Patterns and Scales in Gastrointestinal Microbial Ecology

Gastroenterology

Volumn 136, Issue 6, 2009, Pages 1989-2002

  Camp, J Gray ^a   Kanther, Michelle ^a   Semova, Ivana ^a   Rawls, John F ^a  

^a UNIVERSITY OF NORTH CAROLINA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; BIODIVERSITY; BIOGEOGRAPHY; ECOLOGY; ECOSYSTEM; ENERGY BALANCE; ENVIRONMENTAL FACTOR; GASTROINTESTINAL TRACT; HABITAT; HUMAN; INTESTINE FLORA; LIPID STORAGE; MICROBIAL COMMUNITY; MOLECULAR INTERACTION; NONHUMAN; PHYLOGENY; PRIORITY JOURNAL; SEQUENCE ANALYSIS; SIGNAL TRANSDUCTION;

EID: 65449128399     PISSN: 00165085     EISSN: None     Source Type: Journal    
DOI: 10.1053/j.gastro.2009.02.075     Document Type: Article

References (131)

1. Savage D.C. Microbial ecology of the gastrointestinal tract. Annu Rev Microbiol 31 (1977) 107-133
2. McFall-Ngai M. Are biologists in "future shock"?. Symbiosis integrates biology across domains. Nat Rev Microbiol 6 (2008) 789-792
3. Bäckhed F., Ley R.E., Sonnenburg J.L., et al. Host-bacterial mutualism in the human intestine. Science 307 (2005) 1915-1920
4. Wostmann B.S. Germfree and gnotobiotic models: background and applications (1996), CRC Press, Boca Raton, FL
5. Cheesman S.E., and Guillemin K. We know you are in there: conversing with the indigenous gut microbiota. Res Microbiol 158 (2007) 2-9
6. Kinross J.M., von Roon A.C., Holmes E., et al. The human gut microbiome: implications for future health care. Curr Gastroenterol Rep 10 (2008) 396-403
7. Lederberg J. Infectious history. Science 288 (2000) 287-293
8. Turnbaugh P.J., Ley R.E., Hamady M., et al. The human microbiome project. Nature 449 (2007) 804-810
9. Ley R.E., Turnbaugh P.J., Klein S., et al. Microbial ecology: human gut microbes associated with obesity. Nature 444 (2006) 1022-1023
10. Frank D.N., St Amand A.L., Feldman R.A., et al. Molecular-phylogenetic characterization of microbial community imbalances in human inflammatory bowel diseases. Proc Natl Acad Sci U S A 104 (2007) 13780-13785
11. Eckburg P.B., Bik E.M., Bernstein C.N., et al. Diversity of the human intestinal microbial flora. Science 308 (2005) 1635-1638
12. Bik E.M., Eckburg P.B., Gill S.R., et al. Molecular analysis of the bacterial microbiota in the human stomach. Proc Natl Acad Sci U S A 103 (2006) 732-737
13. Frank D.N., and Pace N.R. Gastrointestinal microbiology enters the metagenomics era. Curr Opin Gastroenterol 24 (2008) 4-10
14. Breitbart M., Hewson I., Felts B., et al. Metagenomic analyses of an uncultured viral community from human feces. J Bacteriol 185 (2003) 6220-6223
15. Dinsdale E.A., Edwards R.A., Hall D., et al. Functional metagenomic profiling of nine biomes. Nature 452 (2008) 629-632
16. Danovaro R., Dell'Anno A., Corinaldesi C., et al. Major viral impact on the functioning of benthic deep-sea ecosystems. Nature 454 (2008) 1084-1087
17. Samuel B.S., and Gordon J.I. A humanized gnotobiotic mouse model of host-archaeal-bacterial mutualism. Proc Natl Acad Sci U S A 103 (2006) 10011-10016
18. Samuel B.S., Hansen E.E., Manchester J.K., et al. Genomic and metabolic adaptations of Methanobrevibacter smithii to the human gut. Proc Natl Acad Sci U S A 104 (2007) 10643-10648
19. Conway de Macario E., and Macario A.J. Methanogenic archaea in health and disease: a novel paradigm of microbial pathogenesis. Int J Med Microbiol 299 (2009) 99-108
20. Scupham A.J., Presley L.L., Wei B., et al. Abundant and diverse fungal microbiota in the murine intestine. Appl Environ Microbiol 72 (2006) 793-801
21. Scanlan P.D., and Marchesi J.R. Micro-eukaryotic diversity of the human distal gut microbiota: qualitative assessment using culture-dependent and -independent analysis of faeces. ISME J 2 (2008) 1183-1193
22. Prosser J.I., Bohannan B.J., Curtis T.P., et al. The role of ecological theory in microbial ecology. Nat Rev Microbiol 5 (2007) 384-392
23. Little A.E., Robinson C.J., Peterson S.B., et al. Rules of engagement: interspecies interactions that regulate microbial communities. Annu Rev Microbiol 62 (2008) 375-401
24. Ley R.E., Peterson D.A., and Gordon J.I. Ecological and evolutionary forces shaping microbial diversity in the human intestine. Cell 124 (2006) 837-848
25. Dethlefsen L., McFall-Ngai M., and Relman D.A. An ecological and evolutionary perspective on human-microbe mutualism and disease. Nature 449 (2007) 811-818
26. Levin S.A. The problem of pattern and scale in ecology. Ecology 73 (1992) 1943-1967
27. Raes J., and Bork P. Molecular eco-systems biology: towards an understanding of community function. Nat Rev Microbiol 6 (2008) 693-699
28. Zengler K., Toledo G., Rappe M., et al. Cultivating the uncultured. Proc Natl Acad Sci U S A 99 (2002) 15681-15686
29. Ingham C.J., Sprenkels A., Bomer J., et al. The micro-Petri dish, a million-well growth chip for the culture and high-throughput screening of microorganisms. Proc Natl Acad Sci U S A 104 (2007) 18217-18222
30. Fox G.E., Magrum L.J., Balch W.E., et al. Classification of methanogenic bacteria by 16S ribosomal RNA characterization. Proc Natl Acad Sci U S A 74 (1977) 4537-4541
31. Lane D.J., Pace B., Olsen G.J., et al. Rapid determination of 16S ribosomal RNA sequences for phylogenetic analyses. Proc Natl Acad Sci U S A 82 (1985) 6955-6959
32. Gevers D., Cohan F.M., Lawrence J.G., et al. Opinion: re-evaluating prokaryotic species. Nat Rev Microbiol 3 (2005) 733-739
33. Willenbrock H., Hallin P.F., Wassenaar T.M., et al. Characterization of probiotic Escherichia coli isolates with a novel pan-genome microarray. Genome Biol 8 (2007) R267
34. Tettelin H., Masignani V., Cieslewicz M.J., et al. Genome analysis of multiple pathogenic isolates of Streptococcus agalactiae: implications for the microbial "pan-genome.". Proc Natl Acad Sci U S A 102 (2005) 13950-13955
35. Medini D., Donati C., Tettelin H., et al. The microbial pan-genome. Curr Opin Genet Dev 15 (2005) 589-594
36. Lozupone C.A., Hamady M., Cantarel B.L., et al. The convergence of carbohydrate active gene repertoires in human gut microbes. Proc Natl Acad Sci U S A 105 (2008) 15076-15081
37. Xu J., Mahowald M.A., Ley R.E., et al. Evolution of symbiotic bacteria in the distal human intestine. PLoS Biol 5 (2007) e156
38. Hughes J.B., Hellmann J.J., Ricketts T.H., et al. Counting the uncountable: statistical approaches to estimating microbial diversity. Appl Environ Microbiol 67 (2001) 4399-4406
39. Lozupone C.A., and Knight R. Species divergence and the measurement of microbial diversity. FEMS Microbiol Rev 32 (2008) 557-578
40. Dethlefsen L., Eckburg P.B., Bik E.M., et al. Assembly of the human intestinal microbiota. Trends Ecol Evol 21 (2006) 517-523
41. Zoetendal E.G., Rajilic-Stojanovic M., and de Vos W.M. High-throughput diversity and functionality analysis of the gastrointestinal tract microbiota. Gut 57 (2008) 1605-1615
42. Marsh T.L. Terminal restriction fragment length polymorphism (T-RFLP): an emerging method for characterizing diversity among homologous populations of amplification products. Curr Opin Microbiol 2 (1999) 323-327
43. Fisher M.M., and Triplett E.W. Automated approach for ribosomal intergenic spacer analysis of microbial diversity and its application to freshwater bacterial communities. Appl Environ Microbiol 65 (1999) 4630-4636
44. Muyzer G. DGGE/TGGE a method for identifying genes from natural ecosystems. Curr Opin Microbiol 2 (1999) 317-322
45. Rinttila T., Kassinen A., Malinen E., et al. 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 (2004) 1166-1177
46. Matsuki T., Watanabe K., Fujimoto J., et al. Use of 16S rRNA gene-targeted group-specific primers for real-time PCR analysis of predominant bacteria in human feces. Appl Environ Microbiol 70 (2004) 7220-7228
47. DeSantis T.Z., Brodie E.L., Moberg J.P., et al. High-density universal 16S rRNA microarray analysis reveals broader diversity than typical clone library when sampling the environment. Microb Ecol 53 (2007) 371-383
48. Harrington C.R., Lucchini S., Ridgway K.P., et al. A short-oligonucleotide microarray that allows improved detection of gastrointestinal tract microbial communities. BMC Microbiol 8 (2008) 195
49. Loy A., Lehner A., Lee N., et al. Oligonucleotide microarray for 16S rRNA gene-based detection of all recognized lineages of sulfate-reducing prokaryotes in the environment. Appl Environ Microbiol 68 (2002) 5064-5081
50. Dethlefsen L., Huse S., Sogin M.L., et al. The pervasive effects of an antibiotic on the human gut microbiota, as revealed by deep 16S rRNA sequencing. PLoS Biol 6 (2008) e280
51. Turnbaugh P.J., Hamady M., Yatsunenko T., et al. A core gut microbiome in obese and lean twins. Nature 457 (2009) 480-484
52. Scupham A.J., Jones J.A., and Wesley I.V. Comparison of DNA extraction methods for analysis of turkey cecal microbiota. J Appl Microbiol 102 (2007) 401-409
53. Watanabe K., Kodama Y., and Harayama S. Design and evaluation of PCR primers to amplify bacterial 16S ribosomal DNA fragments used for community fingerprinting. J Microbiol Methods 44 (2001) 253-262
54. Farrelly V., Rainey F.A., and Stackebrandt E. Effect of genome size and rrn gene copy number on PCR amplification of 16S rRNA genes from a mixture of bacterial species. Appl Environ Microbiol 61 (1995) 2798-2801
55. Sartor R.B. Microbial influences in inflammatory bowel diseases. Gastroenterology 134 (2008) 577-594
56. Sokol H., Lay C., Seksik P., et al. Analysis of bacterial bowel communities of IBD patients: what has it revealed?. Inflamm Bowel Dis 14 (2008) 858-867
57. DiBaise J.K., Zhang H., Crowell M.D., et al. Gut microbiota and its possible relationship with obesity. Mayo Clin Proc 83 (2008) 460-469
58. Medini D., Serruto D., Parkhill J., et al. Microbiology in the post-genomic era. Nat Rev Microbiol 6 (2008) 419-430
59. Turnbaugh P.J., and Gordon J.I. An invitation to the marriage of metagenomics and metabolomics. Cell 134 (2008) 708-713
60. Gill S.R., Pop M., Deboy R.T., et al. Metagenomic analysis of the human distal gut microbiome. Science 312 (2006) 1355-1359
61. Turnbaugh P.J., Ley R.E., Mahowald M.A., et al. An obesity-associated gut microbiome with increased capacity for energy harvest. Nature 444 (2006) 1027-1131
62. Turnbaugh P.J., Bäckhed F., Fulton L., et al. Diet-induced obesity is linked to marked but reversible alterations in the mouse distal gut microbiome. Cell Host Microbe 3 (2008) 213-223
63. Sonnenburg J.L., Xu J., Leip D.D., et al. Glycan foraging in vivo by an intestine-adapted bacterial symbiont. Science 307 (2005) 1955-1959
64. Sonnenburg J.L., Chen C.T., and Gordon J.I. Genomic and metabolic studies of the impact of probiotics on a model gut symbiont and host. PLoS Biol 4 (2006) e413
65. Reigstad C.S., Hultgren S.J., and Gordon J.I. Functional genomic studies of uropathogenic Escherichia coli and host urothelial cells when intracellular bacterial communities are assembled. J Biol Chem 282 (2007) 21259-21267
66. Martens E.C., Chiang H.C., and Gordon J.I. Mucosal glycan foraging enhances fitness and transmission of a saccharolytic human gut bacterial symbiont. Cell Host Microbe 4 (2008) 447-457
67. Bjursell M.K., Martens E.C., and Gordon J.I. Functional genomic and metabolic studies of the adaptations of a prominent adult human gut symbiont, Bacteroides thetaiotaomicron, to the suckling period. J Biol Chem 281 (2006) 36269-36279
68. Verberkmoes N.C., Russell A.L., Shah M., et al. Shotgun metaproteomics of the human distal gut microbiota. ISME J 3 (2009) 179-189
69. Nicholson J.K., Holmes E., and Wilson I.D. Gut microorganisms, mammalian metabolism and personalized health care. Nat Rev Microbiol 3 (2005) 431-438
70. Dumas M.E., Barton R.H., Toye A., et al. Metabolic profiling reveals a contribution of gut microbiota to fatty liver phenotype in insulin-resistant mice. Proc Natl Acad Sci U S A 103 (2006) 12511-12516
71. Claus S.P., Tsang T.M., Wang Y., et al. Systemic multicompartmental effects of the gut microbiome on mouse metabolic phenotypes. Mol Syst Biol 4 (2008) 219
72. Li M., Wang B., Zhang M., et al. Symbiotic gut microbes modulate human metabolic phenotypes. Proc Natl Acad Sci U S A 105 (2008) 2117-2122
73. Hansen S.K., Rainey P.B., Haagensen J.A., et al. Evolution of species interactions in a biofilm community. Nature 445 (2007) 533-536
74. Kim H.J., Boedicker J.Q., Choi J.W., et al. Defined spatial structure stabilizes a synthetic multispecies bacterial community. Proc Natl Acad Sci U S A 105 (2008) 18188-18193
75. Kerr B., Riley M.A., Feldman M.W., et al. Local dispersal promotes biodiversity in a real-life game of rock-paper-scissors. Nature 418 (2002) 171-174
76. Swidsinski A., Sydora B.C., Doerffel Y., et al. Viscosity gradient within the mucus layer determines the mucosal barrier function and the spatial organization of the intestinal microbiota. Inflamm Bowel Dis 13 (2007) 963-970
77. Behrens S., Losekann T., Pett-Ridge J., et al. Linking microbial phylogeny to metabolic activity at the single-cell level by using enhanced element labeling-catalyzed reporter deposition fluorescence in situ hybridization (EL-FISH) and NanoSIMS. Appl Environ Microbiol 74 (2008) 3143-3150
78. Jarrell K.F., and McBride M.J. The surprisingly diverse ways that prokaryotes move. Nat Rev Microbiol 6 (2008) 466-476
79. Keller L., and Surette M.G. Communication in bacteria: an ecological and evolutionary perspective. Nat Rev Microbiol 4 (2006) 249-258
80. Verstraeten N., Braeken K., Debkumari B., et al. Living on a surface: swarming and biofilm formation. Trends Microbiol 16 (2008) 496-506
81. West S.A., Griffin A.S., Gardner A., et al. Social evolution theory for microorganisms. Nat Rev Microbiol 4 (2006) 597-607
82. Dennis A., Kudo T., Kruidenier L., et al. The p50 subunit of NF-kappaB is critical for in vivo clearance of the noninvasive enteric pathogen Citrobacter rodentium. Infect Immun 76 (2008) 4978-4988
83. Rawls J.F., Mahowald M.A., Goodman A.L., et al. In vivo imaging and genetic analysis link bacterial motility and symbiosis in the zebrafish gut. Proc Natl Acad Sci U S A 104 (2007) 7622-7627
84. Balagadde F.K., Song H., Ozaki J., et al. A synthetic Escherichia coli predator-prey ecosystem. Mol Syst Biol 4 (2008) 187
85. Ley R.E., Bäckhed F., Turnbaugh P., et al. Obesity alters gut microbial ecology. Proc Natl Acad Sci U S A 102 (2005) 11070-11075
86. Bäckhed F., Ding H., Wang T., et al. The gut microbiota as an environmental factor that regulates fat storage. Proc Natl Acad Sci U S A 101 (2004) 15718-15723
87. Rawls J.F., Mahowald M.A., Ley R.E., et al. Reciprocal gut microbiota transplants from zebrafish and mice to germ-free recipients reveal host habitat selection. Cell 127 (2006) 423-433
88. Palmer C., Bik E.M., Digiulio D.B., et al. Development of the human infant intestinal microbiota. PLoS Biol 5 (2007) e177
89. Johansson M.E., Phillipson M., Petersson J., et al. The inner of the two Muc2 mucin-dependent mucus layers in colon is devoid of bacteria. Proc Natl Acad Sci U S A 105 (2008) 15064-15069
90. Meyer-Hoffert U., Hornef M.W., Henriques-Normark B., et al. Secreted enteric antimicrobial activity localises to the mucus surface layer. Gut 57 (2008) 764-771
91. Walker A.W., Duncan S.H., Harmsen H.J., et al. The species composition of the human intestinal microbiota differs between particle-associated and liquid phase communities. Environ Microbiol 10 (2008) 3275-3283
92. Molly K., Vande Woestyne M., and Verstraete W. Development of a 5-step multi-chamber reactor as a simulation of the human intestinal microbial ecosystem. Appl Microbiol Biotechnol 39 (1993) 254-258
93. Avery S.V. Microbial cell individuality and the underlying sources of heterogeneity. Nat Rev Microbiol 4 (2006) 577-587
94. Xu J., Bjursell M.K., Himrod J., et al. A genomic view of the human-Bacteroides thetaiotaomicron symbiosis. Science 299 (2003) 2074-2076
95. Coyne M.J., Reinap B., Lee M.M., et al. Human symbionts use a host-like pathway for surface fucosylation. Science 307 (2005) 1778-1781
96. Mazmanian S.K., Liu C.H., Tzianabos A.O., et al. An immunomodulatory molecule of symbiotic bacteria directs maturation of the host immune system. Cell 122 (2005) 107-118
97. Fujiya M., Musch M.W., Nakagawa Y., et al. The Bacillus subtilis quorum-sensing molecule CSF contributes to intestinal homeostasis via OCTN2, a host cell membrane transporter. Cell Host Microbe 1 (2007) 299-308
98. Ley R.E., Hamady M., Lozupone C., et al. Evolution of mammals and their gut microbes. Science 320 (2008) 1647-1651
99. Garrett W.S., Lord G.M., Punit S., et al. Communicable ulcerative colitis induced by T-bet deficiency in the innate immune system. Cell 131 (2007) 33-45
100. Sokol H., Pigneur B., Watterlot L., et al. Faecalibacterium prausnitzii is an anti-inflammatory commensal bacterium identified by gut microbiota analysis of Crohn disease patients. Proc Natl Acad Sci U S A 105 (2008) 16731-16736
101. Lupp C., Robertson M.L., Wickham M.E., et al. Host-mediated inflammation disrupts the intestinal microbiota and promotes the overgrowth of Enterobacteriaceae. Cell Host Microbe 2 (2007) 119-129
102. Kuehl C.J., Wood H.D., Marsh T.L., et al. Colonization of the cecal mucosa by Helicobacter hepaticus impacts the diversity of the indigenous microbiota. Infect Immun 73 (2005) 6952-6961
103. Green J.L., Bohannan B.J., and Whitaker R.J. Microbial biogeography: from taxonomy to traits. Science 320 (2008) 1039-1043
104. Jia W., Li H., Zhao L., et al. Gut microbiota: a potential new territory for drug targeting. Nat Rev Drug Discov 7 (2008) 123-129
105. Neish A.S. Microbes in gastrointestinal health and disease. Gastroenterology 136 (2009) 65-80
106. Baas-Becking L.G.M. Geobiologie of inleiding tot de milieukunde (1934), Vand Stockkum & Zoon
107. de Wit R., and Bouvier T. "Everything is everywhere, but, the environment selects"; what did Baas Becking and Beijerinck really say?. Environ Microbiol 8 (2006) 755-758
108. Penders J., Thijs C., Vink C., et al. Factors influencing the composition of the intestinal microbiota in early infancy. Pediatrics 118 (2006) 511-521
109. Hallstrom M., Eerola E., Vuento R., et al. Effects of mode of delivery and necrotising enterocolitis on the intestinal microflora in preterm infants. Eur J Clin Microbiol Infect Dis 23 (2004) 463-470
110. Gronlund M.M., Lehtonen O.P., Eerola E., et al. Fecal microflora in healthy infants born by different methods of delivery: permanent changes in intestinal flora after cesarean delivery. J Pediatr Gastroenterol Nutr 28 (1999) 19-25
111. Wen L., Ley R.E., Volchkov P.Y., et al. Innate immunity and intestinal microbiota in the development of type 1 diabetes. Nature 455 (2008) 1109-1113
112. Vaishnava S., Behrendt C.L., Ismail A.S., et al. Paneth cells directly sense gut commensals and maintain homeostasis at the intestinal host-microbial interface. Proc Natl Acad Sci U S A 105 (2008) 20858-20863
113. Blaut M., and Clavel T. Metabolic diversity of the intestinal microbiota: implications for health and disease. J Nutr 137 (2007) 751S-755S
114. Viswanathan V.K., Sharma R., and Hecht G. Microbes and their products-physiological effects upon mammalian mucosa. Adv Drug Deliv Rev 56 (2004) 727-762
115. Albiger B., Dahlberg S., Henriques-Normark B., et al. Role of the innate immune system in host defence against bacterial infections: focus on the Toll-like receptors. J Intern Med 261 (2007) 511-528
116. Bates J.M., Akerlund J., Mittge E., et al. Intestinal alkaline phosphatase detoxifies lipopolysaccharide and prevents inflammation in zebrafish in response to the gut microbiota. Cell Host Microbe 2 (2007) 371-382
117. Goldberg R.F., Austen Jr. W.G., Zhang X., et al. Intestinal alkaline phosphatase is a gut mucosal defense factor maintained by enteral nutrition. Proc Natl Acad Sci U S A 105 (2008) 3551-3556
118. Rakoff-Nahoum S., Paglino J., Eslami-Varzaneh F., et al. Recognition of commensal microflora by toll-like receptors is required for intestinal homeostasis. Cell 118 (2004) 229-241
119. Vijay-Kumar M., Sanders C.J., Taylor R.T., et al. Deletion of TLR5 results in spontaneous colitis in mice. J Clin Invest 117 (2007) 3909-3921
120. Neurath M.F., Pettersson S., Meyer zum Buschenfelde K.H., et al. Local administration of antisense phosphorothioate oligonucleotides to the p65 subunit of NF-kappa B abrogates established experimental colitis in mice. Nat Med 2 (1996) 998-1004
121. Greten F.R., Eckmann L., Greten T.F., et al. IKKbeta links inflammation and tumorigenesis in a mouse model of colitis-associated cancer. Cell 118 (2004) 285-296
122. Nenci A., Becker C., Wullaert A., et al. Epithelial NEMO links innate immunity to chronic intestinal inflammation. Nature 446 (2007) 557-561
123. Zaph C., Troy A.E., Taylor B.C., et al. Epithelial-cell-intrinsic IKK-beta expression regulates intestinal immune homeostasis. Nature 446 (2007) 552-556
124. Steinbrecher K.A., Harmel-Laws E., Sitcheran R., et al. Loss of epithelial RelA results in deregulated intestinal proliferative/apoptotic homeostasis and susceptibility to inflammation. J Immunol 180 (2008) 2588-2599
125. Kim S.C., Tonkonogy S.L., Karrasch T., et al. Dual-association of gnotobiotic Il-10-/- mice with 2 nonpathogenic commensal bacteria induces aggressive pancolitis. Inflamm Bowel Dis 13 (2007) 1457-1466
126. Hou B., Reizis B., and DeFranco A.L. Toll-like receptors activate innate and adaptive immunity by using dendritic cell-intrinsic and -extrinsic mechanisms. Immunity 29 (2008) 272-282
127. Hooper L.V., Midtvedt T., and Gordon J.I. How host-microbial interactions shape the nutrient environment of the mammalian intestine. Annu Rev Nutr 22 (2002) 283-307
128. Begley M., Gahan C.G., and Hill C. The interaction between bacteria and bile. FEMS Microbiol Rev 29 (2005) 625-651
129. Ridlon J.M., Kang D.J., and Hylemon P.B. Bile salt biotransformations by human intestinal bacteria. J Lipid Res 47 (2006) 241-259
130. Stevens C.E., and Hume I.D. Contributions of microbes in vertebrate gastrointestinal tract to production and conservation of nutrients. Physiol Rev 78 (1998) 393-427
131. Bäckhed F., Manchester J.K., Semenkovich C.F., et al. Mechanisms underlying the resistance to diet-induced obesity in germ-free mice. Proc Natl Acad Sci U S A 104 (2007) 979-984