Chapter 2 : The Gut Microbiome: Current Understanding and Future Perspectives

MyBook is a cheap paperback edition of the original book and will be sold at uniform, low price.

Ebook: Choose a downloadable PDF or ePub file. Chapter is a downloadable PDF file. File must be downloaded within 48 hours of purchase

Buy this Chapter
Digital (?) $15.00

Preview this chapter:
Zoom in

The Gut Microbiome: Current Understanding and Future Perspectives, Page 1 of 2

| /docserver/preview/fulltext/10.1128/9781555815479/9781555814052_Chap02-1.gif /docserver/preview/fulltext/10.1128/9781555815479/9781555814052_Chap02-2.gif


This chapter complements recent reviews by providing an overview of how the human gut microbiome develops, with a specific emphasis on the colon; some insights into life cycle assessment of gut microbiome structure-function relationships; and description of specific roles that foods might play in modulating these responses. The gastrointestinal (GI) microbiome in many carnivores is, in effect, in competition with the digestive and absorptive processes of the host animal, though the commensal microflora does serve to protect the host from pathogens, principally by colonization resistance. The chapter focuses on distal regions of the human GI tract. The greater abundance of staphylococci in the feces of breast-fed than in those of formula-fed infants may reflect a continuous inoculation of the GI tract of breast-fed infants. Phylogenetic studies employing cloning and sequencing of 16S rRNA genes amplified by PCR have greatly expanded one's knowledge of the diversity and composition of the adult gut microbiome. As noted by Peterson et al., advances in one's abilities to examine gut microbiomes at the RNA, protein, and metabolite levels of investigation will further the mechanistic understanding of microbiome function. In a human trial, Abell et al. noted that the inclusion of resistant starch in the diet significantly increased butyrate and acetate concentrations. The recent advances in genomics and metagenomics provide the opportunity to develop a better understanding of human gut microbiome structure-function relationships and their role in human health and disease, including modulating effects.

Citation: Yu Z, Morrison M. 2009. The Gut Microbiome: Current Understanding and Future Perspectives, p 19-40. In Jaykus L, Wang H, Schlesinger L (ed), Food-Borne Microbes. ASM Press, Washington, DC. doi: 10.1128/9781555815479.ch2

Key Concept Ranking

Bacteria and Archaea
Bacterial Genetics
Restriction Fragment Length Polymorphism
Denaturing Gradient Gel Electrophoresis
Highlighted Text: Show | Hide
Loading full text...

Full text loading...


1. Abell, G. C.,, C. M. Cooke,, C. N. Bennett,, M. A. Conlon, and, A. L. McOrist. 2008. Phylotypes related to Ruminococcus bromii are abundant in the large bowel of humans and increase in response to a diet high in resistant starch. FEMS Microbiol. Ecol. 63:505515.
2. Adlerberth, I.,, D. P. Strachan,, P. M. Matricardi,, S. Ahrne,, L. Orfei,, N. Aberg,, M. R. Perkin,, S. Tripodi,, B. Hesselmar,, R. Saalman,, A. R. Coates,, C. L. Bonanno,, V. Panetta, and, A. E. Wold. 2007. Gut microbiota and development of atopic eczema in 3 European birth cohorts. J. Allergy Clin. Immunol. 120:343350.
3. Ahrne, S.,, E. Lonnermark,, A. E. Wold,, N. Aberg,, B. Hesselmar,, R. Saalman,, I. L. Strannegard,, G. Molin, and, I. Adlerberth. 2005. Lactobacilli in the intestinal microbiota of Swedish infants. Microbes Infect. 7:12561262.
4. Andersson, A. F.,, M. Lindberg,, H. Jakobsson,, F. Backhed,, P. Nyren, and, L. Eng-strand. 2008. Comparative analysis of human gut microbiota by barcoded pyrosequencing. PLoS ONE 3:e2836.
5. 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.
6. 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.
7. Barclay, A. R.,, D. J. Morrison, and, L. T. Weaver. 2008. What is the role of the metabolic activity of the gut microbiota in inflammatory bowel disease? Probing for answers with stable isotopes. J. Pediatr. Gastroenterol. Nutr. 46:486495.
8. Barrangou, R.,, M. A. Azcarate-Peril,, T. Duong,, S. B. Conners,, R. M. Kelly, and, T. R. Klaenhammer. 2006. Global analysis of carbohydrate utilization by Lactobacillus acidophilus using cDNA microarrays. Proc. Natl. Acad. Sci. USA 103:38163821.
9. Belenguer, A.,, S. H. Duncan,, G. Holtrop,, S. E. Anderson,, G. E. Lobley, and, H. J. Flint. 2007. Impact of pH on lactate formation and utilization by human fecal microbial communities. Appl. Environ. Microbiol. 73:65266533.
10. Biavati, B.,, M. Vescovo,, S. Torriani, and, V. Bottazzi. 2000. Bifidobacteria: history, ecology, physiology and applications. Ann. Microbiol. 50:117131.
11. Bjorksten, B.,, E. Sepp,, K. Julge,, T. Voor, and, M. Mikelsaar. 2001. Allergy development and the intestinal microflora during the first year of life. J. Allergy Clin. Immunol. 108:516520.
12. Boehm, G.,, J. Jelinek,, B. Stahl,, K. van Laere,, J. Knol,, S. Fanaro,, G. Moro, and, V. Vigi. 2004. Prebiotics in infant formulas. J. Clin. Gastroenterol. 38:S76S79.
13. Boehm, G.,, M. Lidestri,, P. Casetta,, J. Jelinek,, F. Negretti,, B. Stahl, and, A. Marini. 2002. Supplementation of a bovine milk formula with an oligosaccharide mixture increases counts of faecal bifidobacteria in preterm infants. Arch. Dis. Child. Fet. Neonat. Ed. 86:F178F181.
14. Boehm, G., and, B. Stahl. 2003. Oligosaccharides, p. 203243. In T. Mattila-Sandholm (ed.), Functional Dairy Products. Woodhead Publishing Limited, Cambridge, United Kingdom.
15. Bomba, A.,, Z. Jonecova,, S. Gancarcikova, and, R. Nemcova. 2006. The gastrointestinal microbiota of farm animals, p. 381400. In A. C. Ouwehan and, E. E. Vaughan (ed.), Gastrointestinal Microbiology. Taylor & Francis Group, New York, NY.
16. Bourriaud, C.,, R. J. Robins,, L. Martin,, F. Kozlowski,, E. Tenailleau,, C. Cherbut, and, C. Michel. 2005. Lactate is mainly fermented to butyrate by human intestinal microfloras but inter-individual variation is evident. J. Appl. Microbiol. 99:201212.
17. Bron, P. A.,, D. Molenaar,, W. M. de Vos, and, M. Kleerebezem. 2006. DNA micro-array-based identification of bile-responsive genes in Lactobacillus plantarum. J. Appl. Microbiol. 100:728738.
18. Brunser, O.,, G. Figueroa,, M. Gotteland,, E. Haschke-Becher,, C. Magliola,, F. Rochat,, S. Cruchet,, R. Palframan,, G. Gibson,, F. Chauffard, and, F. Haschke. 2006. Effects of probiotic or prebiotic supplemented milk formulas on fecal microbiota composition of infants. Asia Pac. J. Clin. Nutr. 15:368376.
19. Bullen, C. L., and, A. T. Willis. 1971. Resistance of the breast-fed infant to gastroenteritis. Br. Med. J. 3:338343.
20. Bullen, J. J.,, H. J. Rogers, and, L. Leigh. 1972. Iron-binding proteins in milk and resistance to Escherichia coli infection in infants. Br. Med. J. 1:6975.
21. Chen, K.,, T. Baxter,, W. M. Muir,, M. A. Groenen, and, L. B. Schook. 2007. Genetic resources, genome mapping and evolutionary genomics of the pig (Sus scrofa). Int. J. Biol. Sci. 3:153165.
22. Chierici, R.,, S. Fanaro,, D. Saccomandi, and, V. Vigi. 2003. Advances in the modulation of the microbial ecology of the gut in early infancy. Acta Paediatr. 92:5663.
23. Clarke, J. M.,, D. L. Topping,, A. R. Bird,, G. P. Young, and, L. Cobiac. 2008. Effects of high-amylose maize starch and butyrylated high-amylose maize starch on azoxymethane-induced intestinal cancer in rats. Carcinogenesis 29:21902194.
24. de Vos, W. M.,, P. A. Bron, and, M. Kleerebezem. 2004. Postgenomics of lactic acid bacteria and other food-grade bacteria to discover gut functionality. Curr. Opin. Biotechnol. 15:8693.
25. Dicksved, J.,, J. Halfvarson,, M. Rosenquist,, G. Järnerot,, C. Tysk,, J. Apajalahti,, L. Eng-strand, and, J. K. Jansson. 2008. Molecular analysis of the gut microbiota of identical twins with Crohn’s disease. ISME J. 2:716727.
26. Dunbar, J.,, S. M. Barns,, L. O. Ticknor, and, C. R. Kuske. 2002. Empirical and theoretical bacterial diversity in four Arizona soils. Appl. Environ. Microbiol. 68:30353045.
27. Duncan, S. H.,, A. Barcenilla,, C. S. Stewart,, S. E. Pryde, and, H. J. Flint. 2002. Acetate utilization and butyryl coenzyme A (CoA): acetate-CoA transferase in butyrate-producing bacteria from the human large intestine. Appl. Environ. Microbiol. 68:51865190.
28. Duncan, S. H.,, G. Holtrop,, G. E. Lobley,, A. G. Calder,, C. S. Stewart, and, H. J. Flint. 2004. Contribution of acetate to butyrate formation by human faecal bacteria. Br. J. Nutr. 91:915923.
29. Duncan, S. H.,, P. Louis, and, H. J. Flint. 2007. Cultivable bacterial diversity from the human colon. Lett. Appl. Microbiol. 44:343350.
30. 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.
31. 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.
32. Edwards, C. A., and, A. M. Parrett. 2002. Intestinal flora during the first months of life: new perspectives. Br. J. Nutr. 88(Suppl. 1):S11S18.
33. Euler, A. R.,, D. K. Mitchell,, R. Kline, and, L. K. Pickering. 2005. Prebiotic effect of fructo-oligosaccharide supplemented term infant formula at two concentrations compared with unsupplemented formula and human milk. J. Pediatr. Gastroenterol. Nutr. 40:157164.
34. Falony, G.,, A. Vlachou,, K. Verbrugghe, and, L. De Vuyst. 2006. Cross-feeding between Bifidobacterium longum BB536 and acetate-converting, butyrate-producing colon bacteria during growth on oligofructose. Appl. Environ. Microbiol. 72:78357841.
35. Fanaro, S.,, R. Chierici,, P. Guenini, and, V. Vigi. 2003. Intestinal microflora in early infancy: composition and development. Acta Paediatr. 92:S48S55.
36. Favier, C. F.,, W. M. de Vos, and, A. D. L. Akkermans. 2003. Development of bacterial and bifidobacterial communities in feces of newborn babies. Anaerobe 9:219229.
37. 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.
38. Ferrer, M.,, O. V. Golyshina,, T. N. Chernikova,, A. N. Khachane,, D. Reyes-Duarte,, V. A. Santos,, C. Strompl,, K. Elborough,, G. Jarvis,, A. Neef,, M. M. Yakimov,, K. N. Timmis, and, P. N. Golyshin. 2005. Novel hydrolase diversity retrieved from a metagenome library of bovine rumen microflora. Environ. Microbiol. 7:19962010.
39. Fleischmann, R. D.,, M. D. Adams,, O. White,, R. A. Clayton,, E. F. Kirkness,, A. R. Kerlavage,, C. J. Bult,, J. F. Tomb,, B. A. Dougherty,, J. M. Merrick, et al. 1995. Whole-genome random sequencing and assembly of Haemophilus influenzae Rd. Science 269:496512.
40. Frank, D. N., and, N. R. Pace. 2008. Gastrointestinal microbiology enters the metagenomics era. Curr. Opin. Gastroenterol. 24:410.
41. Frank, D. N.,, A. L. St Amand,, R. A. Feldman,, E. C. Boedeker,, N. Harpaz, and, N. R. Pace. 2007. Molecular-phylogenetic characterization of microbial community imbalances in human inflammatory bowel diseases. Proc. Natl. Acad. Sci. USA 104:1378013785.
42. Gaskins, H. R.,, J. A. Croix,, N. Nakamura, and, G. M. Nava. 2008. Impact of the intestinal microbiota on the development of mucosal defense. Clin. Infect. Dis. 46(Suppl. 2):S80S86; discussion, S144S151.
43. George, M.,, K. E. Nord,, G. Ronquist,, G. Hedenstierna, and, L. Wiklund. 1996. Faecal microflora and urease activity during the first six months of infancy. Upsala J. Med. Sci. 101:233250.
44. Gilbert, J. A.,, D. Field,, Y. Huang,, R. Edwards,, W. Li,, P. Gilna, and, I. Joint. 2008. Detection of large numbers of novel sequences in the metatranscriptomes of complex marine microbial communities. PLoS ONE 3:e3042.
45. 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.
46. Gonzalez, R.,, E. S. Klaassens,, E. Malinen,, W. M. de Vos, and, E. E. Vaughan. 2008. Differential transcriptional response of Bifidobacterium longum to human milk, formula milk, and galactooligosaccharide. Appl. Environ. Microbiol. 74:46864694.
47. Guerin-Danan, C.,, C. Andrieux,, F. Popot,, A. Charpilienne,, P. Vaissade,, C. Gaudichon,, C. Pedone,, C. Bouley, and, O. Szylit. 1997. Pattern of metabolism and composition of the fecal microflora in infants 10 to 18 months old from day care centers. J. Pediatr. Gastroenterol. Nutr. 25:281289.
48. Gupta, A.,, G. P. Mathur, and, J. C. Sobti. 2002. World Health Assembly recommends exclusive breastfeeding for first six months. J. Indian Med. Assoc. 100:510511, 515.
49. Handelsman, J. 2004. Metagenomics: application of genomics to uncultured microorganisms. Microbiol. Mol. Biol. Rev. 68:669685.
50. Harmsen, H. J. M.,, A. C. M. Wildeboer-Veloo,, G. C. Raangs,, A. A. Wagendorp,, N. Klijn,, J. G. Bindels, and, G. W. Welling. 2000. Analysis of intestinal flora development in breast-fed and formula-fed infants by using molecular identification and detection methods. J. Pediatr. Gastroenterol. Nutr. 30:6167.
51. Hashizume, K.,, T. Tsukahara,, K. Yamada,, H. Koyama, and, K. Ushida. 2003. Megasphaera elsdenii JCM1772T normalizes hyperlactate production in the large intestine of fructooligosaccharidefed rats by stimulating butyrate production. J. Nutr. 133:31873190.
52. Hayashi, H.,, M. Sakamoto, and, Y. Benno. 2002. Phylogenetic analysis of the human gut microbiota using 16S rDNA clone libraries and strictly anaerobic culture-based methods. Microbiol. Immunol. 46:535548.
53. Hove, H.,, I. Nordgaard-Andersen, and, P. B. Mortensen. 1994. Faecal DL-lactate concentration in 100 gastrointestinal patients. Scand. J. Gastroenterol. 29:255259.
54. Hume, I. D. 1999. Marsupial Nutrition. Cambridge University Press, Cambridge, United Kingdom.
55. Janssen, R.,, K. A. Krogfelt,, S. A. Cawthraw,, W. van Pelt,, J. A. Wagenaar, and, R. J. Owen. 2008. Host-pathogen interactions in Campylobacter infections: the host perspective. Clin. Microbiol. Rev. 21:505518.
56. Khan, K. M., and, C. A. Edwards. 2005. In vitro fermentation characteristics of a mixture of raftilose and guar gum by human faecal bacteria. Eur. J. Nutr. 44:371376.
57. Klaassens, E. S.,, W. M. de Vos, and, E. E. Vaughan. 2007. Metaproteomics approach to study the functionality of the microbiota in the human infant gastrointestinal tract. Appl. Environ. Microbiol. 73:13881392.
58. Klaenhammer, T. R.,, R. Barrangou,, B. L. Buck,, M. A. Azcarate-Peril, and, E. Altermann. 2005. Genomic features of lactic acid bacteria effecting bioprocessing and health. FEMS Microbiol. Rev. 29:393409.
59. Kleessen, B.,, E. Bezirtzoglou, and, J. Matto. 2000. Culture-based knowledge on biodiversity, development and stability of human gastrointestinal microflora. Microb. Ecol. Health Dis. 12(Suppl. 2):5363.
60. Kleessen, B.,, H. Bunke,, K. Tovar,, J. Noack, and, G. Sawatzki. 1995. Influence of two infant formulas and human milk on the development of faecal flora in newborn infants. Acta Paediatr. 84:13471356.
61. Kles, K. A., and, E. B. Chang. 2006. Short-chain fatty acids impact on intestinal adaptation, inflammation, carcinoma, and failure. Gastroenterology 130:S100S105.
62. Knol, J.,, P. Scholtens,, C. Kafka,, J. Steen-bakkers,, S. Gro,, K. Helm,, M. Klarczyk,, H. Schöpfer,, H.-M. Böckler, and, J. Wells. 2005. Colon microflora in infants fed formula with galacto- and fructo-oligosaccharides: more like breast-fed infants. J. Pediatr. Gastroenterol. Nutr. 40:3642.
63. Koropatkin, N. M.,, E. C. Martens,, J. I. Gordon, and, T. J. Smith. 2008. Starch catabolism by a prominent human gut symbiont is directed by the recognition of amylose helices. Structure 16:11051115.
64. Kunz, C., and, S. Rudloff. 1993. Biological functions of oligosaccharides in human milk. Acta Paediatr. 82:903912.
65. Kurokawa, K.,, T. Itoh,, T. Kuwahara,, K. Oshima,, H. Toh,, A. Toyoda,, H. Takami,, H. Morita,, V. K. Sharma,, T. P. Srivastava,, T. D. Taylor,, H. Noguchi,, H. Mori,, Y. Ogura,, D. S. Ehrlich,, K. Itoh,, T. Takagi,, Y. Sakaki,, T. Hayashi, and, M. Hattori. 2007. Comparative metagenomics revealed commonly enriched gene sets in human gut microbiomes. DNA Res. 14:169181.
66. Lane, D. J.,, B. Pace,, G. J. Olsen,, D. A. Stahl,, M. L. Sogin, and, N. R. Pace. 1985. Rapid determination of 16S ribosomal RNA sequences for phylogenetic analyses. Proc. Natl. Acad. Sci. USA 82:69556959.
67. Larue, R.,, Z. Yu,, V. A. Parisi,, A. R. Egan, and, M. Morrison. 2005. Novel microbial diversity adherent to plant biomass in the herbivore gastrointestinal tract, as revealed by ribosomal intergenic spacer analysis and rrs gene sequencing. Environ. Microbiol. 7:530543.
68. Lentle, R. G.,, K. J. Stafford,, M. S. Kennedy, and, S. J. Haslett. 2002. Rheological properties of digesta suggest little radial or axial mixing in the forestomach of the tammar (Macropus eugenii) and the parma (Macropus parma) wallaby. Physiol. Biochem. Zool. 75:572582.
69. Ley, R. E.,, P. J. Turnbaugh,, S. Klein, and, J. I. Gordon. 2006. Microbial ecology: human gut microbes associated with obesity. Nature 444:10221023.
70. Liepke, C.,, K. Adermann,, M. Raida,, H. J. Mägert,, W. G. Forssmann, and, H. D. Zucht. 2002. Human milk provides peptides highly stimulating the growth of bifidobacteria. Eur. J. Biochem. 269:712718.
71. Lindberg, E.,, I. Adlerberth,, B. Hesselmar,, R. Saalman,, I. L. Strannegard,, N. Aberg, and, A. E. Wold. 2004. High rate of transfer of Staphylococcus aureus from parental skin to infant gut flora. J. Clin. Microbiol. 42:530534.
72. Loh, G.,, M. Eberhard,, R. M. Brunner,, U. Hennig,, S. Kuhla,, B. Kleessen, and, C. C. Metges. 2006. Inulin alters the intestinal micro-biota and short-chain fatty acid concentrations in growing pigs regardless of their basal diet. J. Nutr. 136:11981202.
73. Lonnerdal, B. 2003. Nutritional and physiologic significance of human milk proteins. Am. J. Clin. Nutr. 77:1537S1543S.
74. Louis, P.,, S. H. Duncan,, S. I. McCrae,, J. Millar,, M. S. Jackson, and, H. J. Flint. 2004. Restricted distribution of the butyrate kinase pathway among butyrate-producing bacteria from the human colon. J. Bacteriol. 186:20992106.
75. Lundequist, B.,, C. E. Nord, and, J. Winberg. 1985. The composition of the faecal microflora in breastfed and bottle fed infants from birth to eight weeks. Acta Paediatr. Scand. 74:4551.
76. Macfarlane, S., and, G. T. Macfarlane. 2003. Regulation of short-chain fatty acid production. Proc. Nutr. Soc. 62:6772.
77. Mackie, R. I. 2002. Mutualistic fermentative digestion in the gastrointestinal tract: diversity and evolution. Integr. Comp. Biol. 42:319326.
78. Mackie, R. I.,, A. Sghir, and, H. R. Gaskins. 1999. Developmental microbial ecology of the neonatal gastrointestinal tract. Am. J. Clin. Nutr. 69:1035S1045S.
79. Mackie, R. I.,, B. A. White, and, R. E. Isaacson. 1997. Gastrointestinal Microbiology. Chapman & Hall, New York, NY.
80. 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. Dore. 2006. Reduced diversity of faecal microbiota in Crohn’s disease revealed by a metagenomic approach. Gut 55:205211.
81. Mason, K. L.,, G. B. Huffnagle,, M. C. Noverr, and, J. Y. Kao. 2008. Overview of gut immunology. Adv. Exp. Med. Biol. 635:114.
82. 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.
83. Miller, S. J. 2004. Cellular and physiological effects of short-chain fatty acids. Mini Rev. Med. Chem. 4:839845.
84. 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. Dore, 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.
85. Newburg, D. S. 2000. Oligosaccharides in human milk and bacterial colonization. J. Pediatr. Gastroenterol. Nutr. 30:S8S17.
86. Ninonuevo, M. R.,, Y. Park,, H. Yin,, J. Zhang,, R. E. Ward,, B. H. Clowers,, J. B. German,, S. L. Freeman,, K. Killeen,, R. Grimm, and, C. B. Lebrilla. 2006. A strategy for annotating the human milk glycome. J. Agric. Food Chem. 54:74717480.
87. O’Keefe, S. J. 2008. Nutrition and colonic health: the critical role of the microbiota. Curr. Opin. Gastroenterol. 24:5158.
88. Orrhage, K., and, C. E. Nord. 1999. Factors controlling the bacterial colonization of the intestine in breastfed infants. Acta Paediatr. Suppl. 430:4757.
89. Ouwehand, A. C.,, S. Salminen,, T. Arvola,, T. Ruuska, and, E. Isolauri. 2004. Microbiota composition of the intestinal mucosa: association with fecal microbiota? Microbiol. Immunol. 48:497500.
90. Ouwehand, A. C., and, E. E. Vaughan. 2006. Gastrointestinal Microbiology. Taylor & Francis Group, New York, NY.
91. Palmer, C.,, E. M. Bik,, D. B. Digiulio,, D. A. Relman, and, P. O. Brown. 2007. Development of the human infant intestinal micro-biota. PLoS Biol. 5:e177.
92. Pang, X.,, X. Hua,, Q. Yang,, D. Ding,, C. Che,, L. Cui,, W. Jia,, P. Bucheli, and, L. Zhao. 2007. Inter-species transplantation of gut microbiota from human to pigs. ISME J. 1:156162.
93. Penders, J.,, C. Vink,, C. Driessen,, N. London,, C. Thijs, and, E. E. Stobberingh. 2005. Quantification of Bifidobacterium spp., Escherichia coli and Clostridium difficile in faecal samples of breast-fed and formula-fed infants by real-time PCR. FEMS Microbiol. Lett. 243:141147.
94. Perez, P. F.,, J. Doré,, M. Leclerc,, F. Levenez,, J. Benyacoub,, P. Serrant,, I. Segura-Roggero,, E. J. Schiffrin, and, A. Donnet-Hughes. 2007. Bacterial imprinting of the neonatal immune system: lessons from maternal cells? Pediatrics 119:e724e732.
95. Peterson, D. A.,, D. N. Frank,, N. R. Pace, and, J. I. Gordon. 2008. Metagenomic approaches for defining the pathogenesis of inflammatory bowel diseases. Cell Host Microbe 3:417427.
96. Pillinger, M. H., and, M. J. Blaser. 2007. The language used by Helicobacter pylori to regulate human cells. J. Infect. Dis. 196:69.
97. Pryde, S. E.,, S. H. Duncan,, G. L. Hold,, C. S. Stewart, and, H. J. Flint. 2002. The microbiology of butyrate formation in the human colon. FEMS Microbiol. Lett. 217:133139.
98. Puiman, P., and, B. Stoll. 2008. Animal models to study neonatal nutrition in humans. Curr. Opin. Clin. Nutr. Metabolic Care 11:601606.
99. Riedijk, M. A.,, B. Stoll,, S. Chacko,, H. Schierbeek,, A. L. Sunehag,, J. B. van Goudoever, and, D. G. Burrin. 2007. Methionine transmethylation and transsulfuration in the piglet gastrointestinal tract. Proc. Natl. Acad. Sci. USA 104:34083413.
100. Rinne, M. M.,, M. Gueimonde,, M. Kalliomäki,, U. Hoppu,, S. J. Salminen, and, E. Isolauri. 2005. Similar bifidogenic effects of prebiotic-supplemented partially hydrolyzed infant formula and breastfeeding on infant gut microbiota. FEMS Immunol. Med. Microbiol. 43:5965.
101. Roy, C. C.,, C. L. Kien,, L. Bouthillier, and, E. Levy. 2006. Short-chain fatty acids: ready for prime time? Nutr. Clin. Practice 21:351366.
102. Rueda, R.,, J. Maldonado,, E. Narbona, and, A. Gil. 1998. Neonatal dietary gangliosides. Early Hum. Dev. 53(Suppl.):S135S147.
103. Sakata, S.,, T. Tonooka,, S. Ishizeki,, M. Takada,, M. Sakamoto,, M. Fukuyama, and, Y. Benno. 2005. Culture-independent analysis of fecal microbiota in infants, with special reference to Bifidobacterium species. FEMS Microbiol. Lett. 243:417423.
104. Sakata, T.,, T. Kojima,, M. Fujieda,, M. Takahashi, and, T. Michibata. 2003. Influences of probiotic bacteria on organic acid production by pig caecal bacteria in vitro. Proc. Nutr. Soc. 62:7380.
105. Samuel, B. S., and, J. I. Gordon. 2006. A humanized gnotobiotic mouse model of host-archaeal-bacterial mutualism. Proc. Natl. Acad. Sci. USA 103:1001110016.
106. Satokari, R. M.,, E. E. Vaughan,, C. F. Favier,, J. Dore,, C. Edwards, and, W. M. de Vos. 2002. Diversity of Bifidobacterium and Lactobacillus spp. in breast-fed and formula-fed infants as assessed by 16S rDNA sequence differences. Microb. Ecol. Health Dis. 14:97105.
107. Saulnier, D. M.,, D. Molenaar,, W. M. de Vos,, G. R. Gibson, and, S. Kolida. 2007. Identification of prebiotic fructooligosaccharide metabolism in Lactobacillus plantarum WCFS1 through microarrays. Appl. Environ. Microbiol. 73:17531765.
108. Savage, D. C. 1977. Microbial ecology of the gastrointestinal tract. Annu. Rev. Microbiol. 31:107133.
109. Schell, M. A.,, M. Karmirantzou,, B. Snel,, D. Vilanova,, B. Berger,, G. Pessi,, M. C. Zwahlen,, F. Desiere,, P. Bork,, M. Delley,, R. D. Pridmore, and, F. Arigoni. 2002. The genome sequence of Bifidobacterium longum reflects its adaptation to the human gastrointestinal tract. Proc. Natl. Acad. Sci. USA 99:1442214427.
110. Scheppach, W., and, F. Weiler. 2004. The butyrate story: old wine in new bottles? Curr. Opin. Clin. Nutr. Metabolic Care 7:563567.
111. Seeliger, S.,, P. H. Janssen, and, B. Schink. 2002. Energetics and kinetics of lactate fermentation to acetate and propionate via methylmalonyl-CoA or acrylyl-CoA. FEMS Microbiol. Lett. 211:6570.
112. Sepp, E.,, K. Julge,, M. Vasar,, P. Naaber,, B. Bjorksten, and, M. Mikelsaar. 1997. Intestinal microflora of Estonian and Swedish infants. Acta Paediatr. 86:956961.
113. Sonnenburg, E. D.,, J. L. Sonnenburg,, J. K. Manchester,, E. E. Hansen,, H. C. Chiang, and, J. I. Gordon. 2006. A hybrid two-component system protein of a prominent human gut symbiont couples glycan sensing in vivo to carbohydrate metabolism. Proc. Natl. Acad. Sci. USA 103:88348839.
114. 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. 4:e413.
115. Sonnenburg, J. L.,, J. Xu,, D. D. Leip,, C. H. Chen,, B. P. Westover,, J. Weatherford,, J. D. Buhler, and, J. I. Gordon. 2005. Glycan foraging in vivo by an intestine-adapted bacterial symbiont. Science 307:19551959.
116. Spurlock, M. E., and, N. K. Gabler. 2008. The development of porcine models of obesity and the metabolic syndrome. J. Nutr. 138:397402.
117. Stark, P. L., and, A. Lee. 1982. The microbial ecology of the large bowel of breast-fed and formula-fed infants during the first year of life. J. Med. Microbiol. 15:189203.
118. Stevens, C. E., and, I. D. Hume. 1998. Contributions of microbes in vertebrate gastrointestinal tract to production and conservation of nutrients. Physiol. Rev. 78:393427.
119. Suau, A.,, R. Bonnet,, M. Sutren,, J.-J. Godon,, G. R. Gibson,, M. D. Collins, and, J. Dore. 1999. Direct analysis of genes encoding 16S rRNA from complex communities reveals many novel molecular species within the human gut. Appl. Environ. Microbiol. 65:47994807.
120. Tannock, G. W. 2002. Probiotics and prebiotics: where are we going? p. 139. In G. W. Tannock (ed.), Probiotics and Prebiotics. Caister Academic Press, Wymondham, United Kingdom.
121. Toden, S.,, A. R. Bird,, D. L. Topping, and, M. A. Conlon. 2007. High red meat diets induce greater numbers of colonic DNA doublestrand breaks than white meat in rats: attenuation by high-amylose maize starch. Carcinogenesis 28:23552362.
122. Topping, D. L., and, P. M. Clifton. 2001. Short-chain fatty acids and human colonic function: roles of resistant starch and nonstarch polysaccharides. Physiol. Rev. 81:10311064.
123. Turnbaugh, P. J.,, R. E. Ley,, M. Hamady,, C. M. Fraser-Liggett,, R. Knight, and, J. I. Gordon. 2007. The human microbiome project. Nature 449:804810.
124. Turnbaugh, P. J.,, R. E. Ley,, M. A. Mahowald,, V. Magrini,, E. R. Mardis, and, J. I. Gordon. 2006. An obesity-associated gut microbiome with increased capacity for energy harvest. Nature 444:10271031.
125. van den Broek, L. A.,, S. W. Hinz,, G. Beldman,, J. P. Vincken, and, A. G. Voragen. 2008. Bifidobacterium carbohydrases—their role in breakdown and synthesis of (potential) prebiotics. Mol. Nutr. Food Res. 52:146163.
126. van de Wiele, T.,, N. Boon,, S. Possemiers,, H. Jacobs, and, W. Verstraete. 2007. Inulin-type fructans of longer degree of polymerization exert more pronounced in vitro prebiotic effects. J. Appl. Microbiol. 102:452460.
127. Ventura, M.,, C. Canchaya,, G. F. Fitzgerald,, R. S. Gupta, and, D. van Sinderen. 2007. Genomics as a means to understand bacterial phylogeny and ecological adaptation: the case of bifidobacteria. Antonie van Leeuwenhoek 91:351372.
128. Walter, J.,, M. Mangold, and, G. W. Tannock. 2005. Construction, analysis, and β-glucanase screening of a bacterial artificial chromosome library from the large-bowel microbiota of mice. Appl. Environ. Microbiol. 71:23472354.
129. Wang, M.,, S. Ahrné,, 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. 54:219231.
130. Whitehead, K.,, J. Versalovic,, S. Roos, and, R. A. Britton. 2008. Genomic and genetic characterization of the bile stress response of probiotic Lactobacillus reuteri ATCC 55730. Appl. Environ. Microbiol. 74:18121819.
131. Whitlock, D. R. 2008. Human microbiome: hype or false modesty? Nature 454:690.
132. Wilson, M. 2005. The gastrointestinal tract and its indigenous microbiota, p. 251317. In M. Wilson (ed.), Microbial Inhabitants of Humans. Cambridge University Press, Cambridge, United Kingdom.
133. Wong, J. M.,, R. de Souza,, C. W. Kendall,, A. Emam, and, D. J. Jenkins. 2006. Colonic health: fermentation and short chain fatty acids. J. Clin. Gastroenterol. 40:235243.
134. Xu, J.,, M. K. Bjursell,, J. Himrod,, S. Deng,, L. K. Carmichael,, H. C. Chiang,, L. V. Hooper, and, J. I. Gordon. 2003. A genomic view of the human- Bacteroides thetaiotaomicron symbiosis. Science 299:20742076.
135. Xu, J., and, J. I. Gordon. 2003. Honor thy symbionts. Proc. Natl. Acad. Sci. USA 100:1045210459.
136. Yu, Z.,, M. Yu, and, M. Morrison. 2006. Improved serial analysis of V1 ribosomal sequence tags (SARST-V1) provides a rapid, comprehensive, sequence-based characterization of bacterial diversity and community composition. Environ. Microbiol. 8:603611.
137. Zoetendal, E. G.,, A. D. L. Akkermans,, W. M. Akkermans-van Vliet,, J. A. 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.
138. Zoetendal, E. G.,, B. Cheng,, S. Koike, and, R. I. Mackie. 2004. Molecular microbial ecology of the gastrointestinal tract: from phylogeny to function. Curr. Issues Intest. Microbiol. 5:3147.
139. Zoetendal, E. G.,, C. T. Collier,, S. Koike,, R. I. Mackie, and, H. R. Gaskins. 2004. Molecular ecological analysis of the gastrointestinal microbiota: a review. J. Nutr. 134:465472.


Generic image for table

Numerical abundance of major bacterial groups in infants

Citation: Yu Z, Morrison M. 2009. The Gut Microbiome: Current Understanding and Future Perspectives, p 19-40. In Jaykus L, Wang H, Schlesinger L (ed), Food-Borne Microbes. ASM Press, Washington, DC. doi: 10.1128/9781555815479.ch2
Generic image for table

Microbial genera and species isolated from feces of humans

Citation: Yu Z, Morrison M. 2009. The Gut Microbiome: Current Understanding and Future Perspectives, p 19-40. In Jaykus L, Wang H, Schlesinger L (ed), Food-Borne Microbes. ASM Press, Washington, DC. doi: 10.1128/9781555815479.ch2

This is a required field
Please enter a valid email address
Please check the format of the address you have entered.
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error