A guide to statistical analysis in microbial ecology: A community-focused, living review of multivariate data analyses

FEMS Microbiology Ecology

Volumn 90, Issue 3, 2014, Pages 543-550

  Buttigieg, Pier Luigi ^a,b,c   Ramette, Alban ^a,d,e  

^a HGF MPG Group for Deep Sea Ecology and Technology   (Germany)

^b ALFRED WEGENER INSTITUTE FOR POLAR AND MARINE RESEARCH   (Germany)

^c UNIVERSITY OF BREMEN   (Germany)

^d MAX PLANCK INSTITUTE FOR MARINE MICROBIOLOGY   (Germany)

^e UNIVERSITY OF BERN   (Switzerland)

Author keywords

Complex data; Interactive guide; Multivariate statistics; Online resource

Indexed keywords

ECOLOGY; INTERNET; MICROBIAL CONSORTIUM; MULTIVARIATE ANALYSIS; PRACTICE GUIDELINE; STATISTICS AND NUMERICAL DATA;

ECOLOGY; GUIDELINES AS TOPIC; INTERNET; MICROBIAL CONSORTIA; MULTIVARIATE ANALYSIS;

EID: 84914820443     PISSN: 01686496     EISSN: 15746941     Source Type: Journal    
DOI: 10.1111/1574-6941.12437     Document Type: Article

References (66)

1. Anderson MJ (2001) A new method for non-parametric multivariate analysis of variance. Austral Ecol 26: 32-46.
2. Bertics VJ & Ziebis W (2009) Biodiversity of benthic microbial communities in bioturbated coastal sediments is controlled by geochemical microniches. ISME J 3: 1269-1285.
3. Bienhold C, Boetius A & Ramette A (2012) The energy-diversity relationship of complex bacterial communities in Arctic deep-sea sediments. ISME J 6: 724-732.
4. Böer SI, Hedtkamp SIC, van Beusekom JEE, Fuhrman JA, Boetius A & Ramette A (2009) Time- and sediment depth-related variations in bacterial diversity and community structure in subtidal sands. ISME J 3: 780-791.
5. Borcard D & Legendre P (2002) All-scale spatial analysis of ecological data by means of principal coordinates of neighbour matrices. Ecol Model 153: 51-68.
6. Borcard D, Legendre P & Gillet F (2011) Numerical Ecology with R (Gentleman R, Hornik K & Parmigiani GG, eds), Springer, New York.
7. Caporaso JG, Kuczynski J, Stombaugh J et al. (2010) QIIME allows analysis of high-throughput community sequencing data. Nat Methods 7: 335-336.
8. Clarke KR (1993) Non-parametric multivariate analyses of changes in community structure. Austral Ecol 18: 117-143.
9. Coss RG (2009) Pseudoreplication conventions are testable hypotheses. J Comp Psychol 123: 444-446.
10. Cottenie K & De Meester L (2003) Comment to Oksanen (2001): reconciling Oksanen (2001) and Hurlbert (1984). Oikos 100: 394-396.
11. Dray S, Legendre P & Peres-Neto PR (2006) Spatial modelling: a comprehensive framework for principal coordinate analysis of neighbour matrices (PCNM). Ecol Model 196: 483-493.
12. Dryer DC (1997) Wizards, guides, and beyond. Proceedings of the 2nd International Conference on Intelligent User Interfaces - IUI '97 (Moore J, Edmonds E & Puerta A, eds), pp. 265-268. ACM Press, New York.
13. Frossard A, Gerull L, Mutz M & Gessner MO (2012) Disconnect of microbial structure and function: enzyme activities and bacterial communities in nascent stream corridors. ISME J 6: 680-691.
14. Gobet A, Quince C & Ramette A (2010) Multivariate Cutoff Level Analysis (MultiCoLA) of large community data sets. Nucleic Acids Res 38: e155.
15. Härdle W & Simar L (2007) Applied Multivariate Statistical Analysis, 2nd edn. Springer, Berlin, Heidelberg.
16. Hartmann M, Niklaus PA, Zimmermann S, Schmutz S, Kremer J, Abarenkov K, Lüscher P, Widmer F & Frey B (2013) Resistance and resilience of the forest soil microbiome to logging-associated compaction. ISME J 8: 226-244.
17. Hurlbert SH (1984) Pseudoreplication and the design of ecological field experiments. Ecol Monogr 54: 187-211.
18. Hurlbert SH (2004) On misinterpretations of pseudoreplication and related matters: a reply to Oksanen. Oikos 104: 591-597.
19. Hurlbert SH (2009) The ancient black art and transdisciplinary extent of pseudoreplication. J Comp Psychol 123: 434-443.
20. James F & McCulloch C (1990) Multivariate analysis in ecology and systematics: panacea or Pandora's box? Annu Rev Ecol Syst 21: 129-166.
21. Jombart T, Pontier D & Dufour A-B (2009) Genetic markers in the playground of multivariate analysis. Heredity 102: 330-341.
22. Karsenti E, Acinas SG, Bork P et al. (2011) A holistic approach to marine eco-systems biology. PLoS Biol 9: e1001177.
23. Koehnle TJ & Schank JC (2009) An ancient black art. J Comp Psychol 123: 452-458.
24. Kopp D, Bouchon-Navaro Y, Louis M, Legendre P & Bouchon C (2012) Spatial and temporal variation in a Caribbean herbivorous fish assemblage. J Coast Res 278: 63-72.
25. Kottmann R, Kostadinov I, Duhaime MB, Buttigieg PL, Yilmaz P, Hankeln W, Waldmann J & Glöckner FO (2010) Megx.net: integrated database resource for marine ecological genomics. Nucleic Acids Res 38: D391-D395.
26. Kuczynski J, Lauber CL, Walters WA, Parfrey LW, Clemente JC, Gevers D & Knight R (2012) Experimental and analytical tools for studying the human microbiome. Nat Rev Genet 13: 47-58.
27. Laliberté E (2008) Analyzing or explaining beta diversity? Comment. Ecology 89: 3232-3237.
28. Legendre P (2005a) Analyzing beta diversity: partitioning the spatial variation of community composition data. Ecol Monogr 75: 435-450.
29. Legendre P (2005b) Species associations: the Kendall coefficient of concordance revisited. J Agric Biol Environ Stat 10: 226-245.
30. Legendre P (2007) Studying beta diversity: ecological variation partitioning by multiple regression and canonical analysis. J Plant Ecol 1: 3-8.
31. Legendre P & Anderson MJ (1999) Distance-based redundancy analysis: testing multispecies responses in multifactorial ecological experiments. Ecol Monogr 69: 1-24.
32. Legendre P & Gallagher ED (2001) Ecologically meaningful transformations for ordination of species data. Oecologia 129: 271-280.
33. Legendre P & Legendre L (1998) Numerical Ecology, 2nd edn. Elsevier, Amsterdam.
34. Legendre P & Legendre L (2012) Numerical Ecology, 3rd edn. Elsevier, Amsterdam.
35. Legendre P, Borcard D & Peres-Neto P (2008) Analyzing or explaining beta diversity? Comment. Ecology 89: 3238-3244.
36. McMurdie PJ & Holmes S (2013) phyloseq : an R package for reproducible interactive analysis and graphics of microbiome census data. PLoS ONE 8: e61217.
37. Nuzzo R (2014) Scientific method: statistical errors. Nature 506: 150-152.
38. Økland RHR (2007) Wise use of statistical tools in ecological field studies. Folia Geobot 42: 123-140.
39. Oksanen L (2001) Logic of experiments in ecology: is pseudoreplication a pseudoissue? Oikos 94: 27-38.
40. Oksanen L (2004) The devil lies in details: reply to Stuart Hurlbert. Oikos 104: 598-605.
41. Oksanen J, Blanchet FG, Kindt R, Legendre P, Minchin PR, O'Hara RB, Simpson GL, Solymos P, Stevens MHH & Wagner H (2013) vegan: community Ecology Package. R package version 2.0-7. http://CRAN.R-project.org/package=vegan.
42. Pavoine S, Dufour A-B & Chessel D (2004) From dissimilarities among species to dissimilarities among communities: a double principal coordinate analysis. J Theor Biol 228: 523-537.
43. Pélissier R, Couteron P & Dray S (2008) Analyzing or explaining beta diversity? Ecology 89: 3227-3232.
44. Peres-Neto P, Legendre P, Dray S & Borcard D (2006) Variation partitioning of species data matrices: estimation and comparison of fractions. Ecology 87: 2614-2625.
45. Prosser JI (2010) Replicate or lie. Environ Microbiol 12: 1806-1810.
46. Prosser JI, Bohannan B & Curtis T (2007) The role of ecological theory in microbial ecology. Nat Rev Microbiol 5: 384-392.
47. R Development Core Team (2014) R: A Language and Environment for Statistical Computing. R Foundation for Statistical Computing, Vienna, Austria. http://www.r-project.org/
48. Ramette A (2007) Multivariate analyses in microbial ecology. FEMS Microbiol Ecol 62: 142-160.
49. Rivers AR, Sharma S, Tringe SG, Martin J, Joye SB & Moran MA (2013) Transcriptional response of bathypelagic marine bacterioplankton to the Deepwater Horizon oil spill. ISME J 7: 2315-2329.
50. RStudio Inc. (2014) shiny: Web Application Framework for R. R package version 0.10.2.1. http://CRAN.R-project.org/package=shiny.
51. Rusch DB, Halpern AL, Sutton G et al. (2007) The Sorcerer II Global Ocean Sampling expedition: northwest Atlantic through eastern tropical Pacific. PLoS Biol 5: e77.
52. Schank JC & Koehnle TJ (2009) Pseudoreplication is a pseudoproblem. J Comp Psychol 123: 421-433.
53. Schloss PD, Westcott SL, Ryabin T et al. (2009) Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol 75: 7537-7541.
54. Thioulouse J, Prin Y & Duponnois R (2012) Multivariate analyses in soil microbial ecology: a new paradigm. Environ Ecol Stat 19: 499-520.
55. Tuomisto H & Ruokolainen K (2006) Analyzing or explaining beta diversity? Understanding the targets of different methods of analysis. Ecology 87: 2697-2708.
56. Tuomisto H & Ruokolainen K (2008) Analyzing or explaining beta diversity? Reply. Ecology 89: 3244-3256.
57. Warton DI (2011) Regularized sandwich estimators for analysis of high-dimensional data using generalized estimating equations. Biometrics 67: 116-123.
58. Warton DI & Hudson HM (2004) A MANOVA statistic is just as powerful as distance-based statistics for multivariate abundances. Ecology 85: 858-874.
59. Warton DI, Wright ST & Wang Y (2012) Distance-based multivariate analyses confound location and dispersion effects. Methods Ecol Evol 3: 89-101.
60. Wright S (1934) The method of path coefficients. Ann Math Stat 5: 161-215.
61. Yee TW (2006) Constrained additive ordination. Ecology 87: 203-213.
62. Zhou J, Jiang Y-H, Deng Y, Shi Z, Zhou BY, Xue K, Wu L, He Z & Yang Y (2013) Random sampling process leads to overestimation of β-diversity of microbial communities. mBio 4: e00324-13.
63. Zinger L, Amaral-Zettler LA, Fuhrman JA, Horner-Devine MC, Huse SM, Welch DBM, Martiny JBH, Sogin M, Boetius A & Ramette A (2011) Global patterns of bacterial beta-diversity in seafloor and seawater ecosystems. PLoS ONE 6: e24570.
64. Zinger L, Gobet A & Pommier T (2012) Two decades of describing the unseen majority of aquatic microbial diversity. Mol Ecol 21: 1878-1896.
65. Zou H, Hastie T & Tibshirani R (2006) Sparse principal component analysis. J Comput Graph Stat 15: 265-286.
66. Zuur AF, Ieno EN & Elphick CS (2010) A protocol for data exploration to avoid common statistical problems. Methods Ecol Evol 1: 3-14.