Microbiology in the post-genomic era

Nature Reviews Microbiology

Volumn 6, Issue 6, 2008, Pages 419-430

  Medini, Duccio ^a   Serruto, Davide ^a   Parkhill, Julian ^b   Relman, David A ^c   Donati, Claudio ^a   Moxon, Richard ^d   Falkow, Stanley ^c   Rappuoli, Rino ^a  

^a NOVARTIS VACCINES AND DIAGNOSTICS   (Italy)

^b WELLCOME TRUST SANGER INSTITUTE   (United Kingdom)

^c STANFORD UNIVERSITY   (United States)

^d UNIVERSITY OF OXFORD   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

ANTIBIOTIC AGENT; BACTERIAL DNA; RNA 16S; STREPTOCOCCUS VACCINE;

ANTIBIOTIC RESISTANCE; ARTICLE; BACTERIAL GENETICS; BACTERIAL GENOME; BACTERIAL STRAIN; BACTERIAL TRANSMISSION; BACTERIAL VIRULENCE; BACTERIUM IDENTIFICATION; CLASSIFICATION; DNA DNA HYBRIDIZATION; DNA SEQUENCE; GENE EXPRESSION; GENETIC ANALYSIS; GENETIC VARIABILITY; GENOMICS; HIGH THROUGHPUT SCREENING; HORIZONTAL GENE TRANSFER; HOST PATHOGEN INTERACTION; HUMAN; INTESTINE FLORA; MICROBIAL COMMUNITY; MOLECULAR EVOLUTION; MULTILOCUS ENZYME ELECTROPHORESIS; MULTILOCUS SEQUENCE TYPING; NONHUMAN; PRIORITY JOURNAL; PYROSEQUENCING; RNA ANALYSIS; SEQUENCE DATABASE; SEQUENCE HOMOLOGY; SINGLE NUCLEOTIDE POLYMORPHISM; STREPTOCOCCUS AGALACTIAE;

BACTERIA; DNA, BACTERIAL; ENVIRONMENTAL HEALTH; ENVIRONMENTAL MICROBIOLOGY; EVOLUTION, MOLECULAR; GENOMICS; HUMANS; MICROBIOLOGY;

BACTERIA (MICROORGANISMS);

EID: 43849099955     PISSN: 17401526     EISSN: None     Source Type: Journal    
DOI: 10.1038/nrmicro1901     Document Type: Article

References (92)

1. Dighe, A. S. et al. Comparison of 16S rRNA gene sequences of genus Methanobrevibacter. BMC Microbiol. 4, 20 (2004).
2. Keswani, J. & Whitman, W. B. Relationship of 16S rRNA sequence similarity to DNA hybridization in prokaryotes. Int. J. Syst Evol. Microbiol. 51, 667-678 (2001).
3. Acinas, S. G. et al. Fine-scale phylogenetic architecture of a complex bacterial community. Nature 430, 551-554 (2004).
4. Konstantinidis, K. T., Ramette, A. & Tiedje, J. M. The bacterial species definition in the genomic era. Philos. Trans. R. Soc. Lond. B 361, 1929-1940 (2006).
5. Sacchi, C. T. et al. Sequencing of 16S rRNA gene: A rapid tool for identification of Bacillus anthracis. Emerg. Infect. Dis. 8, 1117-1123 (2002).
6. Huber, H. et al. A new phylum of Archaea represented by a nanosized hyperthermophilic symbiont. Nature 417, 63-67 (2002).
7. Selander, R. K. et al. Methods of multilocus enzyme electrophoresis for bacterial population genetics and systematics. Appl. Environ. Microbiol. 51, 873-884 (1986).
8. Caugant, D. A., Kristiansen. B. E., Froholm, L. O., Bovre, K. & Selander, R. K. Clonall diversity of Neisseria meningiddis from a population of asymptomatic carriers. Infect. Immun. 56, 2060-2068 (1988).
9. Maiden, M. C. et al. Multilocus sequence typing: A portable approach to the identification of clones within populations at pathogenic microorganisms. Proc Natl. Acad. Sci. USA 95, 3140-3145 (1998).
10. Moxon, R., Bayliss, C. & Hood, D. Bacterial contingency loci: The role of simple sequence DNA epeats in bacterial adaptation. Annu. Rev. Genet. 40, 307-333 (2006).
11. Dobrindt, U., Hochhut, B., Hentschel, U. & Hacker, J. Genomic islands in pathogenic and environmental microorganisms. Nature Rev. Microbiol. 2, 414-424 (2004).
12. Falkow, S. in Escherichia coli and Salmonella typhimurium: Cellular and Molecular Biology (eds Neidhardt, F C. et al.) 2723-2729 (ASM, Washington DC, 1996).
13. Urwin, R. et al. Distribution of surface protein variants among hyperinvasive meningococci: Implications for vaccine design. Infect. Immun. 72, 5955-5962 (2004).
14. Caugant, D. A. et al. Genetic diversity in relation to serotype in Escherichid coli. Infect. Immun. 49, 407-413 (1985).
15. Tettelin, H. et al. Genome analysis of multiple pathogenic isolates of Streptococcus agalactiae: Implications for the microbial "pan-genome". Proc. Natl Acad. Sci. USA 102, 13950-13955 (2005).
16. Moorhead, S. M., Dykes, G. A. & Cursons, R. T. An SNP-based PCR assay to differentiate between Listeria monocytogenes lineages derived from phylogenetic analysis of the sigB gene. J. Microbiol. Methods 55, 425-432 (2003).
17. Robertson, G. A. et al. Identification and interrogation of highly informative single nucleotide polymorphism sets defined by bacterial multilocus sequence typing databases. J. Med. Microbiol. 53, 35-45 (2004).
18. Weissman, S. J., Moseley, S. L., Dykhuizen, D. E. & Sokurenko, E. V. Enterobacterial adhesins and the case for studying SNPs in bacteria. Trends Microbiol. 11, 115-117 (2003).
19. Read, T D. et al. Comparative genome sequencing for discovery of novel polymorphisms in Bacillus anthracis. Science 296, 2028-2033 (2002).
20. Alland, D. et al. Modeling bacterial evolution with comparative-genome-based marker systems: Application to Mycobacterfum tuberculosis evolution and pathogenesis. J. Bacteriol. 185 3392-3399 (2003).
21. Gutacker, M. M. et al. Genome-wide analysis of synonymous single nucleotide polymorphisms in Mycobacterium tuberculosis complex organisms: Resolution of genetic relationships among closely related microbial strains. Genetics 162, 1533-1543 (2002).
22. Filliol, I. et al. Global phylogeny of Mycobacterium tuberculosis based on single nucleotide polymorphism (SNP) analysis: insights into tuberculosis evolution, phylogenetic accuracy of other DNA fingerprinting systems, and recommendations for a minimal standard SNP set. J. Bacteriol. 188, 759-772 (2006).
23. Roumagnac, P. et al. Evolutionary history of Salmonella typhi. Science 314, 1301-1304 (2006).
24. Sanger, F., Nicklen, S. & Coulson, A. R. DNA sequencing with chain-terminating inhibitors. Proc. Natl Acad. Sci. USA 74, 5463-5467 (1977).
25. Smith, L. M. et al. Fluorescence detection in automated DNA sequence analysis. Nature 321, 674-679 (1986).
26. Prober, J. M. et al. A system for rapid DNA sequencing with fluorescent chain-terminating dideoxynucleotides: Science 238 336-341 (1987).
27. Madabhushi, R. S. Separation of 4-color DNA sequencing extension prooucts in noncovalently coated capillaries using low viscosity polymer solutions. Electrophoresis 19, 224-230 (1998).
28. Hall, N. Advanced sequencing technologies and their wider impact in microbiology. J. Exp. Biol. 210, 1518-1525 (2007).
29. Schuster, S. C. Next-generation sequencing transforms today's biology. Nature Methods 5, 16-18 (2008).
30. Margulies, M. et al. Genome sequencing in microfabricated high-density picolitre reactors. Nature 437, 376-380 (2005).
31. Shendure, J. et al. Accurate multiplex polony sequencing of an evolved bacterial genome. Science 309, 1728-1732 (2005).
32. Bennett, S. Solexa Ltd. Pharmacogenomics 5, 433-438 (2004).
33. Bennett, S. T., Barnes, C., Cox, A., Davies, L. & Brown, C. Toward the 1,000 dollars human genome. Pharmacogenomics 6, 373-382 (2005).
34. Goldberg, S. M. et al. A Sanger/pyrosequencing hybrid approach for the generation of high-quality draft assemblies of marine microbial genomes. Proc Natl Acad. Sci. USA 103, 11240-11245 (2006).
35. Parkhill, J. et al. The genome sequence of the food-borne pathogen Campylobacter jejuni reveals hypervariable sequences. Nature 403, 665-668 (2000).
36. Gundogdu, O. et al. Re-annotation and re-analysis of the Campylobacter jejuni NCTC 11168 genome sequence. BMC Genomics 8, 162 (2007).
37. Baker, S. & Dougan, G. The genome of Salmonella enterica serovar Typhi. Clin. Infect. Dis. 45 (Suppl. 1), 29-33 (2007).
38. Cerdeno-Tarraga, A. M. et al. Extensive DNA inversions in the B. fragilis genome control variable gene expression. Science 307, 1463-1465 (2005).
39. Bentley, S. D. et al. Sequencing and analysis of the genome of the Whipple's disease bacterium Tropheryma whipplei. Lancet 361, 637-644 (2003).
40. Braslavsky I., Hebert, B., Kartalov, E. & Quake, S. R. Sequence information can be obtained from single DNA molecules. Proc. Natl. Acad. Sci. USA 100, 3960-3964 (2003).
41. Kasianowicz, J. J., Brandin, E., Branton, D. & Deamer, D. W. Characterization of individual polynucleotide molecules using a membrane channel. Proc Natl Acad. Sci. USA 93, 13770-13773 (1996).
42. Storm A. J. et al. Fast DNA translocation through a solid-state nanopore. Nano Lett. 5, 1193-1197 (2005).
43. Storm, A. J., Chen, J. H., Zandbergen, H. W & Dekker, C. Translocation of double-strand DNA through a silicon oxide nanopore. Phys. Rev. E Stat Nonlin. Soft Matter Phys. 71, 051903 (2005).
44. Fraser-Liggett, C. M. Insights on biology and evolution from microbial genome sequencing. Genome Res. 15, 1603-1610 (2005).
45. Perna, N. T. et al. Genome sequence of enterohaemorrhagic Escherichic coli O157:H7. Nature 409, 529-533 (2001).
46. Welch, R. A. et al. Extensive mosaic structure revealed by the complete genome sequence of uropathogenic Eschertchia coli. Proc. Natl. Acad. Sci. USA 99, 17020-17024 (2002).
47. Brochet, M. et al. Genomic diversity and evolution within the species Streptococcus agalactiae. Microbes Infect. 8, 1227-1243 (2006).
48. Brzusikiewicz, E. et al. How to become a uropathogen: Comparative genomic analysis of extraintestinal pathogenic Escherichia coli strains. Proc. Natl. Acad. Sci. USA 103, 12879-12884 (2006).
49. Tettelin, H., Medini, D., Donati, C. & Masignani. V. Towards a universal group B Streptococcus vaccine using multistrain genome analysis. Expert Rev. Vaccines 5, 687-694 (2006).
50. Hogg, J. S. et al. Characterization and modeling of the Hoemophilus influenzae core and supragenomes based on the complete genomic sequences of Rd and 12 clinical nontypeable strains. Genome Biol. 8, R103 (2007).
51. Hiller, N. L. et al. Comparative genomic analyses of seventeen Streptococcus pneumoniae strains: Insights into the pneumococcal supragenome. J. Bacteriol. 189, 8186-8195 (2007).
52. Ochman, H., Lawrence, J. G. & Groisman, E. A. Lateral gene transfer and the nature of bacterial innovation. Nature 405, 299-304 (2000).
53. Maione, D. et al. Identification of a universal group B Streptococcus vaccine by multiple genome screen. Science 309 148-150 (2005).
54. Lauer, P. et al. Genome analysis reveals pili in group B Streptococcus. Science 309, 105 (2005).
55. Handelsman. J. Metagenomics: Application of genomics to uncultured microorganisms, Microbiol. Mol. Biol. Rev. 68, 669-685 (2004).
56. National Research Council. The New Science of Metagenomics: Revealing the Secrets of Our Microbial Planet (the National Academies, Washington DC, 2007).
57. Tringe, S. G. et al. Comparative metagenomics of microbial communities. Science 308, 554-557 (2005).
58. Tyson, G. W. et al. Community structure and metabolism through reconstruction of microbial genornes from the environment. Nature 428, 37-43 (2004).
59. Venber, J. C. et al. Environmental genome shotgun sequencing of the Sargasso Sea. Science 304, 66-74 (2004).
60. Gill, S. R. et al. Metagenomic analysis of the human distal gut microbiome. Science 312, 1355-1359 (2006).
61. Tumbaugh, P. J. et al. An obesity-associated gut microbiome with increased capacity for energy harvest. Nature 444, 1027-1031 (2006).
62. Tringe, S. G. & Rubin, E. M. Metagenomics: DNA sequencing of environmental samples. Nature Rev. Genet. 6, 805-814 (2005).
63. Dethlelsen, L, McFall-Ngai, M. & Relman, D. A. An ecological and evolutionary perspective on human - microbe mutualism and disease. Nature 449, 811-818 (2007).
64. Versalovic, J. & Reiman, D. How bacterial communities expand functional repertoires. PLoS Biol. 4, e430 (2006).
65. Ley. R. E. Peterson, D. A. Cordon, J. I. Ecological and evolutionary forces shaping microbial diversity in the human intestine. Cell 124, 837-848 (2000).
66. Eckburg, P. B. et al. Diversity of the human intestinal microbial flora. Science 308, 1635-1638 (2005).
67. Doolittle W. F. & Papke, R. T. Genomics and the bacterial species problem. Genome Biol. 7, 116 (2006).
68. Goldenfeld, N. & Woese, C. Biology's next revolution. Nature 445, 369 (2007).
69. Alm. R. A. et al. Genomic-sequence comparison of two unrelated isolates of the human gastric pathogen Helicobacterpy lori. Nature 397, 176-180 (1999).
70. Parkhill, J. et al. Complete DNA sequence of a serogroup A strain of Neisseria meningitidis Z2491. Nature 404, 502-506 (2000).
71. Tettelin, H. et al. Complete genome sequence of Neisseria meningitidis serogroup B strain MC58. Science 287, 1809-1815 (2000).
72. Silverman, M., Zieg, J., Hilmen, M. & Simon, M. Phase variation in Salmonella: Genetic analysis of a recombinational switch. Proc Natl Acad. Sci. USA 76, 391-395 (1979).
73. Kuwahara, T. et al. Genomic analysis of Bacteraides fragilis reveals extensive DNA inversions regulating cell surface adaptation. Proc. Natl Acad. Sci. USA 101, 14919-14924 (2004).
74. Chambaud, I. et al. The complete genome sequence of the murine respiratory pathogen Mycoplasma pulmonis. Nucleic Acids Res 29 2145-2153 (2001).
75. Liu, M. et al. Reverse transcriptase-mediated tropism switching in Bordetella bacteriophage. Science 295, 2091-2094 (2002).
76. Medini, D., Donati, C., Tettelin, H., Masignani, V. & Rappuoli, R. The microbial pan-genome. Curr. Opin. Genet. Dev. 15, 589-594 (2005).
77. Rusch. D. B. et al. The Sorcerer II Global Ocean Sampling expedition: Northwest Atlantic through eastern tropical Pacific. PLoS Biol. 5, e77 (2007).
78. Yooseph, S. et al. The Sorcerer II Global Ocean Sampling expedition: Expanding the universe of protein families. PLoS Biol. 5, e16 (2007).
79. Medini, D., Covacci, A. & Donati, C. Protein homology network families reveal step-wise cliversification of Type III and Type IV secretion systems. PloS Comput Biol. 2, e173 (2006).
80. Rappuoli, R. Reverse vaccinology. Curr. Opin. Microbiol. 3, 445-450 (2000).
81. Jolley, K. A., Chan, M. S. & Maiden, M. C. mlstdbNet - distributed multi-locus sequence typing (MLST) databases. BMC Bioinformatics 5, 86 (2004).
82. Didelot, X. & Falush, D. Inference of bacterial microevolution using multilocus sequence data. Genetics 175, 1251-1266 (2007).
83. Didelot, X., Achtman, M., Parkhill, J., Thomson. N. R. & Falush. D. A bimodal pattern of relatedness betvveen. the Salmonella Paratyphi A and Typhi genomes: Convergence or divergence by homologous recombination? Genome Res. 17, 61-68 (2007).
84. Marcy, Y. et al. Dissecting biological "dark matter" with single-cell genetic analysis of rare and uncultivated TM7 microbes from the human mouth. Proc. Natl Acad. Sci. USA 104, 11889-11894 (2007).
85. Dethiefsen, L. & Reiman, D. A. The importance of individuals and scale: moving towards single cell microbiology. Environ. Microbiol. 9 8-10 (2007).
86. Dethlefsen, L., Eckburg, P. B., Bik, E. M. & Reiman, D. A. Assembly of the human intestinal microbiota. Trends Ecol. Evol. 21, 517-523 (2006).
87. Relman, D. A. Genome-wide responses of a pathogenic bacterium to its host. J. Clin. Invest. 110, 1071-1073 (2002).
88. Relman, D. A. & Falkow, S. The meaning and impact of the human genome sequence for microbiology. Trends Microbiol. 9, 206-208 (2001).
89. Turnbaugh, P. J. et al. The Human Microbiome Project. Nature 449, 804-810 (2007).
90. Bentley, S. D. et al. Meningococcal genetic variation mechanisms viewed through comparative analysis of serogroup C strain FAM18. PLaS Genet. 3, e23 (2007).
91. Sacchi, C. T., Whitney, A. M.. Reeves, M. W., Mayer, L. W. & Popovic, T. Sequence diversity of Neisseria meningitidis 16S rRNA genes and use of 16S rRNA gene sequencing as a molecular subtyping tool. J. Clin. Microbiol. 40, 4520-4527 (2002).
92. Deng, W. et al. Comparative genomics of Salmonella enterica serovar Typhi strains Ty2 and CT18. J. Bacteriol. 185, 2330-2337 (2003).