高级搜索

功能宏基因组学在新型抗生素耐药基因研究中的应用进展

,  ,  ,  ,  ,  , 

downloadPDF

上一篇

下一篇

何荣, 原珂, 林里, 杨颖, 邹世春, 栾天罡, 陈保卫. 功能宏基因组学在新型抗生素耐药基因研究中的应用进展[J]. 环境化学, 2019, (7): 1548-1556. doi: 10.7524/j.issn.0254-6108.2018090702
引用本文: 何荣, 原珂, 林里, 杨颖, 邹世春, 栾天罡, 陈保卫. 功能宏基因组学在新型抗生素耐药基因研究中的应用进展[J]. 环境化学, 2019, (7): 1548-1556. doi: 10.7524/j.issn.0254-6108.2018090702
shu
HE Rong, YUAN Ke, LIN Li, YANG Ying, ZOU Shichun, LUAN Tiangang, CHEN Baowei. Functional metagenomics: One of the most robust tools for discovering new antibiotics resistance genes[J]. Environmental Chemistry, 2019, (7): 1548-1556. doi: 10.7524/j.issn.0254-6108.2018090702
Citation: HE Rong, YUAN Ke, LIN Li, YANG Ying, ZOU Shichun, LUAN Tiangang, CHEN Baowei. Functional metagenomics: One of the most robust tools for discovering new antibiotics resistance genes[J]. Environmental Chemistry, 2019, (7): 1548-1556. doi: 10.7524/j.issn.0254-6108.2018090702
shu

功能宏基因组学在新型抗生素耐药基因研究中的应用进展

  • 1. 中山大学海洋科学学院, 广州, 510275;

  • 2. 中山大学生命科学院, 广州, 510275;

  • 3. 中山大学环境科学与工程学院, 广州, 510275

    • 通讯作者: 陈保卫, E-mail: chenbw5@mail.sysu.edu.cn
  • 基金项目:

    国家自然科学基金（21777198）资助.

Functional metagenomics: One of the most robust tools for discovering new antibiotics resistance genes

  • 1. School of Marine Sciences, Sun Yat-Sen University, Guangzhou, 510275, China;

  • 2. School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, China;

  • 3. School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou, 510275, China

    • Corresponding author: CHEN Baowei, chenbw5@mail.sysu.edu.cn
  • Fund Project: Supported by National Natural Science Foundation of China (21777198).

  • 摘要: 抗生素耐药性是二十一世纪人类面对的最严峻的环境健康问题之一.抗生素耐药基因（Antibiotics resistance genes，ARGs）被认为是一类新型环境污染物.当前针对ARGs的主要研究方法有细菌分离和培养法、聚合酶链式反应（Polymerase Chain Reaction，PCR）法、和宏基因组法.然而，仅有功能宏基因组方法能发现新型的ARGs.功能宏基因组方法利用新一代测序技术的高通量的特性，结合分子生物学技术和功能筛选构建有关抗生素耐药性的基因库，通过生物信息学分析高效地发现新型ARGs.本文综述了近来利用功能宏基因组技术筛选新型ARGs的相关研究进展，总结了功能宏基因学相关的技术和方法的优势和限制，并展望了功能宏基因学方法进一步发展的方向.
    Abstract: Antibiotic resistance is one of the greatest challenges on the public health in the world. Currently, antibiotic resistance genes (ARGs) have been regarded as a group of emerging environmental contaminants. The main analytical approaches of ARGs include isolation and incubation of bacterial strains, PCR, and new generation high-throughput sequencing-based metagenomic methods. However, functional metagenomic approach is a robust tool to find the new ARGs that have never been identified. This approach combines the high throughput of new generation sequencing platforms with function identification of constructing gene libraries, which is able to efficiently seek the novel ARGs without any of prior knowledge about the function of them. In this paper, we reviewed research progress on the application of functional metagenomics in the discovery of novel ARGs and summarized the advantages and flaws of current technologies and methods related to functional metagenomics. In final, we provided the perspectives of the future improvement on functional metagenomics.
  • 加载中
  • [1] 朱永官, 欧阳纬莹, 吴楠, 等. 抗生素耐药性的来源与控制对策[J]. 中国科学院院刊, 2015,30(4):509-516.

    ZHU Y G, OUYANG W Y, WU N, et al. Antibiotic resistance:sources and mitigation[J]. Bulletin of the Chinese Academy of Sciences, 2015, 30(4):509-516(in Chinese).

    [2] BOUKI C, VENIERI D, DIAMADOPOULOS E. Detection and fate of antibiotic resistant bacteria in wastewater treatment plants:A review[J]. Ecotoxicology and Environmental Safety, 2013,91:1-9.
    [3] XIONG W, SUN Y, ZHANG T, et al. Antibiotics, antibiotic resistance genes, and bacterial community composition in fresh water aquaculture environment in China[J]. Microbial Ecology, 2015,70(2):425-432.
    [4] BAYM M, LIEBERMAN T D, KELSIC E D, et al. Spatiotemporal microbial evolution on antibiotic landscapes[J]. Science, 2016,353(6304):1147-1151.
    [5] 郑璇, 郑育洪. 国内外超级细菌的研究进展及防控措施[J]. 中国畜牧兽医文摘, 2012,28(1):69-75.

    ZHENG X, ZHENG Y H. Research progresses and controlling measures of superbugs[J]. Chinese Abstracts of Animal Husbandry and Veterinary Medicine, 2012,28(1):69-75(in Chinese).

    [6] PRUDEN A, PEI R, STORTEBOOM H, et al. Antibiotic resistance genes as emerging contaminants:Studies in northern colorado[J]. Environmental Science & Technology, 2006,40(23):7445-7450.
    [7] COUGHLAN L M, COTTER P D, et al. Biotechnological applications of functional metagenomics in the food and pharmaceutical industries[J]. Frontiers in Microbiology, 2015,6:672.
    [8] VIKESLAND P J, PRUDEN A, ALVAREZ P J J, et al. Toward a comprehensive strategy to mitigate dissemination of environmental sources of antibiotic resistance[J]. Environmental Science & Technology, 2017,51(22):13061-13069.
    [9] PRUDEN A, ARABI M, STORTEBOOM H N. Correlation between upstream human activities and riverine antibiotic resistance genes[J]. Environmental Science & Technology, 2012,46(21):11541-11549.
    [10] CHENG G, HU Y, YIN Y, et al. Functional screening of antibiotic resistance genes from human gut microbiota reveals a novel gene fusion[J]. FEMS Microbiol Lett, 2012,336(1):11-16.
    [11] UFARTA L, POTOCKI-VERONESE G, LAVILLE A L. Discovery of new protein families and functions:New challenges in functional metagenomics for biotechnologies and microbial ecology[J]. Frontiers in Microbiology, 2015,6:563.
    [12] Dos Santos, KNUPP D F, ISTVAN P, et al. Functional metagenomics as a tool for identification of new antibiotic resistance genes from natural environments[J]. Microbial Ecology, 2017,73(2):479-491.
    [13] PEHRSSON E C, FORSBERG K J, GIBSON M K, et al. Novel resistance functions uncovered using functional metagenomic investigations of resistance reservoirs[J]. Frontiers in Microbiology, 2013,4(145):145.
    [14] WANG W, XU S, REN Z, et al. Application of metagenomics in the human gut microbiome[J]. World Journal of Gastroenterology, 2015,21(3):803-814.
    [15] PENDERS J, STOBBERINGH E E, SAVELKOUL P H M, et al. The human microbiome as a reservoir of antimicrobial resistance[J]. Frontiers in Microbiology, 2013,4(1):87.
    [16] FOUHY F, OGILVIE L A, JONES B V, et al. Identification of aminoglycoside and β-lactam resistance genes from within an infant gut functional metagenomic Library[J]. Plos One, 2014,9(9):e108016
    [17] PHUONG H, THI P, NONAKA, et al. Detection of the sul1, sul2, and sul3 genes in sulfonamide-resistant bacteria from wastewater and shrimp ponds of north Vietnam[J]. Science of the Total Environment, 2008,405(1-3):377-384.
    [18] SHARMA V K, JOHNSON N, CIZMAS L, et al. A review of the influence of treatment strategies on antibiotic resistant bacteria and antibiotic resistance genes[J]. Chemosphere, 2016,150:702-714.
    [19] GIGER W. Hydrophilic and amphiphilic water pollutants:using advanced analytical methods for classic and emerging contaminants[J]. Analytical and Bioanalytical Chemistry, 2009,393(1):37-44.
    [20] LAPARA T M, BURCH T R, MCNAMARA P J, et al. Tertiary-Treated municipal wastewater is a significant point source of antibiotic resistance genes into duluth-superior harbor[J]. Environmental Science & Technology, 2011,45(22):9543-9549.
    [21] LUO Y, MAO D, RYSZ M, et al. Trends in antibiotic resistance genes occurrence in the Haihe River, China[J]. Environ Sci Technol, 2010,44(19):7220-7225.
    [22] AMOS G C A, ZHANG L, HAWKEY P M, et al. Functional metagenomic analysis reveals rivers are a reservoir for diverse antibiotic resistance genes[J]. Veterinary Microbiology, 2014,171(3-4):441-447.
    [23] HEUER H, SCHMITT H, SMALLA K. Antibiotic resistance gene spread due to manure application on agricultural fields[J]. Current Opinion in Microbiology, 2011,14(3):236-243
    [24] WICHMANN F, UDIKOVIC-KOLIC N, ANDREW S, et al. Diverse antibiotic resistance genes in dairy cow manure[J]. MBio, 2014,5(2):379-382.
    [25] LECLERCQ S O, WANG C, ZHU Y, et al. Diversity of the tetracycline mobilome within a chinese pig manure sample[J]. Applied and Environmental Microbiology, 2016,82(21):6454-6462.
    [26] LAKAY F M, BOTHA A, PRIOR B A. Comparative analysis of environmental DNA extraction and purification methods from different humic acid-rich soils[J]. Journal of Applied Microbiology, 2007,102(1):265-273.
    [27] BERTRAND H, POLY F, VAN V T, et al. High molecular weight DNA recovery from soils prerequisite for biotechnological metagenomic library construction[J]. Journal of Microbiological Methods, 2005,62(1):1-11.
    [28] UDIKOVIC-KOLIC N, WICHMANN F, BRODERICK N A, et al. Bloom of resident antibiotic-resistant bacteria in soil following manure fertilization[J]. Proceedings of the National Academy of Sciences, 2014,111(42):15202-15207.
    [29] SU J Q, WEI B, XU C Y, et al. Functional metagenomic characterization of antibiotic resistance genes in agricultural soils from China[J]. Environment International, 2014,65:9-15.
    [30] NASRIN S, GANJI S, KAKIRDE K S, et al. Chloramphenicol derivatives with antibacterial activity identified by functional metagenomics[J]. Journal of Natural Products, 2018,81(6):1321-1332.
    [31] SALIMRAJ R, ZHANG L, HINCHLIFFE P, et al. Structural and biochemical characterization of rm3, a subclass b3 metallo-β-lactamase identified from a functional metagenomic Study[J]. Antimicrobial agents and chemotherapy, 2016,60(10):5828-5840.
    [32] LAU C H, van ENGELEN K, GORDON S, et al. Novel antibiotic resistance determinants from agricultural soil exposed to antibiotics widely used in human medicine and animal farming[J]. Applied and Environmental Microbiology, 2017,83(16):e0989-17.
    [33] FORSBERG K J, PATEL S, GIBSON M K, et al. Bacterial phylogeny structures soil resistomes across habitats[J]. Nature, 2014,509(7502):612-616.
    [34] WANG S, GAO X, GAO Y, et al. Tetracycline resistance genes identified from distinct soil environments in China by functional metagenomics[J]. Front Microbiol, 2017,8:1-9.
    [35] FORSBERG K J, REYES A, WANG B, et al. The Shared antibiotic resistome of soil bacteria and human pathogens[J]. Science, 2012,337(6098):1107-1111.
    [36] MOORE A M, PATEL S, FORSBERG K J, et al. Pediatric fecal microbiota harbor diverse and novel antibiotic resistance genes[J]. PLoS ONE, 2013,8(11):e78822.
    [37] HATOSY S M, MARTINY A C. The ocean as a global reservoir of antibiotic resistance genes[J]. Applied and Environmental Microbiology, 2015,81(21):7593-7599.
    [38] VERCAMMEN K, GARCIA-ARMISEN T, GOEDERS N, et al. Identification of a metagenomic gene cluster containing a new class A beta-lactamase and toxin-antitoxin systems[J]. Microbiologyopen, 2013,2(4):674-683.
    [39] YOU Y, HILPERT M, WARD M J. Identification of tet45, a tetracycline efflux pump, from a poultry-litter-exposed soil isolate and persistence of tet(45) in the soil[J]. Journal of Antimicrobial Chemotherapy, 2013,68(9):1962-1969.
    [40] VERSLUIS D, RODRIGUEZ DE EVGRAFOV M, SOMMER M O A, et al. Sponge microbiota are a reservoir of functional antibiotic resistance genes[J]. Frontiers in Microbiology, 2016,7:1848.
    [41] COURTOIS S, CAPPELLANO C M, BALL M, et al. Recombinant environmental libraries provide access to microbial diversity for drug discovery from natural products[J]. Applied and Environmental Microbiology, 2003,69(1):49-55.
    [42] COURTOIS S, FROSTEGARD A, GORANSSON P, et al. Quantification of bacterial subgroups in soil:comparison of DNA extracted directly from soil or from cells previously released by density gradient centrifugation[J]. Environ Microbiol, 2001,3(7):431-439.
    [43] LEVER M A, TORTI A, EICKENBUSCH P, et al. A modular method for the extraction of DNA and RNA, and the separation of DNA pools from diverse environmental sample types[J]. Frontiers in Microbiology, 2015,6(476):476.
    [44] LI H, ZHANG Y, ZHANG C G, et al. Effect of petroleum-containing wastewater irrigation on bacterial diversities and enzymatic activities in a paddy soil irrigation area[J]. Journal of Environment Quality, 2005,34(3):1073-1080.
    [45] ROBE P, NALIN R, CAPELLANO C, et al. Extraction of DNA from soil[J]. European Journal of Soil Biology, 2003,39(4):183-190.
    [46] ZHANG B, LI M, MA L, et al. A widely applicable protocol for DNA isolation from fecal samples[J]. Biochemical Genetics, 2006,44(11-12):494-503.
    [47] LI M, GONG J, COTTRILL M, et al. Evaluation of QIAamp® DNA Stool Mini Kit for ecological studies of gut microbiota[J]. Journal of Microbiological Methods, 2003,54(1):13-20.
    [48] LEE LE JIE, ABDULLAH M. Optimization of genomic DNA shearing by sonication for next-generation sequencing library preparation[J]. AsPac J. Mol. Biol. Biotechnol, 2014,22(3):200-208.
    [49] MCGARVEY K M, QUEITSCH K, FIELDS S. Wide variation in antibiotic resistance proteins identified by functional metagenomic screening of a soil DNA library[J]. Applied and Environmental Microbiology, 2012,78(6):1708-1714.
    [50] RIESENFELD C S, GOODMAN R M, HANDELSMAN J. Uncultured soil bacteria are a reservoir of new antibiotic resistance genes[J]. Environmental Microbiology, 2004,6(9):981-989.
    [51] MULLANY P. Functional metagenomics for the investigation of antibiotic resistance[J]. Virulence, 2014,5(3):443-447.
    [52] BIVER S. Bacillus subtilis as a tool for screening soil metagenomic libraries for antimicrobial activities[J]. Journal of Microbiology and Biotechnology, 2013,23(6):850-855.
    [53] STREIT W R, SCHMITZ R A. Metagenomics-the key to the uncultured microbes Wolfgang R Streit 1,2 and Ruth A Schmitz1[J]. Current Opinion in Microbiology, 2004, 7:492-498.
    [54] CHUNG E J, LIM H K, KIM J C, et al. Forest soil metagenome gene cluster involved in antifungal activity expression in Escherichia coli[J]. Appl Environ Microbiol, 2008,74(3):723-730.
    [55] DEVIRGILⅡS C, ZINNO P, STIRPE M, et al. Functional screening of antibiotic resistance genes from a representative metagenomic library of food fermenting microbiota[J]. BioMed Research International, 2014,2014:1-9.
    [56] van ELSAS J D, COSTA R, JANSSON J, et al. The metagenomics of disease-suppressive soils-experiences from the METACONTROL project[J]. Trends in Biotechnology, 2008,26(11):591-601.
    [57] MIRETE S, MORGANTE V, EDUARDO GONZALEZ-PASTOR J. Functional metagenomics of extreme environments[J]. Current Opinion In Biotechnology, 2016,38:143-149.
    [58] MCMAHON M D, GUAN C, HANDELSMAN J, et al. Metagenomic analysis of streptomyces lividans reveals host-dependent functional expression[J]. Applied and Environmental Microbiology, 2012,78(10):3622-3629.
    [59] WILHARM G, LEPKA D, FABER F, et al. A simple and rapid method of bacterial transformation[J]. Journal of Microbiological Methods, 2010,80(2):215-216.
    [60] AUNE T E V, AACHMANN F L. Methodologies to increase the transformation efficiencies and the range of bacteria that can be transformed[J]. Applied Microbiology and Biotechnology, 2010,85(5):1301-1313.
    [61] WU N, MATAND K, KEBEDE B, et al. Enhancing DNA electrotransformation efficiency in Escherichia coli DH10B electrocompetent cells[J]. Electronic Journal of Biotechnology, 2010,13(5):11.
    [62] SARASWAT M, GRAND R S, PATRICK W M. Desalting DNA by drop dialysis increases library size upon transformation[J]. Bioscience, Biotechnology, and Biochemistry, 2013,77(2):402-404.
    [63] AHMAD I, RUBBAB T, DEEBA F, et al. Optimization of E. coli culture conditions for efficient DNA uptake by electroporation[J]. Turkish Journal of Biology, 2014,38:568-573.
    [64] 高立红, 史亚利, 厉文辉, 等. 抗生素环境行为及其环境效应研究进展[J]. 环境化学, 2013,39(9):1619-1633.

    GAO L H, SHI Y L, LI W H, et al. Research progresses on environmental behavior and effects of antibiotics[J]. Environmental Chemistry, 2013, 39(9):1619-1633(in Chinese).

    [65] LANGIN A, ALEXY R, KONIG A, et al. Deactivation and transformation products in biodegradability testing of β-lactams amoxicillin and piperacillin[J]. Chemosphere, 2009,75(3):347-354.
    [66] ANDREWS J M. Determination of minimum inhibitory concentrations[J]. Journal of Antimicrobial Chemotherapy, 2001,481:5-16.
    [67] 王兴春, 杨致荣, 王敏, 等. 高通量测序技术及其应用[J]. 中国生物工程杂志, 2012,32(1):109-114.

    WANG X C, YANG Z R, WANG M, et al. High-throughput sequencing technologies and their application[J]. China Biotechnology, 2012, 32(1):109-114(in Chinese).

    [68] 曹晨霞, 韩琬, 张和平. 第三代测序技术在微生物研究中的应用[J]. 微生物学通报, 2016,43(10):2269-2276.

    CAO C X, HAN W, ZHANG H P. Application of third generation sequencing technology to microbial research[J]. Microbiology, 2016, 43(10):2269-2276(in Chinese).

    [69] 张得芳, 马秋月, 尹佟明, 等. 第三代测序技术及其应用[J]. 中国生物工程杂志, 2013,33(5):125-131.

    ZHANG D F, MA Q Y, YI D M, et al. Third-generation sequencing technologies and their application[J]. China Biotechnology, 2013, 33(5):125-131(in Chinese).

    [70] LIAO Y, LIN S, LIN H. Completing bacterial genome assemblies:Strategy and performance comparisons[J]. Scientific Reports, 2015,5(1):8747.
    [71] ZERBINO D R, BIRNEY E. Velvet:Algorithms for de novo short read assembly using de Bruijn graphs[J]. Genome Research, 2008,18(5):821-829.
    [72] VAN GOETHEM M W, PIERNEEF R, BEZUIDT O K I, et al. A reservoir of ‘historical’ antibiotic resistance genes in remote pristine Antarctic soils[J]. Microbiome, 2018,6(1):40.
    [73] FINN R D, CLEMENTS J, EDDY S R. HMMER web server:Interactive sequence similarity searching[J]. Nucleic Acids Research, 2011,39(suppl):W29-W37.
    [74] GIBSON M K, FORSBERG K J, DANTAS G. Improved annotation of antibiotic resistance determinants reveals microbial resistomes cluster by ecology[J]. 2015,9(1):207-216.
  • 加载中
WeChat 点击查看大图
计量
  • 文章访问数:  2416
  • HTML全文浏览数:  2416
  • PDF下载数:  90
  • 施引文献:  0
出版历程
  • 收稿日期:  2018-09-07

功能宏基因组学在新型抗生素耐药基因研究中的应用进展

    通讯作者: 陈保卫, E-mail: chenbw5@mail.sysu.edu.cn
  • 1. 中山大学海洋科学学院, 广州, 510275;
  • 2. 中山大学生命科学院, 广州, 510275;
  • 3. 中山大学环境科学与工程学院, 广州, 510275
  • 收稿日期:  2018-09-07
基金项目:

国家自然科学基金（21777198）资助.

摘要: 抗生素耐药性是二十一世纪人类面对的最严峻的环境健康问题之一.抗生素耐药基因（Antibiotics resistance genes，ARGs）被认为是一类新型环境污染物.当前针对ARGs的主要研究方法有细菌分离和培养法、聚合酶链式反应（Polymerase Chain Reaction，PCR）法、和宏基因组法.然而，仅有功能宏基因组方法能发现新型的ARGs.功能宏基因组方法利用新一代测序技术的高通量的特性，结合分子生物学技术和功能筛选构建有关抗生素耐药性的基因库，通过生物信息学分析高效地发现新型ARGs.本文综述了近来利用功能宏基因组技术筛选新型ARGs的相关研究进展，总结了功能宏基因学相关的技术和方法的优势和限制，并展望了功能宏基因学方法进一步发展的方向.

English Abstract

    全文HTML

参考文献 (74)

目录

/

返回文章
返回

Copyright © 2019 中国科学院生态环境研究中心