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Chapter 2 : The Human Intestinal Microbiota and Its Impact on Health

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Abstract:

Although microbes are everywhere and, in theory, they all may have an impact on human health, microbial diversity is so enormous that it is hardly possible to describe all of them. This chapter focuses on the microbes residing in gastrointestinal (GI) tract that are collectively termed the microbiota, since these have the most intimate interaction with human body and, therefore, have a prominent impact on human health. It has been observed that the predominant bacterial composition in feces of healthy adult individuals is relatively stable over time. In contrast to healthy adults, however, severely disturbed and/or unstable fecal microbiotas can be correlated with humans with GI tract disorders, such as Crohn’s disease (CD), ulcerative colitis (UC), and intestinal bowel syndrome (IBS). Bacteria related to known butyrate-producing bacteria predominated in a live fraction, while bacteria affiliated with , , and were more abundant in dead fractions. These are important findings, since they link phylogenetic information of the GI bacteria to activity. Although metagenomic analysis has shown their power for revealing the coding potential of the microbiome, and the genome of the entire microbial ecosystem, further functional studies, such as metaproteomics, have been reported but show limitations in our predictive capacity. Hence, there is a great need to integrate all available reductionist and global, cultivation- and molecular-based approaches to finally describe and understand micro companions throughout the journey on planet Earth.

Citation: Rajilić-Stojanović M, de Vos W, Zoetendal E. 2008. The Human Intestinal Microbiota and Its Impact on Health, p 11-32. In Zengler K (ed), Accessing Uncultivated Microorganisms. ASM Press, Washington, DC. doi: 10.1128/9781555815509.ch2

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Citation: Rajilić-Stojanović M, de Vos W, Zoetendal E. 2008. The Human Intestinal Microbiota and Its Impact on Health, p 11-32. In Zengler K (ed), Accessing Uncultivated Microorganisms. ASM Press, Washington, DC. doi: 10.1128/9781555815509.ch2
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Image of FIGURE 2
FIGURE 2

SSU rRNA-based phylogenetic tree representing the diversity of the human GI microbiota. Each phylum is presented as a distinct phylogenetic group except for the , which are presented by four phylogenetic groups. The reference bar indicates 10% sequence divergence.

Citation: Rajilić-Stojanović M, de Vos W, Zoetendal E. 2008. The Human Intestinal Microbiota and Its Impact on Health, p 11-32. In Zengler K (ed), Accessing Uncultivated Microorganisms. ASM Press, Washington, DC. doi: 10.1128/9781555815509.ch2
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Image of FIGURE 3
FIGURE 3

(A) Ratio of the average hybridization signals obtained by the analysis of fecal DNA and RNA. Less active phylogenetic groups (higher hybridization signals with DNA) are presented as left-oriented bars, while active phylogenetic groups (higher hybridization signal with RNA) are presented with right-oriented bars. Relative composition of the total microbiota (B) and active microbiota (C).

Citation: Rajilić-Stojanović M, de Vos W, Zoetendal E. 2008. The Human Intestinal Microbiota and Its Impact on Health, p 11-32. In Zengler K (ed), Accessing Uncultivated Microorganisms. ASM Press, Washington, DC. doi: 10.1128/9781555815509.ch2
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Image of FIGURE 4
FIGURE 4

PCA triplot depicting the microbiota of healthy adults (○) (D1–D9), patients with IBS (◆) (IBS1–IBS9), and patients with UC (■) (UC1–UC9). Percentage values at the axes indicate contribution of the principal components to the explanation of total variance in the dataset; phylogenetic groups named after cultivated representative that contributed at least 60% to the explanatory axis used in the plot are presented as vectors, while centroides of the plot describe health status of subjects.

Citation: Rajilić-Stojanović M, de Vos W, Zoetendal E. 2008. The Human Intestinal Microbiota and Its Impact on Health, p 11-32. In Zengler K (ed), Accessing Uncultivated Microorganisms. ASM Press, Washington, DC. doi: 10.1128/9781555815509.ch2
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References

/content/book/10.1128/9781555815509.ch02
1. Acinas, S. G.,, L. A. Marcelino,, V. Klepac-Ceraj, and, M. F. Polz. 2004. Divergence and redundancy of 16S rRNA sequences in genomes with multiple rrn operons. J. Bacteriol. 186:26292635.
2. Albert, M. J.,, V. I. Mathan, and, S. J. Baker. 1980. Vitamin B12 synthesis by human small intestinal bacteria. Nature 238:781782.
3. Amann, R. I.,, B. J. Binder,, R. J. Olson,, S. W. Chisholm,, R. Devereux, and, D. A. Stahl. 1990. Combination of 16S rRNA-targeted oligonucleotide probes with flow cytometry for analyzing mixed microbial populations. Appl. Environ. Microbiol. 56:19191925.
4. Andoh, A.,, S. Sakata,, Y. Koizumi,, K. Mitsuyama,, Y. Fujiyama, and, Y. Benno. 2007. Terminal restriction fragment length polymorphism analysis of the diversity of fecal microbiota in patients with ulcerative colitis. Inflamm. Bowel. Dis. 13:955962.
5. Apajalahti, J. H.,, A. Kettunen,, P. H. Nurminen,, H. Jatila, and, W. E. Holben. 2003. Selective plating underestimates abundance and shows differential recovery of bifidobacterial species from human feces. Appl. Environ. Microbiol. 69:57315735.
6. Aranda-Michel, J., and, R. A. Giannella. 1999. Acute diarrhea: a practical review. Am. J. Med. 106:670.
7. Ashby, M. N.,, J. Rine,, E. F. Mongodin,, K. E. Nelson, and, D. Dimster-Denk. 2007. Serial analysis of rRNA genes and the unexpected dominance of rare members of microbial communities. Appl. Environ. Microbiol. 73:45324542.
8. Bäckhed, F.,, R. E. Ley,, J. L. Sonnenburg,, D. A. Peterson, and, J. I. Gordon. 2005. Host-bacterial mutualism in the human intestine. Science 307:19151920.
9. Bakir, M. A.,, M. Sakamoto,, M. Kitahara,, M. Matsumoto, and, Y. Benno. 2006. Bacteroides dorei sp. nov., isolated from human faeces. Int. J. Syst. Evol. Microbiol. 56:16391643.
10. Barcenilla, A.,, S. E. Pryde,, J. C. Martin,, S. H. Duncan,, C. S. Stewart,, C. Henderson, and, H. J. Flint. 2000. Phylogenetic relationships of butyrate-producing bacteria from the human gut. Appl. Environ. Microbiol. 66:16541661.
11. Ben-Amor, K. 2004. Ph.D. thesis. Microbial ecophysiology of the human intestinal tract: a flow cytometric approach, p. 166. Laboratory of Microbiology, Wageningen University, Wageningen, The Netherlands.
12. Ben-Amor, K.,, P. Breeuwer,, P. Verbaarschot,, F. M. Rombouts,, A. D. L. Akkermans,, W. M. De Vos, and, T. Abee. 2002. Multiparametric flow cytometry and cell sorting for the assessment of viable, injured, and dead bifidobacterium cells during bile salt stress. Appl. Environ. Microbiol. 68:52095216.
13. Ben-Amor, K.,, H. G. Heilig,, H. Smidt,, E. E. Vaughan,, T. Abee, and, W. M. de Vos. 2005. Genetic diversity of viable, injured, and dead fecal bacteria assessed by fluorescence-activated cell sorting and 16S rRNA gene analysis. Appl. Environ. Microbiol. 71:46794689.
14. Bengmark, S. 1998. Ecological control of the gastrointestinal tract. The role of probiotic flora. Gut 42:27.
15. Bengtson, M. B.,, T. Ronning,, M. H. Vatn, and, J. R. Harris. 2006. Irritable bowel syndrome in twins: genes and environment. Gut 55:17541759.
16. Bik, E. M.,, P. B. Eckburg,, S. R. Gill,, K. E. Nelson,, E. A. Purdom,, F. Francois,, G. Perez-Perez,, M. J. Blaser, and, D. A. Relman. 2006. Molecular analysis of the bacterial microbiota in the human stomach. Proc. Natl. Acad. Sci. 103:732737.
17. Breitbart, M.,, I. Hewson,, B. Felts,, J. M. Mahaffy,, J. Nulton,, P. Salamon, and, F. Rohwer. 2003. Metagenomic analyses of an uncultured viral community from human feces. J. Bacteriol. 185:62206223.
18. Button, D. K., and, B. R. Robertson. 2001. Determination of DNA content of aquatic bacteria by flow cytometry. Appl. Environ. Microbiol. 67:16361645.
19. Carvalho, M. D. G. S.,, P. L. Shewmaker,, A. G. Steigerwalt,, R. E. Morey,, A. J. Sampson,, K. Joyce,, T. J. Barrett,, L. M. Teixeira, and, R. R. Facklam. 2006. Enterococcus caccae sp. nov., isolated from human stools. Int. J. Syst. Evol. Microbiol. 56:15051508.
20. Chiesa, C.,, L. Pacifico,, F. Nanni,, A. M. Renzi, and, G. Ravagnan. 1993. Yersinia pseudotuberculosis in Italy. Attempted recovery from 37, 666 samples. Microbiol. Immunol. 37:391394.
21. Cho, J. C.,, K. L. Vergin,, R. M. Morris, and, S. J. Giovannoni. 2004. Lentisphaera araneosa gen. nov., sp. nov, a transparent exopolymer producing marine bacterium, and the description of a novel bacterial phylum, Lentisphaerae. Environ. Microbiol. 6:611621.
22. Cummings, J. H., and, G. T. Macfarlane. 1997. Colonic microflora: nutrition and health. Nutrition 13:476.
23. Derrien, M. 2007. Ph.D. thesis. Mucin utilisation and host interactions of the novel intestinal microbe Akkermansia muciniphila, p. 164. Laboratory of Microbiology, Wageningen University, Wageningen, The Netherlands.
24. Derrien, M.,, E. E. Vaughan,, C. M. Plugge, and, W. M. de Vos. 2004. Akkermansia muciniphila gen. nov., sp. nov., a human intestinal mucin-degrading bacterium. Int. J. Syst. Evol. Microbiol 54:14691476.
25. DeSantis, T. Z.,, E. L. Brodie,, J. P. Moberg,, I. X. Zubieta,, Y. M. Piceno, and, G. L. Andersen. 2007. High-density universal 16S rRNA microarray analysis reveals broader diversity than typical clone library when sampling the environment. Microb. Ecol. 53:371383.
26. DeSantis, T. Z.,, P. Hugenholtz,, N. Larsen,, M. Rojas,, E. L. Brodie,, K. Keller,, T. Huber,, D. Dalevi,, P. Hu, and, G. L. Andersen. 2006. Green-genes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB. Appl. Environ. Microbiol. 72:50695072.
27. de Vries, M. C. 2006. Ph.D. thesis. Analyzing global gene expression of Lactobacillus plantarum in the human gastrointestinal tract, p. 160. Laboratory of Microbiology, Wageningen University, Wageningen, The Netherlands.
28. Dobell, C. A. 1920. The discovery of the intestinal protozoa of man. Proc. R. Soc. Med. 13:115.
29. Duncan, S. H.,, R. I. Aminov,, K. P. Scott,, P. Louis,, T. B. Stanton, and, H. J. Flint. 2006. Proposal of Roseburia faecis sp. nov., Roseburia hominis sp. nov. and Roseburia inulinivorans sp. nov., based on isolates from human faeces. Int. J. Syst. Evol. Microbiol. 56:24372441.
30. Duncan, S. H.,, G. L. Hold,, A. Barcenilla,, C. S. Stewart, and, H. J. Flint. 2002a. Roseburia intestinalis sp. nov., a novel saccharolytic, butyrate-producing bacterium from human faeces. Int. J. Syst. Evol. Microbiol. 52:16151620.
31. Duncan, S. H.,, G. L. Hold,, H. Harmsen,, C. S. Stewart, and, H. J. Flint. 2002b. Growth requirements and fermentation products of Fusobacterium prausnitzii, and a proposal to reclassify it as Faecalibacterium prausnitzii gen. nov., comb. nov. Int. J. Syst. Evol. Microbiol. 52:21412146.
32. Duncan, S. H.,, P. Louis, and, H. J. Flint. 2004. Lactate-utilizing bacteria, isolated from human feces, that produce butyrate as a major fermentation product. Appl. Environ. Microbiol. 70:58105817.
33. Duncan, S. H.,, P. Louis, and, H. J. Flint. 2007. Cultivable bacterial diversity from the human colon. Lett. Appl. Microbiol. 44:343350.
34. Eckburg, P. B.,, E. M. Bik,, C. N. Bernstein,, E. Purdom,, L. Dethlefsen,, M. Sargent,, S. R. Gill,, K. E. Nelson, and, D. A. Relman. 2005. Diversity of the human intestinal microbial flora. Science 308:16351638.
35. Egert, M.,, B. Wagner,, T. Lemke,, A. Brune, and, M. W. Friedrich. 2003. Microbial community structure in midgut and hindgut of the humus-feeding larva of Pachnoda ephippiata (Coleoptera: Scarabaeidae). Appl. Environ. Microbiol. 69:66596668.
36. Favier, C. F.,, E. E. Vaughan,, W. M. de Vos, and, A. D. L. Akkermans. 2002. Molecular monitoring of succession of bacterial communities in human neonates. Appl. Environ. Microbiol. 68:219226.
37. Fernandez, A. S.,, S. A. Hashsham,, S. L. Dollhopf,, L. Raskin,, O. Glagoleva,, F. B. Dazzo,, R. F. Hickey,, C. S. Criddle, and, J. M. Tiedje. 2000. Flexible community structure correlates with stable community function in methanogenic bioreactor communities perturbed by glucose. Appl. Environ. Microbiol. 66:40584067.
38. Fogel, G. B.,, C. R. Collins,, J. Li, and, C. F. Brunk. 1999. Prokaryotic genome size and SSU rDNA copy number: estimation of microbial relative abundance from a mixed population. Microb. Ecol. 38:93113.
39. Franks, A. H.,, H. J. M. Harmsen,, G. C. Raangs,, G. J. Jansen,, F. Schut, and, G. W. Welling. 1998. Variations of bacterial populations in human feces measured by fluorescent in situ hybridization with group-specific 16S rRNA-targeted oligonucleotide probes. Appl. Environ. Microbiol. 64:33363345.
40. Freitas, R. A. 1999. Navigational Alimentography. Landes Bioscience, Georgetown, TX.
41. Gill, S. R.,, M. Pop,, R. T. Deboy,, P. B. Eckburg,, P. J. Turnbaugh,, B. S. Samuel,, J. I. Gordon,, D. A. Relman,, C. M. Fraser-Liggett, and, K. E. Nelson. 2006. Metagenomic analysis of the human distal gut microbiome. Science 312:13551359.
42. Gloux, K.,, M. Leclerc,, H. Iliozer,, R. L’Haridon,, C. Manichanh,, G. Corthier,, R. Nalin,, H. M. Blottière, and, J. Doré. 2007. Development of high-throughput phenotyping of metagenomic clones from the human gut microbiome for modulation of eukaryotic cell growth. Appl. Environ. Microbiol. 73:37343737.
43. Gophna, U.,, K. Sommerfeld,, S. Gophna,, W. F. Doolittle, and, S. J. O. Veldhuyzen van Zanten. 2006. Differences between tissue-associated intestinal microfloras of patients with Crohn’s disease and ulcerative colitis. J. Clin. Microbiol. 44:41364141.
44. Guschin, D. Y.,, B. K. Mobarry,, D. Proudnikov,, D. A. Stahl,, B. E. Rittmann, and, A. D. Mirzabekov. 1997. Oligonucleotide microchips as genosensors for determinative and environmental studies in microbiology. Appl. Environ. Microbiol. 63:23972402.
45. Guyton, A. C. 1985. Anatomy and Physiology. Saunders College Pub., Philadelphia, PA.
46. Gwee, K. A. 2005. Irritable bowel syndrome in developing countries—a disorder of civilization or colonization? Neurogastroent. Motil. 27:317324.
47. Halfvarson, J.,, L. Bodin,, C. Tysk,, E. Lindberg, and, G. Jarnerot. 2003. Inflammatory bowel disease in a Swedish twin cohort: a long-term follow-up of concordance and clinical characteristics. Gastroenterology 124:1767.
48. Haller, D. 2006. Intestinal epithelial cell signalling and host-derived negative regulators under chronic inflammation: to be or not to be activated determines the balance towards commensal bacteria. Neurogastroenterol. Motil. 18:184199.
49. Handelsman, J. 2004. Metagenomics: application of genomics to uncultured microorganisms. Microbiol. Mol. Biol. Rev. 68:669685.
50. Hold, G. L.,, A. Schwiertz,, R. I. Aminov,, M. Blaut, and, H. J. Flint. 2003. Oligonucleotide probes that detect quantitatively significant groups of butyrate-producing bacteria in human feces. Appl. Environ. Microbiol. 69:43204324.
51. Hooper, L. V., and, J. I. Gordon. 2001. Commensal host-bacterial relationships in the gut. Science 292:11151118.
52. Hooper, L. V.,, J. Xu,, P. G. Falk,, T. Midtvedt, and, J. I. Gordon. 1999. A molecular sensor that allows a gut commensal to control its nutrient foundation in a competitive ecosystem. Proc. Natl. Acad. Sci. USA 96:98339838.
53. Horz, H. P.,, M. E. Vianna,, B. P. F. A. Gomes, and, G. Conrads. 2005. Evaluation of universal probes and primer sets for assessing total bacterial load in clinical samples: general implications and practical use in endodontic antimicrobial therapy. J. Clin. Microbiol. 43:53325337.
54. Hugenholtz, P.,, G. W. Tyson,, R. I. Webb,, A. M. Wagner, and, L. L. Blackall. 2001. Investigation of candidate division TM7, a recently recognized major lineage of the domain bacteria with no known pure-culture representatives. Appl. Environ. Microbiol. 67:411419.
55. Ingham, C. J.,, M. van den Ende,, P. C. Wever, and, P. M. Schneeberger. 2006. Rapid antibiotic sensitivity testing and trimethoprim-mediated filamentation of clinical isolates of the Enterobacteriaceae assayed on a novel porous culture support. J. Med. Microbiol. 55:15111519.
56. Jones, B. V., and, J. Marchesi. 2007. Transposon-aided capture (TRACA) of plasmids resident in the human gut mobile metagenome. Nat. Methods 4:5561.
57. Justesen, T.,, O. H. Nielsen, and, P. A. Krasilnikoff. 1984. Normal cultivable microflora in upper jejunal fluid in children without gastrointestinal disorders. J. Pediatr. Gastroenterol. Nutr. 3:683686.
58. Kazor, C. E.,, P. M. Mitchell,, A. M. Lee,, L. N. Stokes,, W. J. Loesche,, F. E. Dewhirst, and, B. J. Paster. 2003. Diversity of bacterial populations on the tongue dorsa of patients with halitosis and healthy patients. J. Clin. Microbiol. 41:558563.
59. Kenzaka, T.,, S. Tamaki,, N. Yamaguchi,, K. Tani, and, M. Nasu. 2005. Recognition of individual genes in diverse microorganisms by cycling primed in situ amplification. Appl. Environ. Microbiol. 71:72367244.
60. King, T. S.,, M. Elia, and, J. O. Hunter. 1998. Abnormal colonic fermentation in irritable bowel syndrome. Lancet 352:1187.
61. Kirjavainen, P. V.,, E. Apostolou,, T. Arvola,, S. J. Salminen,, G. R. Gibson, and, E. Isolauri. 2001. Characterizing the composition of intestinal microflora as a prospective treatment target in infant allergic disease. FEMS Immunol. Med. Microbiol. 32:1.
62. Klaassens, E. S.,, W. M. de Vos, and, E. E. Vaughan. 2006. A metaproteomics approach to study the functionality of the microbiota in the human infant gastrointestinal tract. Appl. Environ. Microbiol.: AEM.0192101906.
63. Klappenbach, J. A.,, P. R. Saxman,, J. R. Cole, and, T. M. Schmidt. 2001. rrndb: the ribosomal RNA operon copy number database. Nucleic Acids Res. 29:181184.
64. Lay, C.,, L. Rigottier-Gois,, K. Holmstrom,, M. Rajilic,, E. E. Vaughan,, W. M. de Vos,, M. D. Collins,, R. Thiel,, P. Namsolleck,, M. Blaut, and, J. Doré. 2005. Colonic microbiota signatures across five northern European countries. Appl. Environ. Microbiol. 71:41534155.
65. Leitch, E. C.,, A. W. Walker,, S. H. Duncan,, G. Holtrop, and, H. J. Flint. 2007. Selective colonization of insoluble substrates by human faecal bacteria. Environ. Microbiol. 9:667679.
66. Ley, R. E.,, P. J. Turnbaugh,, S. Klein, and, J. I. Gordon. 2006. Microbial ecology: human gut microbes associated with obesity. Nature 444:10221023.
67. Loy, A., and, L. Bodrossy. 2006. Highly parallel microbial diagnostics using oligonucleotide microarrays. Clin. Chim. Acta 363:106.
68. Macfarlane, G. T.,, J. H. Cummings, and, C. Alison. 1986. Protein degradation by human intestinal bacteria. J. Gen. Microbiol. 132:16471656.
69. Macfarlane, G. T.,, G. R. Gibson, and, S. Macfar-lane. 1994. Short chain fatty acid and lactate production by human intestinal bacteria grown in batch and continuous culture. In H. J. Binder,, J. H. Cummings, and, K. H. Soergel (ed.), Short Chain Fatty Acids. Kluwer Publishing, London, United Kingdom.
70. Manichanh, C.,, L. Rigottier-Gois,, E. Bonnaud,, K. Gloux,, E. Pelletier,, L. Frangeul,, R. Nalin,, C. Jarrin,, P. Chardon,, P. Marteau,, J. Roca, and, J. Doré. 2006. Reduced diversity of faecal microbiota in Crohn’s disease revealed by a metagenomic approach. Gut 55:205211.
71. Marchesi, J. R.,, E. Holmes,, F. Khan,, S. Kochhar,, P. Scanlan,, F. Shanahan,, I. D. Wilson, and, Y. Wang. 2007. Rapid and noninvasive metabonomic characterization of inflammatory bowel disease. J. Proteome Res. 6:546551.
72. Matsuda, K.,, H. Tsuji,, T. Asahara,, Y. Kado, and, K. Nomoto. 2007. Sensitive quantitative detection of commensal bacteria by rRNA-targeted reverse transcription-PCR. Appl. Environ. Microbiol. 73:3239.
73. Matsuki, T.,, K. Watanabe,, J. Fujimoto, Y. Miyamoto,, T. Takada,, K. Matsumoto,, H. Oyaizu, and, T. Ryuichiro. 2002. Development of 16S rRNA-gene-targeted group-specific primers for the detection and identification of predominant bacteria in human feces. Appl. Environ. Microbiol. 68:54455451.
74. Matsuki, T.,, K. Watanabe,, J. Fujimoto,, T. Takada, and, R. Tanaka. 2004. Use of 16S rRNA gene-targeted group-specific primers for real-time PCR analysis of predominant bacteria in human feces. Appl. Environ. Microbiol. 70:72207228.
75. Matsumoto, T.,, T. Hayasak,, Y. Nishimura,, M. Nakamura,, T. Takeda,, Y. Tabuchi,, M. Obinata,, T. Hanawa, and, H. Yamada. 2006. Butyrate induces necrotic cell death in murine colonic epithelial cell MCE301. Biol. Pharm. Bull. 29:20412045.
76. Mättö, J.,, L. Maunuksela,, K. Kajander,, A. Palva,, R. Korpela,, A. Kassinen, and, M. Saarela. 2005. Composition and temporal stability of gastrointestinal microbiota in irritable bowel syndrome—a longitudinal study in IBS and control subjects. FEMS Immunol. Med. Microbiol. 43:213222.
77. Maukonen, J.,, R. Satokari,, J. Mättö,, H. Söder-lund,, T. Mattila-Sandholm, and, M. Saarela. 2006. Prevalence and temporal stability of selected clostridial groups in irritable bowel syndrome in relation to predominant faecal bacteria. J. Med. Microbiol. 55:625633.
78. McGarr, S. E.,, J. M. Ridlon, and, P. B. Hylemon. 2005. Diet, anaerobic bacterial metabolism, and colon cancer: a review of the literature. J. Clin. Gastroenterol. 39:98109.
79. Mitsuoka, T. 1992. Intestinal flora and aging. Nutr. Rev. 50:438446.
80. Mohan, R.,, P. Namsolleck,, P. A. Lawson,, M. Osterhoff,, M. D. Collins,, C.-A. Alpert, and, M. Blaut. 2006. Clostridium asparagiforme sp. nov., isolated from a human faecal sample. Syst. Appl. Microbiol. 29:292.
81. Moore, W. E. C., and, L. V. Holdeman. 1974a. Human fecal flora: the normal flora of 20 Japanese-Hawaiians. Appl. Microbiol. 27:961979.
82. Moore, W. E. C., and, L. V. Holdeman. 1974b. Special problems associated with the isolation and identification of intestinal bacteria in fecal flora studies. Am. J. Clin. Nutr. 27:14501455.
83. Mueller, S.,, K. Saunier,, C. Hanisch,, E. Norin,, L. Alm,, T. Midtvedt,, A. Cresci,, S. Silvi,, C. Orpianesi,, M. C. Verdenelli,, T. Clavel,, C. Koebnick,, H.-J. F. Zunft,, J. Doré, and, M. Blaut. 2006. Differences in fecal microbiota in different European study populations in relation to age, gender, and country: a cross-sectional study. Appl. Environ. Microbiol. 72:10271033.
84. Müller, H. E. 1986. Occurrence and pathogenic role of Morganella-Proteus-Providencia group bacteria in human feces. J. Clin. Microbiol. 23:404405.
85. Neufeld, J. D.,, W. W. Mohn, and, V. de Lorenzo. 2006. Composition of microbial communities in hexachlorocyclohexane (HCH) contaminated soils from Spain revealed with a habitat-specific microarray. Environ. Microbiol. 8:126140.
86. Nicholson, J. K.,, E. Holmes, and, I. D. Wilson. 2005. Gut microorganisms, mammalian metabolism and personalized health care. Nat. Rev. Microbiol. 3:431438.
87. Noverr, M. C., and, G. B. Huffnagle. 2004. Does the microbiota regulate immune responses outside the gut? Trends Microbiol. 12:562568.
88. Noverr, M. C., and, G. B. Huffnagle. 2005. The “microflora hypothesis” of allergic diseases. Clin. Exp. Allergy 35:15111520.
89. Ott, S. J.,, M. Musfeldt,, D. F. Wenderoth,, J. Hampe,, O. Brant,, U. R. Folsch,, K. N. Timmis, and, S. Schreiber. 2004. Reduction in diversity of the colonic mucosa associated bacterial microflora in patients with active inflammatory bowel disease. Gut 53:685693.
90. Palmer, C.,, E. M. Bik,, D. B. Digiulio,, D. A. Relman, and, P. O. Brown. 2007. Development of the human infant intestinal microbiota. PLoS Biol. 5:e177.
91. Palmer, C.,, E. M. Bik,, M. B. Eisen,, P. B. Eckburg,, T. R. Sana,, P. K. Wolber,, D. A. Relman, and, P. O. Brown. 2006. Rapid quantitative profiling of complex microbial populations. Nucleic Acids Res. 34:e5.
92. Parracho, H. M. R. T.,, M. O. Bingham,, G. R. Gibson, and, A. L. McCartney. 2005. Differences between the gut microflora of children with autistic spectrum disorders and that of healthy children. J. Med. Microbiol. 54:98991.
93. Paster, B. J.,, S. K. Boches,, J. L. Galvin,, R. E. Ericson,, C. N. Lau,, V. A. Levanos,, A. Sahasrabudhe, and, F. E. Dewhirst. 2001. Bacterial diversity in human subgingival plaque. J. Bacteriol. 183:37703783.
94. Phillips, M. L. 2006. Interdomain interactions: dissecting animal-bacterial symbioses. BioScience 56:376381.
95. Podar, M.,, C. B. Abulencia,, M. Walcher,, D. Hutchison,, K. Zengler,, J. A. Garcia,, T. Holland,, D. Cotton,, L. Hauser, and, M. Keller. 2007. Targeted access to the genomes of low-abundance organisms in complex microbial communities. Appl. Environ. Microbiol. 73:32053214.
96. Raghunathan, A.,, H. R. Ferguson,, C. J. Bornarth,, W. Song,, M. Driscoll, and, R. S. Lasken. 2005. Genomic DNA amplification from a single bacterium. Appl. Environ. Microbiol. 71:33423347.
97. Rajilić-Stojanović, M. 2007. Ph.D. thesis. Diversity of the human gastrointestinal microbiota: novel perspectives from high throughput analyses, p. 216. Laboratory of Microbiology, Wageningen University, Wageningen, The Netherlands.
98. Rajilić-Stojanović, M.,, H. Smidt, and, W. M. de Vos. 2007. Diversity of the human gastrointestinal tract microbiota revisited. Environ. Microbiol. 9:21252136.
99. Rakoff-Nahoum, S.,, J. Paglino,, F. Eslami-Varzaneh,, S. Edberg, and, R. Medzhitov. 2004. Recognition of commensal microflora by toll-like receptors is required for intestinal homeostasis. Cell 118:229.
100. Ram, R. J.,, N. C. Verberkmoes,, M. P. Thelen,, G. W. Tyson,, B. J. Baker,, R. C. Blake,, M. Shah,, R. L. Hettich, and, J. F. Banfield. 2005. Community proteomics of a natural microbial biofilm. Science 308:19151920.
101. Ramotar, K.,, J. M. Conly,, H. Chubb, and, T. J. Louie. 1984. Production of menaquinones by intestinal anaerobes. J. Infect. Dis. 150:213218.
102. Rappé, M. S., and, S. J. Giovannoni. 2004. The uncultured microbial majority. Annu. Rev. Microbiol. 57:369394.
103. Rinttilä, T.,, A. Kassinen,, E. Malinen,, L. Krogius, and, A. Palva. 2004. Development of an extensive set of 16S rDNA-targeted primers for quantification of pathogenic and indigenous bacteria in faecal samples by real-time PCR. J. Appl. Microbiol. 97:11661177.
104. Roediger, W. E. W. 1980. Role of anaerobic bacteria in the metabolic welfare of the colonic mucosa in man. Gut 21:793798.
105. Sacchi, C. T.,, D. Alber,, P. Dull,, E. A. Mothershed,, A. M. Whitney,, G. A. Barnett,, T. Popovic, and, L. W. Mayer. 2005. High level of sequence diversity in the 16S rRNA genes of Haemophilus influenzae isolates is useful for molecular subtyping. J. Clin. Microbiol. 43:37343742.
106. Sakuma, K.,, M. Kitahara,, R. Kibe,, M. Sakamoto, and, Y. Benno. 2006. Clostridium glycyrrhizinilyticum sp. nov., a glycyrrhizin-hydrolysing bacterium isolated from human faeces. Microbiol. Immunol. 50:481485.
107. Salzman, N. H.,, H. de Jong,, Y. Paterson,, H. J. M. Harmsen,, G. W. Welling, and, N. A. Bos. 2002. Analysis of 16S libraries of mouse gastrointestinal microflora reveals a large new group of mouse intestinal bacteria. Microbiology 148:36513660.
108. Sartor, R. B. 2006. Mechanisms of disease: pathogenesis of Crohn’s disease and ulcerative colitis. Nat. Clin. Pract. Gastroenterol. Hepatol. 3:390407.
109. Scheppach, W., and, F. Weiler. 2004. The butyrate story: old wine in new bottles? Curr. Opin. Clin. Nutr. Metab. Care. 7:563567.
110. Seksik, P.,, L. Rigottier-Gois,, G. Gramet,, M. Sutren,, P. Pochart,, P. Marteau,, R. Jian, and, J. Doré. 2003. Alterations of the dominant faecal bacterial groups in patients with Crohn’s disease of the colon. Gut 52:237242.
111. Sepehri, S.,, R. Kotlowski,, C. N. Bernstein, and, D. O. Krause. 2007. Microbial diversity of inflamed and noninflamed gut biopsy tissues in inflammatory bowel disease. Inflamm. Bowel Dis. 13:675683.
112. Smoot, L. M.,, J. C. Smoot,, H. Smidt,, P. A. Noble,, M. Könneke,, Z. A. McMurry, and, D. A. Stahl. 2005. DNA microarrays as salivary diagnostic tools for characterizing the oral cavity’s microbial community. Adv. Dent. Res. 18:611.
113. Sokol, H.,, P. Seksik,, L. Rigottier-Gois,, C. Lay,, P. Lepage,, I. Podglajen,, P. Marteau, and, J. Doré. 2006. Specificities of the fecal microbiota in inflammatory bowel disease. Inflamm. Bowel Dis. 12:106111.
114. Song, Y.,, E. Kononen,, M. Rautio,, C. Liu,, A. Bryk,, E. Eerola, and, S. M. Finegold. 2006. Alistipes onderdonkii sp. nov. and Alistipes shahii sp. nov., of human origin. Int. J. Syst. Evol. Microbiol. 56:19851990.
115. Sonnenburg, J. L.,, C. T. Chen, and, J. I. Gordon. 2006. Genomic and metabolic studies of the impact of probiotics on a model gut symbiont and host. PLoS Biol. 12:e413.
116. Sood, A.,, V. Midha,, N. Sood,, A. S. Bhatia, and, G. Avasthi. 2003. Incidence and prevalence of ulcerative colitis in Punjab, North India. Gut 52:15871590.
117. Suau, A.,, V. Rochet,, A. Sghir,, G. Gramet,, S. Brewaeys,, M. Sutren,, L. Rigottier-Gois, and, J. Doré. 2001. Fusobacterium prausnitzii and related species represent a dominant group within the human fecal flora. Syst. Appl. Microbiol. 24:139145.
118. Tajima, K.,, S. Arai,, K. Ogata,, T. Nagamine,, H. Matsui,, M. Namakura,, R. I. Aminov, and, Y. Benno. 2000. Rumen bacterial community transition during adaptation to high-grain diet. Anaerobe 6:273284.
119. Tannock, G. W.,, K. Munro,, R. Bibiloni,, M. A. Simon,, P. Hargreaves,, P. Gopal,, H. Harmsen, and, G. Welling. 2004. Impact of consumption of oligosaccharide-containing biscuits on the fecal microbiota of humans. Appl. Environ. Microbiol. 70:21292136.
120. Tannock, G. W.,, K. Munro,, H. J. M. Harmsen,, G. W. Welling,, J. Smart, and, P. K. Gopal. 2000. Analysis of the fecal microflora of human subjects consuming a probiotic product containing Lacto-bacillus rhamnosus DR20. Appl. Environ. Microbiol. 66:25782588.
121. Thomsen, T. R.,, B. V. Kjellerup,, J. L. Nielsen,, P. Hugenholtz, and, P. H. Nielsen. 2002. In situ studies of the phylogeny and physiology of filamentous bacteria with attached growth. Environ. Microbiol. 4:383391.
122. Uchiyama, T.,, T. Abe,, T. Ikemura, and, K. Watanabe. 2005. Substrate-induced gene-expression screening of environmental metagenome libraries for isolation of catabolic genes. Nat. Biotechnol. 23:8893.
123. van der Waaij, D. 1989. The ecology of the human intestine and its consequences for overgrowth by pathogens such as Clostridium difficile. Ann. Rev. Microbiol. 43:6987.
124. van Tongeren, S. P.,, J. P. Slaets,, H. J. Harmsen, and, G. W. Welling. 2005. Fecal microbiota composition and frailty. Appl Environ Microbiol 71:64386442.
125. Vanhoutte, T.,, G. Huys,, E. Brandt, and, J. Swings. 2004. Temporal stability analysis of the microbiota in human feces by denaturing gradient gel electrophoresis using universal and group-specific 16S rRNA gene primers. FEMS Microbiol. Ecol. 48:437446.
126. Vaughan, E. E.,, H. G. H. J. Heilig,, K. Ben-Amor, and, W. M. de Vos. 2005. Diversity, vitality and activities of intestinal lactic acid bacteria and bifidobacteria assessed by molecular approaches. FEMS Microbiol. Rev. 29:477.
127. Venter, J. C.,, K. Remington,, J. F. Heidelberg,, A. L. Halpern,, D. Rusch,, J. A. Eisen,, D. Wu,, I. Paulsen,, K. E. Nelson,, W. Nelson,, D. E. Fouts,, S. Levy,, A. H. Knap,, M. W. Lomas,, K. Nealson,, O. White,, J. Peterson,, J. Hoffman,, R. Parsons,, H. Baden-Tillson,, C. Pfannkoch,, Y.- H. Rogers, and, H. O. Smith. 2004. Environmental genome shotgun sequencing of the Sargasso Sea. Science 304:6674.
128. Wagner, M.,, A. Loy,, M. Klein,, N. Lee,, N. B. Ramsing,, D. A. Stahl,, M. W. Friedrich, and, R. L. Jared. 2005. Functional marker genes for identification of sulfate-reducing prokaryotes. Methods. Enzymol. 397:469489.
129. Wagner, M.,, H. Smidt,, A. Loy, and, J. Zhou. 2007. Unravelling microbial communities with DNA-microarrays: challenges and future directions. Microb. Ecol. 53:498506.
130. Wang, M.,, S. Ahrne,, B. Jeppsson, and, G. Molin. 2005. Comparison of bacterial diversity along the human intestinal tract by direct cloning and sequencing of 16S rRNA genes. FEMS Microbiol. Ecol. 54:219.
131. Williamson, L. L.,, B. R. Borlee,, P. D. Schloss,, C. Guan,, H. K. Allen, and, J. Handelsman. 2005. Intracellular screen to identify metagenomic clones that induce or inhibit a quorum-sensing biosensor. Appl. Environ. Microbiol. 71:63356344.
132. Woese, C. R. 1987. Bacterial evolution. Microbiol. Rev. 51:221271.
133. Woese, C. R.,, O. Kandler, and, M. L. Wheelis. 1990. Towards a natural system of organisms: proposal for the domains Archaea, Bacteria, and Eucarya. Proc. Natl. Acad. Sci. USA 87:45764579.
134. Zengler, K.,, G. Toledo,, M. Rappé,, J. Elkins,, E. J. Mathur,, J. M. Short, and, M. Keller. 2002. Cultivating the uncultured. Proc. Natl. Acad. Sci. USA 99:1568115685.
135. Zhou, J. 2003. Microarrays for bacterial detection and microbial community analysis. Curr. Opin. Microbiol. 6:288.
136. Zoetendal, E. G.,, A. D. Akkermans,, W. M. Akkermans-van Vliet,, A. J. G. M. de Visser, and, W. M. de Vos. 2001. The host genotype affects the bacterial community in the human gastrointestinal tract. Microb. Ecol. Health Dis. 13:129134.
137. Zoetendal, E. G.,, A. D. Akkermans, and, W. M. de Vos. 1998. Temperature gradient gel electrophoresis analysis of 16S rRNA from human fecal samples reveals stable and host-specific communities of active bacteria. Appl. Environ. Microbiol. 64:38543859.
138. Zoetendal, E. G.,, C. M. Plugge,, A. D. L. Akkermans, and, W. M. de Vos. 2003. Victivallis vadensis gen. nov., sp. nov., a sugar-fermenting anaerobe from human faeces. Int. J. Syst. Evol. Microbiol. 53:211215.
139. Zwirglmaier, K.,, W. Ludwig, and, K. H. Schleifer. 2004. Recognition of individual genes in a single bacterial cell by fluorescence in situ hybridization—RING-FISH. Mol. Microbiol. 51:8996.

Tables

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TABLE 1

Approximate dimensions of the human GI tract and corresponding microbiota density ( ).

Citation: Rajilić-Stojanović M, de Vos W, Zoetendal E. 2008. The Human Intestinal Microbiota and Its Impact on Health, p 11-32. In Zengler K (ed), Accessing Uncultivated Microorganisms. ASM Press, Washington, DC. doi: 10.1128/9781555815509.ch2

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