UniFrac: A new phylogenetic method for comparing microbial communities

Applied and Environmental Microbiology

Volumn 71, Issue 12, 2005, Pages 8228-8235

  Lozupone, Catherine ^a   Knight, Rob ^a  

^a UNIVERSITY OF COLORADO   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CLONING; ECOLOGY; ENVIRONMENTAL ENGINEERING; RNA; SEDIMENTS; WATER;

MARINE SEDIMENTS; PHYLOGENETIC INFORMATION; PHYLOGENETIC TREE;

MICROBIOLOGY;

ICE; RIBOSOME RNA; SEA WATER; WATER;

COMPARATIVE STUDY; METHODOLOGY; MICROBIAL COMMUNITY;

ARTICLE; BACTERIUM ISOLATE; CHEMISTRY; CLONE; GENE LIBRARY; GEOGRAPHY; MICROFLORA; NONHUMAN; PHYLOGENY; RNA SEQUENCE; SEDIMENT; WATER SAMPLING;

BACTERIA; GENETIC TECHNIQUES; GEOGRAPHY; PHYLOGENY; RNA, RIBOSOMAL, 16S;

BACTERIA (MICROORGANISMS);

EID: 29144464937     PISSN: 00992240     EISSN: None     Source Type: Journal    
DOI: 10.1128/AEM.71.12.8228-8235.2005     Document Type: Article

References (45)

1. Acinas, S. G., V. Klepac-Ceraj, D. E. Hunt, C. Pharino, I. Ceraj, D. L. Distel, and M. F. Polz. 2004. Fine-scale phylogenetic architecture of a complex bacterial community. Nature 430:551-554.
2. Bano, N., and J. T. Hollibaugh. 2002. Phylogenetic composition of bacterioplankton assemblages from the Arctic Ocean. Appl. Environ. Microbiol. 68:505-518.
3. Bowman, J. P., S. A. McCammon, M. V. Brown, D. S. Nichols, and T. A. McMeekin. 1997. Diversity and association of psychrophilic bacteria in Antarctic sea ice. Appl. Environ. Microbiol. 63:3068-3078.
4. Bowman, J. P., S. A. McCammon, J. A. Gibson, L. Robertson, and P. D. Nichols. 2003. Prokaryotic metabolic activity and community structure in Antarctic continental shelf sediments. Appl. Environ. Microbiol. 69:2448-2462.
5. Bowman, J. P., and R. D. McCuaig. 2003. Biodiversity, community structural shifts, and biogeography of prokaryotes within Antarctic continental shelf sediment. Appl. Environ. Microbiol. 69:2463-2483.
6. Brinkmeyer, R., K. Knittel, J. Jurgens, H. Weyland, R. Amann, and E. Helmke. 2003. Diversity and structure of bacterial communities in Arctic versus Antarctic pack ice. Appl. Environ. Microbiol. 69:6610-6619.
7. Brown, M. V., and J. P. Bowman. 2001. A molecular phylogenetic survey of sea-ice microbial communities (SIMCO). FEMS Microbiol. Ecol. 35:267-275.
8. Eilers, H., J. Pernthaler, F. O. Glöckner, and R. Amann. 2000. Culturability and in situ abundance of pelagic bacteria from the North Sea. Appl. Environ. Microbiol. 66:3044-3051.
9. Felsenstein, J. 2004. Inferring phylogenies. Sinauer Associates, Inc., Sunderland, Mass.
10. Ferguson, R. L., E. N. Buckley, and A. V. Palumbo. 1984. Response of marine bacterioplankton to differential filtration and confinement. Appl. Environ. Microbiol. 47:49-55.
11. Fuhrman, J. A., K. McCallum, and A. A. Davis. 1993. Phylogenetic diversity of subsurface marine microbial communities from the Atlantic and Pacific oceans. Appl. Environ. Microbiol. 59:1294-1302.
12. Giovannoni, S. J., and M. Rappé. 2000. Evolution, diversity, and molecular ecology of marine prokaryotes, p. 47-84. In D. L. Kirchman (ed.), Microbial ecology of the oceans. John Wiley & Sons, Inc., New York, N.Y.
13. Glöckner, F. O., E. Zaichikov, N. Belkova, L. Denissova, J. Pernthaler, A. Pernthaler, and R. Amann. 2000. Comparative 16S rRNA analysis of lake bacterioplankton reveals globally distributed phylogenetic clusters including an abundant group of actinobacteria. Appl. Environ. Microbiol. 66:5053-5065.
14. Helmke, E., and H. Weyland. 1995. Bacteria in sea ice and underlying water of the eastern Weddell Sea in midwinter. Mar. Ecol. Prog. Ser. 117:269-287.
15. Hugenholtz, P. 2002. Exploring prokaryotic diversity in the genomic era. Genome Biol. 3:reviews0003.
16. Hughes, J. B., J. J. Hellmann, T. H. Ricketts, and B. J. Bohannan. 2001. Counting the uncountable: statistical approaches to estimating microbial diversity. Appl. Environ. Microbiol. 67:4399-4406.
17. Hur, I., and J. Chun. 2004. A method for comparing multiple bacterial community structures from 16S rDNA clone library sequences. J. Microbiol. 42:9-13.
18. Jannasch, H. W., and G. E. Jones. 1959. Bacterial populations in sea water as determined by different methods of enumeration. Limnol. Oceanogr. 4:128-139.
19. Junge, K., F. Imhoff, T. Staley, and J. W. Deming. 2002. Phylogenetic diversity of numerically important Arctic sea-ice bacteria cultured at subzero temperature. Microb. Ecol. 43:315-328.
20. Juretschko, S., A. Loy, A. Lehner, and M. Wagner. 2002. The microbial community composition of a nitrifying-denitrifying activated sludge from an industrial sewage treatment plant analyzed by the full-cycle rRNA approach. Syst. Appl. Microbiol. 25:84-99.
21. Kanawaga, T. 2003. Bias and artifacts in multitemplate polymerase chain reaction. J. Biosci. Bioeng. 96:317-323.
22. Kelly, K. M., and A. Y. Chistoserdov. 2001. Phylogenetic analysis of the succession of bacterial communities in the Great South Bay (Long Island). FEMS Microbiol. Ecol. 35:85-95.
23. Krzanowski, W. J. 2000. Principles of multivariate analysis. A user's perspective. Oxford University Press, Oxford, United Kingdom.
24. Ley, R. E., F. Backhed, P. Turnbaugh, C. A. Lozupone, R. D. Knight, and J. I. Gordon. 2005. Obesity alters gut microbial ecology. Proc. Natl. Acad. Sci. USA 102:11070-11075.
25. Li, L., C. Kato, and K. Horikoshi. 1999. Microbial diversity in sediments collected from the deepest cold-seep area, the Japan Trench. Mar. Biotechnol. (New York) 1:391-400.
26. Ludwig, W., O. Strunk, R. Westram, L. Richter, H. Meier, Yadhukumar, A. Buchner, T. Lai, S. Steppi, G. Jobb, W. Förster, I. Brettske, S. Gerber, A. W. Ginhart, O. Gross, S. Grumann, S. Hermann, R. Jost, A. König, T. Liss, R. Lüssmann, M. May, B. Nonhoff, B. Reichel, R. Strehlow, A. Stamatakis, N. Stuckmann, A. Vilbig, M. Lenke, T. Ludwig, A. Bode, and K. H. Schleifer. 2004. ARB: a software environment for sequence data. Nucleic Acids Res. 32:1363-1371.
27. Magurran, A. E. 1988. Ecological diversity and its measurement. Princeton University Press, Princeton, N.J.
28. Magurran, A. E. 2004. Measuring biological diversity. Blackwell, Oxford, United Kingdom.
29. Maidak, B. L., J. R. Cole, T. G. Lilburn, C. T. Parker, Jr., P. R. Saxman, R. J. Farris, G. M. Garrity, G. J. Olsen, T. M. Schmidt, and J. M. Tiedje. 2001. The RDP-II (Ribosomal Database Project). Nucleic Acids Res. 29:173-174.
30. Martin, A. P. 2002. Phylogenetic approaches for describing and comparing the diversity of microbial communities. Appl. Environ. Microbiol. 68:3673-3682.
31. Massana, R., A. E. Murray, C. M. Preston, and E. F. DeLong. 1997. Vertical distribution and phylogenetic characterization of marine planktonic archaea in the Santa Barbara Channel. Appl. Environ. Microbiol. 63:50-56.
32. Mullins, T. D., T. B. Britschgi, R. L. Krest, and S. J. Giovannoni. 1995. Genetic comparisons reveal the same unknown bacterial lineages in Atlantic and Pacific bacterioplankton communities. Limnol. Oceanogr. 40:148-158.
33. Nübel, U., F. Garcia-Pichel, M. Kuhl, and G. Muyzer. 1999. Quantifying microbial diversity: morphotypcs, 16S rRNA genes, and carotenoids of oxygenic phototrophs in microbial mats. Appl. Environ. Microbiol. 65:422-430.
34. Pace, N. R. 1997. A molecular view of microbial diversity and the biosphere. Science 276:734-740.
35. Pace, N. R., D. A. Stahl, D. J. Lane, and G. J. Olsen. 1986. The analysis of natural microbial populations by ribosomal RNA sequences. Adv. Microb. Ecol. 9:1-55.
36. Pace, N. R., D. A. Stahl, D. J. Lane, and G. J. Olsen. 1985. Analyzing natural microbial populations by rRNA sequences. ASM News 51:4-12.
37. Rappé, M. S., and S. J. Giovannoni. 2003. The uncultured microbial majority. Annu. Rev. Microbiol. 57:369-394.
38. Ravenschlag, K., K. Sahm, J. Pernthaler, and R. Amann. 1999. High bacterial diversity in permanently cold marine sediments. Appl. Environ. Microbiol. 65:3982-3989.
39. Schloss, P. D., B. R. Larget, and J. Handelsman. 2004. Integration of microbial ecology and statistics: a test to compare gene libraries. Appl. Environ. Microbiol. 70:5485-5492.
40. Singleton, D. R., M. A. Furlong, S. L. Rathbun, and W. B. Whitman. 2001. Quantitative comparisons of 16S rRNA gene sequence libraries from environmental samples. Appl. Environ. Microbiol. 67:4374-4376.
41. Spear, J. R., J. J. Walker, T. M. McCollom, and N. R. Pace. 2005. Hydrogen and bioenergetics in the Yellowstone geothermal ecosystem. Proc. Natl. Acad. Sci. USA 102:2555-2560.
42. Staley, J. T., and J. J. Gosink. 1999. Poles apart: biodiversity and biogeography of sea ice bacteria. Annu. Rev. Microbiol. 53:189-215.
43. von Wintzingerode, F., U. B. Göbel, and E. Stackebrandt. 1997. Determination of microbial diversity in environmental samples: pitfalls of PCR-based rRNA analysis. FEMS Microbiol. Rev. 21:213-229.
44. Wheeler, P. A., M. Gosselin, E. Sherr, D. Thibault, D. L. Kirchman, R. Benner, and T. E. Whitledge. 1996. Active cycling of organic carbon in the central Arctic Ocean. Nature 380:697-699.
45. Zwart, G., W. D. Hiorns, B. A. Methe, M. P. Van Agterveld, R. Huismans, S. C. Nold, J. P. Zehr, and H. J. Laanbroek. 1998. Nearly identical 16S rRNA sequences recovered from lakes in North America and Europe indicate the existence of clades of globally distributed freshwater bacteria. Syst. Appl. Microbiol. 21:546-556.