The human gut microbiome: Current knowledge, challenges, and future directions

Translational Research

Volumn 160, Issue 4, 2012, Pages 246-257

  Dave, Maneesh ^a   Higgins, Peter D ^b   Middha, Sumit ^a   Rioux, Kevin P ^c  

^a MAYO CLINIC   (United States)

^b UNIVERSITY OF MICHIGAN MEDICAL SCHOOL   (United States)

^c UNIVERSITY OF CALGARY   (Canada)

Author keywords

[No Author keywords available]

Indexed keywords

CIPROFLOXACIN;

BIOINFORMATICS; DIABETES MELLITUS; ECOLOGY; ENTERITIS; GENOME; HUMAN; INTESTINE FLORA; IRRITABLE COLON; MICROBIOME; NONHUMAN; OBESITY; PRIORITY JOURNAL; REVIEW; SEQUENCE ANALYSIS;

EID: 84866423583     PISSN: 19315244     EISSN: 18781810     Source Type: Journal    
DOI: 10.1016/j.trsl.2012.05.003     Document Type: Review

References (82)

1. E.F. DeLong, and N.R. Pace Environmental diversity of bacteria and archaea Syst Biol 50 2001 470 478
2. R.E. Ley, D.A. Peterson, and J.I. Gordon Ecological and evolutionary forces shaping microbial diversity in the human intestine Cell 124 2006 837 848
3. D.C. Savage Microbial ecology of the gastrointestinal tract Annu Rev Microbiol 31 1977 107 133
4. W.B. Whitman, D.C. Coleman, and W.J. Wiebe Prokaryotes: the unseen majority Proc Natl Acad Sci U S A 95 1998 6578 6583
5. F. Backhed, R.E. Ley, J.L. Sonnenburg, D.A. Peterson, and J.I. Gordon Host-bacterial mutualism in the human intestine Science 307 2005 1915 1920
6. A. Reyes, M. Haynes, and N. Hanson Viruses in the faecal microbiota of monozygotic twins and their mothers Nature 466 2010 334 338
7. J. Lederberg, and A.T. McCray 'Ome sweet 'omics - a genealogical treasury of words Scientist 15 2001 8 9
8. J. Handelsman Metagenomics: application of genomics to uncultured microorganisms Microbiol Mol Biol Rev 68 2004 669 685
9. Metagenomics Co The New Science of Metagenomics: Revealing the Secrets of Our Microbial Planet 2007 The National Academies Press Washington, DC
10. P.J. Turnbaugh, R.E. Ley, M. Hamady, C.M. Fraser-Liggett, R. Knight, and J.I. Gordon The human microbiome project Nature 449 2007 804 810
11. K.E. Nelson, G.M. Weinstock, and S.K. Highlander A catalog of reference genomes from the human microbiome Science 328 2010 994 999
12. E.M. Bik, P.B. Eckburg, and S.R. Gill Molecular analysis of the bacterial microbiota in the human stomach Proc Natl Acad Sci U S A 103 2006 732 737
13. M.G. Dominguez-Bello, M.J. Blaser, R.E. Ley, and R. Knight Development of the human gastrointestinal microbiota and insights from high-throughput sequencing Gastroenterology 140 2011 1713 1719
14. A.S. Neish Microbes in gastrointestinal health and disease Gastroenterology 136 2009 65 80
15. W.E. Moore, and L.V. Holdeman Human fecal flora: the normal flora of 20 Japanese-Hawaiians Appl Microbiol 27 1974 961 979
16. H. Hayashi, M. Sakamoto, and Y. Benno Phylogenetic analysis of the human gut microbiota using 16S rDNA clone libraries and strictly anaerobic culture-based methods Microbiol Immunol 46 2002 535 548
17. L. Dethlefsen, M. McFall-Ngai, and D.A. Relman An ecological and evolutionary perspective on human-microbe mutualism and disease Nature 449 2007 811 818
18. C.R. Woese, and G.E. Fox Phylogenetic structure of the prokaryotic domain: the primary kingdoms Proc Natl Acad Sci U S A 74 1977 5088 5090
19. A. Nocker, M. Burr, and A.K. Camper Genotypic microbial community profiling: a critical technical review Microb Ecol 54 2007 276 289
20. V.B. Young, and T.M. Schmidt Antibiotic-associated diarrhea accompanied by large-scale alterations in the composition of the fecal microbiota J Clin Microbiol 42 2004 1203 1206
21. J.R. Cole, B. Chai, and R.J. Farris The ribosomal database project (RDP-II): introducing myRDP space and quality controlled public data Nucleic Acids Res 35 2007 D169 D172
22. M. Ronaghi, M. Uhlen, and P. Nyren A sequencing method based on real-time pyrophosphate Science 281 363 1998 5
23. M. Achtman, and M. Wagner Microbial diversity and the genetic nature of microbial species Nat Rev Microbiol 6 2008 431 440
24. P.D. Schloss, and S.L. Westcott Assessing and improving methods used in operational taxonomic unit-based approaches for 16S rRNA gene sequence analysis Appl Environ Microbiol 77 2011 3219 3226
25. M.R. Rondon, P.R. August, and A.D. Bettermann Cloning the soil metagenome: a strategy for accessing the genetic and functional diversity of uncultured microorganisms Appl Environ Microbiol 66 2000 2541 2547
26. M. Hamady, and R. Knight Microbial community profiling for human microbiome projects: tools, techniques, and challenges Genome Res 19 2009 1141 1152
27. J. Barriuso, J.R. Valverde, and R.P. Mellado Estimation of bacterial diversity using next generation sequencing of 16S rDNA: a comparison of different workflows BMC Bioinformatics 12 2011 473
28. J.C. Wooley, and Y. Ye Metagenomics: Facts and Artifacts, and Computational Challenges* J Comput Sci Technol 25 1 2009 71 81
29. P.H. Degnan, and H. Ochman Illumina-based analysis of microbial community diversity Isme J 6 1 2012 183 194
30. C. Quince, A. Lanzen, and T.P. Curtis Accurate determination of microbial diversity from 454 pyrosequencing data Nat Methods 6 9 2009 639 641
31. J.G. Caporaso, J. Kuczynski, and J. Stombaugh QIIME allows analysis of high-throughput community sequencing data Nat Methods 7 5 2010 335 336
32. P.D. Schloss, S.L. Westcott, and T. Ryabin Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities Appl Environ Microbiol 75 23 2009 7537 7541
33. G.B. Gloor, R. Hummelen, and J.M. Macklaim Microbiome profiling by illumina sequencing of combinatorial sequence-tagged PCR products PLoS One 5 10 2010 e15406
34. A.K. Waljee, and P.D. Higgins Machine learning in medicine: a primer for physicians Am J Gastroenterol 105 6 2010 1224 1226
35. K. Krampis, T. Booth, and B. Chapman Cloud BioLinux: pre-configured and on-demand bioinformatics computing for the genomics community BMC Bioinformatics 13 2012 42
36. D.A. Peterson, D.N. Frank, N.R. Pace, and J.I. Gordon Metagenomic approaches for defining the pathogenesis of inflammatory bowel diseases Cell Host Microbe 3 2008 417 427
37. P.J. Turnbaugh, M. Hamady, and T. Yatsunenko A core gut microbiome in obese and lean twins Nature 457 2009 480 484
38. M. Arumugam, J. Raes, and E. Pelletier Enterotypes of the human gut microbiome Nature 473 2011 174 180
39. E. Biagi, L. Nylund, and M. Candela Through ageing, and beyond: gut microbiota and inflammatory status in seniors and centenarians PLoS One 5 2010 e10667
40. S. Mueller, K. Saunier, and C. Hanisch Differences in fecal microbiota in different European study populations in relation to age, gender, and country: a cross-sectional study Appl Environ Microbiol 72 2006 1027 1033
41. J.E. Koenig, A. Spor, and N. Scalfone Succession of microbial consortia in the developing infant gut microbiome Proc Natl Acad Sci U S A 108 Suppl 1 2011 4578 4585
42. M.J. Claesson, S. Cusack, and O. O'Sullivan Composition, variability, and temporal stability of the intestinal microbiota of the elderly Proc Natl Acad Sci U S A 108 Suppl 1 2011 4586 4591
43. G.W. Tannock, K. Munro, H.J. Harmsen, G.W. Welling, J. Smart, and P.K. Gopal Analysis of the fecal microflora of human subjects consuming a probiotic product containing Lactobacillus rhamnosus DR20 Appl Environ Microbiol 66 2000 2578 2588
44. P.D. Scanlan, F. Shanahan, C. O'Mahony, and J.R. Marchesi Culture-independent analyses of temporal variation of the dominant fecal microbiota and targeted bacterial subgroups in Crohn's disease J Clin Microbiol 44 2006 3980 3988
45. J.G. Caporaso, C.L. Lauber, and E.K. Costello Moving pictures of the human microbiome Genome Biol 12 2011 R50
46. A.W. Walker, S.H. Duncan, H.J.M. Harmsen, G. Holtrop, G.W. Welling, and H.J. Flint The species composition of the human intestinal microbiota differs between particle-associated and liquid phase communities Environ Microbiol 10 2008 3275 3283
47. P. Lepage, P. Seksik, and M. Sutren Biodiversity of the mucosa-associated microbiota is stable along the distal digestive tract in healthy individuals and patients with IBD Inflamm Bowel Dis 11 2005 473 480
48. P.B. Eckburg, E.M. Bik, and C.N. Bernstein Diversity of the human intestinal microbial flora Science 308 2005 1635 1638
49. P. Gillevet, M. Sikaroodi, A. Keshavarzian, and E.A. Mutlu Quantitative assessment of the human gut microbiome using multitag pyrosequencing Chem Biodivers 7 2010 1065 1075
50. P. Marteau, P. Pochart, J. Dore, C. Bera-Maillet, A. Bernalier, and G. Corthier Comparative study of bacterial groups within the human cecal and fecal microbiota Appl Environ Microbiol 67 2001 4939 4942
51. M. Dave, L.A. Johnson, and S.T. Walk A randomised trial of sheathed versus standard forceps for obtaining uncontaminated biopsy specimens of microbiota from the terminal ileum Gut 60 2011 1043 1049
52. V. Mai, B. Greenwald, J.G. Morris Jr., J.P. Raufman, and O.C. Stine Effect of bowel preparation and colonoscopy on post-procedure intestinal microbiota composition Gut 55 2006 1822 1823
53. 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
54. G.D. Wu, J.D. Lewis, and C. Hoffmann Sampling and pyrosequencing methods for characterizing bacterial communities in the human gut using 16S sequence tags BMC Microbiol 10 2010 206
55. L.F. Roesch, G. Casella, and O. Simell Influence of fecal sample storage on bacterial community diversity Open Microbiol J 3 2009 40 46
56. E.G. Zoetendal, H.G. Heilig, and E.S. Klaassens Isolation of DNA from bacterial samples of the human gastrointestinal tract Nat Protoc 1 2006 870 873
57. J. Ahn, L. Yang, and B.J. Paster Oral microbiome profiles: 16S rRNA pyrosequencing and microarray assay comparison PLoS One 6 2011 e22788
58. Z. Pei, E.J. Bini, L. Yang, M. Zhou, F. Francois, and M.J. Blaser Bacterial biota in the human distal esophagus Proc Natl Acad Sci U S A 101 2004 4250 4255
59. H. Hayashi, R. Takahashi, T. Nishi, M. Sakamoto, and Y. Benno Molecular analysis of jejunal, ileal, caecal and recto-sigmoidal human colonic microbiota using 16S rRNA gene libraries and terminal restriction fragment length polymorphism J Med Microbiol 54 2005 1093 1101
60. M.G. Dominguez-Bello, E.K. Costello, and M. Contreras Delivery mode shapes the acquisition and structure of the initial microbiota across multiple body habitats in newborns Proc Natl Acad Sci U S A 107 2010 11971 11975
61. R.E. Ley, M. Hamady, and C. Lozupone Evolution of mammals and their gut microbes Science 320 2008 1647 1651
62. B.D. Muegge, J. Kuczynski, and D. Knights Diet drives convergence in gut microbiome functions across mammalian phylogeny and within humans Science 332 2011 970 974
63. G. Erwin, A.D.L.A. Zoetendal, W.M. Akkermans-van Vliet, J.A.G.M. de Visser, and W.M. de Vos The host genotype affects the bacterial community in the human gastrointestinal tract Microb Ecol Health Dis 13 2001 129 134
64. C. Palmer, E.M. Bik, D.B. DiGiulio, D.A. Relman, and P.O. Brown Development of the human infant intestinal microbiota PLoS Biol 5 2007 e177
65. E. Biagi, L. Nylund, and M. Candela Through ageing, and beyond: gut microbiota and inflammatory status in seniors and centenarians PLoS One 5 2010 e10667
66. G.D. Wu, J. Chen, and C. Hoffmann Linking long-term dietary patterns with gut microbial enterotypes Science 334 2011 105 108
67. 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
68. 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 U S A 108 Suppl 1 2011 4554 4561
69. C. Jernberg, S. Lofmark, C. Edlund, and J.K. Jansson Long-term ecological impacts of antibiotic administration on the human intestinal microbiota Isme J 1 2007 56 66
70. D.A. Antonopoulos, S.M. Huse, H.G. Morrison, T.M. Schmidt, M.L. Sogin, and V.B. Young Reproducible community dynamics of the gastrointestinal microbiota following antibiotic perturbation Infect Immun 77 2009 2367 2375
71. A. Salonen, W.M. de Vos, and A. Palva Gastrointestinal microbiota in irritable bowel syndrome: present state and perspectives Microbiology 156 2010 3205 3215
72. R. Vanderploeg, R. Panaccione, S. Ghosh, and K. Rioux Influences of intestinal bacteria in human inflammatory bowel disease Infect Dis Clin North Am 24 2010 977 993
73. B.J. Meijer, and L.A. Dieleman Probiotics in the treatment of human inflammatory bowel diseases: update 2011 J Clin Gastroenterol 45 Suppl 2011 S139 S144
74. A. Sood, V. Midha, and G.K. Makharia The probiotic preparation, VSL#3 induces remission in patients with mild-to-moderately active ulcerative colitis Clin Gastroenterol Hepatol 7 2009 1202 1209
75. A. Tursi, G. Brandimarte, and A. Papa Treatment of relapsing mild-to-moderate ulcerative colitis with the probiotic VSL#3 as adjunctive to a standard pharmaceutical treatment: a double-blind, randomized, placebo-controlled study Am J Gastroenterol 105 2010 2218 2227
76. W. Kruis, P. Fric, and J. Pokrotnieks Maintaining remission of ulcerative colitis with the probiotic Escherichia coli Nissle 1917 is as effective as with standard mesalazine Gut 53 2004 1617 1623
77. P. Gionchetti, F. Rizzello, and A. Venturi Oral bacteriotherapy as maintenance treatment in patients with chronic pouchitis: a double-blind, placebo-controlled trial Gastroenterology 119 2000 305 309
78. P. Moayyedi, A.C. Ford, and N.J. Talley The efficacy of probiotics in the therapy of irritable bowel syndrome: a systematic review Gut 59 2010 325 332
79. D.M. Brenner, M.J. Moeller, W.D. Chey, and P.S. Schoenfeld The utility of probiotics in the treatment of irritable bowel syndrome: a systematic review Am J Gastroenterol 104 2009 1033 1049
80. N. Hoveyda, C. Heneghan, K.R. Mahtani, R. Perera, N. Roberts, and P. Glasziou A systematic review and meta-analysis: probiotics in the treatment of irritable bowel syndrome BMC Gastroenterol 9 2009 15
81. L.V. McFarland, and S. Dublin Meta-analysis of probiotics for the treatment of irritable bowel syndrome World J Gastroenterol 14 2008 2650 2661
82. P.J. Whorwell, L. Altringer, and J. Morel Efficacy of an encapsulated probiotic Bifidobacterium infantis 35624 in women with irritable bowel syndrome Am J Gastroenterol 101 2006 1581 1590