The human microbiome project, personalized medicine and the birth of pharmacomicrobiomics

Current Pharmacogenomics and Personalized Medicine

Volumn 8, Issue 3, 2010, Pages 182-193

  Rizkallah, Mariam Reyad ^a   Saad, Rama ^b,c   Aziz, Ramy Karam ^a  

^a CAIRO UNIVERSITY   (Egypt)

^b Ministry of Antiquities   (Egypt)

^c CAIRO UNIVERSITY   (Egypt)

Author keywords

Metagenomics; Microbiome; Microbiota; Next generation sequencing; Personalized medicine; Pharmacogenomics

Indexed keywords

DNA 16S;

ANTIBIOTIC THERAPY; ARTICLE; BACTERIAL GENOME; BACTERIAL MUTATION; DIABETIC FOOT; DIAGNOSTIC VALUE; DNA SEQUENCE; DRUG DISPOSITION; HEALTH CARE FINANCING; HUMAN; HUMAN GENOME; HUMAN GENOME PROJECT; HUMAN MICROBIOME PROJECT; IMMUNE DEFICIENCY; METAGENOMICS; MICROBIAL DIVERSITY; MICROBIOME; PHARMACOGENOMICS;

EID: 78649294933     PISSN: 18756921     EISSN: 18756913     Source Type: Journal    
DOI: 10.2174/187569210792246326     Document Type: Article

References (128)

1. Ring HZ, Kwok PY, Cotton RG. Human Variome Project: an international collaboration to catalogue human genetic variation. Pharmacogenomics 2006; 7(7): 969-72.
2. Anonymous (Editorial). What is the human variome project? Nat Genet 2007; 39(4): 423.
3. Cotton RG, Auerbach AD, Axton M, et al. GENETICS. The Human Variome Project. Science 2008; 322(5903): 861-2.
4. Nebert DW, Zhang G, Vesell ES. From human genetics and genomics to pharmacogenetics and pharmacogenomics: past lessons, future directions. Drug Metab Rev 2008; 40(2): 187-224.
5. Adams MD, Celniker SE, Holt RA, et al. The genome sequence of Drosophila melanogaster. Science 2000; 287(5461): 2185-95.
6. C. elegans Sequencing Consortium. Genome sequence of the nematode C. elegans: a platform for investigating biology. Science 1998; 282(5396): 2012-8.
7. Yu J, Hu S, Wang J, et al. A draft sequence of the rice genome (Oryza sativa L. ssp. indica). Science 2002; 296(5565): 79-92.
8. Goff SA, Ricke D, Lan TH, et al. A draft sequence of the rice genome (Oryza sativa L. ssp. japonica). Science 2002; 296(5565): 92-100.
9. Savage DC. Microbial ecology of the gastrointestinal tract. Annu Rev Microbiol 1977; 31: 107-33.
10. Peterson J, Garges S, Giovanni M, et al. The NIH Human Microbiome Project. Genome Res 2009; 19(12): 2317-23.
11. Ley RE, Peterson DA, Gordon JI. Ecological and evolutionary forces shaping microbial diversity in the human intestine. Cell 2006; 124(4): 837-48.
12. Stone M. NIH builds substantial human microbiome project. Microbes 2009; 4(10): 451-56.
13. Lander ES, Linton LM, Birren B, et al. Initial sequencing and analysis of the human genome. Nature 2001; 409(6822): 860-921.
14. Venter JC, Adams MD, Myers EW, et al. The sequence of the human genome. Science 2001; 291(5507): 1304-51.
15. Davies J. In a map for human life, count the microbes, too. Science 2001; 291(5512): 2316.
16. Relman DA, Falkow S. The meaning and impact of the human genome sequence for microbiology. Trends Microbiol 2001; 9(5): 206-8.
17. Human Genome Project Information. Available from: http://www. ornl.gov/sci/techresources/Human_Genome/home.shtml [Accessed June 20, 2010]
18. Ronaghi M. Pyrosequencing sheds light on DNA sequencing. Genome Res 2001; 11(1): 3-11.
19. Shendure J, Porreca GJ, Reppas NB, et al. Accurate multiplex polony sequencing of an evolved bacterial genome. Science 2005; 309(5741): 1728-32.
20. Bennett S. Solexa Ltd. Pharmacogenomics 2004; 5(4): 433-8.
21. Margulies M, Egholm M, Altman WE, et al. Genome sequencing in microfabricated high-density picolitre reactors. Nature 2005; 437(7057): 376-80.
22. Riesenfeld CS, Schloss PD, Handelsman J. Metagenomics: genomic analysis of microbial communities. Annu Rev Genet 2004; 38: 525-52.
23. Handelsman J. Metagenomics: application of genomics to uncultured microorganisms. Microbiol Mol Biol Rev 2004; 68(4): 669-85.
24. Edwards RA, Rohwer F. Viral metagenomics. Nat Rev Microbiol 2005; 3(6): 504-10.
25. The International Human Microbiome Consortium. Available from:http://www.human-microbiome.org [Accessed June 20, 2010].
26. The International Human Microbiome Consortium: Goal. Available from: http://www.human-microbiome.org/index.php?id=25 [Accessed June 20, 2010].
27. The International Human Microbiome Consortium: Organisation. Available from: http://www.human-microbiome.org/index.php? id=27 [Accessed June 20, 2010].
28. The International Human Microbiome Consortium: Membership. Available from: http://www.human-microbiome.org/index.php? id=28 [Accessed June 20, 2010].
29. Metagenomics of the Human Intestinanl Tract. Available from: http://www.metahit.eu [Accessed June 20, 2010].
30. Qin J, Li R, Raes J, et al. A human gut microbial gene catalogue established by metagenomic sequencing. Nature 2010; 464(7285): 59-65.
31. Grice EA, Kong HH, Conlan S, et al. Topographical and temporal diversity of the human skin microbiome. Science 2009; 324(5931): 1190-2.
32. Turnbaugh PJ, Hamady M, Yatsunenko T, et al. A core gut microbiome in obese and lean twins. Nature 2009; 457(7228): 480-4.
33. Vijay-Kumar M, Aitken JD, Carvalho FA, et al. Metabolic syndrome and altered gut microbiota in mice lacking Toll-like receptor 5. Science 2010; 328(5975): 228-31.
34. Frank DN, Feazel LM, Bessesen MT, et al. The human nasal microbiota and Staphylococcus aureus carriage. PLoS ONE 2010; 5(5): e10598.
35. Turnbaugh PJ, Ridaura VK, Faith JJ, et al. The effect of diet on the human gut microbiome: a metagenomic analysis in humanized gnotobiotic mice. Sci Transl Med 2009; 1(6): 6ra14.
36. Tuohy KM, Gougoulias C, Shen Q, et al. Studying the human gut microbiota in the trans-omics era--focus on metagenomics and metabonomics. Curr Pharm Des 2009; 15(13): 1415-27.
37. Wilson ID. Drugs, bugs, and personalized medicine: pharmacometabonomics enters the ring. Proc Natl Acad Sci USA 2009; 106(34): 14187-8.
38. Kendall AI. Some observations on the study of the intestinal bacteria. J Biol Chem 1909; 6: 499-507.
39. Aziz RK. A hundred-year-old insight into the gut microbiome! Gut Pathog 2009; 1(1): 21.
40. Integrated Microbial Genomes: Human Microbiome Project. Available from: http://www.hmpdacc-resources.org/cgi-bin/img_hmp/main.cgi[Accessed June 20, 2010].
41. Human Microbiome Project: Documentation and SOPs. Available from: http://hmpdacc.org/sops.php [Accessed June 20, 2010].
42. Traces Archives. Available from: http://www.ncbi.nlm.nih.gov/ Traces/home [Accessed June 20, 2010].
43. Arola H, Koivula T, Karvonen AL, et al. Low trehalase activity is associated with abdominal symptoms caused by edible mushrooms. Scand J Gastroenterol 1999; 34(9): 898-903.
44. Hehemann JH, Correc G, Barbeyron T, et al. Transfer of carbohydrate-active enzymes from marine bacteria to Japanese gut microbiota. Nature 2010; 464(7290): 908-12.
45. Clayton TA, Baker D, Lindon JC, et al. Pharmacometabonomic identification of a significant host-microbiome metabolic interaction affecting human drug metabolism. Proc Natl Acad Sci USA 2009; 106(34): 14728-33.
46. Wilson ID, Nicholson JK. The role of gut microbiota in drug response. Curr Pharm Des 2009; 15(13): 1519-23.
47. Backhed F, Ding H, Wang T, et al. The gut microbiota as an environmental factor that regulates fat storage. Proc Natl Acad Sci USA 2004; 101(44): 15718-23.
48. Turnbaugh PJ, Ley RE, Mahowald MA, et al. An obesityassociated gut microbiome with increased capacity for energy harvest. Nature 2006; 444(7122): 1027-31.
49. Oakley BB, Fiedler TL, Marrazzo JM, et al. Diversity of human vaginal bacterial communities and associations with clinically defined bacterial vaginosis. Appl Environ Microbiol 2008; 74(15): 4898-909.
50. Turnbaugh PJ, Gordon JI. The core gut microbiome, energy balance and obesity. J Physiol 2009; 587(Pt 17): 4153-8.
51. Guarner F, Malagelada JR. Gut flora in health and disease. Lancet 2003; 361(9356): 512-9.
52. Zaura E, Keijser BJ, Huse SM, et al. Defining the healthy core microbiome of oral microbial communities. BMC Microbiol 2009; 9: 259.
53. Takeshita T, Suzuki N, Nakano Y, et al. Relationship between oral malodor and the global composition of indigenous bacterial populations in saliva. Appl Environ Microbiol 2010; 76(9): 2806-14.
54. Pacheco-Fowler V, Gaonkar T, Wyer PC, et al. Antiseptic impregnated endotracheal tubes for the prevention of bacterial colonization. J Hosp Infect 2004; 57(2): 170-4.
55. Day WA, Maurelli AT. Black holes and antivirulence genes: selection for gene loss as part of the evolution of bacterial pathogens. In: Seifert HS, Dirita VJ, Eds. Evolution of Microbial Pathogens. Washington DC: ASM Press 2006.
56. Maurelli AT. Black holes, antivirulence genes, and gene inactivation in the evolution of bacterial pathogens. FEMS Microbiol Lett 2007; 267(1): 1-8.
57. Qu A, Brulc JM, Wilson MK, et al. Comparative metagenomics reveals host specific metavirulomes and horizontal gene transfer elements in the chicken cecum microbiome. PLoS ONE 2008; 3(8): e2945.
58. Otto M. Staphylococcus epidermidis--the 'accidental' pathogen. Nat Rev Microbiol 2009; 7(8): 555-67.
59. Sommer MO, Dantas G, Church GM. Functional characterization of the antibiotic resistance reservoir in the human microflora. Science 2009; 325(5944): 1128-31.
60. Siefert JL. Defining the mobilome. Methods Mol Biol 2009; 532: 13-27.
61. Ellner JJ, Goldberger MJ, Parenti DM. Mycobacterium avium infection and AIDS: a therapeutic dilemma in rapid evolution. J Infect Dis 1991; 163(6): 1326-35.
62. Bhambri S, Bhambri A, Del Rosso JQ. A typical mycobacterial cutaneous infections. Dermatol Clin 2009; 27(1): 63-73.
63. Williams MM, Yakrus MA, Arduino MJ, et al. Structural analysis of biofilm formation by rapidly and slowly growing nontuberculous mycobacteria. Appl Environ Microbiol 2009; 75(7): 2091-8.
64. Grice EA, Kong HH, Renaud G, et al. A diversity profile of the human skin microbiota. Genome Res 2008; 18(7): 1043-50.
65. Cogen AL, Nizet V, Gallo RL. Skin microbiota: a source of disease or defence? Br J Dermatol 2008; 158(3): 442-55.
66. Lin YT, Wang CT, Chiang BL. Role of bacterial pathogens in atopic dermatitis. Clin Rev Allergy Immunol 2007; 33(3): 167-77.
67. Scharschmidt TC, List K, Grice EA, et al. Matriptase-deficient mice exhibit ichthyotic skin with a selective shift in skin microbiota. J Invest Dermatol 2009; 129(10): 2435-42.
68. Bek-Thomsen M, Lomholt HB, Kilian M. Acne is not associated with yet-uncultured bacteria. J Clin Microbiol 2008; 46(10): 3355-60.
69. Domingo P, Fontanet A, Sanchez F, et al. Morbidity associated with long-term use of totally implantable ports in patients with AIDS. Clin Infect Dis 1999; 29(2): 346-51.
70. Verhulst NO, Beijleveld H, Knols BG, et al. Cultured skin microbiota attracts malaria mosquitoes. Malar J 2009; 8(1): 302.
71. Jakubovics NS, Gill SR, Vickerman MM, et al. Role of hydrogen peroxide in competition and cooperation between Streptococcus gordonii and Actinomyces naeslundii. FEMS Microbiol Ecol 2008; 66(3): 637-44.
72. Avila M, Ojcius DM, Yilmaz O. The oral microbiota: living with a permanent guest. DNA Cell Biol 2009; 28(8): 405-11.
73. Filoche S, Wong L, Sissons CH. Oral biofilms: emerging concepts in microbial ecology. J Dent Res 2010; 89(1): 8-18.
74. Ghannoum MA, Jurevic RJ, Mukherjee PK, et al. Characterization of the oral fungal microbiome (mycobiome) in healthy individuals. PLoS Pathog 2010; 6(1): e1000713.
75. Muto M, Hitomi Y, Ohtsu A, et al. Acetaldehyde production by non-pathogenic Neisseria in human oral microflora: implications for carcinogenesis in upper aerodigestive tract. Int J Cancer 2000; 88(3): 342-50.
76. Meurman JH, Uittamo J. Oral micro-organisms in the etiology of cancer. Acta Odontol Scand 2008; 66(6): 321-6.
77. Rasmussen TT, Kirkeby LP, Poulsen K, et al. Resident aerobic microbiota of the adult human nasal cavity. APMIS 2000; 108(10): 663-75.
78. Kirtsreesakul V, Tuntaraworasin J, Thamjarungwong B. Microbiology and antimicrobial susceptibility patterns of commensal flora in the middle nasal meatus. Ann Otol Rhinol Laryngol 2008; 117(12): 914-8.
79. Chen Y, Xu X, Fu J, et al. [Perliminary study on the aerobes distribution of nasal cavity from the healthy children and adults]. Lin Chung Er Bi Yan Hou Tou Jing Wai Ke Za Zhi 2007; 21(23): 1068-9.
80. Craven DE, Chroneou A, Zias N, et al. Ventilator-associated tracheobronchitis: the impact of targeted antibiotic therapy on patient outcomes. Chest 2009; 135(2): 521-8.
81. van Belkum A, Emonts M, Wertheim H, et al. The role of human innate immune factors in nasal colonization by Staphylococcus aureus. Microbes Infect 2007; 9(12-13): 1471-7.
82. Eckburg PB, Bik EM, Bernstein CN, et al. Diversity of the human intestinal microbial flora. Science 2005; 308(5728): 1635-8.
83. Rakoff-Nahoum S, Paglino J, Eslami-Varzaneh F, et al. Recognition of commensal microflora by toll-like receptors is required for intestinal homeostasis. Cell 2004; 118(2): 229-41.
84. Chen Y, Blaser MJ. Helicobacter pylori colonization is inversely associated with childhood asthma. J Infect Dis 2008; 198(4): 553-60.
85. Reibman J, Marmor M, Filner J, et al. Asthma is inversely associated with Helicobacter pylori status in an urban population. PLoS ONE 2008; 3(12): e4060.
86. Cover TL, Blaser MJ. Helicobacter pylori in health and disease. Gastroenterology 2009; 136(6): 1863-73.
87. McGarr SE, Ridlon JM, Hylemon PB. Diet, anaerobic bacterial metabolism, and colon cancer: a review of the literature. J Clin Gastroenterol 2005; 39(2): 98-109.
88. Cummings JH, Macfarlane GT, Macfarlane S. Intestinal bacteria and ulcerative colitis. Curr Issues Intest Microbiol 2003; 4(1): 9-20.
89. Andoh A, Fujiyama Y. Therapeutic approaches targeting intestinal microflora in inflammatory bowel disease. World J Gastroenterol 2006; 12(28): 4452-60.
90. Subramanian S, Campbell BJ, Rhodes JM. Bacteria in the pathogenesis of inflammatory bowel disease. Curr Opin Infect Dis 2006; 19(5): 475-84.
91. Singh J, Rivenson A, Tomita M, et al. Bifidobacterium longum, a lactic acid-producing intestinal bacterium inhibits colon cancer and modulates the intermediate biomarkers of colon carcinogenesis. Carcinogenesis 1997; 18(4): 833-41.
92. O'Mahony L, Feeney M, O'Halloran S, et al. Probiotic impact on microbial flora, inflammation and tumour development in IL-10 knockout mice. Aliment Pharmacol Ther 2001; 15(8): 1219-25.
93. Jia W, Li H, Zhao L, et al. Gut microbiota: a potential new territory for drug targeting. Nat Rev Drug Discov 2008; 7(2): 123-9.
94. Zhou X, Bent SJ, Schneider MG, et al. Characterization of vaginal microbial communities in adult healthy women using cultivationindependent methods. Microbiology 2004; 150(Pt 8): 2565-73.
95. Chassot F, Negri MF, Svidzinski AE, et al. Can intrauterine contraceptive devices be a Candida albicans reservoir? Contraception 2008; 77(5): 355-9.
96. Yang X, Xie L, Li Y, et al. More than 9,000,000 unique genes in human gut bacterial community: estimating gene numbers inside a human body. PLoS ONE 2009; 4(6): e6074.
97. Fierer N, Lauber CL, Zhou N, et al. Forensic identification using skin bacterial communities. Proc Natl Acad Sci USA 2010; 107(14): 6477-81.
98. Hill DA, Hoffmann C, Abt MC, et al. Metagenomic analyses reveal antibiotic-induced temporal and spatial changes in intestinal microbiota with associated alterations in immune cell homeostasis. Mucosal Immunol 2009; 3(2): 148-58.
99. Martin FP, Rezzi S, Pere-Trepat E, et al. Metabolic effects of dark chocolate consumption on energy, gut microbiota, and stress-related metabolism in free-living subjects. J Proteome Res 2009; 8: 5568-79.
100. Palmer C, Bik EM, Digiulio DB, et al. Development of the Human Infant Intestinal Microbiota. PLoS Biol 2007; 5(7): e177.
101. Rezzi S, Ramadan Z, Martin FP, et al. Human metabolic phenotypes link directly to specific dietary preferences in healthy individuals. J Proteome Res 2007; 6(11): 4469-77.
102. Bader MS. Diabetic foot infection. Am Fam Physician 2008; 78(1): 71-9.
103. Kinney MA, Yentzer BA, Fleischer AB Jr, et al. Trends in the treatment of acne vulgaris: are measures being taken to avoid antimicrobial resistance? J Drugs Dermatol 2010; 9(5): 519-24.
104. Wolrath H, Forsum U, Larsson PG, et al. Analysis of bacterial vaginosis-related amines in vaginal fluid by gas chromatography and mass spectrometry. J Clin Microbiol 2001; 39(11): 4026-31.
105. Verstraelen H, Verhelst R. Bacterial vaginosis: an update on diagnosis and treatment. Expert Rev Anti Infect Ther 2009; 7(9): 1109-24.
106. Raes J, Bork P. Molecular eco-systems biology: towards an understanding of community function. Nat Rev Microbiol 2008; 6(9): 693-9.
107. Mathan VI, Wiederman J, Dobkin JF, et al. Geographic differences in digoxin inactivation, a metabolic activity of the human anaerobic gut flora. Gut 1989; 30(7): 971-7.
108. Bowey E, Adlercreutz H, Rowland I. Metabolism of isoflavones and lignans by the gut microflora: a study in germ-free and human flora associated rats. Food Chem Toxicol 2003; 41(5): 631-6.
109. Delgado S, Ruas-Madiedo P, Suarez A, et al. Interindividual differences in microbial counts and biochemical-associated variables in the feces of healthy Spanish adults. Dig Dis Sci 2006; 51(4): 737-43.
110. Cevc G, Vierl U. Nanotechnology and the transdermal route: A state of the art review and critical appraisal. J Control Release 2010; 141(3): 277-99.
111. Stingley RL, Zou W, Heinze TM, et al. Metabolism of azo dyes by human skin microbiota. J Med Microbiol 2009; 59(Pt 1): 108-14.
112. Chung KT, Fulk GE, Egan M. Reduction of azo dyes by intestinal anaerobes. Appl Environ Microbiol 1978; 35(3): 558-62.
113. Jones JJ, Falkinham JO 3rd. Decolorization of malachite green and crystal violet by waterborne pathogenic mycobacteria. Antimicrob Agents Chemother 2003; 47(7): 2323-6.
114. Steidler L. Delivery of therapeutic proteins to the mucosa using genetically modified microflora. Expert Opin Drug Deliv 2005; 2(4): 737-46.
115. Kotloff KL, Wasserman SS, Jones KF, et al. Clinical and microbiological responses of volunteers to combined intranasal and oral inoculation with a Streptococcus gordonii carrier strain intended for future use as a group A Streptococcus vaccine. Infect Immun 2005; 73(4): 2360-6.
116. Davydov L, Yermolnik M, Cuni LJ. Warfarin and amoxicillin/ clavulanate drug interaction. Ann Pharmacother 2003; 37(3): 367-70.
117. Jones RD. Bacterial resistance and topical antimicrobial wash products. Am J Infect Control 1999; 27(4): 351-63.
118. Neely AN, Gardner J, Durkee P, et al. Are topical antimicrobials effective against bacteria that are highly resistant to systemic antibiotics? J Burn Care Res 2009; 30(1): 19-29.
119. Aziz RK, Nizet V. Pathogen microevolution in high resolution. Sci Transl Med 2010; 2(16): 16ps4.
120. International HapMap Consortium. The International HapMap Project. Nature 2003; 426(6968): 789-96.
121. Park J, Hwang S, Lee YS, et al. SNP@Ethnos: a database of ethnically variant single-nucleotide polymorphisms. Nucleic Acids Res 2007; 35(Database issue): D711-5.
122. Kaput J, Cotton RG, Hardman L, et al. Planning the human variome project: the Spain report. Hum Mutat 2009; 30(4): 496-510.
123. Hall CB, Caserta MT, Schnabel K, et al. Chromosomal integration of human herpesvirus 6 is the major mode of congenital human herpesvirus 6 infection. Pediatrics 2008; 122(3): 513-20.
124. D'Costa VM, McGrann KM, Hughes DW, et al. Sampling the antibiotic resistome. Science 2006; 311(5759): 374-7.
125. Wright GD. The antibiotic resistome: the nexus of chemical and genetic diversity. Nat Rev Microbiol 2007; 5(3): 175-86.
126. Bennett ST, Barnes C, Cox A, et al. Toward the 1,000 dollars human genome. Pharmacogenomics 2005; 6(4): 373-82.
127. Butler D. Human genome at ten: Science after the sequence. Nature 2010; 465(7301): 1000-1.
128. Fischetti VA, Nelson D, Schuch R. Reinventing phage therapy: are the parts greater than the sum? Nat Biotechnol 2006; 24(12): 1508-11.