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Chapter 34 : Phylogenetic Diversity of Microbial Pathogens

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Abstract:

Culture methods remain significantly inadequate in duplicating the physiological needs of microorganisms and, in particular, environmental microorganisms. With the advent of sequence-based (molecular) phylogeny has come the ability to detect and analyze the compositions of microbial communities without reliance on in vitro microbial cultivation. Pathogenic microorganisms often elicit host tissue pathology and clinical manifestations as they propagate in privileged anatomic sites. Comparative rRNA analysis depends upon selection of an appropriate group of homologous sequences, rigorous sequence alignment with preservation of conserved secondary structures, and use of appropriate phylogenetic inference methods. Several features make ss rRNA molecules useful and reliable evolutionary clocks. First, they are ubiquitous among living cells, and they do not seem to be transferred horizontally among mixed populations. Second, the function of the molecule is essential, and as a result, its secondary and tertiary structures are highly conserved. Third, these molecules are large enough to contain sufficient information content for comparisons among diverse organisms. The phylogeny of the Whipple's disease bacillus reveals a second theme that may be common to previously uncultivated microbial pathogens. On the basis of a culture-independent analysis of bacterial diversity within soil, it is not surprising that previously unidentified human microbial pathogens would be found in this environment.

Citation: Relman D. 1994. Phylogenetic Diversity of Microbial Pathogens, p 507-517. In Miller V, Kaper J, Portnoy D, Isberg R (ed), Molecular Genetics of Bacterial Pathogenesis. ASM Press, Washington, DC. doi: 10.1128/9781555818340.ch34

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Nucleic Acid Amplification Techniques
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16s rRNA Sequencing
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Gram-Positive Bacteria
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Figures

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Figure 1

Evolutionary tree of the domain on the basis of comparative analysis of 16S rRNA sequences. A revised organization of this domain was published recently ( ). The divisions that contain organisms known to be pathogenic for humans are underlined. Line segment length is proportional to the number of fixed point mutations in the rRNA, and thus reflects evolutionary distance.

Citation: Relman D. 1994. Phylogenetic Diversity of Microbial Pathogens, p 507-517. In Miller V, Kaper J, Portnoy D, Isberg R (ed), Molecular Genetics of Bacterial Pathogenesis. ASM Press, Washington, DC. doi: 10.1128/9781555818340.ch34
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Image of Figure 2
Figure 2

Proposed analysis of the human commensal microbial flora found in the subgingival crevice. This experiment is designed to address the question, to what extent does cultivation yield an accurate representation of microbial diversity in this human anatomic niche?

Citation: Relman D. 1994. Phylogenetic Diversity of Microbial Pathogens, p 507-517. In Miller V, Kaper J, Portnoy D, Isberg R (ed), Molecular Genetics of Bacterial Pathogenesis. ASM Press, Washington, DC. doi: 10.1128/9781555818340.ch34
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References

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1. Amann, R. I.,, L. Krumholz,, and D. A. Stahl. 1990. Fluorescent-oligonucleotide probing of whole cells for determinative, phylogenetic, and environmental studies in microbiology. J. Bacteriol. 172: 762 770.
2. Azad, A. F.,, J. J. Sacci,, W. M. Nelson,, G. A. Dasch,, E. T. Schmidtmann,, and M. Carl. 1992. Genetic characterization and transovarial transmission of a typhus-like rickettsia found in cat fleas. Proc. Natl. Acad. Sci. USA 89: 43 46.
3. Barns, S. M.,, R. E. Fundyga,, M. W. Jeffries,, and N. R. Pace. 1994. Remarkable archaeal diversity detected in a Yellowstone National Park hot spring environment. Proc. Natl. Acad. Sci. USA 91: 1609 1613.
4. Boddinghaus, B.,, T. Rogall,, T. Flohr,, H. Blocker,, and E. C. Bottger. 1990. Detection and identification of mycobacteria by amplification of rRNA. J. Clin. Microbiol. 28: 1751 1759.
5. Chen, K.,, H. Neimark,, P. Rumore,, and C. R. Steinman. 1989. Broad range DNA probes for detecting and amplifying eubacterial nucleic acids. FEMS Microbiol. Lett. 48: 19 24.
6. Cockerel), C. J.,, and P. E. LeBoit. 1990. Bacillary angiomatosis: a newly characterized, pseudoneo-plastic, infectious, cutaneous vascular disorder. J. Am. Acad. Dermatol. 22: 501 512.
7. DeLong, E. F.,, G. S. Wickham,, and N. R. Pace. 1989. Phylogenetic stains: ribosomal RNA-based probes for the identification of single cells. Science 243: 1360 1363. ( Erratum, 245:1312.)
8. Dewhirst, F. E.,, C. K. Chen,, B. J. Paster,, and J. J. Zambon. 1993. Phytogeny of species in the family Neisseriaceae isolated from human dental plaque and description of Kingella orale sp. nov. Int. J. Syst. Bacteriol. 43: 490 499.
9. Dewhirst, F. E.,, B. J. Paster,, I. Olsen,, and G. J. Fraser. 1992. Phylogeny of 54 representative strains of species in the family Pasteurellaceae as determined by comparison of 16S rRNA sequences. J. Bacteriol. 174: 2002 2013.
10. Dewhirst, F. E.,, B. J. Paster,, I. Olsen,, and G. J. Fraser. 1993. Phylogeny of the Pasteurellaceae as determined by comparison of 16S ribosomal ribonucleic acid sequences. Int. J. Med. Microbiol. Virol. Parasitol. Infect. Dis. 279: 35 44.
11. Dobbins, W. O. 1987. Whipple's Disease. Charles C Thomas, Springfield, Ill..
12. Dorsch, M.,, D. Lane,, and E. Stackebrandt. 1992. Toward a phylogeny of the genus Vibrio based on 16S rRNA sequences. Int. J. Syst. Bacteriol. 42: 58 63.
13. Ennis, P. D.,, J. Zemmour,, R. D. Salter,, and P. Parham. 1990. Rapid cloning of HLA-A,B cDNA by using the polymerase chain reaction: frequency and nature of errors produced in amplification. Proc. Natl. Acad. Sci. USA 87: 2833 2837.
14. Evans, A. S. 1976. Causation and disease: the Henle-Koch postulates revisited. Yale J. Biol. Med. 49: 175 195.
15. Fox, G. E.,, E. Stackebrandt,, R. B. Hespell,, J. Gibson,, J. Maniloff,, T. A. Dyer,, R. S. Wolfe,, W. E. Balch,, R. S. Tanner,, L. J. Magrum,, L. B. Zablen,, R. Blakemore,, R. Gupta,, L. Bonen,, B. J. Lewis,, D. A. Stahl,, K. R. Luehrsen,, K. N. Chen,, and C. R. Woese. 1980. The phylogeny of prokaryotes. Science 209: 457 463.
16. Fox, G. E.,, J. D. Wisotzkey,, and P. J. Jurtshuk. 1992. How close is close: 16S rRNA sequence identity may not be sufficient to guarantee species identity. Int. J. Syst. Bacteriol. 42: 166 170.
17. Fuhrman, J. A.,, K. McCallum,, and A. A. Davis. 1992. Novel major archaebacterial group from marine plankton. Nature (London) 356: 148 149.
18. Giovannoni, S. J.,, T. B. Britschgi,, C. L. Moyer,, and K. G. Field. 1990. Genetic diversity in Sargasso Sea bacterioplankton. Nature (London) 345: 60 63.
19. Giovannoni, S. J.,, E. F. DeLong,, G. J. Olsen,, and N. R. Pace. 1988. Phylogenetic group-specific oligodeoxynucleotide probes for identification of single microbial cells J. Bacteriol. 170: 720 726. ( Erratum, 170:2418.)
20. Gold, T. 1992. The deep, hot biosphere. Proc. Natl. Acad. Sci. USA 89: 6045 6049.
21. Gray, M. W. 1992. The endosymbiont hypothesis revisited. Int. Rev. Cytol. 141: 233 357.
22. Greer, C. E.,, S. L. Peterson,, N. B. Kiviat,, and M. M. Manos. 1991. PCR amplification from paraffin-embedded tissues: effects of fixative and fixation time. Am. J. Clin. Pathol. 95: 117 124.
23. Gutell, R. R.,, B. Weiser,, C. R. Woese,, and H. F. Noller. 1985. Comparative anatomy of 16-S-like ribosomal RNA. Prog. Nucleic Acids Res. Mol. Biol. 32: 155 216.
24. Ibrahim, A.,, B. M. Goebel,, W. Liesack,, M. Griffiths,, and E. Stackebrandt. 1993. The phylogeny of the genus Yersinia based on 16S rDNA sequences. FEMS Microbiol. Lett. 114: 173 177.
25. James, B. D.,, G. J. Olsen,, and N. R. Pace. 1989. Phylogenetic comparative analysis of RNA secondary structure. Methods Enzymol. 180: 227 239.
26. Koehler, J. E.,, C. A. Glaser,, and J. W. Tappero. 1994. Rochalimaea henselae infection. A new zoonosis with the domestic cat as reservoir. JAMA 271: 531 535.
27. Koehler, J. E.,, F. D. Quinn,, T. G. Berger,, P. E. LeBoit,, and J. W. Tappero. 1992. Isolation of Rochalimaea species from cutaneous and osseous lesions of bacillary angiomatosis. N. Engl. J. Med. 327: 1625 1631.
28. Lane, D. J.,, B. Pace,, G. J. Olsen,, D. A. Stahl,, M. L. Sogin,, and N. R. Pace. 1985. Rapid determination of 16S ribosomal RNA sequences for phylogenetic analyses. Proc. Natl. Acad. Sci. USA 82: 6955 6959.
29. Liesack, W.,, and E. Stackebrandt. 1992. Occurrence of novel groups of the domain Bacteria as revealed by analysis of genetic material isolated from an Australian terrestrial environment. J. Bacteriol. 174: 5072 5078.
30. Medlin, L.,, H. J. Elwood,, S. Stickel,, and M. L. Sogin. 1988. The characterization of enzymatically amplified eukaryotic 16S-like rRNA-coding regions. Gene 71: 491 499.
31. Mylvaganam, S.,, and P. P. Dennis. 1992. Sequence heterogeneity between the two genes encoding 16S rRNA from the halophilic archaebacterium Haloarcula marismortui. Genetics 130: 399 410.
32. Olsen, G. J.,, D. J. Lane,, S. J. Giovannoni,, N. R. Pace,, and D. A. Stahl. 1986. Microbial ecology and evolution: a ribosomal RNA approach. Annu. Rev. Microbiol. 40: 337 365.
33. Olsen, G. J.,, and C. R. Woese. 1993. Ribosomal RNA: a key to phylogeny. FASEBJ. 7: 113 231.
34. Olsen, G. J.,, C. R. Woese,, and R. Overbeek. 1994. The winds of (evolutionary) change: breathing new life into microbiology. J. Bacteriol. 176: 1 6.
35. Paabo, S.,, R. G. Higuchi,, and A. C. Wilson. 1989. Ancient DNA and the polymerase chain reaction. The emerging field of molecular archaeology. /. Biol. Chem. 264: 9709 9712.
36. Paabo, S.,, D. M. Irwin,, and A. C. Wilson. 1990. DNA damage promotes jumping between templates during enzymatic amplification. J. Biol. Chem. 265: 4718 4721.
37. Paster, B. J.,, F. E. Dewhirst,, W. G. Weisburg,, L. A. Tordoff,, G. J. Fraser,, R. B. HespeU,, T. B. Stanton,, L. Zablen,, L. Mandelco,, and C. R. Woese. 1991. Phylogenetic analysis of the spirochetes. J. Bacteriol. 173: 6101 6109.
38. Pitulle, C.,, M. Dorsch,, J. Kazda,, J. Wolters,, and E. Stackebrandt. 1992. Phylogeny of rapidly growing members of the genus Mycobacterium. Int. J. Syst. Bacteriol. 42: 337 343.
39. Regnery, R. L.,, B. E. Anderson,, J. E. Clarridge HI,, M. C. Rodriguez-Barradas,, D. C. Jones,, and J. H. Carr. 1992. Characterization of a novel Rochalimaea species, R. henselae sp. nov., isolated from blood of a febrile, human immunodeficiency virus-positive patient. J. Clin. Microbiol. 30: 265 274.
40. Regnery, R. L.,, C. L. Spruill,, and B. D. Plikaytis. 1991. Genotypic identification of rickettsiae and estimation of intraspecies sequence divergence for portions of two rickettsial genes. J. Bacteriol. 173: 1576 1589.
41. Relman, D. A. 1993. The identification of uncultured microbial pathogens. J. Infect. Dis. 168: 1 8.
42. Relman, D. A., 1993. Universal bacterial 16S rDNA amplification and sequencing, p. 489 495. In D. H. Persing,, T. F. Smith,, F. C. Tenover,, and T. J. White (ed.), Diagnostic Molecular Microbiology: Principles and Applications. American Society for Microbiology, Washington, D.C..
43. Relman, D. A.,, P. W. Lepp,, K. N. Sadler,, and T. M. Schmidt. 1992. Phylogenetic relationships among the agent of bacillary angiomatosis, Bartonella bacilliformis, and other alpha-proteobacteria. Mol. Microbiol. 6: 1801 1807.
44. Relman, D. A.,, J. S. Loutit,, T. M. Schmidt,, S. Falkow,, and L. S. Tompkins. 1990. The agent of bacillary angiomatosis. An approach to the identification of uncultured pathogens. N. Engl. J. Med. 323: 1573 1580.
45. Relman, D. A.,, T. M. Schmidt,, R. P. MacDermott,, and S. Falkow. 1992. Identification of the uncultured bacillus of Whipple's disease. N. Engl. J. Med. 327: 293 301.
46. Schmidt, T. M.,, E. F. DeLong,, and N. R. Pace. 1991. Analysis of a marine picoplankton community by 16S rRNA gene cloning and sequencing. J. Bacteriol. 173: 4371 4378.
47. Schmidt, T. M.,, and D. A. Relman. 1994. Phylogenetic identification of uncultured pathogens using ribosomal RNA sequences. Methods Enzymol. 235: 205 222.
48. Stahl, D. A.,, and J. W. Urbance. 1990. The division between fast- and slow-growing species corresponds to natural relationships among the mycobacteria. J. Bacteriol. 172: 116 124.
49. Stanier, R. Y.,, and C. B. vanNiel. 1941. The main outlines of bacterial classification. J. Bacteriol. 42: 437 466.
50. Stoler, M. H.,, T. A. Bonfiglio,, R. T. Steigbigel,, and M. Pereira. 1983. An atypical subcutaneous infection associated with acquired immune deficiency syndrome. Am. J. Clin. Pathol. 80: 714 718.
51. Strom, R. L.,, and R. P. Gruninger. 1983. AIDS with Mycobacterium avium-intracellulare lesions resembling those of Whipple's disease. N. Engl. J. Med. 309: 1323 1324. (Letter.)
52. Turner, S.,, W. T. Burger,, S. J. Giovannoni,, L. R. Mur,, and N. R. Pace. 1989. The relationship of a prochlorophyte Prochlorothrix hollandica to green chloroplasts. Nature (London) 337: 380 382.
53. Wang, H. H.,, D. Tollerud,, D. Danar,, P. Hanff,, K. Gottesdiener,, and S. Rosen. 1986. Another Whipple-like disease in AIDS? N. Engl. J. Med. 314: 1577 1578. (Letter.)
54. Ward, D. M.,, M. M. Bateson,, R. Weller,, and A. L. Ruff-Roberts. 1992. Ribosomal RNA analysis of microorganisms as they occur in nature. Adv. Microb. Ecol. 12: 219 286.
55. Ward, D. M.,, R. Weller,, and M. M. Bateson. 1990. 16S rRNA sequences reveal numerous uncultured microorganisms in a natural community. Nature (London) 345: 63 65.
56. Weisburg, W. G.,, S. M. Barns,, D. A. Pelletier,, and D. J. Lane. 1991. 16S ribosomal DNA amplification for phylogenetic study. J. Bacteriol. 173: 697 703.
57. Weisburg, W. G.,, M. E. Dobson,, J. E. Samuel,, G. A. Dasch,, L. P. Mallavia,, O. Baca,, L. Mandelco,, J. E. Sechrest,, E. Weiss,, and C. R. Woese. 1989. Phylogenetic diversity of the rickettsiae. J. Bacteriol. 171: 4202 4206.
58. Weisburg, W. G.,, C. R. Woese,, M. E. Dobson,, and E. Weiss. 1985. A common origin of rickettsiae and certain plant pathogens. Science 230: 556 558.
59. Whipple, G. H. 1907. A hitherto undescribed disease characterized anatomically by deposits of fat and fatty acids in the intestinal and mesenteric lymphatic tissues. Johns Hopkins Hosp. Bull. 18: 382 391.
60. Williams, S. G.,, J. J. Saccl,, M. E. Schriefer,, E. M. Andersen,, K. K. Fujioka,, F. J. Sorvillo,, A. R. Burr,, and A. F. Azad. 1992. Typhus and typhuslike rickettsiae associated with opossums and their fleas in Los Angeles County, California. J. Clin. Microbiol. 30: 1758 1762.
61. Wilson, K. H.,, R. Blitchington,, R. Frothingham,, and J. A. Wilson. 1991. Phylogeny of the Whipple's-disease-associated bacterium. Lancet 338: 474 475.
62. Wilson, K. H.,, R. B. Blitchington,, and R. C. Greene. 1990. Amplification of bacterial 16S ribosomal DNA with polymerase chain reaction. J. Clin. Microbiol. 28: 1942 1946.
63. Woese, C. R. 1987. Bacterial evolution. Microbiol. Rev. 51: 221 271.
64. Woese, C. R.,, O. Kandler,, and M. L. Wheelis. 1990. Towards a natural system of organisms: proposal for the domains Archaea, Bacteria, and Eucarya. Proc. Natl. Acad. Sci. USA 87: 4576 4579.

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