期:2013-02-26 接受日期:2013-05-09 出版日期:2013-07-02
  • 通讯作者: 杨云锋 E-mail:yangyf@tsinghua.edu.cn

Recent advancement in microbial environmental research using metagenomics tools

Xin Sun, Ying Gao, Yunfeng Yang*()   

  1. State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084
  • Received:2013-02-26 Accepted:2013-05-09 Online:2013-07-02
  • Contact: Yang Yunfeng E-mail:yangyf@tsinghua.edu.cn

宏基因组学以环境中微生物的基因组的总和为研究对象, 从而规避了传统方法中绝大部分微生物不能培养的缺陷, 因此近年来在环境微生物学研究中得到了广泛应用。本文重点介绍了宏基因组学技术中关键的两类技术: 即以罗氏454及Illumina为代表的高通量测序技术和以基因芯片(GeoChip)为代表的基因芯片技术在微生物研究中的应用。测序技术可以发现新物种和新基因, 但由于测序深度有限, 定量性差, 不易发现低丰度物种, 且易受污染物干扰。芯片技术很好地克服了这些局限, 但不易于发现新基因。本文介绍了这些技术近年来在气候变化、水处理工程系统、极端环境、人体肠道、石油污染修复、生物冶金等方面取得的部分代表性成果。在此基础上, 对宏基因组技术在环境微生物研究方面的未来发展方向提出了预判和展望。我们认为由于两种技术各自的优缺点, 今后将两类技术结合起来的综合研究会越来越多。另外, 由于大量数据的处理方法已成为制约宏基因组学发展的瓶颈, 相应的生物信息学技术开发将是未来科研的热点和难点。

关键词: 宏基因组学, 生物信息学, 高通量测序, 基因芯片

Metagenomics is the study of microbial meta-genomes from environmental samples, which is independent on the ability to cultivate microbes in the laboratory. It provides a new way of examining the microbial world and has been widely used in microbiological research for the past decade. Sequencing-based metagenomic technology, represented by 454 and Illumina sequencing platforms, and microarray-based technology, often using GeoChip, are two of the most commonly used technologies in metagenomics. Sequencing-based technologies are capable of detecting new microbes and genes, but are limited with regard to sequence depth and quantification, and present problems of contamination when used on complex microbial communities. Microarray-based technologies are complementary to sequencing-based technologies in regard to advantages and disadvantages. They have been widely used, for example, in studies of climate change, energy, engineering, metallurgy, extreme environments and human health. However, their use in examining the extremely complex and diverse microbial world merits further technical development, with a focus on integrating both technologies and the development of appropriate bioinformatics tools.

Key words: metagenomics, bioinformatics, high-throughput sequencing, GeoChip

表1

高通量测序和基因芯片技术的性能比较"

方法 Technologies 高通量测序Sequencing 基因芯片Microarray
准确性 Accuracy 高 High 高 High
全面性 Coverage 高 High 高 High
信息深度 Depth 高 High 高 High
定量性 Quantification 低 Low 高 High
发现新物种
Detecting new species/genes
有 Yes 无 No
受污染物干扰
Interference by contaminants
高 High 低 Low
受群落主要物种干扰
Interference by abundant species
高 High 低 Low
1 Austin EE, Castro HF, Sides KE, Schadt CW, Classen AT (2009) Assessment of 10 years of CO2 fumigation on soil microbial communities and function in a sweetgum plantation.Soil Biology and Biochemistry, 41, 514-520.
2 Backhed F, Ding H, Wang T, Hooper LV, Koh GY, Nagy A, Semenkovich CF, Gordon JI (2004) The gut microbiota as an environmental factor that regulates fat storage. Proceedings of the National Academy of Sciences,USA, 101, 15718-15723.
3 Bartram AK, Lynch MD, Stearns JC, Moreno-Hagelsieb G, Neufeld JD (2011) Generation of multimillion-sequence 16S rRNA gene libraries from complex microbial communities by assembling paired-end illumina reads.Applied and Environmental Microbiology, 77, 3846-3852.
4 Chu H, Fierer N, Lauber CL, Caporaso J, Knight R, Grogan P (2010) Soil bacterial diversity in the Arctic is not fundamentally different from that found in other biomes.Environmental Microbiology, 12, 2998-3006.
5 Claesson MJ, Jeffery IB, Conde S, Power SE, O’Connor EM, Cusack S, Harris HMB, Coakley M, Lakshminarayanan B, O’Sullivan O (2012) Gut microbiota composition correlates with diet and health in the elderly.Nature, 488, 178-184.
6 Danovaro R, Corinaldesi C, Dell'anno A, Fuhrman JA, Middelburg JJ, Noble RT, Suttle CA (2011) Marine viruses and global climate change.FEMS Microbiology Review, 35, 993-1034.
7 Deng Y, Jiang YH, Yang Y, He Z, Luo F, Zhou J (2012) Molecular ecological network analyses.BMC Bioinfo- rmatics, 13, 113.
8 Dos Santos HF, Cury JC, Do Carmo FL, Dos Santos AL, Tiedje J, van Elsas JD, Rosado AS, Peixoto RS (2011) Mangrove bacterial diversity and the impact of oil contamination revealed by pyrosequencing: bacterial proxies for oil pollution.PLoS ONE, 6, e16943.
9 Fang H, Cai L, Yu Y, Zhang T (2013) Metagenomic analysis reveals the prevalence of biodegradation genes for organic pollutants in activated sludge.Bioresource Technology, 129, 209-218.
10 Faust K, Raes J (2012) Microbial interactions: from networks to models.Nature Reviews Microbiology, 10, 538-550.
11 Gill SR, Pop M, Deboy RT, Eckburg PB, Turnbaugh PJ, Samuel BS, Gordon JI, Relman DA, Fraser-Liggett CM, Nelson KE (2006a) Metagenomic analysis of the human distal gut microbiome.Science, 312, 1355-1359.
12 Handelsman J, Rondon MR, Brady SF, Clardy J, Goodman RM (1998) Molecular biological access to the chemistry of unknown soil microbes: a new frontier for natural products.Chemistry & Biology, 5, R245-R249.
13 Hazen TC, Dubinsky EA, DeSantis TZ, Andersen GL, Piceno YM, Singh N, Jansson JK, Probst A, Borglin SE, Fortney JL (2010) Deep-sea oil plume enriches indigenous oil-degrading bacteria.Science, 330, 204-208.
14 He Z, Gentry TJ, Schadt CW, Wu L, Liebich J, Chong SC, Huang Z, Wu W, Gu B, Jardine P, Criddle C, Zhou J (2007) GeoChip: a comprehensive microarray for investigating biogeochemical, ecological and environmental processes.The ISME Journal, 1, 67-77.
15 He ZL, Piceno Y, Deng Y, Xu MY, Lu ZM, Desantis T, Andersen G, Hobbie SE, Reich PB, Zhou JZ (2012) The phylogenetic composition and structure of soil microbial communities shifts in response to elevated carbon dioxide.The ISME Journal, 6, 259-272.
16 He ZL, Xu MY, Deng Y, Kang SD, Kellogg L, Wu LY, van Nostrand JD, Hobbie SE, Reich PB, Zhou J (2010) Metagenomic analysis reveals a marked divergence in the structure of belowground microbial communities at elevated CO2.Ecology Letters, 13, 564-575.
17 Howitt MR, Garrett WS (2012) A complex microworld in the gut: gut microbiota and cardiovascular disease connectivity.Nature Medicine, 18, 1188-1189.
18 Hugenholtz P, Tyson GW (2008) Microbiology: metagenomics.Nature, 455, 481-483.
19 Jones DS, Albrecht HL, Dawson KS, Schaperdoth I, Freeman KH, Pi Y, Pearson A, Macalady JL (2012) Community genomic analysis of an extremely acidophilic sulfur-oxidizing biofilm.The ISME Journal, 6, 158-170.
20 Kellenberger E (2001) Exploring the unkown—The silent revolution of microbiology.EMBO Reports, 2, 5-7.
21 Kostka JE, Prakash O, Overholt WA, Green SJ, Freyer G, Canion A, Delgardio J, Norton N, Hazen TC, Huettel M (2011) Hydrocarbon-degrading bacteria and the bacterial community response in Gulf of Mexico beach sands impacted by the Deepwater Horizon oil spill.Applied and Environmental Microbiology, 77, 7962-7974.
22 Kuang JL, Huang LN, Chen LX, Hua ZS, Li SJ, Hu M, Li JT, Shu WS (2013) Contemporary environmental variation determines microbial diversity patterns in acid mine drainage.The ISME Journal, 7, 1038-1050.
23 Liang Y, Li G, Van Nostrand JD, He Z, Wu L, Deng Y, Zhang X, Zhou J (2009a) Microarray-based analysis of microbial functional diversity along an oil contamination gradient in oil field.FEMS Microbiology Ecology, 70, 324-333.
24 Liang Y, Nostrand JDV, Wang J, Zhang X, Zhou J, Li G (2009b) Microarray-based functional gene analysis of soil microbial communities during ozonation and biodegradation of crude oil.Chemosphere, 75, 193-199.
25 Liang Y, Van Nostrand JD, Deng Y, He Z, Wu L, Zhang X, Li G, Zhou J (2011) Functional gene diversity of soil microbial communities from five oil-contaminated fields in China.The ISME Journal, 5, 403-413.
26 Logares R, Haverkamp THA, Kumar S, Lanzén A, Nederbragt AJ, Quince C, Kauserud H (2012). Environmental microbiology through the lens of high-throughput DNA sequencing: synopsis of current platforms and bioinformatics approaches.Journal of Microbiological Methods, 91, 106-113.
27 Lu Z, Deng Y, Van Nostrand JD, He Z, Voordeckers J, Zhou A, Lee Y-J, Mason OU, Dubinsky EA, Chavarria KL, Tom LM, Fortney JL, Lamendella R, Jansson JK, D'Haeseleer P, Hazen TC, Zhou J (2012) Microbial gene functions enriched in the Deepwater Horizon deep-sea oil plume.The ISME Journal, 6, 451-460.
28 Luo CW, Tsementzi D, Kyrpides N, Read T, Konstantinidis KT (2012) Direct comparisons of Illumina vs. Roche 454 sequencing technologies on the same microbial community DNA sample.PLoS ONE, 7, e30087.
29 Mackelprang R, Waldrop MP, DeAngelis KM, David MM, Chavarria KL, Blazewicz SJ, Rubin EM, Jansson JK (2011) Metagenomic analysis of a permafrost microbial community reveals a rapid response to thaw.Nature, 480, 368-371.
30 Qin J, Li Y, Cai Z, Li S, Zhu J, Zhang F, Liang S, Zhang W, Guan Y, Shen D, Peng Y, Zhang D, Jie Z, Wu W, Qin Y, Xue W, Li J, Han L, Lu D, Wu P, Dai Y, Sun X, Li Z, Tang A, Zhong S, Li X, Chen W, Xu R, Wang M, Feng Q, Gong M, Yu J, Zhang Y, Zhang M, Hansen T, Sanchez G, Raes J, Falony G, Okuda S, Almeida M, LeChatelier E, Renault P, Pons N, Batto J-M, Zhang Z, Chen H, Yang R, Zheng W, Li S, Yang H, Wang J, Ehrlich SD, Nielsen R, Pedersen O, Kristiansen K, Wang J (2012) A metagenome-wide association study of gut microbiota in type 2 diabetes.Nature, 490, 55-60.
31 Schloissnig S, Arumugam M, Sunagawa S, Mitreva M, Tap J, Zhu A, Waller A, Mende DR, Kultima JR, Martin J, Kota K, Sunyaev SR, Weinstock GM, Bork P (2013) Genomic variation landscape of the human gut microbiome.Nature, 493, 45-50.
32 Shen L (申丽), Liu XD (刘学端), Qiu GZ (邱冠周) (2008) 16s rDNA based microbial diversity analysis of eleven acid mine drainages obtained from three Chinese copper mines.Chinese Journal of Biotechnology(生物工程学报), 24, 968-974. (in Chinese with English abstract)
33 Shi P, Jia S, Zhang X, Zhang T, Cheng S, Li A (2013) Metagenomic insights into chlorination effects on microbial antibiotic resistance in drinking water.Water Research, 47, 111-120.
34 Simister R, Taylor MW, Tsai P, Fan L, Bruxner TJ, Crowe ML, Webster N (2012) Thermal stress responses in the bacterial biosphere of the Great Barrier Reef sponge, Rhopaloeides odorabile.Environmental Microbiology, 14, 3232-3246.
35 Simon C, Daniel R (2011) Metagenomic analyses: past and future trends.Applied and Environmental Microbiology, 77, 1153-1161.
36 Smith MG, Gianoulis TA, Pukatzki S, Mekalanos JJ, Ornston LN, Gerstein M, Snyder M (2007) New insights into Acinetobacter baumannii pathogenesis revealed by high-density pyrosequencing and transposon mutagenesis.Genes & Development, 21, 601-614.
37 Turnbaugh PJ, Ley RE, Mahowald MA, Magrini V, Mardis ER, Gordon JI (2006) An obesity-associated gut microbiome with increased capacity for energy harvest.Nature, 444, 1027-1031.
38 Van Nostrand JD, Wu W-M, Wu L, Deng Y, Carley J, Carroll S, He Z, Gu B, Luo J, Criddle CS, Watson DB, Jardine PM, Marsh TL, Tiedje JM, Hazen TC, Zhou J (2009) GeoChip-based analysis of functional microbial communities during the reoxidation of a bioreduced uranium-contaminated aquifer.Environmental Microbiology, 11, 2611-2626.
39 Waldron PJ, Wu L, Van Nostrand JD, Schadt CW, He Z, Watson DB, Jardine PM, Palumbo AV, Hazen TC, Zhou J (2009) Functional gene array-based analysis of microbial community structure in groundwaters with a gradient of contaminant levels.Environmental Science & Technology, 43, 3529-3534.
40 Wang F, Zhou H, Meng J, Peng X, Jiang L, Sun P, Zhang C, Van Nostrand JD, Deng Y, He Z, Wu L, Zhou J, Xiao X (2009) GeoChip-based analysis of metabolic diversity of microbial communities at the Juan de Fuca Ridge hydrothermal vent.Proceedings of the National Academy of Sciences, USA, 106, 4840-4845.
41 Willing BP, Dicksved J, Halfvarson J, Andersson AF, Lucio M, Zheng Z, Järnerot G, Tysk C, Jansson JK, Engstrand L (2010) A pyrosequencing study in twins shows that gastrointestinal microbial profiles vary with inflammatory bowel disease phenotypes. Gastroenterology, 139, 1844-1854. e1.
42 Wommack KE, Bhavsar J, Ravel J (2008) Metagenomics: read length matters.Applied and Environmental Microbiology, 74, 1453-1463.
43 Xie J, He Z, Liu X, Liu X, Van Nostrand JD, Deng Y, Wu L, Zhou J, Qiu G (2011) GeoChip-based analysis of the functional gene diversity and metabolic potential of microbial communities in acid mine drainage.Applied and Environmental Microbiology, 77, 991-999.
44 Xing WL (邢婉丽), Cheng J (程京) (2004) Biochip Technology (生物芯片技术). Tsinghua University Press, Beijing. (in Chinese)
45 Yang Y, Wu L, Lin Q, Yuan M, Xu D, Yu H, Hu Y, Duan J, Li X, He Z, Xue K, Van Nostrand JD, Wang S, Zhou J (2013) Responses of the functional structure of soil microbial community to livestock grazing in the Tibetan alpine grassland.Global Change Biology, 19, 637-648.
46 Ye L, Zhang T (2013) Bacterial communities in different sections of a municipal wastewater treatment plant revealed by 16S rDNA 454 pyrosequencing.Applied Microbiology and Biotechnology, 97, 2681-2690.
47 Ye L, Zhang T, Wang T, Fang Z (2012) Microbial structures, functions, and metabolic pathways in wastewater treatment bioreactors revealed using high-throughput sequencing.Environmental Science & Technology, 46, 13244-13252.
48 Yin H, Cao L, Qiu G, Wang D, Kellogg L, Zhou J, Dai Z, Liu X (2007) Development and evaluation of 50-mer oligonucleotide arrays for detecting microbial populations in Acid Mine Drainages and bioleaching systems.Journal of Microbiological Methods, 70, 165-178.
49 Zengler K, Palsson BO (2012) A road map for the development of community systems (CoSy) biology.Nature Reviews. Microbiology, 10, 366-372.
50 Zhou J, Deng Y, Luo F, He Z, Tu Q, Zhi X (2010) Functional molecular ecological networks.mBio, 1, e00169-10.
51 Zhou J, Deng Y, Luo F, He Z, Yang Y (2011) Phylogenetic molecular ecological network of soil microbial communities in response to elevated CO2.MBio, 2, e00122-11
52 Zhou J, Thompson DK, Xu Y, Tiedje JM (2004) Microbial Functional Genomics. Wiley-Liss, New York.
53 Zhou J, Xue K, Xie J, Deng Y, Wu L, Cheng X, Fei S, Deng S, He Z, Van Nostrand JD, Luo Y (2012) Microbial mediation of carbon-cycle feedbacks to climate warming.Nature Climate Change, 2, 106-110.
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