Measures of phylogenetic differentiation provide robust and complementary insights into microbial communities

ISME Journal

Volumn 7, Issue 1, 2013, Pages 173-183

  Parks, Donovan H ^a   Beiko, Robert G ^a  

^a DALHOUSIE UNIVERSITY   (Canada)

Author keywords

diversity; community ecology; metagenomics; phylogenetic diversity; similarity indices

Indexed keywords

COMPARATIVE STUDY; DATA SET; ECOLOGICAL MODELING; MEASUREMENT METHOD; MICROBIAL COMMUNITY; PHYLOGENETICS; SPATIOTEMPORAL ANALYSIS; SPECIES DIVERSITY; TAXONOMY; THRESHOLD;

ARTICLE; BACTERIUM; BIOLOGICAL MODEL; CLASSIFICATION; COMPUTER PROGRAM; ECOLOGY; GENETICS; HUMAN; METAGENOME; METHODOLOGY; MICROBIOLOGY; PHYLOGENY;

BACTERIA; ECOLOGY; ENVIRONMENTAL MICROBIOLOGY; HUMANS; METAGENOME; MODELS, BIOLOGICAL; PHYLOGENY; SOFTWARE;

EID: 84871385708     PISSN: 17517362     EISSN: 17517370     Source Type: Journal    
DOI: 10.1038/ismej.2012.88     Document Type: Article

References (43)

1. Barr JJ, Slater FR, Fukushima T, Bond PL. (2010). Evidence for bacteriophage activity causing community and performance changes in a phosphorus-removal activated sludge. FEMS Microbiol Ecol 74: 631-642.
2. Bryant JA, Lamanna C, Morlon H, Kerkhoff AJ, Enquist BJ, Green JL. (2008). Microbes on mountainsides: contrasting elevational patterns of bacterial and plant diversity. Proc Natl Acad Sci USA 105: 11505-11511.
3. Caporaso JG, Lauber CL, Costello EK, Berg-Lyons D, Gonzalez A, Stombaugh J et al. (2011). Moving pictures of the human microbiome. Genome Biol 12: R50.
4. Clarke KR, Warwick RM. (1998). A taxonomic distinctness index and its statistical properties. J Appl Ecol 35: 523-531.
5. Cock PJ, Antao T, Chang JT, Chapman BA, Cox CJ, Dalke A et al. (2009). Biopython: freely available Python tools for computational molecular biology and bioinformatics. Bioinformatics 25: 1422-1423.
6. Costello EK, Lauber CL, Hamady M, Fierer N, Gordon JI, Knight R. (2009). Bacterial community variation in human body habitats across space and time. Science 329: 1694-1697.
7. Crozier RH, Dunnett LJ, Agapow PM. (2005). Phylogenetic biodiversity assessment based on systematic nomenclature. Evol Bioninform Online 1: 11-36.
8. DeSantis TZ, Hugenholtz P, Keller K, Brodie EL, Larsen N, Piceno YM et al. (2006). NAST: a multiple sequence alignment server for comparative analysis of 16S rRNA genes. Nucleic Acids Res 34: W394-W399.
9. Dethlefsen L, Huse S, Sogin ML, Relman DA. (2008). The pervasive effects of an antibiotic on the human gut microbiota, as revealed by deep 16S rRNA sequencing. PLoS Biol 6: e280.
10. Faith DP, Baker AM. (2007). Phylogenetic diversity (PD) and biodiversity conservation: some bioinformatics challenges. Evol Bioinform Online 17: 121-128.
11. Fierer N, Lauber CL, Zhou N, Daniel M, Costello EK, Knight R. (2010). Forensic identification using skin bacterial communities. Proc Natl Acad Sci USA 107: 6477-6481.
12. Graham CH, Fine PVA. (2008). Phylogenetic beta diversity: linking ecological and evolutionary processes across space in time. Ecol Lett 11: 1265-1277.
13. Green JL, Plotkin JB. (2007). A statistical theory for sampling species abundances. Ecol Lett 10: 1037-1045.
14. Hamady M, Lozupone C, Knight R. (2010). Fast UniFrac: facilitating high-throughput phylogenetic analyses of microbial communities including analysis of pyrosequencing and PhyloChip data. ISME J 4: 17-27.
15. Horner-Devine MC, Bohannan BJM. (2006). Phylogenetic clustering and overdispersion in bacterial communities. Ecology 87: S100-S108.
16. Kluge AG, Farris JS. (1969). Quantitative phyletics and the evolution of anurans. Syst Zool 18: 1-32.
17. Koleff P, Gaston KJ, Lennon JJ. (2003). Measuring beta diversity for presence absence data. J Anim Ecol 72: 367-382.
18. Kuczynski J, Liu Z, Lozupone C, McDonald D, Fierer N, Knight R. (2010). Microbial community resemblance methods differ in their ability to detect biologically relevant patterns. Nat Methods 7: 813-819.
19. Lauber CL, Hamady M, Knight R, Fierer N. (2009). Pyrosequencing-based assessment of soil pH as a predictor of soil bacterial community composition at the continental scale. Appl Environ Microbiol 75: 5111-5120.
20. Legendre P, Legendre L. (1998). Numerical Ecology, 2nd English edn. Elsevier: Amsterdam, The Netherlands.
21. Lozupone C, Knight R. (2005). UniFrac: a new phylogenetic method for comparing microbial communities. Appl Environ Microbiol 71: 8228-8235.
22. Lozupone CA, Hamady M, Kelley ST, Knight R. (2007). Quantitative and qualitative b diversity measures lead to different insights into factors that structure microbial communities. Appl Environ Microbiol 73: 1576-1585.
23. Lozupone CA, Hamady M, Knight R. (2006). UniFrac - An online tool for comparing microbial community diversity in a phylogenetic context. BMC Bioinformatics 7: 371.
24. Lozupone CA, Knight R. (2007). Global patterns in bacterial diversity. Proc Natl Acad Sci USA 104: 11436-11440.
25. Magurran AE. (2004). Measuring Biological Diversity. Blackwell Publishing: Oxford, UK.
26. Martin AP. (2002). Phylogenetic approaches for describing and comparing the diversity of microbial communities. Appl Environ Microbiol 68: 3673-3682.
27. Martiny JB, Bohannan BJM, Brown JH, Colwell RK, Fuhrman JA, Green JL et al. (2006). Microbial biogeography: putting microorganisms on the map. Nat Rev Microbiol 4: 102-112.
28. Nipperess DA, Faith DP, Barton K. (2010). Resemblance in phylogenetic diversity among ecological assemblages. J Veg Sci 21: 809-820.
29. Pielou EC. (1984). The interpretation of ecological data: a primer of classification and ordination. John Wiley and Sons.
30. Plotkin JB, Muller-Landau HC (eds). (2002). Sampling the species composition of a landscape. Ecology 83: 3344-3356.
31. Plotkin JB, Muller-Landau H. (2002). Sampling the species composition of a landscape. Ecology 83: 3344-3356.
32. Price MN, Dehal PS, Arkin AP. (2009). FastTree: computing large minimum-evolution trees with profiles instead of a distance matrix. Mol Biol Evol 26: 1641-1650.
33. Root HT, Nelson PR. (2011). Does phylogenetic distance aid in detecting environmental gradients related to species composition? J Veg Sci 22: 1143-1148.
34. Rousk J, Baath E, Brookes PC, Lauber CL, Lozupone C, Caporaso JG et al. (2010). Soil bacterial and fungal communities across a pH gradient in an arable soil. ISME J 4: 1340-1351.
35. Schloss PD. (2008). Evaluating different approaches that test whether microbial communities have the same structure. ISME J 2: 265-275.
36. Schloss PD, Handelsman J. (2004). Status of the microbial census. Mol Biol Rev 68: 686-691.
37. Schloss PD, Westcott SL, Ryabin T, Hall JR, Hartmann M, Hollister EB et al. (2009). Introducing mothur: opensource, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol 75: 7537-7541.
38. Slater FR, Johnson CR, Blackall LL, Beiko RG, Bond PL. (2010). Monitoring associations between clade-level variation, overall community structure and ecosystem function in enhanced biological phosphorus removal (EBPR) systems using terminalrestriction fragment length polymorphism (T-RFLP). Water Res 44: 4908-4923.
39. Stackebrandt E, Goebel BM. (1994). Taxonomic Note: A place for DNA-DNA reassociation and 16S rRNA sequence analysis in the present species definition in bacteriology. Int J Syst Bacteriol 44: 846-849.
40. Swenson NG. (2011). Phylogenetic beta diversity metrics, trait evolution and inferring the functional beta diversity of communities. PLOS One 6: e21264.
41. Turnbaugh PJ, Hamady M, Yatsunenko T, Cantarel BL, Duncan A, Ley RE et al. (2009). A core gut microbiome in obese and lean twins. Nature 457: 480-484.
42. Ubeda C, Taur Y, Jeng RR, Equinda MJ, Son T, Samstein M et al. (2010). Vancomycin-resistant Enterococcus domination of intestinal microbiota is enabled by antibiotic treatment in mice and precedes bloodstream invasion in humans. J Clin Invest 120: 4332-4341.
43. Webb CO, Ackerly DD, Kembel SW. (2008). Phylocom: software for the analysis of phylogenetic community structure and trait evolution. Bioinformatics 24: 2098-2100.