Advancing our understanding of the human microbiome using QIIME

Methods in Enzymology

Volumn 531, Issue , 2013, Pages 371-444

  Navas Molina, José A ^a   Peralta Sánchez, Juan M ^b   González, Antonio ^b   McMurdie, Paul J ^c   Vázquez Baeza, Yoshiki ^b   Xu, Zhenjiang ^b   Ursell, Luke K ^b   Lauber, Christian ^g   Zhou, Hongwei ^d   Song, Se Jin ^b   Huntley, James ^b   Ackermann, Gail L ^b   Berg Lyons, Donna ^b   Holmes, Susan ^c   Caporaso, J Gregory ^e,f   Knight, Rob ^b  

^a UCB 450   (United States)

^b UNIVERSITY OF COLORADO   (United States)

^c STANFORD UNIVERSITY   (United States)

^d SOUTHERN MEDICAL UNIVERSITY   (China)

^e NORTHERN ARIZONA UNIVERSITY   (United States)

^f ARGONNE NATIONAL LABORATORY   (United States)

^g NONE   (United States)

Author keywords

Highthroughput sequencing; Microbial community analyses; Microbial ecology; Microbiome; QIIME

Indexed keywords

RNA 16S; RNA 18S;

ARTICLE; BIOINFORMATICS; COMPUTER PROGRAM; DNA SEQUENCE; GENE SEQUENCE; HUMAN; METAGENOMICS; MICROBIAL COMMUNITY; MICROBIOME; NONHUMAN; PIPELINE; PRACTICE GUIDELINE; PRIORITY JOURNAL; PROTEIN ANALYSIS; QUALITY CONTROL; QUANTITATIVE INSIGHTS INTO MICROBIAL ECOLOGY; SEQUENCE ALIGNMENT; TIME SERIES ANALYSIS; WORKFLOW;

MUS;

HIGHTHROUGHPUT SEQUENCING; MICROBIAL COMMUNITY ANALYSES; MICROBIAL ECOLOGY; MICROBIOME; QIIME;

ANIMALS; BACTERIA; COMPUTATIONAL BIOLOGY; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; HUMANS; MICE; MICROBIOTA; PHYLOGENY; SOFTWARE;

EID: 84884577945     PISSN: 00766879     EISSN: 15577988     Source Type: Book Series    
DOI: 10.1016/B978-0-12-407863-5.00019-8     Document Type: Chapter

References (107)

1. Allaire, J., Horner, J., Marti, V., & Porte, N. (2013). Markdown: Markdown rendering for R. From http://CRAN.R-project.org/package=markdown.
2. S.F. Altschul, W. Gish, W. Miller, E.W. Myers, and D.J. Lipman Basic local alignment search tool Journal of Molecular Biology 215 3 1990 403 410
3. M. Arumugam, J. Raes, E. Pelletier, D. Le Paslier, T. Yamada, and D.R. Mende Enterotypes of the human gut microbiome Nature 473 7346 2011 174 180
4. R.M. Atlas, and R. Bartha Microbial ecology: Fundamentals and applications 4th ed. 1998 Benjamin/Cummings Menlo Park, CA/Harlow
5. N.A. Bokulich, S. Subramanian, J.J. Faith, D. Gevers, J.I. Gordon, and R. Knight Quality-filtering vastly improves diversity estimates from Illumina amplicon sequencing Nature Methods 10 1 2013 57 59
6. L. Breiman Random forests Machine Learning 45 1 2001 5 32
7. J.G. Caporaso, K. Bittinger, F.D. Bushman, T.Z. DeSantis, G.L. Andersen, and R. Knight PyNAST: A flexible tool for aligning sequences to a template alignment Bioinformatics 26 2 2010 266 267
8. J.G. Caporaso, J. Kuczynski, J. Stombaugh, K. Bittinger, F.D. Bushman, and E.K. Costello QIIME allows analysis of high-throughput community sequencing data Nature Methods 7 5 2010 335 336
9. J.G. Caporaso, C.L. Lauber, E.K. Costello, D. Berg-Lyons, A. Gonzalez, and J. Stombaugh Moving pictures of the human microbiome Genome Biology 12 5 2011 R50
10. J.G. Caporaso, C.L. Lauber, W.A. Walters, D. Berg-Lyons, J. Huntley, and N. Fierer Ultra-high-throughput microbial community analysis on the Illumina HiSeq and MiSeq platforms ISME Journal 6 8 2012 1621 1624
11. F.A. Carvalho, O. Koren, J.K. Goodrich, M.E. Johansson, I. Nalbantoglu, and J.D. Aitken Transient inability to manage proteobacteria promotes chronic gut inflammation in TLR5-deficient mice Cell Host & Microbe 12 2 2012 139 152
12. J. Chakerian, and S. Holmes Computational tools for evaluating phylogenetic and hierarchical clustering trees Journal of Computational and Graphical Statistics 21 3 2012 581 599
13. V.B. Chen, I.W. Davis, and D.C. Richardson KING (Kinemage, Next Generation): A versatile interactive molecular and scientific visualization program Protein Science 18 11 2009 2403 2409
14. J.R. Cole, Q. Wang, E. Cardenas, J. Fish, B. Chai, and R.J. Farris The Ribosomal Database Project: Improved alignments and new tools for rRNA analysis Nucleic Acids Research 37 Database issue 2009 D141 D145
15. C. De Filippo, D. Cavalieri, M. Di Paola, M. Ramazzotti, J.B. Poullet, and S. Massart Impact of diet in shaping gut microbiota revealed by a comparative study in children from Europe and rural Africa Proceedings of the National Academy of Sciences of the United States of America 107 33 2010 14691 14696
16. T.Z. DeSantis, P. Hugenholtz, N. Larsen, M. Rojas, E.L. Brodie, and K. Keller Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB Applied and Environmental Microbiology 72 7 2006 5069 5072
17. L. Dethlefsen, and D.A. Relman Incomplete recovery and individualized responses of the human distal gut microbiota to repeated antibiotic perturbation Proceedings of the National Academy of Sciences of the United States of America 108 Suppl. 1 2011 4554 4561
18. R. Diaz Heijtz, S. Wang, F. Anuar, Y. Qian, B. Bjorkholm, and A. Samuelsson Normal gut microbiota modulates brain development and behavior Proceedings of the National Academy of Sciences of the United States of America 108 7 2011 3047 3052
19. M.G. Dominguez-Bello, E.K. Costello, M. Contreras, M. Magris, G. Hidalgo, and N. Fierer Delivery mode shapes the acquisition and structure of the initial microbiota across multiple body habitats in newborns Proceedings of the National Academy of Sciences of the United States of America 107 26 2010 11971 11975
20. M. Drancourt, C. Bollet, A. Carlioz, R. Martelin, J.P. Gayral, and D. Raoult 16S ribosomal DNA sequence analysis of a large collection of environmental and clinical unidentifiable bacterial isolates Journal of Clinical Microbiology 38 10 2000 3623 3630
21. P.B. Eckburg, and D.A. Relman The role of microbes in Crohn's disease Clinical Infectious Diseases 44 2 2007 256 262
22. R.C. Edgar MUSCLE: Multiple sequence alignment with high accuracy and high throughput Nucleic Acids Research 32 5 2004 1792 1797
23. R.C. Edgar Search and clustering orders of magnitude faster than BLAST Bioinformatics 26 19 2010 2460 2461
24. R.C. Edgar, B.J. Haas, J.C. Clemente, C. Quince, and R. Knight UCHIME improves sensitivity and speed of chimera detection Bioinformatics 27 16 2011 2194 2200
25. J. Evans, L. Sheneman, and J. Foster Relaxed neighbor joining: A fast distance-based phylogenetic tree construction method Journal of Molecular Evolution 62 6 2006 785 792
26. D.P. Faith Conservation evaluation and phylogenetic diversity Biological Conservation 61 1 1992 1 10
27. N. Fierer, M. Hamady, C.L. Lauber, and R. Knight The influence of sex, handedness, and washing on the diversity of hand surface bacteria Proceedings of the National Academy of Sciences of the United States of America 105 46 2008 17994 17999
28. N. Fierer, C.L. Lauber, N. Zhou, D. McDonald, E.K. Costello, and R. Knight Forensic identification using skin bacterial communities Proceedings of the National Academy of Sciences of the United States of America 107 14 2010 6477 6481
29. D.N. Frank BARCRAWL and BARTAB: Software tools for the design and implementation of barcoded primers for highly multiplexed DNA sequencing BMC Bioinformatics 10 2009 362
30. D. Gevers, R. Knight, J.F. Petrosino, K. Huang, A.L. McGuire, and B.W. Birren The Human Microbiome Project: A community resource for the healthy human microbiome PLoS Biology 10 8 2012 e1001377
31. J.A. Gilbert, F. Meyer, D. Antonopoulos, P. Balaji, C.T. Brown, and C.T. Brown Meeting report: The terabase metagenomics workshop and the vision of an Earth microbiome project Standards in Genomic Sciences 3 3 2010 243 248
32. J.A. Gilbert, F. Meyer, J. Jansson, J. Gordon, N. Pace, and J. Tiedje The Earth Microbiome Project: Meeting report of the "1 EMP meeting on sample selection and acquisition" at Argonne National Laboratory October 6 2010 Standards in Genomic Sciences 3 3 2010 249 253
33. A. Gonzalez, and R. Knight Advancing analytical algorithms and pipelines for billions of microbial sequences Current Opinion in Biotechnology 23 1 2012 64 71
34. A. Gonzalez, J. Stombaugh, C.L. Lauber, N. Fierer, and R. Knight SitePainter: A tool for exploring biogeographical patterns Bioinformatics 28 3 2012 436 438
35. J.C. Gower Some distance properties of latent root and vector methods used in multivariate analysis Biometrika 53 1966 325 338
36. B.J. Haas, D. Gevers, A.M. Earl, M. Feldgarden, D.V. Ward, and G. Giannoukos Chimeric 16S rRNA sequence formation and detection in Sanger and 454-pyrosequenced PCR amplicons Genome Research 21 3 2011 494 504
37. M. Hamady, and R. Knight Microbial community profiling for Human Microbiome Projects: Tools, techniques, and challenges Genome Research 19 7 2009 1141 1152
38. M. Hamady, J.J. Walker, J.K. Harris, N.J. Gold, and R. Knight Error-correcting barcoded primers for pyrosequencing hundreds of samples in multiplex Nature Methods 5 3 2008 235 237
39. K.M. Hewitt, F.L. Mannino, A. Gonzalez, J.H. Chase, J.G. Caporaso, and R. Knight Bacterial diversity in two Neonatal Intensive Care Units (NICUs) PLoS One 8 1 2013 e54703
40. Human Microbiome Project Consortium A framework for human microbiome research Nature 486 7402 2012 215 221
41. Human Microbiome Project Consortium Structure, function and diversity of the healthy human microbiome Nature 486 7402 2012 207 214
42. L. Jost Partitioning diversity into independent alpha and beta components Ecology 88 10 2007 2427 2439
43. K. Katoh, K. Misawa, K. Kuma, and T. Miyata MAFFT: A novel method for rapid multiple sequence alignment based on fast Fourier transform Nucleic Acids Research 30 14 2002 3059 3066
44. W.J. Kent BLAT - The BLAST-like alignment tool Genome Research 12 4 2002 656 664
45. D. Knights, E.K. Costello, and R. Knight Supervised classification of human microbiota FEMS Microbiology Reviews 35 2 2011 343 359
46. D. Knights, J. Kuczynski, E.S. Charlson, J. Zaneveld, M.C. Mozer, and R.G. Collman Bayesian community-wide culture-independent microbial source tracking Nature Methods 8 9 2011 761 763
47. D. Knights, J. Kuczynski, O. Koren, R.E. Ley, D. Field, and R. Knight Supervised classification of microbiota mitigates mislabeling errors ISME Journal 5 4 2011 570 573
48. J.E. Koenig, A. Spor, N. Scalfone, A.D. Fricker, J. Stombaugh, and R. Knight Succession of microbial consortia in the developing infant gut microbiome Proceedings of the National Academy of Sciences of the United States of America 108 Suppl. 1 2011 4578 4585
49. O. Koren, J.K. Goodrich, T.C. Cullender, A. Spor, K. Laitinen, and H.K. Backhed Host remodeling of the gut microbiome and metabolic changes during pregnancy Cell 150 3 2012 470 480
50. J. Kuczynski, E.K. Costello, D.R. Nemergut, J. Zaneveld, C.L. Lauber, and D. Knights Direct sequencing of the human microbiome readily reveals community differences Genome Biology 11 5 2010 210
51. J. Kuczynski, C.L. Lauber, W.A. Walters, L.W. Parfrey, J.C. Clemente, and D. Gevers Experimental and analytical tools for studying the human microbiome Nature Reviews. Genetics 13 1 2012 47 58
52. J. Kuczynski, Z. Liu, C. Lozupone, D. McDonald, N. Fierer, and R. Knight Microbial community resemblance methods differ in their ability to detect biologically relevant patterns Nature Methods 7 10 2010 813 819
53. M.A. Larkin, G. Blackshields, N.P. Brown, R. Chenna, P.A. McGettigan, and H. McWilliam Clustal W and Clustal X version 2.0 Bioinformatics 23 21 2007 2947 2948
54. F. Leisch Sweave: Dynamic generation of statistical reports using literate data analysis B.R. Wolfgang Härdle, Compstat: Proceedings in computational statistics 2002 Physica-Verlag Heidelberg, Germany 575 580
55. R.E. Ley, F. Backhed, P. Turnbaugh, C.A. Lozupone, R.D. Knight, and J.I. Gordon Obesity alters gut microbial ecology Proceedings of the National Academy of Sciences of the United States of America 102 31 2005 11070 11075
56. R.E. Ley, M. Hamady, C. Lozupone, P.J. Turnbaugh, R.R. Ramey, and J.S. Bircher Evolution of mammals and their gut microbes Science 320 5883 2008 1647 1651
57. W. Li, and A. Godzik Cd-hit: A fast program for clustering and comparing large sets of protein or nucleotide sequences Bioinformatics 22 13 2006 1658 1659
58. W. Li, L. Jaroszewski, and A. Godzik Clustering of highly homologous sequences to reduce the size of large protein databases Bioinformatics 17 3 2001 282 283
59. A. Liaw, and M. Wiener Classification and Regression by randomForest R News: The Newsletter of the R Project 2 3 2002 4
60. Z. Liu, T.Z. DeSantis, G.L. Andersen, and R. Knight Accurate taxonomy assignments from 16S rRNA sequences produced by highly parallel pyrosequencers Nucleic Acids Research 36 18 2008 e120
61. T. Loua Atlas statistique de la population de Paris 1873 J. Dejey & Cie Paris
62. C.A. Lozupone, M. Hamady, S.T. Kelley, and R. Knight Quantitative and qualitative beta diversity measures lead to different insights into factors that structure microbial communities Applied and Environmental Microbiology 73 5 2007 1576 1585
63. C. Lozupone, and R. Knight UniFrac: A new phylogenetic method for comparing microbial communities Applied and Environmental Microbiology 71 12 2005 8228 8235
64. C.A. Lozupone, and R. Knight Species divergence and the measurement of microbial diversity FEMS Microbiology Reviews 32 4 2008 557 578
65. C. Lozupone, M.E. Lladser, D. Knights, J. Stombaugh, and R. Knight UniFrac: An effective distance metric for microbial community comparison ISME Journal 5 2 2011 169 172
66. W. Ludwig, O. Strunk, R. Westram, L. Richter, H. Meier, and Yadhukumar ARB: A software environment for sequence data Nucleic Acids Research 32 4 2004 1363 1371
67. K.V. Mardia, J.T. Kent, and J. Bibby Multivariate analysis 1979 Academic Press London
68. D. McDonald, J.C. Clemente, J. Kuczynski, J.R. Rideout, J. Stombaugh, and D. Wendel The Biological Observation Matrix (BIOM) format or: How I learned to stop worrying and love the ome-ome Gigascience 1 1 2012 7
69. D. McDonald, M.N. Price, J. Goodrich, E.P. Nawrocki, T.Z. DeSantis, and A. Probst An improved Greengenes taxonomy with explicit ranks for ecological and evolutionary analyses of bacteria and archaea ISME Journal 6 3 2012 610 618
70. P.G. McLean, G.E. Bergonzelli, S.M. Collins, and P. Bercik Targeting the microbiota-gut-brain axis to modulate behavior: Which bacterial strain will translate best to humans? Proceedings of the National Academy of Sciences of the United States of America 109 4 2012 E174 author reply E176
71. P.J. McMurdie, and S. Holmes phyloseq: An R package for reproducible interactive analysis and graphics of microbiome census data PLoS One 8 4 2013 e61217
72. B.D. Muegge, J. Kuczynski, D. Knights, J.C. Clemente, A. Gonzalez, and L. Fontana Diet drives convergence in gut microbiome functions across mammalian phylogeny and within humans Science 332 6032 2011 970 974
73. E.P. Nawrocki, D.L. Kolbe, and S.R. Eddy Infernal 1.0: Inference of RNA alignments Bioinformatics 25 10 2009 1335 1337
74. G.J. Olsen, N. Larsen, and C.R. Woese The ribosomal RNA database project Nucleic Acids Research 19 Suppl. 1991 2017 2021
75. G.J. Olsen, R. Overbeek, N. Larsen, T.L. Marsh, M.J. McCaughey, and M.A. Maciukenas The Ribosomal Database Project Nucleic Acids Research 20 Suppl. 1992 2199 2200
76. E. Paradis, J. Claude, and K. Strimmer APE: Analyses of phylogenetics and evolution in R language Bioinformatics 20 2 2004 289 290
77. M. Pirrung, R. Kennedy, J.G. Caporaso, J. Stombaugh, D. Wendel, and R. Knight TopiaryExplorer: Visualizing large phylogenetic trees with environmental metadata Bioinformatics 27 21 2011 3067 3069
78. M.N. Price, P.S. Dehal, and A.P. Arkin FastTree: Computing large minimum evolution trees with profiles instead of a distance matrix Molecular Biology and Evolution 26 7 2009 1641 1650
79. C. Quast, E. Pruesse, P. Yilmaz, J. Gerken, T. Schweer, and P. Yarza The SILVA ribosomal RNA gene database project: Improved data processing and web-based tools Nucleic Acids Research 41 D1 2013 D590 D596
80. C. Quince, A. Lanzen, T.P. Curtis, R.J. Davenport, N. Hall, and I.M. Head Accurate determination of microbial diversity from 454 pyrosequencing data Nature Methods 6 9 2009 639 641
81. C. Quince, A. Lanzen, R.J. Davenport, and P.J. Turnbaugh Removing noise from pyrosequenced amplicons BMC Bioinformatics 12 2011 38
82. S. Rajaram, and Y. Oono NeatMap - non-clustering heat map alternatives in R BMC Bioinformatics 11 2010 45
83. J. Ravel, P. Gajer, L. Fu, C.K. Mauck, S.S. Koenig, and J. Sakamoto Twice-daily application of HIV microbicides alter the vaginal microbiota MBio 3 6 2012 e00370-12
84. J. Reeder, and R. Knight Rapidly denoising pyrosequencing amplicon reads by exploiting rank-abundance distributions Nature Methods 7 9 2010 668 669
85. L.F. Roesch, R.R. Fulthorpe, A. Riva, G. Casella, A.K. Hadwin, and A.D. Kent Pyrosequencing enumerates and contrasts soil microbial diversity ISME Journal 1 4 2007 283 290
86. D.C. Savage Microbial ecology of the gastrointestinal tract Annual Review of Microbiology 31 1977 107 133
87. P.D. Schloss, and J. Handelsman Introducing DOTUR, a computer program for defining operational taxonomic units and estimating species richness Applied and Environmental Microbiology 71 3 2005 1501 1506
88. P.D. Schloss, and J. Handelsman Introducing SONS, a tool for operational taxonomic unit-based comparisons of microbial community memberships and structures Applied and Environmental Microbiology 72 10 2006 6773 6779
89. P.D. Schloss, S.L. Westcott, T. Ryabin, J.R. Hall, M. Hartmann, and E.B. Hollister Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities Applied and Environmental Microbiology 75 23 2009 7537 7541
90. P. Shannon, A. Markiel, O. Ozier, N.S. Baliga, J.T. Wang, and D. Ramage Cytoscape: A software environment for integrated models of biomolecular interaction networks Genome Research 13 11 2003 2498 2504
91. M.I. Smith, T. Yatsunenko, M.J. Manary, I. Trehan, R. Mkakosya, and J. Cheng Gut microbiomes of Malawian twin pairs discordant for kwashiorkor Science 339 6119 2013 548 554
92. P.H.A. Sneath, and R.R. Sokal Numerical taxonomy: The principles and practice of numerical classification 1973 Freeman San Francisco
93. D.A. Soergel, N. Dey, R. Knight, and S.E. Brenner Selection of primers for optimal taxonomic classification of environmental 16S rRNA gene sequences ISME Journal 6 7 2012 1440 1444
94. Sogin, M., Welch, D. M., & Huse, S. (2009). The visualization and analysis of microbial population structures. From http://vamps.mbl.edu.
95. R.R. Sokal, and P.H.A. Sneath Principles of numerical taxonomy 1963 W.H. Freeman San Francisco
96. M.D. Spencer, T.J. Hamp, R.W. Reid, L.M. Fischer, S.H. Zeisel, and A.A. Fodor Association between composition of the human gastrointestinal microbiome and development of fatty liver with choline deficiency Gastroenterology 140 3 2011 976 986
97. A. Stamatakis, T. Ludwig, and H. Meier RAxML-III: A fast program for maximum likelihood-based inference of large phylogenetic trees Bioinformatics 21 4 2005 456 463
98. R.C. Tryon Cluster analysis 1939 Edwards Bros. Ann Arbor, MI
99. P.J. Turnbaugh, M. Hamady, T. Yatsunenko, B.L. Cantarel, A. Duncan, and R.E. Ley A core gut microbiome in obese and lean twins Nature 457 7228 2009 480 484
100. P.J. Turnbaugh, R.E. Ley, M. Hamady, C.M. Fraser-Liggett, R. Knight, and J.I. Gordon The Human Microbiome Project Nature 449 7164 2007 804 810
101. A.J. Vinten, R.R. Artz, N. Thomas, J.M. Potts, L. Avery, and S.J. Langan Comparison of microbial community assays for the assessment of stream biofilm ecology Journal of Microbiological Methods 85 3 2011 190 198
102. Q. Wang, G.M. Garrity, J.M. Tiedje, and J.R. Cole Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy Applied and Environmental Microbiology 73 16 2007 5261 5267
103. R.H. Whittaker Vegetation of the Siskiyou Mountains, Oregon and California Ecological Monographs 30 3 1960 280 338
104. R.H. Whittaker Evolution and measurement of species diversity Taxon 21 2/3 1972 213 251
105. H. Wickham ggplot2: Elegant graphics for data analysis Use R! Vol. 6991 2009 Springer New York
106. L. Wilkinson, and M. Friendly The history of the cluster heat map The American Statistician 63 2 2009 179 184
107. Y. Xie Dynamic documents with R and knitr 2013 Chapman and Hall/CRC London, United Kingdom