Conducting a microbiome study

Cell

Volumn 158, Issue 2, 2014, Pages 250-262

  Goodrich, Julia K ^a   Di Rienzi, Sara C ^a   Poole, Angela C ^a   Koren, Omry ^a   Walters, William A ^b   Caporaso, J Gregory ^c,d   Knight, Rob ^e   Ley, Ruth E ^a  

^a Department of Obstetrics Gynecology   (United States)

^b UNIVERSITY OF COLORADO SCHOOL OF MEDICINE   (United States)

^c NORTHERN ARIZONA UNIVERSITY   (United States)

^d ARGONNE NATIONAL LABORATORY   (United States)

^e UNIVERSITY OF COLORADO   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

RNA 16S; DNA;

ALGORITHM; ARTICLE; CLASSIFICATION; CLUSTER ANALYSIS; DATA ANALYSIS; DATA BASE; DIZYGOTIC TWINS; DNA CONTAMINATION; DNA EXTRACTION; DNA SEQUENCE; ENVIRONMENTAL FACTOR; GENE AMPLIFICATION; GENE SEQUENCE; GENOTYPE; HEREDITY; HUMAN; IMMUNE SYSTEM; MATERNAL EFFECT; METAGENOMICS; MICROBIAL DIVERSITY; MICROBIOME; MICROFLORA; MODEL; MONOZYGOTIC TWINS; NONHUMAN; OBESITY; PHENOTYPE; POLYMERASE CHAIN REACTION; PRINCIPAL COORDINATE ANALYSIS; PRIORITY JOURNAL; RESEARCH; RNA GENE; SAMPLING; SEQUENCE ANALYSIS; STUDY DESIGN; CONTAMINATION; MATERNAL BEHAVIOR; PILOT STUDY;

ANIMALS; ARCHAEA; BACTERIA; GUIDELINES AS TOPIC; HUMANS; MICROBIOLOGICAL TECHNIQUES; MICROBIOTA; POLYMERASE CHAIN REACTION; RIBOTYPING;

EID: 84904569753     PISSN: 00928674     EISSN: 10974172     Source Type: Journal    
DOI: 10.1016/j.cell.2014.06.037     Document Type: Review

References (102)

1. K. Abarenkov, R. Henrik Nilsson, K.H. Larsson, I.J. Alexander, U. Eberhardt, S. Erland, K. Høiland, R. Kjøller, E. Larsson, and T. Pennanen et al. The UNITE database for molecular identification of fungi - recent updates and future perspectives New Phytol. 186 2010 281 285
2. S.G. Acinas, R. Sarma-Rupavtarm, V. Klepac-Ceraj, and M.F. Polz PCR-induced sequence artifacts and bias: insights from comparison of two 16S rRNA clone libraries constructed from the same sample Appl. Environ. Microbiol. 71 2005 8966 8969
3. D. Aird, M.G. Ross, W.S. Chen, M. Danielsson, T. Fennell, C. Russ, D.B. Jaffe, C. Nusbaum, and A. Gnirke Analyzing and minimizing PCR amplification bias in Illumina sequencing libraries Genome Biol. 12 2011 R18
4. S.V. Angiuoli, M. Matalka, A. Gussman, K. Galens, M. Vangala, D.R. Riley, C. Arze, J.R. White, O. White, and W.F. Fricke CloVR: a virtual machine for automated and portable sequence analysis from the desktop using cloud computing BMC Bioinformatics 12 2011 356
5. M. Arumugam, J. Raes, E. Pelletier, D. Le Paslier, T. Yamada, D.R. Mende, G.R. Fernandes, J. Tap, T. Bruls, J.M. Batto MetaHIT Consortium Enterotypes of the human gut microbiome Nature 473 2011 174 180
6. G. Bai, P. Gajer, M. Nandy, B. Ma, H. Yang, J. Sakamoto, M.H. Blanchard, J. Ravel, and R.M. Brotman Comparison of storage conditions for human vaginal microbiome studies PLoS ONE 7 2012 e36934
7. A.K. Benson, S.A. Kelly, R. Legge, F. Ma, S.J. Low, J. Kim, M. Zhang, P.L. Oh, D. Nehrenberg, and K. Hua et al. Individuality in gut microbiota composition is a complex polygenic trait shaped by multiple environmental and host genetic factors Proc. Natl. Acad. Sci. USA 107 2010 18933 18938
8. D. Blankenberg, G. Von Kuster, N. Coraor, G. Ananda, R. Lazarus, M. Mangan, A. Nekrutenko, and J. Taylor Galaxy: a web-based genome analysis tool for experimentalists Curr. Protoc. Mol. Biol. Unit 19 2010 11 21
9. N.A. Bokulich, S. Subramanian, J.J. Faith, D. Gevers, J.I. Gordon, R. Knight, D.A. Mills, and J.G. Caporaso Quality-filtering vastly improves diversity estimates from Illumina amplicon sequencing Nat. Methods 10 2013 57 59
10. N.A. Bokulich, J.H. Thorngate, P.M. Richardson, and D.A. Mills Microbial biogeography of wine grapes is conditioned by cultivar, vintage, and climate Proc. Natl. Acad. Sci. USA 2013
11. 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 2010 266 267
12. J.G. Caporaso, J. Kuczynski, J. Stombaugh, K. Bittinger, F.D. Bushman, E.K. Costello, N. Fierer, A.G. Peña, J.K. Goodrich, and J.I. Gordon et al. QIIME allows analysis of high-throughput community sequencing data Nat. Methods 7 2010 335 336
13. J.G. Caporaso, R. Knight, and S.T. Kelley Host-associated and free-living phage communities differ profoundly in phylogenetic composition PLoS ONE 6 2011 e16900
14. J.G. Caporaso, C.L. Lauber, E.K. Costello, D. Berg-Lyons, A. Gonzalez, J. Stombaugh, D. Knights, P. Gajer, J. Ravel, and N. Fierer et al. Moving pictures of the human microbiome Genome Biol. 12 2011 R50
15. J.G. Caporaso, C.L. Lauber, W.A. Walters, D. Berg-Lyons, J. Huntley, N. Fierer, S.M. Owens, J. Betley, L. Fraser, and M. Bauer et al. Ultra-high-throughput microbial community analysis on the Illumina HiSeq and MiSeq platforms ISME J. 6 2012 1621 1624
16. I.M. Carroll, T. Ringel-Kulka, J.P. Siddle, T.R. Klaenhammer, and Y. Ringel Characterization of the fecal microbiota using high-throughput sequencing reveals a stable microbial community during storage PLoS ONE 7 2012 e46953
17. F.A. Carvalho, O. Koren, J.K. Goodrich, M.E. Johansson, I. Nalbantoglu, J.D. Aitken, Y. Su, B. Chassaing, W.A. Walters, and A. González et al. Transient inability to manage proteobacteria promotes chronic gut inflammation in TLR5-deficient mice Cell Host Microbe 12 2012 139 152
18. B. Chassaing, J.D. Aitken, A.T. Gewirtz, and M. Vijay-Kumar Gut microbiota drives metabolic disease in immunologically altered mice Adv. Immunol. 116 2012 93 112
19. I. Cho, S. Yamanishi, L. Cox, B.A. Methé, J. Zavadil, K. Li, Z. Gao, D. Mahana, K. Raju, and I. Teitler et al. Antibiotics in early life alter the murine colonic microbiome and adiposity Nature 488 2012 621 626
20. J.C. Clemente, L.K. Ursell, L.W. Parfrey, and R. Knight The impact of the gut microbiota on human health: an integrative view Cell 148 2012 1258 1270
21. J.R. Cole, Q. Wang, E. Cardenas, J. Fish, B. Chai, R.J. Farris, A.S. Kulam-Syed-Mohideen, D.M. McGarrell, T. Marsh, G.M. Garrity, and J.M. Tiedje The Ribosomal Database Project: improved alignments and new tools for rRNA analysis Nucleic Acids Res. 37 Database issue 2009 D141 D145
22. S.M. Collins, M. Surette, and P. Bercik The interplay between the intestinal microbiota and the brain Nat. Rev. Microbiol. 10 2012 735 742
23. HMPC (Human Microbiome Project Consortium) A framework for human microbiome research Nature 486 2012 215 221
24. Consortium, H.M.P.; Human Microbiome Project Consortium Structure, function and diversity of the healthy human microbiome Nature 486 2012 207 214
25. E.K. Costello, C.L. Lauber, M. Hamady, N. Fierer, J.I. Gordon, and R. Knight Bacterial community variation in human body habitats across space and time Science 326 2009 1694 1697
26. E.K. Costello, K. Stagaman, L. Dethlefsen, B.J. Bohannan, and D.A. Relman The application of ecological theory toward an understanding of the human microbiome Science 336 2012 1255 1262
27. F.B. Dean, S. Hosono, L. Fang, X. Wu, A.F. Faruqi, P. Bray-Ward, Z. Sun, Q. Zong, Y. Du, and J. Du et al. Comprehensive human genome amplification using multiple displacement amplification Proc. Natl. Acad. Sci. USA 99 2002 5261 5266
28. L. Dethlefsen, and D.A. Relman Incomplete recovery and individualized responses of the human distal gut microbiota to repeated antibiotic perturbation Proc. Natl. Acad. Sci. USA 108 Suppl 1 2011 4554 4561
29. L. Dethlefsen, S. Huse, M.L. Sogin, and D.A. Relman The pervasive effects of an antibiotic on the human gut microbiota, as revealed by deep 16S rRNA sequencing PLoS Biol. 6 2008 e280
30. S.C. Di Rienzi, I. Sharon, K.C. Wrighton, O. Koren, L.A. Hug, B.C. Thomas, J.K. Goodrich, J.T. Bell, T.D. Spector, J.F. Banfield, and R.E. Ley The human gut and groundwater harbor non-photosynthetic bacteria belonging to a new candidate phylum sibling to Cyanobacteria Elife 2 2013 e01102
31. R.C. Edgar MUSCLE: multiple sequence alignment with high accuracy and high throughput Nucleic Acids Res. 32 2004 1792 1797
32. R.C. Edgar Search and clustering orders of magnitude faster than BLAST Bioinformatics 26 2010 2460 2461
33. R.C. Edgar, B.J. Haas, J.C. Clemente, C. Quince, and R. Knight UCHIME improves sensitivity and speed of chimera detection Bioinformatics 27 2011 2194 2200
34. J.J. Faith, J.L. Guruge, M. Charbonneau, S. Subramanian, H. Seedorf, A.L. Goodman, J.C. Clemente, R. Knight, A.C. Heath, and R.L. Leibel et al. The long-term stability of the human gut microbiota Science 341 2013 1237439
35. J. Friedman, and E.J. Alm Inferring correlation networks from genomic survey data PLoS Comput. Biol. 8 2012 e1002687
36. M.K. Friswell, H. Gika, I.J. Stratford, G. Theodoridis, B. Telfer, I.D. Wilson, and A.J. McBain Site and strain-specific variation in gut microbiota profiles and metabolism in experimental mice PLoS ONE 5 2010 e8584
37. W.S. Garrett, G.M. Lord, S. Punit, G. Lugo-Villarino, S.K. Mazmanian, S. Ito, J.N. Glickman, and L.H. Glimcher Communicable ulcerative colitis induced by T-bet deficiency in the innate immune system Cell 131 2007 33 45
38. B. Giardine, C. Riemer, R.C. Hardison, R. Burhans, L. Elnitski, P. Shah, Y. Zhang, D. Blankenberg, I. Albert, and J. Taylor et al. Galaxy: a platform for interactive large-scale genome analysis Genome Res. 15 2005 1451 1455
39. J. Goecks, A. Nekrutenko, J. Taylor Galaxy Team Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences Genome Biol. 11 2010 R86
40. S.A. Goff, M. Vaughn, S. McKay, E. Lyons, A.E. Stapleton, D. Gessler, N. Matasci, L. Wang, M. Hanlon, and A. Lenards et al. The iPlant Collaborative: Cyberinfrastructure for Plant Biology Front. Plant Sci. 2 2011 34
41. B.J. Haas, D. Gevers, A.M. Earl, M. Feldgarden, D.V. Ward, G. Giannoukos, D. Ciulla, D. Tabbaa, S.K. Highlander, E. Sodergren Human Microbiome Consortium Chimeric 16S rRNA sequence formation and detection in Sanger and 454-pyrosequenced PCR amplicons Genome Res. 21 2011 494 504
42. 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 Nat. Methods 5 2008 235 237
43. S.A. Handley, L.B. Thackray, G. Zhao, R. Presti, A.D. Miller, L. Droit, P. Abbink, L.F. Maxfield, A. Kambal, and E. Duan et al. Pathogenic simian immunodeficiency virus infection is associated with expansion of the enteric virome Cell 151 2012 253 266
44. B.L. Hurwitz, L. Deng, B.T. Poulos, and M.B. Sullivan Evaluation of methods to concentrate and purify ocean virus communities through comparative, replicated metagenomics Environ. Microbiol. 15 2013 1428 1440
45. I.D. Iliev, V.A. Funari, K.D. Taylor, Q. Nguyen, C.N. Reyes, S.P. Strom, J. Brown, C.A. Becker, P.R. Fleshner, and M. Dubinsky et al. Interactions between commensal fungi and the C-type lectin receptor Dectin-1 influence colitis Science 336 2012 1314 1317
46. I.I. Ivanov, K. Atarashi, N. Manel, E.L. Brodie, T. Shima, U. Karaoz, D. Wei, K.C. Goldfarb, C.A. Santee, and S.V. Lynch et al. Induction of intestinal Th17 cells by segmented filamentous bacteria Cell 139 2009 485 498
47. P.J. Jack, R.N. Amos-Ritchie, A. Reverter, G. Palacios, P.L. Quan, O. Jabado, T. Briese, W.I. Lipkin, and D.B. Boyle Microarray-based detection of viruses causing vesicular or vesicular-like lesions in livestock animals Vet. Microbiol. 133 2009 145 153
48. F. Karlsson, V. Tremaroli, J. Nielsen, and F. Bäckhed Assessing the human gut microbiota in metabolic diseases Diabetes 62 2013 3341 3349
49. R. Knight, J. Jansson, D. Field, N. Fierer, N. Desai, J.A. Fuhrman, P. Hugenholtz, D. van der Lelie, F. Meyer, and R. Stevens et al. Unlocking the potential of metagenomics through replicated experimental design Nat. Biotechnol. 30 2012 513 520
50. D. Knights, E.K. Costello, and R. Knight Supervised classification of human microbiota FEMS Microbiol. Rev. 35 2011 343 359
51. D. Knights, K.G. Lassen, and R.J. Xavier Advances in inflammatory bowel disease pathogenesis: linking host genetics and the microbiome Gut 62 2013 1505 1510
52. O. Koren, A. Spor, J. Felin, F. Fåk, J. Stombaugh, V. Tremaroli, C.J. Behre, R. Knight, B. Fagerberg, R.E. Ley, and F. Bäckhed Human oral, gut, and plaque microbiota in patients with atherosclerosis Proc. Natl. Acad. Sci. USA 108 Suppl 1 2011 4592 4598
53. O. Koren, J.K. Goodrich, T.C. Cullender, A. Spor, K. Laitinen, H.K. Bäckhed, A. Gonzalez, J.J. Werner, L.T. Angenent, and R. Knight et al. Host remodeling of the gut microbiome and metabolic changes during pregnancy Cell 150 2012 470 480
54. O. Koren, D. Knights, A. Gonzalez, L. Waldron, N. Segata, R. Knight, C. Huttenhower, and R.E. Ley A guide to enterotypes across the human body: meta-analysis of microbial community structures in human microbiome datasets PLoS Comput. Biol. 9 2013 e1002863
55. 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 Nat. Methods 7 2010 813 819
56. J. Kuczynski, C.L. Lauber, W.A. Walters, L.W. Parfrey, J.C. Clemente, D. Gevers, and R. Knight Experimental and analytical tools for studying the human microbiome Nat. Rev. Genet. 13 2012 47 58
57. D.J. Lahr, and L.A. Katz Reducing the impact of PCR-mediated recombination in molecular evolution and environmental studies using a new-generation high-fidelity DNA polymerase Biotechniques 47 2009 857 866
58. R.S. Lasken Single-cell genomic sequencing using Multiple Displacement Amplification Curr. Opin. Microbiol. 10 2007 510 516
59. C.L. Lauber, N. Zhou, J.I. Gordon, R. Knight, and N. Fierer Effect of storage conditions on the assessment of bacterial community structure in soil and human-associated samples FEMS Microbiol. Lett. 307 2010 80 86
60. T.D. Lawley, S. Clare, A.W. Walker, M.D. Stares, T.R. Connor, C. Raisen, D. Goulding, R. Rad, F. Schreiber, and C. Brandt et al. Targeted restoration of the intestinal microbiota with a simple, defined bacteriotherapy resolves relapsing Clostridium difficile disease in mice PLoS Pathog. 8 2012 e1002995
61. R.E. Ley, F. Bäckhed, P. Turnbaugh, C.A. Lozupone, R.D. Knight, and J.I. Gordon Obesity alters gut microbial ecology Proc. Natl. Acad. Sci. USA 102 2005 11070 11075
62. R.E. Ley, P.J. Turnbaugh, S. Klein, and J.I. Gordon Microbial ecology: human gut microbes associated with obesity Nature 444 2006 1022 1023
63. R.E. Ley, M. Hamady, C. Lozupone, P.J. Turnbaugh, R.R. Ramey, J.S. Bircher, M.L. Schlegel, T.A. Tucker, M.D. Schrenzel, R. Knight, and J.I. Gordon Evolution of mammals and their gut microbes Science 320 2008 1647 1651
64. C.A. Lozupone, and R. Knight Species divergence and the measurement of microbial diversity FEMS Microbiol. Rev. 32 2008 557 578
65. C.A. Lozupone, J.I. Stombaugh, J.I. Gordon, J.K. Jansson, and R. Knight Diversity, stability and resilience of the human gut microbiota Nature 489 2012 220 230
66. D.S. Lundberg, S.L. Lebeis, S.H. Paredes, S. Yourstone, J. Gehring, S. Malfatti, J. Tremblay, A. Engelbrektson, V. Kunin, and T.G. del Rio et al. Defining the core Arabidopsis thaliana root microbiome Nature 488 2012 86 90
67. D.S. Lundberg, S. Yourstone, P. Mieczkowski, C.D. Jones, and J.L. Dangl Practical innovations for high-throughput amplicon sequencing Nat. Methods 10 2013 999 1002
68. C.F. Maurice, H.J. Haiser, and P.J. Turnbaugh Xenobiotics shape the physiology and gene expression of the active human gut microbiome Cell 152 2013 39 50
69. D. McDonald, M.N. Price, J. Goodrich, E.P. Nawrocki, T.Z. DeSantis, A. Probst, G.L. Andersen, R. Knight, and P. Hugenholtz An improved Greengenes taxonomy with explicit ranks for ecological and evolutionary analyses of bacteria and archaea ISME J. 6 2012 610 618
70. P.J. McMurdie, and S. Holmes Waste Not, Want Not: Why Rarefying Microbiome Data is Inadmissible PLoS Comput. Biol. 10 2013 e1003531
71. M.J. Morowitz, V.J. Denef, E.K. Costello, B.C. Thomas, V. Poroyko, D.A. Relman, and J.F. Banfield Strain-resolved community genomic analysis of gut microbial colonization in a premature infant Proc. Natl. Acad. Sci. USA 108 2011 1128 1133
72. G. Palacios, P.L. Quan, O.J. Jabado, S. Conlan, D.L. Hirschberg, Y. Liu, J. Zhai, N. Renwick, J. Hui, and H. Hegyi et al. Panmicrobial oligonucleotide array for diagnosis of infectious diseases Emerg. Infect. Dis. 13 2007 73 81
73. J.A. Peiffer, A. Spor, O. Koren, Z. Jin, S.G. Tringe, J.L. Dangl, E.S. Buckler, and R.E. Ley Diversity and heritability of the maize rhizosphere microbiome under field conditions Proc. Natl. Acad. Sci. USA 110 2013 6548 6553
74. C. Quast, E. Pruesse, P. Yilmaz, J. Gerken, T. Schweer, P. Yarza, J. Peplies, and F.O. Glöckner The SILVA ribosomal RNA gene database project: improved data processing and web-based tools Nucleic Acids Res. 41 Database issue 2013 D590 D596
75. C. Quince, A. Lanzen, R.J. Davenport, and P.J. Turnbaugh Removing noise from pyrosequenced amplicons BMC Bioinformatics 12 2011 38
76. J.F. Rawls, M.A. Mahowald, R.E. Ley, and J.I. Gordon Reciprocal gut microbiota transplants from zebrafish and mice to germ-free recipients reveal host habitat selection Cell 127 2006 423 433
77. J. Reeder, and R. Knight Rapidly denoising pyrosequencing amplicon reads by exploiting rank-abundance distributions Nat. Methods 7 2010 668 669
78. A. Reyes, M. Haynes, N. Hanson, F.E. Angly, A.C. Heath, F. Rohwer, and J.I. Gordon Viruses in the faecal microbiota of monozygotic twins and their mothers Nature 466 2010 334 338
79. V.K. Ridaura, J.J. Faith, F.E. Rey, J. Cheng, A.E. Duncan, A.L. Kau, N.W. Griffin, V. Lombard, B. Henrissat, and J.R. Bain et al. Gut microbiota from twins discordant for obesity modulate metabolism in mice Science 341 2013 1241214
80. A. Salonen, J. Nikkilä, J. Jalanka-Tuovinen, O. Immonen, M. Rajilić-Stojanović, R.A. Kekkonen, A. Palva, and W.M. de Vos Comparative analysis of fecal DNA extraction methods with phylogenetic microarray: effective recovery of bacterial and archaeal DNA using mechanical cell lysis J. Microbiol. Methods 81 2010 127 134
81. D.C. Savage Microbial ecology of the gastrointestinal tract Annu. Rev. Microbiol. 31 1977 107 133
82. P.D. Schloss, and J. Handelsman Introducing DOTUR, a computer program for defining operational taxonomic units and estimating species richness Appl. Environ. Microbiol. 71 2005 1501 1506
83. P.D. Schloss, S.L. Westcott, T. Ryabin, J.R. Hall, M. Hartmann, E.B. Hollister, R.A. Lesniewski, B.B. Oakley, D.H. Parks, and C.J. Robinson et al. Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities Appl. Environ. Microbiol. 75 2009 7537 7541
84. M.J. Sergeant, C. Constantinidou, T. Cogan, C.W. Penn, and M.J. Pallen High-throughput sequencing of 16S rRNA gene amplicons: effects of extraction procedure, primer length and annealing temperature PLoS ONE 7 2012 e38094
85. R. Sipos, A.J. Székely, M. Palatinszky, S. Révész, K. Márialigeti, and M. Nikolausz Effect of primer mismatch, annealing temperature and PCR cycle number on 16S rRNA gene-targetting bacterial community analysis FEMS Microbiol. Ecol. 60 2007 341 350
86. B. Smith, N. Li, A.S. Andersen, H.C. Slotved, and K.A. Krogfelt Optimising bacterial DNA extraction from faecal samples: comparison of three methods Open Microbiol. J. 5 2011 14 17
87. M.I. Smith, T. Yatsunenko, M.J. Manary, I. Trehan, R. Mkakosya, J. Cheng, A.L. Kau, S.S. Rich, P. Concannon, and J.C. Mychaleckyj et al. Gut microbiomes of Malawian twin pairs discordant for kwashiorkor Science 339 2013 548 554
88. 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 J. 6 2012 1440 1444
89. M.A. Tanner, B.M. Goebel, M.A. Dojka, and N.R. Pace Specific ribosomal DNA sequences from diverse environmental settings correlate with experimental contaminants Appl. Environ. Microbiol. 64 1998 3110 3113
90. P.J. Turnbaugh, R.E. Ley, M.A. Mahowald, V. Magrini, E.R. Mardis, and J.I. Gordon An obesity-associated gut microbiome with increased capacity for energy harvest Nature 444 2006 1027 1031
91. P.J. Turnbaugh, M. Hamady, T. Yatsunenko, B.L. Cantarel, A. Duncan, R.E. Ley, M.L. Sogin, W.J. Jones, B.A. Roe, and J.P. Affourtit et al. A core gut microbiome in obese and lean twins Nature 457 2009 480 484
92. C. Ubeda, Y. Taur, R.R. Jenq, M.J. Equinda, T. Son, M. Samstein, A. Viale, N.D. Socci, M.R. van den Brink, M. Kamboj, and E.G. Pamer Vancomycin-resistant Enterococcus domination of intestinal microbiota is enabled by antibiotic treatment in mice and precedes bloodstream invasion in humans J. Clin. Invest. 120 2010 4332 4341
93. S. Vaishnava, M. Yamamoto, K.M. Severson, K.A. Ruhn, X. Yu, O. Koren, R. Ley, E.K. Wakeland, and L.V. Hooper The antibacterial lectin RegIIIgamma promotes the spatial segregation of microbiota and host in the intestine Science 334 2011 255 258
94. M. Vijay-Kumar, J.D. Aitken, F.A. Carvalho, T.C. Cullender, S. Mwangi, S. Srinivasan, S.V. Sitaraman, R. Knight, R.E. Ley, and A.T. Gewirtz Metabolic syndrome and altered gut microbiota in mice lacking Toll-like receptor 5 Science 328 2010 228 231
95. L. Wen, R.E. Ley, P.Y. Volchkov, P.B. Stranges, L. Avanesyan, A.C. Stonebraker, C. Hu, F.S. Wong, G.L. Szot, and J.A. Bluestone et al. Innate immunity and intestinal microbiota in the development of Type 1 diabetes Nature 455 2008 1109 1113
96. J.J. Werner, O. Koren, P. Hugenholtz, T.Z. DeSantis, W.A. Walters, J.G. Caporaso, L.T. Angenent, R. Knight, and R.E. Ley Impact of training sets on classification of high-throughput bacterial 16s rRNA gene surveys ISME J. 6 2012 94 103
97. J.J. Werner, D. Zhou, J.G. Caporaso, R. Knight, and L.T. Angenent Comparison of Illumina paired-end and single-direction sequencing for microbial 16S rRNA gene amplicon surveys ISME J. 6 2012 1273 1276
98. E.S. Wright, L.S. Yilmaz, and D.R. Noguera DECIPHER, a search-based approach to chimera identification for 16S rRNA sequences Appl. Environ. Microbiol. 78 2012 717 725
99. G.D. Wu, J.D. Lewis, C. Hoffmann, Y.Y. Chen, R. Knight, K. Bittinger, J. Hwang, J. Chen, R. Berkowsky, and L. Nessel et al. Sampling and pyrosequencing methods for characterizing bacterial communities in the human gut using 16S sequence tags BMC Microbiol. 10 2010 206
100. G.D. Wu, J. Chen, C. Hoffmann, K. Bittinger, Y.Y. Chen, S.A. Keilbaugh, M. Bewtra, D. Knights, W.A. Walters, and R. Knight et al. Linking long-term dietary patterns with gut microbial enterotypes Science 334 2011 105 108
101. P. Yilmaz, R. Kottmann, D. Field, R. Knight, J.R. Cole, L. Amaral-Zettler, J.A. Gilbert, I. Karsch-Mizrachi, A. Johnston, and G. Cochrane et al. Minimum information about a marker gene sequence (MIMARKS) and minimum information about any (x) sequence (MIxS) specifications Nat. Biotechnol. 29 2011 415 420
102. C. Zong, S. Lu, A.R. Chapman, and X.S. Xie Genome-wide detection of single-nucleotide and copy-number variations of a single human cell Science 338 2012 1622 1626