Advertisement

Molecular Microecological Techniques

  • Zongxin Ling
  • Charlie Xiang
Chapter
Part of the Advanced Topics in Science and Technology in China book series (ATSTC)

Abstract

Recent researches have shown that microbes associated with the human body are approximately 10 times more numerous than our own cells and contain, in aggregate, about 100 times more genes. This has led to the viewpoint that humans and our microbial symbionts should be considered as “superorganisms”. Some microbes cause disease, but the overwhelming majority are either innocuous or play a vital role in human development, physiology, immunity, and nutrition. However, the overall extent of bacterial diversity in different microhabitats, such as the oral cavity, urogenital tract, skin, gastrointestinal tract, nasal passages and so on, has not been studied extensively yet. The traditional microbiological techniques, such as bacterial cultivation in combination with accurate molecular identification, could not keep pace with our demands for understanding the real world of the field. Despite the rapid development in microbiology, the basic requirements for microecological studies have tremendous limitations. However, these limitations can be overcome with the advent of molecular ecology techniques based on sequence comparisons of nucleic acids (DNA and RNA) and can be used to provide molecular characteristics, while also providing a classification scheme that predicts phylogenetic relationships at the same time. Either direct or in combination with microbial cultivation, the benefits of molecular methods for microecological studies are apparent, which can acquire new and more detailed information about the microbial communities in different microhabitats.

Keywords

Microbial Community Bacterial Vaginosis Terminal Restriction Fragment Length Polymorphism Microb Ecol Specific Microhabitat 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

References

  1. [1]
    Dethlefsen L, McFall-Ngai M, Relman D A. An ecological and evolutionary perspective on human-microbe mutualism and disease. Nature, 2007, 449: 811–818.PubMedCrossRefGoogle Scholar
  2. [2]
    Turnbaugh P J, Ley R E, Hamady M, et al. The human microbiome project. Nature, 2007, 449: 804–810.PubMedCentralPubMedCrossRefGoogle Scholar
  3. [3]
    Ling Z, Liu X, Luo Y, et al. Pyrosequencing analysis of the human microbiota of healthy Chinese undergraduates. BMC Genomics, 2013, 14: 390.PubMedCentralPubMedCrossRefGoogle Scholar
  4. [4]
    Gill S R, Pop M, Deboy R T, et al. Metagenomic analysis of the human distal gut microbiome. Science, 2006, 312: 1355–1359.PubMedCentralPubMedCrossRefGoogle Scholar
  5. [5]
    Cash H L, Whitham C V, Behrendt C L, et al. Symbiotic bacteria direct expression of an intestinal bactericidal lectin. Science, 2006, 313: 1126–1130.PubMedCentralPubMedCrossRefGoogle Scholar
  6. [6]
    Ley R E, Peterson D A, Gordon J I. Ecological and evolutionary forces shaping microbial diversity in the human intestine. Cell, 2006, 124: 837–848.PubMedCrossRefGoogle Scholar
  7. [7]
    Ley R E, Turnbaugh P J, Klein S, et al. Microbial ecology: Human gut microbes associated with obesity. Nature, 2006, 444: 1022–1023.PubMedCrossRefGoogle Scholar
  8. [8]
    Mazmanian S K, Liu C H, Tzianabos A O, et al. An immunomodulatory molecule of symbiotic bacteria directs maturation of the host immune system. Cell, 2005, 122:107–118.PubMedCrossRefGoogle Scholar
  9. [9]
    Turnbaugh P J, Ley R E, Mahowald M A, et al. An obesity-associated gut microbiome with increased capacity for energy harvest. Nature, 2006, 444: 1027–1031.PubMedCrossRefGoogle Scholar
  10. [10]
    Turnbaugh P J, Hamady M, Yatsunenko T, et al. A core gut microbiome in obese and lean twins. Nature, 2009, 457: 480–484.PubMedCentralPubMedCrossRefGoogle Scholar
  11. [11]
    Frank D N, St Amand A L, Feldman R A, et al. Molecular-phylogenetic characterization of microbial community imbalances in human inflammatory bowel diseases. Proc Natl Acad Sci USA, 2007, 104: 13780–13785.PubMedCentralPubMedCrossRefGoogle Scholar
  12. [12]
    Wen L, Ley R E, Volchkov P Y, et al. Innate immunity and intestinal microbiota in the development of Type 1 diabetes. Nature, 2008, 455: 1109–1113.PubMedCentralPubMedCrossRefGoogle Scholar
  13. [13]
    Ordovas J M, Mooser V. Metagenomics: The role of the microbiome in cardiovascular diseases. Curr Opin Lipidol, 2006, 17: 157–161.PubMedCrossRefGoogle Scholar
  14. [14]
    Zhao L, Shen J. Whole-body systems approaches for gut microbiota-targeted, preventive healthcare. J Biotechnol, 2010, 149: 183–190.PubMedCrossRefGoogle Scholar
  15. [15]
    Kurokawa K, Itoh T, Kuwahara T, et al. Comparative metagenomics revealed commonly enriched gene sets in human gut microbiomes. DNA Res, 2007, 14: 169–181.PubMedCentralPubMedCrossRefGoogle Scholar
  16. [16]
    Nicholson J K, Holmes E, Wilson I D. Gut microorganisms, mammalian metabolism and personalized health care. Nat Rev Microbiol, 2005, 3: 431–438.PubMedCrossRefGoogle Scholar
  17. [17]
    Riesenfeld C S, Schloss P D, Handelsman J. Metagenomics: Genomic analysis of microbial communities. Annu Rev Genet, 2004, 38: 525–552.PubMedCrossRefGoogle Scholar
  18. [18]
    Hill J E, Goh S H, Money D M, et al. Characterization of vaginal microflora of healthy, nonpregnant women by chaperonin-60 sequence-based methods. Am J Obstet Gynecol, 2005, 193(3 Pt 1): 682–692.PubMedCrossRefGoogle Scholar
  19. [19]
    Schellenberg J, Links M G, Hill J E, et al. Pyrosequencing of the chaperonin-60 universal target as a tool for determining microbial community composition. Appl Environ Microbiol, 2009, 75: 2889–2898.PubMedCentralPubMedCrossRefGoogle Scholar
  20. [20]
    Li M, Wang B, Zhang M, et al. Symbiotic gut microbes modulate human metabolic phenotypes. Proc Natl Acad Sci USA, 2008, 105: 2117–2122.PubMedCentralPubMedCrossRefGoogle Scholar
  21. [21]
    Meyer M, Stenzel U, Hofreiter M. Parallel tagged sequencing on the 454 platform. Nat Protoc, 2008, 3: 267–278.PubMedCrossRefGoogle Scholar
  22. [22]
    von Bubnoff A. Next-generation sequencing: The race is on. Cell, 2008, 132: 721–723.CrossRefGoogle Scholar
  23. [23]
    Edwards R A, Rodriguez-Brito B, Wegley L, et al. Using pyrosequencing to shed light on deep mine microbial ecology. BMC Genomics, 2006, 7: 57.PubMedCentralPubMedCrossRefGoogle Scholar
  24. [24]
    Roesch L F, Fulthorpe R R, Riva A, et al. Pyrosequencing enumerates and contrasts soil microbial diversity. ISME J, 2007, 1: 283–290.PubMedCentralPubMedGoogle Scholar
  25. [25]
    Roh S W, Kim K H, Nam Y D, et al. Investigation of archaeal and bacterial diversity in fermented seafood using barcoded pyrosequencing. ISME J, 2010, 4: 1–16.PubMedCrossRefGoogle Scholar
  26. [26]
    Fierer N, Hamady M, Lauber C L, et al. The influence of sex, handedness, and washing on the diversity of hand surface bacteria. Proc Natl Acad Sci USA, 2008, 105: 17994–17999.PubMedCentralPubMedCrossRefGoogle Scholar
  27. [27]
    Dowd S E, Sun Y, Secor P R, et al. Survey of bacterial diversity in chronic wounds using pyrosequencing, DGGE, and full ribosome shotgun sequencing. BMC Microbiol, 2008, 8: 43.PubMedCentralPubMedCrossRefGoogle Scholar
  28. [28]
    Keijser B J, Zaura E, Huse S M, et al. Pyrosequencing analysis of the oral microflora of healthy adults. J Dent Res, 2008, 87: 1016–1020.PubMedCrossRefGoogle Scholar
  29. [29]
    Ling Z, Kong J, Jia P, et al. Analysis of oral microbiota in children with dental caries by PCR-DGGE and barcoded pyrosequencing. Microb Ecol, 2010, 60: 677–690.PubMedCrossRefGoogle Scholar
  30. [30]
    Liu W T, Marsh T L, Cheng H, et aL Characterization of microbial diversity by determining terminal restriction fragment length polymorphisms of genes encoding 16S rRNA. Appl Environ Microbiol, 1997, 63: 4516–4522.PubMedCentralPubMedGoogle Scholar
  31. [31]
    Field K G, Bernhard A E, Brodeur T J. Molecular approaches to microbiological monitoring: Fecal source detection. Environ Monit Assess, 2003, 81: 313–326.PubMedCrossRefGoogle Scholar
  32. [32]
    Kirk J L, Beaudette L A, Hart M, et al. Methods of studying soil microbial diversity. J Microbiol Methods, 2004, 58: 169–188.PubMedCrossRefGoogle Scholar
  33. [33]
    Lukow T, Dunfield P F, Liesack W. Use of the T-RFLP technique to assess spatial and temporal changes in the bacterial community structure within an agricultural soil planted with transgenic and non-transgenic potato plants. FEMS Microbiol Ecol, 2000, 32: 241–247.CrossRefGoogle Scholar
  34. [34]
    McCartney A L. Application of molecular biological methods for studying probiotics and the gut flora. Br J Nutr, 2002, 88 Suppl 1: S29-S37.CrossRefGoogle Scholar
  35. [35]
    Sakamoto M, Hayashi H, Benno Y. Terminal restriction fragment length polymorphism analysis for human fecal microbiota and its application for analysis of complex bifidobacterial communities. Microbiol Immunol, 2003, 47: 133–142.PubMedCrossRefGoogle Scholar
  36. [36]
    Sakamoto M, Rocas I N, Siqueira J F, Jr., et al. Molecular analysis of bacteria in asymptomatic and symptomatic endodontic infections. Oral Microbiol Immunol, 2006, 21: 112–122.PubMedCrossRefGoogle Scholar
  37. [37]
    Marsh T L. Terminal restriction fragment length polymorphism (T-RFLP): An emerging method for characterizing diversity among homologous populations of amplification products. Curr Opin Microbiol, 1999, 2: 323–327.PubMedCrossRefGoogle Scholar
  38. [38]
    Dorigo U, Volatier L, Humbert J F. Molecular approaches to the assessment of biodiversity in aquatic microbial communities. Water Res, 2005, 39: 2207–2218.PubMedCrossRefGoogle Scholar
  39. [39]
    Kent A D, Smith D J, Benson B J, et al. Web-based phylogenetic assignment tool for analysis of terminal restriction fragment length polymorphism profiles of microbial communities. Appl Environ Microbiol, 2003, 69: 6768–6776.PubMedCentralPubMedCrossRefGoogle Scholar
  40. [40]
    Zhou X, Brown C J, Abdo Z, et al. Differences in the composition of vaginal microbial communities found in healthy Caucasian and black women. ISME J, 2007, 1: 121–133.PubMedCrossRefGoogle Scholar
  41. [41]
    Culman S W, Bukowski R, Gauch H G, et al. T-REX: Software for the processing and analysis of T-RFLP data. BMC Bioinformatics, 2009, 10: 171.PubMedCentralPubMedCrossRefGoogle Scholar
  42. [42]
    Qian P Y, Thiyagarajan V, Lau S C K, et al. Relationship between bacterial community profile in biofilm and attachment of the acorn barnacle Balanus amphitrite. Aquat Microb Ecol, 2003, 33: 225–237.CrossRefGoogle Scholar
  43. [43]
    Zhang R, Thiyagarajan V, Qian P Y. Evaluation of terminal-restriction fragment length polymorphism analysis in contrasting marine environments. FEMS Microbiol Ecol, 2008, 65: 169–178.PubMedCrossRefGoogle Scholar
  44. [44]
    Engebretson J J, Moyer C L. Fidelity of select restriction endonucleases in determining microbial diversity by terminal-restriction fragment length polymorphism. Appl Environ Microbiol, 2003, 69: 4823–4829.PubMedCentralPubMedCrossRefGoogle Scholar
  45. [45]
    Egert M, Friedrich M W. Formation of pseudo-terminal restriction fragments, a PCR-related bias affecting terminal restriction fragment length polymorphism analysis of microbial community structure. Appl Environ Microbiol, 2003, 69: 2555–2562.PubMedCentralPubMedCrossRefGoogle Scholar
  46. [46]
    Lueders T, Friedrich M W. Evaluation of PCR amplification bias by terminal restriction fragment length polymorphism analysis of small-subunit rRNA and mcrA genes by using defined template mixtures of methanogenic pure cultures and soil DNA extracts. Appl Environ Microbiol, 2003, 69: S320-S326.PubMedCentralPubMedCrossRefGoogle Scholar
  47. [47]
    Borresen A L, Hovig E, Brogger A. Detection of base mutations in genomic DNA using denaturing gradient gel electrophoresis (DGGE) followed by transfer and hybridization with gene-specific probes. Mutat Res, 1988, 202: 77–83.PubMedCrossRefGoogle Scholar
  48. [48]
    Cariello N F, Scott J K, Kat A G, et al. Resolution of a missense mutant in human genomic DNA by denaturing gradient gel electrophoresis and direct sequencing using in vitro DNA amplification: HPRT Munich. Am J Hum Genet, 1988, 42: 726–734.PubMedCentralPubMedGoogle Scholar
  49. [49]
    Sheffield V C, Cox D R, Lerman L S, et al. Attachment of a 40-base-pair G + C-rich sequence (GC-clamp) to genomic DNA fragments by the polymerase chain reaction results in improved detection of single-base changes. Proc Natl Acad Sci USA, 1989, 86: 232–236.PubMedCentralPubMedCrossRefGoogle Scholar
  50. [50]
    Fischer S G, Lerman L S. DNA fragments differing by single base-pair substitutions are separated in denaturing gradient gels: correspondence with melting theory. Proc Natl Acad Sci USA, 1983, 80: 1579–1583.PubMedCentralPubMedCrossRefGoogle Scholar
  51. [51]
    Yamamoto M, Kameda A, Matsuura N, et al. A separation method for DNA computing based on concentration control. New Generat Comput, 2002, 20: 251–261.CrossRefGoogle Scholar
  52. [52]
    Janda J M, Abbott S L. 16S rRNA gene sequencing for bacterial identification in the diagnostic laboratory: Pluses, perils, and pitfalls. J Clin Microbiol, 2007, 45: 2761–2764.PubMedCentralPubMedCrossRefGoogle Scholar
  53. [53]
    Huys G, Vanhoutte T, Vandamme P. Application of sequence-dependent electrophoresis fingerprinting in exploring biodiversity and population dynamics of human intestinal microbiota: What can be revealed? Interdiscip Perspect Infect Dis, 2008, 2008: 597–603.Google Scholar
  54. [54]
    Yu Z, Morrison M. Comparisons of different hypervariable regions of rrs genes for use in fingerprinting of microbial communities by PCR-denaturing gradient gel electrophoresis. Appl Environ Microbiol, 2004, 70: 4800–4806.PubMedCentralPubMedCrossRefGoogle Scholar
  55. [55]
    Amp F, Miambi E. Cluster analysis, richness and biodiversity indexes derived from denaturing gradient gel electrophoresis fingerprints of bacterial communities demonstrate that traditional maize fermentations are driven by the transformation process. Int J Food Microbiol, 2000, 60: 91–97.PubMedCrossRefGoogle Scholar
  56. [56]
    Boon N, Windt W, Verstraete W, et al. Evaluation of nested PCR-DGGE (denaturing gradient gel electrophoresis) with group-specific 16S rRNA primers for the analysis of bacterial communities from different wastewater treatment plants. FEMS Microbiol Ecol, 2002, 39: 101–112.PubMedGoogle Scholar
  57. [57]
    Suzuki M T, Giovannoni S J. Bias caused by template annealing in the amplification of mixtures of 16S rRNA genes by PCR. Appl Environ Microbiol, 1996, 62: 625–630.PubMedCentralPubMedGoogle Scholar
  58. [58]
    Ling Z, Kong J, Liu F, et al. Molecular analysis of the diversity of vaginal microbiota associated with bacterial vaginosis. BMC Genomics, 2010, 11: 488.PubMedCentralPubMedCrossRefGoogle Scholar
  59. [59]
    Ling Z, Liu X, Chen X, et al. Diversity of cervicovaginal microbiota associated with female lower genital tract infections. Microb Ecol, 2011, 61: 704–714.PubMedCrossRefGoogle Scholar
  60. [60]
    Muyzer G, de Waal E C, Uitterlinden A G. Profiling of complex microbial populations by denaturing gradient gel electrophoresis analysis of polymerase chain reaction-amplified genes coding for 16S rRNA. Appl Environ Microbiol, 1993, 59: 695–700.PubMedCentralPubMedGoogle Scholar
  61. [61]
    Muyzer G. DGGE/TGGE a method for identifying genes from natural ecosystems. Curr Opin Microbiol, 1999, 2: 317–322.PubMedCrossRefGoogle Scholar
  62. [62]
    Hayes V M, Wu Y, Osinga J, et al. Improvements in gel composition and electrophoretic conditions for broad-range mutation analysis by denaturing gradient gel electrophoresis. Nucleic Acids Res, 1999, 27: e29.PubMedCentralPubMedCrossRefGoogle Scholar
  63. [63]
    Moore W E, Holdeman L V, Cato E P, et al. Comparative bacteriology of juvenile periodontitis. Infect Immun, 1985, 48: 507–519.PubMedCentralPubMedGoogle Scholar
  64. [64]
    Paster B J, Boches S K, Galvin J L, et al. Bacterial diversity in human subgingival plaque. J Bacteriol, 2001, 183: 3770–3783.PubMedCentralPubMedCrossRefGoogle Scholar
  65. [65]
    Li Y, Ku C Y, Xu J, et al. Survey of oral microbial diversity using PCR-based denaturing gradient gel electrophoresis. J Dent Res, 2005, 84: 559–564.PubMedCrossRefGoogle Scholar
  66. [66]
    DeLong E F, Wickham G S, Pace N R. Phylogenetic stains: ribosomal RNA-based probes for the identification of single cells. Science, 1989, 243: 1360–1363.PubMedCrossRefGoogle Scholar
  67. [67]
    Amann R I, Krumholz L, Stahl D A. Fluorescent-oligonucleotide probing of whole cells for determinative, phylogenetic, and environmental studies in microbiology. J Bacteriol, 1990, 172: 762–770.PubMedCentralPubMedGoogle Scholar
  68. [68]
    Moter A, Gobel U B. Fluorescence in situ hybridization (FISH) for direct visualization of microorganisms. J Microbiol Methods, 2000, 41: 85–112.PubMedCrossRefGoogle Scholar
  69. [69]
    Amann R I, Ludwig W, Schleifer K H. Phylogenetic identification and in situ detection of individual microbial cells without cultivation. Microbiol Rev, 1995, 59: 143–169.PubMedCentralPubMedGoogle Scholar
  70. [70]
    Hugenholtz P, Tyson G W, Blackall L L. Design and evaluation of 16S rRNA-targeted oligonucleotide probes for fluorescence in situ hybridization. Methods Mol Biol, 2002, 179: 29–42.PubMedGoogle Scholar
  71. [71]
    Amann R, Ludwig W. Ribosomal RNA-targeted nucleic acid probes for studies in microbial ecology. FEMS Microbiol Rev, 2000, 24: 555–565.PubMedCrossRefGoogle Scholar
  72. [72]
    Ludwig W, Strunk O, Westram R, et al. ARB: a software environment for seauence data. Nucleic Acids Res. 2004, 32(4): 1363–1371.PubMedCentralPubMedCrossRefGoogle Scholar
  73. [73]
    Navin N, Grubor V, Hicks J, et al. PROBER: Oligonucleotide FISH probe design software. Bioinformatics, 2006, 22: 2437–2438.PubMedCrossRefGoogle Scholar
  74. [74]
    Maruyama A, Sunamura M. Simultaneous direct counting of total and specific microbial cells in seawater, using a deep-sea microbe as target. Appl Environ Microbiol, 2000, 66: 2211–2215.PubMedCentralPubMedCrossRefGoogle Scholar
  75. [75]
    Southwick P L, Ernst L A, Tauriello E W, et al. Cyanine dye labeling reagents--carboxymethylindocyanine succinimidyl esters. Cytometry, 1990, 11: 418–430.PubMedCrossRefGoogle Scholar
  76. [76]
    Yilmaz S, Haroon M F, Rabkin B A, et al. Fixation-free fluorescence in situ hybridization for targeted enrichment of microbial populations. ISME J, 2010, 4: 1352–1356.PubMedCrossRefGoogle Scholar
  77. [77]
    Fredricks D N, Fiedler T L, Marrazzo J M. Molecular identification of bacteria associated with bacterial vaginosis. N Engl J Med, 2005, 353: 1899–1911.PubMedCrossRefGoogle Scholar
  78. [78]
    Wagner M, Haider S. New trends in fluorescence in situ hybridization for identification and functional analyses of microbes. Curr Opin Biotechnol, 2012, 23: 96–102.PubMedCrossRefGoogle Scholar
  79. [79]
    Amann R, Fuchs B M, Behrens S. The identification of microorganisms by fluorescence in situ hybridisation. Curr Opin Biotechnol, 2001, 12: 231–236.PubMedCrossRefGoogle Scholar
  80. [80]
    Gentry T J, Wickham G S, Schadt C W, et al. Microarray applications in microbial ecology research. Microb Ecol, 2006, 52: 159–175.PubMedCrossRefGoogle Scholar
  81. [81]
    Schena M, Shalon D, Davis R W, et al. Quantitative monitoring of gene expression patterns with a complementary DNA microarray. Science, 1995, 270: 467–470.PubMedCrossRefGoogle Scholar
  82. [82]
    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: 291–299.PubMedCrossRefGoogle Scholar
  83. [83]
    Wilson K H, Wilson W J, Radosevich J L, et al. High-density microarray of small-subunit ribosomal DNA probes. Appl Environ Microbiol, 2002, 68: 2535–2541.PubMedCentralPubMedCrossRefGoogle Scholar
  84. [84]
    Brodie E L, Desantis T Z, Joyner D C, et al. Application of a high-density oligonucleotide microarray approach to study bacterial population dynamics during uranium reduction and reoxidation. Appl Environ Microbiol, 2006, 72: 6288–6298.PubMedCentralPubMedCrossRefGoogle Scholar
  85. [85]
    DeSantis T Z, Brodie E L, Moberg J P, et al. High-density universal 16S rRNA microarray analysis reveals broader diversity than typical clone library when sampling the environment. Microb Ecol, 2007, 53: 371–383.PubMedCrossRefGoogle Scholar
  86. [86]
    Wagner M, Smidt H, Loy A, et al. Unravelling microbial communities with DNA-microarrays: challenges and future directions. Microb Ecol, 2007, 53: 498–506.PubMedCrossRefGoogle Scholar
  87. [87]
    Bodrossy L, Sessitsch A. Oligonucleotide microarrays in microbial diagnostics. Curr Opin Microbiol, 2004, 7: 245–254.PubMedCrossRefGoogle Scholar
  88. [88]
    Rajilic-Stojanovic M, Smidt H, de Vos W M. Diversity of the human gastrointestinal tract microbiota revisited. Environ Microbiol, 2007, 9: 2125–2136.PubMedCrossRefGoogle Scholar
  89. [89]
    Schloss P D, Handelsman J. Status of the microbial census. Microbiol Mol Biol Rev, 2004, 68: 686–691.PubMedCentralPubMedCrossRefGoogle Scholar
  90. [90]
    Frias-Lopez J, Shi Y, Tyson G W, et al. Microbial community gene expression in ocean surface waters. Proc Natl Acad Sci USA, 2008, 105: 3805–3810.PubMedCentralPubMedCrossRefGoogle Scholar
  91. [91]
    Wu L, Thompson D K, Li G, et al. Development and evaluation of functional gene arrays for detection of selected genes in the environment. Appl Environ Microbiol, 2001, 67: 5780–5790.PubMedCentralPubMedCrossRefGoogle Scholar
  92. [92]
    Sebat J L, Colwell F S, Crawford R L. Metagenomic profiling: microarray analysis of an environmental genomic library. Appl Environ Microbiol, 2003, 69: 4927–4934.PubMedCentralPubMedCrossRefGoogle Scholar
  93. [93]
    Park S J, Kang C H, Chae J C, et al. Metagenome microarray for screening of fosmid clones containing specific genes. FEMS Microbiol Lett, 2008, 284: 28–34.PubMedCrossRefGoogle Scholar
  94. [94]
    Rajilic-Stojanovic M, Heilig H G, Molenaar D, et al. Development and application of the human intestinal tract chip, a phylogenetic microarray: analysis of universally conserved phylotypes in the abundant microbiota of young and elderly adults. Environ Microbiol, 2009, 11: 1736–1751.PubMedCentralPubMedCrossRefGoogle Scholar
  95. [95]
    Zoetendal E G, Rajilic-Stojanovic M, de Vos W M. High-throughput diversity and functionality analysis of the gastrointestinal tract microbiota. Gut, 2008, 57: 1605–1615.PubMedCrossRefGoogle Scholar
  96. [96]
    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: 67–77.PubMedCrossRefGoogle Scholar
  97. [97]
    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: 1167–1179.PubMedCrossRefGoogle Scholar
  98. [98]
    Lee Y J, van Nostrand J D, Tu Q, et al. The PathoChip, a functional gene array for assessing pathogenic properties of diverse microbial communities. ISME J, 2013, 7: 1974–1984.PubMedCentralPubMedCrossRefGoogle Scholar
  99. [99]
    He Z, Van Nostrand J D, Zhou J. Applications of functional gene microarrays for profiling microbial communities. Curr Opin Biotechnol, 2012, 23: 460–466.PubMedCrossRefGoogle Scholar
  100. [100]
    Chandler D P, Jarrell A E. Automated purification and suspension array detection of 16S rRNA from soil and sediment extracts by using tunable surface microparticles. Appl Environ Microbiol, 2004, 70: 2621–2631.PubMedCentralPubMedCrossRefGoogle Scholar
  101. [101]
    Liu R H, Yang J, Lenigk R, et al. Self-contained, fully integrated biochip for sample preparation, polymerase chain reaction amplification, and DNA microarray detection. Anal Chem, 2004, 76: 1824–1831.PubMedCrossRefGoogle Scholar
  102. [102]
    Liu W T, Zhu L. Environmental microbiology-on-a-chip and its future impacts. Trends Biotechnol, 2005, 23: 174–179.PubMedCrossRefGoogle Scholar
  103. [103]
    Jayaraman A, Hall C K, Genzer J. Computer simulation study of molecular recognition in model DNA microarrays. Biophys J, 2006, 91: 2227–2236.PubMedCentralPubMedCrossRefGoogle Scholar
  104. [104]
    Liu W T, Mirzabekov A D, Stahl D A. Optimization of an oligonucleotide microchip for microbial identification studies: A non-equilibrium dissociation approach. Environ Microbiol, 2001, 3: 619–629.PubMedGoogle Scholar
  105. [105]
    Pozhitkov A E, Stedtfeld R D, Hashsham S A, et al. Revision of the nonequilibrium thermal dissociation and stringent washing approaches for identification of mixed nucleic acid targets by microarrays. Nucleic Acids Res, 2007, 35: e70.PubMedCentralPubMedCrossRefGoogle Scholar
  106. [106]
    von Wintzingerode F, Gobel U B, Stackebrandt E. Determination of microbial diversity in environmental samples: pitfalls of PCR-based rRNA analysis. FEMS Microbiol Rev, 1997, 21: 213–229.CrossRefGoogle Scholar
  107. [107]
    Wang G C, Wang Y. The frequency of chimeric molecules as a consequence of PCR co-amplification of 16S rRNA genes from different bacterial species. Microbiology, 1996, 142 (Pt 5): 1107–1114.PubMedCrossRefGoogle Scholar
  108. [108]
    Pryde S E, Richardson A J, Stewart C S, et al. Molecular analysis of the microbial diversity present in the colonic wall, colonic lumen, and cecal lumen of a pig. Appl Environ Microbiol, 1999, 65: 5372–5377.PubMedCentralPubMedGoogle Scholar
  109. [109]
    Wang Q, Garrity G M, Tiedje J M, et al. Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy. Appl Environ Microbiol, 2007, 73: 5261–5267.PubMedCentralPubMedCrossRefGoogle Scholar
  110. [110]
    Zhu X Y, Zhong T, Pandya Y, et al. 16S rRNA-based analysis of microbiota from the cecum of broiler chickens. Appl Environ Microbiol, 2002, 68: 124–137.PubMedCentralPubMedCrossRefGoogle Scholar
  111. [111]
    Handelsman J. Metagenomics: Application of genomics to uncultured microorganisms. Microbiol Mol Biol Rev, 2004, 68: 669–685.PubMedCentralPubMedCrossRefGoogle Scholar
  112. [112]
    Venter J C, Remington K, Heidelberg J F, et al. Environmental genome shotgun sequencing of the Sargasso Sea. Science, 2004, 304: 66–74.PubMedCrossRefGoogle Scholar
  113. [113]
    Grice E A, Segre J A. The human microbiome: Our second genome. Annual review of genomics and human genetics, 2012, 13: 151–170.PubMedCentralPubMedCrossRefGoogle Scholar
  114. [114]
    Nelson K E, Weinstock G M, Highlander S K, et al. A catalog of reference genomes from the human microbiome. Science, 2010, 328: 994–999.PubMedCrossRefGoogle Scholar
  115. [115]
    Qin J, Li R, Raes J, et al. A human gut microbial gene catalogue established by metagenomic sequencing. Nature, 2010, 464: 59–65.PubMedCentralPubMedCrossRefGoogle Scholar
  116. [116]
    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 USA, 2006, 103: 12115–12120.PubMedCentralPubMedCrossRefGoogle Scholar
  117. [117]
    Shokralla S, Spall J L, Gibson J F, et al. Next-generation sequencing technologies for environmental DNA research. Molecular ecology, 2012, 21: 1794–1805.PubMedCrossRefGoogle Scholar
  118. [118]
    Hajibabaei M, Shokralla S, Zhou X, et al. Environmental barcoding: A next-generation sequencing approach for biomonitoring applications using river benthos. PloS one 2011, 6(4): e17497.PubMedCentralPubMedCrossRefGoogle Scholar
  119. [119]
    Egan A N, Schlueter J, Spooner D M. Applications of next-generation sequencing in plant biology. American Journal of Botany, 2012, 99: 175–185.PubMedCrossRefGoogle Scholar
  120. [120]
    Zhang J, Chiodini R, Badr A, et al. The impact of next-generation sequencing on genomics. Journal of genetics and genomics = Yi chuan xue bao, 2011, 38: 95–109.PubMedCentralPubMedCrossRefGoogle Scholar
  121. [121]
    Glenn T C. Field guide to next-generation DNA sequencers. Molecular ecology resources, 2011, 11: 759–769.PubMedCrossRefGoogle Scholar
  122. [122]
    Margulies M, Egholm M, Altman W E, et al. Genome sequencing in microfabricated high-density nicolitre reactors. Nature, 2005, 437: 376–380.PubMedCentralPubMedGoogle Scholar
  123. [123]
    Rothberg J M, Leamon J H. The development and impact of 454 sequencing. Nat Biotechnol, 2008, 26: 1117–1124.PubMedCrossRefGoogle Scholar
  124. [124]
    Rothberg J M, Hinz W, Rearick T M, et al. An integrated semiconductor device enabling non-optical genome sequencing. Nature, 2011, 475: 348–352.PubMedCrossRefGoogle Scholar
  125. [125]
    Howden B P, McEvoy C R, Allen D L, et al. Evolution of multidrug resistance during Staphylococcus aureus infection involves mutation of the essential two component regulator WalKR. PLoS Pathog, 2011, 7: e1002359.PubMedCentralPubMedCrossRefGoogle Scholar
  126. [126]
    Mardis E R. The impact of next-generation sequencing technology on genetics. Trends Genet, 2008, 24: 133–141.PubMedCrossRefGoogle Scholar
  127. [127]
    Ashelford K, Eriksson M E, Allen C M, et al. Full genome re-sequencing reveals a novel circadian clock mutation in Arabidopsis. Genome Biol, 2011, 12: R28.PubMedCentralPubMedCrossRefGoogle Scholar
  128. [128]
    Shulaev V, Sargent D J, Crowhurst R N, et al. The genome of woodland strawbeny (Fragaria vesca). Nat Genet, 2011, 43: 109–116.PubMedCentralPubMedCrossRefGoogle Scholar
  129. [129]
    Shendure J, Porreca G J, Reppas N B, et al. Accurate multiplex polony sequencing of an evolved bacterial genome. Science, 2005, 309: 1728–1732.PubMedCrossRefGoogle Scholar
  130. [130]
    Liu L, Li Y, Li S, et al. Comparison of next-generation sequencing systems. J Biomed Biotechnol, 2012, 2012: 251364.PubMedCentralPubMedGoogle Scholar
  131. [131]
    Ku C S, Roukos D H. From next-generation sequencing to nanopore sequencing technology: paving the way to personalized genomic medicine. Expert Rev Med Devices, 2013, 10: 1–6.PubMedCrossRefGoogle Scholar
  132. [132]
    Harris T D, Buzby P R, Babcock H, et al. Single-molecule DNA sequencing of a viral genome. Science, 2008, 320: 106–109.PubMedCrossRefGoogle Scholar
  133. [133]
    Eid J, Fehr A, Gray J, et al. Real-time DNA sequencing from single polymerase molecules. Science, 2009, 323: 133–138.PubMedCrossRefGoogle Scholar
  134. [134]
    Flusberg B A, Webster D R, Lee J H, et al. Direct detection of DNA methylation during single-molecule, real-time sequencing. Nat Methods, 2010, 7: 461–465.PubMedCentralPubMedCrossRefGoogle Scholar

Copyright information

© Zhejiang University Press, Hangzhou and Springer-Verlag Berlin Heidelberg 2014

Authors and Affiliations

  • Zongxin Ling
    • 1
    • 2
  • Charlie Xiang
    • 1
    • 2
  1. 1.The State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, the First Affiliated Hospital, School of MedicineZhejiang UniversityHangzhouChina
  2. 2.Collaborative Innovation Center for Diagnosis and Treatment of Infectious DiseasesHangzhouChina

Personalised recommendations