Composition and function of the human-associated microbiota

Nutrition Reviews

Volumn 67, Issue SUPPL. 2, 2009, Pages

  Bik, Elisabeth M ^a  

^a STANFORD UNIVERSITY SCHOOL OF MEDICINE   (United States)

Author keywords

Human associated microbiota; Intestinal microbiota; Ribosomal genes

Indexed keywords

CONFERENCE PAPER; ENTEROPATHY; HUMAN; IMMUNE SYSTEM; INTESTINE FLORA; LARGE INTESTINE; MICROBIAL DIVERSITY; MICROFLORA; MOUTH FLORA; NONHUMAN; SKIN FLORA; BACTERIAL PHENOMENA AND FUNCTIONS; BACTERIUM; CLASSIFICATION; GASTROINTESTINAL DISEASE; GASTROINTESTINAL TRACT; GROWTH, DEVELOPMENT AND AGING; IMMUNOLOGY; MICROBIOLOGY; REVIEW; SIGNAL TRANSDUCTION; SYMBIOSIS;

PROBIOTIC AGENT;

BACTERIA; BACTERIAL PHYSIOLOGICAL PHENOMENA; GASTROINTESTINAL DISEASES; GASTROINTESTINAL TRACT; HUMANS; PROBIOTICS; SIGNAL TRANSDUCTION; SYMBIOSIS;

EID: 77949681033     PISSN: 00296643     EISSN: 17534887     Source Type: Journal    
DOI: 10.1111/j.1753-4887.2009.00237.x     Document Type: Conference Paper

References (49)

1. Savage DC. Microbial ecology of the gastrointestinal tract. Annu Rev Microbiol. 1977;31:107-133.
2. Dethlefsen L, McFall-Ngai M, Relman DA. An ecological and evolutionary perspective on human-microbe mutualism and disease. Nature. 2007;449:811-818.
3. Miller TL, Wolin MJ, de Macario EC, Macario AJL. Isolation of Methanobrevibacter smithii from human feces. Appl Environ Microbiol. 1982;43:227-232.
4. Scanlan PD, Marchesi JR. Micro-eukaryotic diversity of the human distal gut microbiota: Qualitative assessment using culture-dependent and -independent analysis of faeces. ISME J. 2008;2:1183-1193.
5. Tappenden KA, Deutsch AS. The physiological relevance of the intestinal microbiota - contributions to human health. J Am Coll Nutr. 2007;26(Suppl):S679- S683.
6. Flint HJ, Duncan SH, Scott KP, Louis P. Interactions and competition within the microbial community of the human colon: Links between diet and health. Environ Microbiol. 2007;9: 1101-1111.
7. Wostmann BS. The germfree animal in nutritional studies. Annu Rev Nutr. 1981;1:257-279.
8. Hooper LV, Midtvedt T, Gordon JI. How host-microbial interactions shape the nutrient environment of the mammalian intestine. Annu Rev Nutr. 2002;22:283-307.
9. Robert C, Bernalier-Donadille A. The cellulolytic microflora of the human colon: Evidence of microcrystalline cellulosedegrading bacteria in methane excreting subjects. FEMS Microbiol Ecol. 2003;46:81-89.
10. Xu J, Bjursell MK, Himrod J, et al. A genomic view of the human-Bacteroides thetaiotaomicron symbiosis. Science. 2003;299:2074-2076.
11. Cho KH, Cho D, Wang GR, Salyers AA. New regulatory gene that contributes to control of Bacteroides thetaiotaomicron starch utilization genes. J Bacteriol. 2001;183:7198-7205.
12. Pryde SE, Duncan SH, Hold GL, Stewart CS, Flint HJ. The microbiology of butyrate formation in the human colon. FEMS Microbiol Lett. 2002;217:133-139.
13. Bäckhed F, Ding H, Wang T, et al. The gut microbiota as an environmental factor that regulates fat storage. Proc Natl Acad Sci. 2004;101:15718-15723.
14. Hill MJ. Intestinal flora and endogenous vitamin synthesis. Eur J Cancer Prev. 1997;6(Suppl):S43-S45.
15. van der Waaij D, Berghuis-de Vries JM, Lekkerkerkvan der Wees JEC. Colonization resistance of the digestive tract in conventional and antibiotic-treated mice. J Hyg. 1971;69:405-411.
16. Stecher B, Hardt WD. The role of microbiota in infectious disease. Trends Microbiol. 2008;16:107-114.
17. Hooper LV. Bacterial contributions to mammalian gut development. Trends Microbiol. 2004;12:129-134.
18. Macpherson AJ, Harris NL. Interactions between commensal intestinal bacteria and the immune system. Nature Rev Immunol. 2004;4:478-485.
19. Mazmanian SK, Liu CH, Tzianabos AO, Kasper DL. An immunomodulatory molecule of symbiotic bacteria directs maturation of the host immune system. Cell. 2005;122:107-118.
20. Rakoff-Nahoum S, Paglino J, Eslami-Varzaneh F, Edberg S, Medzhitov R. Recognition of commensal microflora by tolllike receptors is required for intestinal homeostasis. Cell. 2004;118:229-241.
21. Staley JT, Konopka A. Measurement of in situ activities of nonphotosynthetic microorganisms in aquatic and terrestrial habitats. Annu Rev Microbiol. 1985;39:321-346.
22. Hugenholtz P. Exploring prokaryotic diversity in the genomic era. Genome Biol. 2002;3:Reviews S0003.
23. Schloss PD, Handelsman J. Status of the microbial census. Microbiol Mol Biol Rev. 2004;68:686-691.
24. Olsen GJ, Lane DJ, Giovannoni SJ, Pace NR, Stahl DA. Microbial ecology and evolution: A ribosomal RNA approach. Annu Rev Microbiol. 1986;40:337-365.
25. Woese CR, Fox GE. Phylogenetic structure of the prokaryotic domain: The primary kingdoms. Proc Natl Acad Sci USA. 1977;75:5088-5090.
26. Relman DA, Loutit JS, Schmidt TM, Falkow S, Tompkins LS. The agent of bacillary angiomatosis. An approach to the identification of uncultured pathogens. N Engl J Med. 1990;323: 1573-1580.
27. Palmer C, Bik EM, Eisen MB, et al. Rapid quantitative profiling of complex microbial populations. Nucleic Acids Res. 2006; 34:e5.
28. Spiegelman D, Whissell G, Greer CW. A survey of the methods for the characterization of microbial consortia and communities. Can J Microbiol. 2005;51:355-386.
29. Dethlefsen L, Eckburg PB, Bik EM, Relman DA. Assembly of the human intestinal microbiota. Trends Ecol Evol. 2006; 21:517-523.
30. Rappe MS, Giovannoni SJ. The uncultured microbial majority. Ann Rev Microbiol. 2003;57:369-394.
31. Giovannoni SJ, Stingl U. Molecular diversity and ecology of microbial plankton. Nature. 2005;437:343-348.
32. Schloss PD, Handelsman J. Towards a census of bacteria in soil. PloS Comp Biol. 2006;2:e92.
33. Spear JR, Walker JJ, McCollom TM, Pace NR. Hydrogen and bioenergetics in theYellowstone geothermal ecosystem. Proc Natl Acad Sci USA. 2005;102:2555-2560.
34. Kelley ST, Theisen U, Angenent LT, Amand AS, Pace NR. Molecular analysis of shower curtain biofilm microbes. Appl Environ Microbiol. 2004;70:4187-4192.
35. Gao Z, Ch T, Pei Z, Blaser MJ. Molecular analysis of human forearm superficial skin bacterial biota. Proc Natl Acad Sci USA. 2007;104:2927-2932.
36. Seymour GJ, Ford PJ, Cullinan MP, Leishman S, Yamazaki K. Relationship between periodontal infections and systemic disease. Clin Microbiol Infect. 2007;13(Suppl 4):S3-S10.
37. Aas JA, Paster BJ, Stokes LN, Olsen I, Dewhirst FE. Defining the normal bacterial flora of the oral cavity. J Clin Microbiol. 2005;43:5721-5732.
38. Pei Z, Bini EJ, Yang L, Zhou M, Francois F, Blaser MJ. Bacterial biota in the human distal esophagus. Proc Natl Acad Sci USA. 2004;101:4250-4255.
39. Bik EM, Eckburg PB, Gill SR, et al. Molecular analysis of the bacterial microbiota in the human stomach. Proc Natl Acad Sci USA. 2006;103:732-737.
40. Eckburg PB, Bik EM, Bernstein CN, et al. Diversity of the human intestinal microbial flora. Science. 2005;308:1635-1638.
41. Rajilic-Stojanovic M, Smidt H, de Vos WM. Diversity of the human gastrointestinal tract microbiota revisited. Env Microbiol. 2007;9:2125-2136. (Pubitemid 47222128)
42. Palmer C, Bik EM, Digiulio DB, Relman DA, Brown PO. Development of the human infant intestinal microbiota. PLoS Biol. 2007;5:e177.
43. Turnbaugh PJ, Ley RE, Mahowald MA, Magrini V, Mardis ER, Gordon JI. An obesity-associated gut microbiome with increased capacity for energy harvest. Nature. 2006;444: 1027-1031.
44. Ley RE, Bäckhed F, Turnbaugh P, Lozupone CA, Knight RD, Gordon JI. Obesity alters gut microbial ecology. Proc Natl Acad Sci USA. 2005;102:11070-11075.
45. Ley RE, Turnbaugh PJ, Klein S, Gordon JI. Microbial ecology: Human gut microbes associated with obesity. Nature. 2006; 444:1022-1023.
46. Gill H, Prasad J. Probiotics, immunomodulation, and health benefits. Adv Exp Med Biol. 2008;606:423-454.
47. Gill SR, Pop M, DeBoy RT, et al. Metagenomic analysis of the human distal gut microbiome. Science. 2006;312:1355-1359.
48. Sogin ML, Morrison HG, Huber JA, et al. Microbial diversity in the deep sea and the underexplored "rare biosphere". Proc Natl Acad Sci USA. 2006;103:12115-12120.
49. Andersson AF, Lindberg M, Jakobsson H, Backhed F, Nyren P, Engstrand L. Comparative analysis of human gut microbiota by barcoded pyrosequencing. PLoS ONE. 2008;3:e2836.