The normal microbiota of the human gastrointestinal tract: History of analysis, succession, and dietary influences

Gastrointestinal Microbiology

Volumn , Issue , 2006, Pages 51-74

  McCartney, Anne L ^a   Gibson, Glenn R ^a  

^a UNIVERSITY OF READING   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 77955655135     PISSN: None     EISSN: None     Source Type: Book    
DOI: None     Document Type: Chapter

References (79)

1. Simon GL, Gorbach SL. Intestinal flora in health and disease. Gastroenterology 1984; 86:174-193.
2. Macfarlane GT, Cummings JH. The colonic flora, fermentation, and large bowel digestive function. In: Phillips SF, Pemberton JH, Shorter RG, eds. The Large Intestine: Physiology, Pathophysiology, and Disease. New York: Raven Press Ltd, 1991:51-92.
3. Tannock GW. An Introduction to Microbes Inhabiting the Human Body. London: Chapman & Hall, 1995.
4. Mitsuoka T. Intestinal flora and human health. Asia Pacific J Clin Nutr 1996; 5:2-9.
5. 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.
6. Holzapfel WH, Haberer P, Snel J, Schillinger U, Huis in’t Veld JHJ. Overview of gut flora and probiotics. Int J Food Microbiol 1998; 41:85-101.
7. Rabiu BA, Gibson GR. Carbohydrates: a limit on bacterial diversity within the colon. Biol Rev 2002; 77:443-453.
8. Guarner F, Malagelada J-R. Gut flora in health and disease. Lancet 2003; 361:512-519.
9. Blaser MJ, Kirschner D. Dynamics of Helicobacter pylori colonization in relation to the host response. Proc Natl Acad Sci USA 1999; 96:8359-8364.
10. Coconnier M-H, Lievin V, Hemery E, Servin AL. Antagonistic activity against Helicobacter infection in vitro and in vivo by the human Lactobacillus acidophilus strain LB. Appl Environ Microbiol 1998; 64:4573-4580.
11. Gibson GR, McCartney AL. Modification of the gut flora by dietary means. Biochem Soc Trans 1998; 26:222-228.
12. Marshall BJ. Helicobacter pylori. Am J Gastroenterol 1994; 89:S116-S128.
13. Bourlioux P, Koletzko B, Guarner F, Braesco V. The intestine and its microflora are partners for the protection of the host: report on the Danone Symposium “The Intelligent Intestine,” held in Paris, June 14, 2002. Am J Clin Nutr 2003; 78:675-683.
14. Macfarlane GT, Macfarlane S, Gibson GR. Validation of three-stage continuous culture system for investigating the effect of retention time on the ecology and metabolism of bacteria in the human colon. Microb Ecol 1998; 35:180-187.
15. Suau A, Bonnet R, Sutren M, et al. Direct analysis of genes encoding 16S rRNA from complex communities reveals many novel molecular species within the human gut. Appl Environ Microbiol 1999; 65:4799-4807.
16. Moore WEC, Holdeman LV. Discussion of current bacteriological investigations of the relationships between intestinal flora, diet, and colon cancer. Cancer Res 1975; 35:3418-3420.
17. Salminen S, Bouley C, Boutron-Ruault M-C, et al. Functional food science and gastrointestinal physiology and function. Br J Nutr 1998; 80:S147-S171.
18. Metges CC. Contribution of microbial amino acids to amino acid homeostasis of the host. J Nutr 2000; 130:1857S-1864S.
19. Gordon JI, Hooper LV, McNevin MS, Wong M, Bry L. Epithelial cell growth and differentiation. III. Promoting diversity in the intestine: conversations between the microflora, epithelium, and diffuse GALT. Am J Physiol 1997; 273:G565-G570.
20. Borruel N, Casellas F, Antolín M, et al. Effects of nonpathogenic bacteria on cytokine secretion by human intestinal mucosa. Am J Gastroenterol 2003; 98:865-870.
21. Perdigón G, Maldonado Galdeano C, Valdez JC, Medici M. Interaction of lactic acid bacteria with the gut immune system. Eur J Clin Nutr 2002; 56:S21-S26.
22. Tannock GW. The acquisition of the normal microflora of the gastrointestinal tract. In: Gibson SAW, ed. Human Health: The Contribution of Microorganisms. London: Springer-Verlag, 1994:1-16.
23. Bezirtzoglou E. The intestinal microflora during the first weeks of life. Anaerobe 1997; 3:173-177.
24. Mountzouris KC, McCartney AL, Gibson GR. Intestinal microflora of human infants and current trends for its nutritional modulation. Br J Nutr 2002; 87:405-420.
25. Salminen S, Gibson GR, McCartney AL, Isolauri E. Influence of mode of delivery on gut microbiota composition in seven year old children. Gut 2004; 53:1388-1389.
26. Biavati B, Sgorbati B, Scardovi V. The Genus Bifidobacterium. In: Balows A, Trüper HG, Dworkin M, Harder W, Schleifer KH, eds. The Prokaryotes. A Handbook on the Biology of Bacteria: Ecophysiology, Isolation, Identification, Applications. 2nd ed., Vol. 1. New York: Springer-Verlag, 1992:816-833.
27. Scardovi V. Genus Bifidobacterium Orla-Jensen 1924, 472AL. In: Sneath PHA, Mair NS, Sharpe ME, Holt JG, eds. In: Bergey’s Manual of Systematic Bacteriology, Vol. 2. Baltimore: Williams and Wilkins, 1986:1418-1434.
28. Edwards CA, Parrett AM. Intestinal flora during the first months of life: new perspectives. Br J Nutr 2002; 88:S11-S18.
29. Salminen S, Bouley C, Boutron Ruault M-C, et al. Functional food science and gastrointestinal physiology and function. Br J Nutr 1998; 80:S147-S171.
30. Kleessen B, Bunke H, Tovar K, Noack J, Sawatzki G. Influence of two infant formulas and human milk on the development of the faecal flora in newborn infants. Acta Paediatrica 1995; 84:1347-1356.
31. Mitsuoka T, Kaneuchi C. Ecology of the bifidobacteria. Am J Clin Nutr 1977; 30:1799-1810.
32. Stark PL, Lee A. The microbial ecology of the large bowel of breast-fed and formula-fed infants during the first year of life. J Med Microbiol 1982; 15:189-203.
33. Yoshioka H, Fujita K, Sakata H, Murono K, Iseki K. Development of the normal intestinal flora and its clinical significance in infants and children. Bifidobacteria Microflora 1991; 2:33-39.
34. Boehm G, Lidestri M, Casetta P, et al. Supplementation of a bovine milk formula with an oligosaccharide mixture increases counts of faecal bifidobacteria in preterm infants. Arch Dis Child 2002; 86:178-181.
35. Harmsen HJM, Wildeboer-Veloc ACM, Raangs GC, et al. Analysis of intestinal flora development in breast-fed and formula-fed infants by using molecular identification and detection methods. J Pediatr Gastroenterol Nutr 2000; 30:61-67.
36. Drasar BS, Jenkins DJA. Bacteria, diet, and large bowel cancer. Am J Clin Nutr 1976; 29:1410-1416.
37. Finegold SM, Sutter VL. Fecal flora in different populations, with special reference to diet. Am J Clin Nutr 1978; 31:S116-S122.
38. Hill MJ, Drasar BS, Aries V, Crowther JS, Hawksworth G, Williams REO. Bacteria and aetiology of cancer of large bowel. Lancet 1971; 1:95-100.
39. Aries V, Crowther JS, Drasar BS, Hill MJ, Williams REO. Bacteria and the aetiology of cancer of the large bowel. Gut 1969; 10:334-335.
40. Moore WEC, Cato EP, Holdeman LV. Some current concepts in intestinal bacteriology. Am J Clin Nutr 1978; 31:S33-S42.
41. Finegold SM, Attebery HR, Sutter VL. Effect of diet on human fecal flora: comparison of Japanese and American diets. Am J Clin Nutr 1974; 27:1456-1469.
42. Holdeman LV, Good IJ, Moore WEC. Human fecal flora: variation in bacterial composition within individuals and a possible effect of emotional stress. Appl Environ Microbiol 1976; 31:359-375.
43. Hentges DJ, Maier BR, Burton GC, Flynn MA, Tsutakawa RK. Effect of a high-beef diet on the fecal flora of humans. Cancer Res 1977; 37:568-571.
44. Cummings JH. Dietary fibre and the intestinal microflora. In: Hallgren B, ed. Nutrition and the Intestinal Flora. Stockholm: Almqvist and Wiksell International, 1983:77-86.
45. Bornside GH. Stability of human fecal flora. Am J Clin Nutr 1978; 31:S141-S144.
46. Hartley CL, Clements HM, Linton KB. Escherichia coli in the faecal flora of man. J Appl Bacteriol 1977; 43:261-269.
47. Mason TG, Richardson G. A review. Escherichia coli and the human gut: some ecological considerations. J Appl Bacteriol 1981; 51:1-16.
48. McBurney WT, McCartney AL, Apun K, McConnell MA, Tannock GW. Perturbation of the enterobacterial microflora detected by molecular analysis. Microb Ecol Health Dis 1999; 11:175-179.
49. Shooter RA, Bettelheim KA, Lennox-King SMJ, O’Farrell S. Escherichia coli serotypes in the faeces of healthy adults over a period of several months. J Hyg 1977; 78:95-98.
50. Wallick H, Stuart CA. Antigenic relationships of Escherichia coli isolated from one individual. J Bacteriol 1943; 45:121-126.
51. Kimura K, McCartney AL, McConnell MA, Tannock GW. Analysis of fecal populations of bifidobacteria and lactobacilli and investigation of the immunological responses of their human hosts to the predominant strains. Appl Environ Microbiol 1997; 63:3394-3398.
52. McCartney AL, Wenzhi W, Tannock GW. Molecular analysis of the composition of the bifidobacterial and lactobacillus microflora of humans. Appl Environ Microbiol 1996; 62:4608-4613.
53. Matsuki T, Watanabe K, Fujimoto J, et al. Development of 16S rRNA-gene-targeted groupspecific primers for the detection and identification of predominant bacteria in human feces. Appl Environ Microbiol 2002; 68:5445-5451.
54. Tannock GW. Analysis of the intestinal microflora using molecular methods. Eur J Clin Nutr 2002; 56:S44-S49.
55. Vaughan EE, Schut F, Heilig HGHJ, Zoetendal EG, de Vos WM, Akkermans ADL. A molecular view of the intestinal microflora. Curr Issues Intest Microbiol 2000; 1:1-12.
56. Zoetendal EG, Akkermans ADL, de Vos WM. Temperature gradient gel electrophoresis analysis of 16S rRNA from human fecal samples reveals stable and host-specific communities of active bacteria. Appl Environ Microbiol 1998; 64:3854-3859.
57. Blaut M, Collins MD, Welling GW, Doré J, van Loo J, de Vos W. Molecular biological methods for studying the gut microflora: the EU human gut flora project. Br J Nutr 2002; 87:S203-S211.
58. Wilson KH, Blitchington RB. Human colonic flora studied by ribosomal DNA sequence analysis. Appl Environ Microbiol 1996; 62:2273-2278.
59. Konstantinov SR, Fitzsimons N, Vaughan EE, Akkermans ADL. From composition to functionality of the intestinal microbial communities. In: Tannock GW, ed. Probiotics and Prebiotics. Where are we Going?. Norfolk, U.K.: Caister Academic Press, 2002:59-84.
60. Satokari RM, Vaughan EE, Akkermans ADL, Saarela M, de Vos WM. Bifidobacterial diversity in human feces detected by genus-specific PCR and denaturing gradient gel electrophoresis. Appl Environ Microbiol 2001; 67:504-513.
61. Walter J, Hertel C, Tannock GW, Lis CM, Munro K, Hammes WP. Detection of Lactobacillus, Pediococcus, Leuconostoc, and Weissella species in human feces by using group-specific PCR primers and denaturing gradient gel electrophoresis. Appl Environ Microbiol 2001; 67:2578-2585.
62. Zoetendal EG, Akkermans ADL, Akkermans, van Vliet WM, de Visser JAGM, de Vos WM. The host genotype affects the bacterial community in the human gastrointestinal tract. Microb Ecol Health Dis 2001; 13:129-134.
63. Favier CF, Vaughan EE, de Vos WM, Akkermans ADL. Molecular monitoring of succession of bacterial communities in human neonates. Appl Environ Microbiol 2002; 68:219-226.
64. Heilig HGHJ, Zoetendal EG, Vaughan EE, Marteau P, Akkermans ADL, de Vos WM. Molecular diversity of Lactobacillus spp. and other lactic acid bacteria in the human intestine as determined by specific amplification of 16S ribosomal DNA. Appl Environ Microbiol 2002; 68:114-123.
65. Zoetendal EG, von Wright A, Vilpponen-Salmela T, Ben-Amor K, Akkermans ADL, de Vos WM. Mucosa-associated bacteria in the human gastrointestinal tract are uniformly distributed along the colon and differ from the community recovered from faeces. Appl Environ Microbiol 2002; 68:3401-3407.
66. Wang R-F, Cao W-W, Cerniglia CE. PCR detection and quantitation of predominant anaerobic bacteria in human and animal fecal samples. Appl Environ Microbiol 1996; 62:1242-1247.
67. Germond J-E, Mamin O, Mollet B. Species specific identification of nine human Bifidobacterium spp. in feces. Syst Appl Microbiol 2002; 25:536-543.
68. Matsuki T, Watanabe K, Tanaka R, Fukuda M, Oyaizu H. Distribution of bifidobacterial species in human intestinal microflora examined 16S rRNA-gene-targeted species-specific primers. Appl Environ Microbiol 1999; 65:4506-4512.
69. Requena T, Burton J, Matsuki T, et al. Identification, detection, and enumeration of human Bifidobacterium species by PCR targeting the transaldolase gene. Appl Environ Microbiol 2002; 68:2420-2427.
70. Harmsen HJM, Welling GW. In: Tannock GW, ed. Probiotics and Prebiotics. Where are we going?. Norfolk, U.K.: Caister Academic Press, 2002:41-58.
71. Marteau P, Pochart P, Doré J, Béra-Maillet C, Bernalier A, Corthier G. Comparative study of bacterial groups within the human cecal and fecal microflora. Appl Environ Microbiol 2001; 67:4939-4942.
72. Franks AH, Harmsen HJM, Raangs GC, Jansen GJ, Schut F, Welling GW. Variations of bacterial populations in human feces measured by fluorescence in situ hybridization with group-specific 16S rRNA-targeted oligonucleotide probes. Appl Environ Microbiol 1998; 64:3336-3345.
73. Harmsen HJM, Raangs GC, He T, Degener JE, Welling GW. Extensive set of 16S rRNA-based probes for detection of bacteria in human feces. Appl Environ Microbiol 2002; 68:2982-2990.
74. Sghir A, Gramet G, Suau A, Rochet V, Pochart P, Dore J. Quantification of bacterial groups within human fecal flora by oligonucleotide probe hybridization. Appl Environ Microbiol 2000; 66:2263-2266.
75. Suau A, Rochet V, Sghir A, et al. Fusobacterium prausnitzii and related species represent a dominant group within the human fecal flora. Syst Appl Microbiol 2001; 24:139-145.
76. Zoetendal EG, Ben-Amor K, Harmsen HJM, Schut F, Akkermans ADL, de Vos WM. Quantification of uncultured Ruminococcus obeum-like bacteria in human fecal samples by fluorescent in situ hybridization and flow cytometry using 16S rRNA-targeted probes. Appl Environ Microbiol 2002; 68:4225-4232.
77. Wang R-F, Beggs ML, Robertson LH, Cerniglia CE. Design and evaluation of oligonucleotidemicroarray method for the detection of human intestinal bacteria in fecal samples. FEMS Microbiol Lett 2002; 213:175-182.
78. Wang R-F, Kim S-J, Robertson LH, Cerniglia CE. Development of a membrane-assay method for the detection of intestinal bacteria in fecal samples. Mol Cell Probes 2002; 16:341-350.
79. Tannock GW. Molecular assessment of intestinal microflora. Am J Clin Nutr 2001; 73:410S-414S.