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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. 172:762770.
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 89:4346.
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: 16091613.
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. 28:17511759.
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. 48:1924.
6. Cockerel), C. J.,, and P. E. LeBoit. 1990. Bacillary angiomatosis: a newly characterized, pseudoneo-plastic, infectious, cutaneous vascular disorder. J. Am. Acad. Dermatol. 22:501512.
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 243:13601363. (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. 43:490499.
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. 174:20022013.
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. 279:3544.
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. 42:5863.
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 87:28332837.
14. Evans, A. S. 1976. Causation and disease: the Henle-Koch postulates revisited. Yale J. Biol. Med. 49:175195.
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 209:457463.
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. 42:166170.
17. Fuhrman, J. A.,, K. McCallum,, and A. A. Davis. 1992. Novel major archaebacterial group from marine plankton. Nature (London) 356:148149.
18. Giovannoni, S. J.,, T. B. Britschgi,, C. L. Moyer,, and K. G. Field. 1990. Genetic diversity in Sargasso Sea bacterioplankton. Nature (London) 345:6063.
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. 170:720726. (Erratum, 170:2418.)
20. Gold, T. 1992. The deep, hot biosphere. Proc. Natl. Acad. Sci. USA 89:60456049.
21. Gray, M. W. 1992. The endosymbiont hypothesis revisited. Int. Rev. Cytol. 141:233357.
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. 95:117124.
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. 32:155216.
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. 114:173177.
25. James, B. D.,, G. J. Olsen,, and N. R. Pace. 1989. Phylogenetic comparative analysis of RNA secondary structure. Methods Enzymol. 180:227239.
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 271:531535.
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. 327:16251631.
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: 69556959.
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. 174:50725078.
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 71:491499.
31. Mylvaganam, S.,, and P. P. Dennis. 1992. Sequence heterogeneity between the two genes encoding 16S rRNA from the halophilic archaebacterium Haloarcula marismortui. Genetics 130:399410.
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. 40:337365.
33. Olsen, G. J.,, and C. R. Woese. 1993. Ribosomal RNA: a key to phylogeny. FASEBJ. 7:113231.
34. Olsen, G. J.,, C. R. Woese,, and R. Overbeek. 1994. The winds of (evolutionary) change: breathing new life into microbiology. J. Bacteriol. 176:16.
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. 264:97099712.
36. Paabo, S.,, D. M. Irwin,, and A. C. Wilson. 1990. DNA damage promotes jumping between templates during enzymatic amplification. J. Biol. Chem. 265:47184721.
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. 173:61016109.
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. 42:337343.
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: 265274.
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. 173:15761589.
41. Relman, D. A. 1993. The identification of uncultured microbial pathogens. J. Infect. Dis. 168:18.
42. Relman, D. A., 1993. Universal bacterial 16S rDNA amplification and sequencing, p. 489495. 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. 6:18011807.
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. 323:15731580.
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. 327:293301.
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. 173:43714378.
47. Schmidt, T. M.,, and D. A. Relman. 1994. Phylogenetic identification of uncultured pathogens using ribosomal RNA sequences. Methods Enzymol. 235:205222.
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. 172:116124.
49. Stanier, R. Y.,, and C. B. vanNiel. 1941. The main outlines of bacterial classification. J. Bacteriol. 42:437466.
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. 80:714718.
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. 309:13231324. (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) 337:380382.
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. 314:15771578. (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. 12:219286.
55. Ward, D. M.,, R. Weller,, and M. M. Bateson. 1990. 16S rRNA sequences reveal numerous uncultured microorganisms in a natural community. Nature (London) 345:6365.
56. Weisburg, W. G.,, S. M. Barns,, D. A. Pelletier,, and D. J. Lane. 1991. 16S ribosomal DNA amplification for phylogenetic study. J. Bacteriol. 173:697703.
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. 171:42024206.
58. Weisburg, W. G.,, C. R. Woese,, M. E. Dobson,, and E. Weiss. 1985. A common origin of rickettsiae and certain plant pathogens. Science 230:556558.
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. 18:382391.
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. 30:17581762.
61. Wilson, K. H.,, R. Blitchington,, R. Frothingham,, and J. A. Wilson. 1991. Phylogeny of the Whipple's-disease-associated bacterium. Lancet 338:474475.
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. 28:19421946.
63. Woese, C. R. 1987. Bacterial evolution. Microbiol. Rev. 51:221271.
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: 45764579.

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