Ecology and physiology of the intestinal tract

Current Topics in Microbiology and Immunology

Volumn 358, Issue , 2013, Pages 247-272

  Blaut, Michael ^a  

^a GERMAN INSTITUTE OF HUMAN NUTRITION   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

ALPHA GALACTOSIDASE; ALPHA GLUCOSIDASE; ALPHA MANNOSIDASE; AMYLASE; BETA FRUCTOFURANOSIDASE; BETA GALACTOSIDASE; BETA GLUCOSIDASE; BETA GLUCURONIDASE; BILE ACID; CARBOHYDRATE; CHONDROITIN SULFATE; ENDO 1,2 BETA XYLANASE; ENZYME; FUCOSE; GALACTOSE; GLUCURONIC ACID; GLYCOPROTEIN; GLYCOSIDASE; HYALURONIC ACID; ISOFLAVONE DERIVATIVE; LIGNAN DERIVATIVE; MALTOSE; MUCIN; N ACETYLGALACTOSAMINE; OLIGOSACCHARIDE; POLYPHENOL; POLYSACCHARIDE; RIBOSE; UNCLASSIFIED DRUG; XENOBIOTIC AGENT;

ACTINOBACTERIA; ARTICLE; ASCOMYCETES; BACTERIAL PHENOMENA AND FUNCTIONS; BACTERIUM CULTURE; BACTEROIDETES; CARBOHYDRATE DIET; COLON; COLORECTAL CANCER; CORE MICROBIOME; CROHN DISEASE; ECOLOGICAL SPECIALIZATION; ENZYME SUBSTRATE; EURYARCHAEOTA; FIRMICUTES; FUSOBACTERIA; HOST PATHOGEN INTERACTION; HUMAN; INFLAMMATORY BOWEL DISEASE; INTESTINE; INTESTINE FLORA; METAGENOMICS; MICROBIAL METABOLISM; NEPHROLITHIASIS; NONHUMAN; NUTRITION; PATHOGENESIS; PHYSICAL CHEMISTRY; PLANT METABOLISM; PRIORITY JOURNAL; PROTEIN METABOLISM; PROTEOBACTERIA; ULCERATIVE COLITIS; VERRUCOMICROBIA; ANIMAL; BACTERIUM; ECOSYSTEM; METABOLISM; METAGENOME; MICROBIOLOGY; REVIEW;

ANIMALS; BACTERIA; BACTERIAL PHYSIOLOGICAL PHENOMENA; ECOSYSTEM; HUMANS; INTESTINES; METAGENOME;

MLCS; MLOWN;

EID: 84880155188     PISSN: 0070217X     EISSN: None     Source Type: Book Series    
DOI: 10.1007/82_2011_192     Document Type: Article

References (98)

1. Adlercreutz H, Mazur W (1997) Phyto-oestrogens and Western diseases. Ann. Med. 29:95-120
2. Allison MJ, Dawson KA, Mayberry WR et al (1985) Oxalobacter formigenes gen. nov., sp. nov.: oxalate-degrading anaerobes that inhabit the gastrointestinal tract. Arch Microbiol 141:1-7
3. Alpert C, Scheel J, Engst W et al (2009) Adaptation of protein expression by Escherichia coli in the gastrointestinal tract of gnotobiotic mice. Environ Microbiol 11:751-761
4. Amann R, Springer N, Ludwig W et al (1991) Identification in situ and phylogeny of uncultured bacterial endosymbionts. Nature 351:161-164
5. Arts IC, Hollman PC (2005) Polyphenols and disease risk in epidemiologic studies. Am J Clin Nutr 81:317S-325S
6. Arumugam M, Raes J, Pelletier E et al (2011) Enterotypes of the human gut microbiome. Nature 473:174-180
7. Atkinson C, Berman S, Humbert O et al (2004) In vitro incubation of human feces with daidzein and antibiotics suggests interindividual differences in the bacteria responsible for equol production. J Nutr 134:596-599
8. Axelson M, Sjövall J, Gustafsson BE et al (1982) Origin of lignans in mammals and identification of a precursor from plants. Nature 298:659-660
9. Baughn AD, Malamy MH (2004) The strict anaerobe Bacteroides fragilis grows in and benefits from nanomolar concentrations of oxygen. Nature 427:441-444
10. Bik EM, Eckburg PB, Gill SR et al. (2006) Molecular analysis of the bacterial microbiota in the human stomach. In: Proceedings of National Academy of Science U S A 103:732-737
11. Blaut M, Collins MD, Welling GW et al (2002) Molecular biological methods for studying the gut microbiota: the EU human gut flora project. Br J Nutr 2:S203-S211
12. Blaut M, Braune A, Wunderlich S et al (2006) Mutagenicity of arbutin in mammalian cells after activation by human intestinal bacteria. Food Chem Toxicol 44:1940-1947
13. Bokkenheuser VD, Winter J, Finegold SM et al (1979) New markers for Eubacterium lentum. Appl Environ Microbiol 37:1001-1006
14. Bry L, Falk PG, Midtvedt T et al (1996) A model of host-microbial interactions in an open mammalian ecosystem. Science 273:1380-1383
15. Cheng Q, Hwa V, Salyers AA (1992) A locus that contributes to colonization of the intestinal tract by Bacteroides thetaiotaomicron contains a single regulatory gene (chuR) that links two polysaccharide utilization pathways. J Bacteriol 174:7185-7193
16. Cheng Q, Yu MC, Reeves AR et al (1995) Identification and characterization of a Bacteroides gene, csuF, which encodes an outer membrane protein that is essential for growth on chondroitin sulfate. J Bacteriol 177:3721-3727
17. Chiang YC, Pai WY, Chen CY et al (2008) Use of primers based on the heat shock protein genes hsp70, hsp40, and hsp10, for the detection of bovine mastitis pathogens Streptococcus agalactiae, Streptococcus uberis and Streptococcus bovis. Mol Cell Probes 22:262-266
18. Cho KH, Cho D, Wang GR et al (2001) New regulatory gene that contributes to control of Bacteroides thetaiotaomicron starch utilization genes. J Bacteriol 183:7198-7205
19. Clavel T, Henderson G, Alpert CA et al (2005) Intestinal bacterial communities that produce active estrogen-like compounds enterodiol and enterolactone in humans. Appl Environ Microbiol 71:6077-6085
20. Clavel T, Henderson G, Engst W et al (2006a) Phylogeny of human intestinal bacteria that activate the dietary lignan secoisolariciresinol diglucoside. FEMS Microbiol Ecol 55:471-478
21. Clavel T, Borrmann D, Braune A et al (2006b) Occurrence and activity of human intestinal bacteria involved in the conversion of dietary lignans. Anaerobe 12:140-147
22. Clavel T, Lippman R, Gavini F et al (2007) Clostridium saccharogumia sp. nov. and Lactonifactor longoviformis gen. nov., sp. nov., two novel human faecal bacteria involved in the conversion of the dietary phytoestrogen secoisolariciresinol diglucoside. Syst Appl Microbiol 30:16-26
23. Collado MC, Derrien M, Isolauri E et al (2007) Intestinal integrity and Akkermansia muciniphila, a mucin-degrading member of the intestinal microbiota present in infants, adults, and the elderly. Appl Environ Microbiol 73:7767-7770
24. Corfield AP, Wagner SA, Clamp JR et al (1992) Mucin degradation in the human colon: production of sialidase, sialate O-acetylesterase, N-acetylneuraminate lyase, arylesterase, and glycosulfatase activities by strains of fecal bacteria. Infect Immun 60:3971-3978
25. Cummings JH (1994) Anatomy and physiology of the human colon. In: ILSI Workshop on colonic microflora: nutrition and health, Barcelona, Spain
26. Cummings JH (1995) Short chain fatty acids. In: Gibson GR, Macfarlane GT (eds) Human colonic bacteria: role in nutrition physiology and pathology. CRC Press, Boca Raton, pp 101-130
27. Cummings JH, Pomare EW, Branch WJ et al (1987) Short chain fatty acids in human large intestine, portal, hepatic and venous blood. Gut 28:1221-1227
28. Deisinger PJ, Hill TS, English JC (1996) Human exposure to naturally occurring hydroquinone. J Toxicol Environ Health 47:31-46
29. Derrien M, Vaughan EE, Plugge CM et al (2004) Akkermansia muciniphila gen. nov., sp. nov., a human intestinal mucin-degrading bacterium. Int J Syst Evol Microbiol 54:1469-1476
30. Doré J, Sghir A, Hannequart-Gramet G et al (1998) Design and evaluation of a 16S rRNAtargeted oligonucleotide probe for specific detection and quantitation of human faecal Bacteroides populations. Syst Appl Microbiol 21:65-71
31. Eckburg PB, Bik EM, Bernstein CN et al (2005) Diversity of the human intestinal microbial flora. Science 308:1635-1638
32. Falk PG, Hooper LV, Midtvedt T et al (1998) Creating and maintaining the gastrointestinal ecosystem: what we know and need to know from gnotobiology. Microbiol Mol Biol Rev 62:1157-1170
33. Filipe MI (1979) Mucins in the human gastrointestinal epithelium: a review. Invest Cell Pathol 2:195-216
34. Finegold SM, Attebery HR, Sutter VL (1974) Effect of diet on human fecal flora: comparison of Japanese and American diets. Am J Clin Nutr 27:1456-1469
35. Finegold SM, Sutter VL, Mathisen GE (1983) Normal indigenous intestinal flora. In: Hentges DJ (ed) Human intestinal microflora in health and disease. Academic Press, New York, pp 3-31
36. Franks AH, Harmsen HJM, Raangs GC et al (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 64:3336-3345
37. Gibson GR (1999) Dietary modulation of the human gut microflora using the prebiotics oligofructose and inulin. J Nutr 129:1438S-1441S
38. Gibson SA, McFarlan C, Hay S et al (1989) Significance of microflora in proteolysis in the colon. Appl Environ Microbiol 55:679-683
39. Gibson GR, Beatty ER, Wang X et al (1995) Selective stimulation of bifidobacteria in the human colon by oligofructose and inulin. Gastroenterology 108:975-982
40. Gill SR, Pop M, Deboy RT et al (2006) Metagenomic analysis of the human distal gut microbiome. Science 312:1355-1359
41. Gniechwitz D, Brueckel B, Reichardt N et al (2007) Coffee dietary fiber contents and structural characteristics as influenced by coffee type and technological and brewing procedures. J Agric Food Chem 55:11027-11034
42. Hansson GC, Johansson ME (2010) The inner of the two Muc2 mucin-dependent mucus layers in colon is devoid of bacteria. Gut Microbes 1:51-54
43. Hespell RB, Smith CJ (1983) Utilization of nitrogen sources by gastrointestinal tract bacteria. In: Hentges DJ (ed) Human intestinal microflora in health and disease. Academic Press, New York, p 21
44. Hillman K, Whyte AL, Stewart CS (1993) Dissolved oxygen in the porcine gastrointestinal tract. Lett. Appl. Microbiol. 16:299-302
45. Holdeman LV, Moore WE (1972) Roll-tube techniques for anaerobic bacteria. Am J Clin Nutr 25:1314-1317
46. Hooper LV, Xu J, Falk PG et al. (1999) A molecular sensor that allows a gut commensal to control its nutrient foundation in a competitive ecosystem. In: In: Proceedings of National Academy of Science U S A 96:9833-9838
47. Hughes R, Magee EA, Bingham S (2000) Protein degradation in the large intestine: relevance to colorectal cancer. Curr Issues Intest Microbiol 1:51-58
48. Hungate RE (1950) The anaerobic mesophilic cellulolytic bacteria. Bacteriol Rev 14:1-49
49. Hwa V, Salyers AA (1992) Evidence for differential regulation of genes in the chondroitin sulfate utilization pathway of Bacteroides thetaiotaomicron. J Bacteriol 174:342-344
50. Joshi S, Agte V (1995) Digestibility of dietary fiber components in vegetarian men. Plant Foods Hum Nutr 48:39-44
51. Kline KA, Falker S, Dahlberg S et al (2009) Bacterial adhesins in host-microbe interactions. Cell Host Microbe 5:580-592
52. Kotarski SF, Linz J, Braun DM et al (1985) Analysis of outer membrane proteins which are associated with growth of Bacteroides thetaiotaomicron on chondroitin sulfate. J Bacteriol 163:1080-1086
53. Kumar R, Mukherjee M, Bhandari M et al (2002) Role of Oxalobacter formigenes in calcium oxalate stone disease: a study from North India. Eur Urol 41:318-322
54. Ley RE, Peterson DA, Gordon JI (2006a) Ecological and evolutionary forces shaping microbial diversity in the human intestine. Cell 124:837-848
55. Ley RE, Turnbaugh PJ, Klein S et al (2006b) Human gut microbes associated with obesity. Nature 444:1022-1023
56. Linn S, Chan T, Lipeski L et al (1983) Isolation and characterization of two chondroitin lyases from Bacteroides thetaiotaomicron. J Bacteriol 156:859-866
57. MacDonald IA, Jellett JF, Mahony DE et al (1979) Bile salt 3 alpha- and 12 alpha-hydroxysteroid dehydrogenases from Eubacterium lentum and related organisms. Appl Environ Microbiol 37:992-1000
58. Macfarlane GT, Cummings JH, Allison C (1986) Protein degradation by human intestinal bacteria. J Gen Microbiol 132:1647-1656
59. Martens EC, Chiang HC, Gordon JI (2008) Mucosal glycan foraging enhances fitness and transmission of a saccharolytic human gut bacterial symbiont. Cell Host Microbe 4:447-457
60. Maruo T, Sakamoto M, Ito C et al (2008) Adlercreutzia equolifaciens gen. nov., sp. nov., an equol-producing bacterium isolated from human faeces, and emended description of the genus Eggerthella. Int J Syst Evol Microbiol 58:1221-1227
61. Matthies A, Blaut M, Braune A (2009) Isolation of a human intestinal bacterium capable of daidzein and genistein conversion. Appl Environ Microbiol 75:1740-1744
62. McCann KS (2000) The diversity-stability debate. Nature 405:228-233
63. Mittal RD, Kumar R, Mittal B et al (2003) Stone composition, metabolic profile and the presence of the gut-inhabiting bacterium Oxalobacter formigenes as risk factors for renal stone formation. Med Princ Pract 12:208-213
64. Qin J, Li R, Raes J et al (2010) A human gut microbial gene catalogue established by metagenomic sequencing. Nature 464:59-65
65. Rajilic-Stojanovic M, Heilig HG, Molenaar D et al (2009) Development and application of the human intestinal tract chip, a phylogenetic microarray: analysis of universally conserved phylotypes in the abundant microbiota of young and elderly adults. Environ Microbiol 11:1736-1751
66. Reeves AR, Wang GR, Salyers AA (1997) Characterization of four outer membrane proteins that play a role in utilization of starch by Bacteroides thetaiotaomicron. J Bacteriol 179:643-649
67. Reichardt N, Gniechwitz D, Steinhart H et al (2009) Characterization of high molecular weight coffee fractions and their fermentation by human intestinal microbiota. Mol Nutr Food Res 53:287-299
68. Ridlon JM, Kang DJ, Hylemon PB (2006) Bile salt biotransformations by human intestinal bacteria. J Lipid Res 47:241-259
69. Round JL, Mazmanian SK (2009) The gut microbiota shapes intestinal immune responses during health and disease. Nat Rev Immunol 9:313-323
70. Sajilata MG, Singhal RS, Kulkarni PR (2006) Resistant starch -a review. Compr Rev Food Sci F 5:1-17
71. Salyers AA, Kotarski SF (1980) Induction of chondroitin sulfate lyase activity in Bacteroides thetaiotaomicron. J Bacteriol 143:781-788
72. Salyers AA, O'Brien M (1980) Cellular location of enzymes involved in chondroitin sulfate breakdown by Bacteroides thetaiotaomicron. J Bacteriol 143:772-780
73. Salyers AA, Pajeau M (1989) Competitiveness of different polysaccharide utilization mutants of Bacteroides thetaiotaomicron in the intestinal tracts of germfree mice. Appl Environ Microbiol 55:2572-2578
74. Salyers AA, West SE, Vercellotti JR et al (1977) Fermentation of mucins and plant polysaccharides by anaerobic bacteria from the human colon. Appl Environ Microbiol 34:529-533
75. Sartor RB (2006) Mechanisms of disease: pathogenesis of Crohn's disease and ulcerative colitis. Nat Clin Pract Gastroenterol Hepatol 3:390-407
76. Schoefer L, Mohan R, Braune A et al (2002) Anaerobic C-ring cleavage of genistein and daidzein by Eubacterium ramulus. FEMS Microbiol. Lett. 208:197-202
77. Setchell KD, Clerici C (2010) Equol: history, chemistry, and formation. J Nutr 140:1355S-1362S
78. Shipman JA, Cho KH, Siegel HA et al (1999) Physiological characterization of SusG, an outer membrane protein essential for starch utilization by Bacteroides thetaiotaomicron. J Bacteriol 181:7206-7211
79. Shipman JA, Berleman JE, Salyers AA (2000) Characterization of four outer membrane proteins involved in binding starch to the cell surface of Bacteroides thetaiotaomicron. J Bacteriol 182:5365-5372
80. Sidhu H, Schmidt ME, Cornelius JG et al (1999) Direct correlation between hyperoxaluria/oxalate stone disease and the absence of the gastrointestinal tract-dwelling bacterium Oxalobacter formigenes: possible prevention by gut recolonization or enzyme replacement therapy. J Am Soc Nephrol 10:S334-S340
81. Slavin JL, Brauer PM, Marlett JA (1981) Neutral detergent fiber, hemicellulose and cellulose digestibility in human subjects. J Nutr 111:287-297
82. Sokol H, Pigneur B, Watterlot L et al. (2008) Faecalibacterium prausnitzii is an antiinflammatory commensal bacterium identified by gut microbiota analysis of Crohn disease patients. In: Proceedings of National Academy of Science, U S A 105:16731-16736
83. Sokol H, Seksik P, Furet JP et al (2009) Low counts of Faecalibacterium prausnitzii in colitis microbiota. Inflamm Bowel Dis 15:1183-1189
84. Suau A, Bonnet R, Sutren M et al (1999) Direct analysis of genes encoding 16S rRNA from complex communities reveals many novel molecular species within the human gut. Appl Environ Microbiol 65:4799-4807
85. Suau A, Rochet V, Sghir A et al (2001) Fusobacterium prausnitzii and related species represent a dominant group within the human fecal flora. Syst Appl Microbiol 24:139-145
86. Tanaka H, Hashiba H, Kok J et al (2000) Bile salt hydrolase of Bifidobacterium longumbiochemical and genetic characterization. Appl Environ Microbiol 66:2502-2512
87. Troxel SA, Sidhu H, Kaul P et al (2003) Intestinal Oxalobacter formigenes colonization in calcium oxalate stone formers and its relation to urinary oxalate. J Endourol 17:173-176
88. Turnbaugh PJ, Ley RE, Mahowald MA et al (2006) An obesity-associated gut microbiome with increased capacity for energy harvest. Nature 444:1027-1031
89. Turnbaugh PJ, Hamady M, Yatsunenko T et al (2009) A core gut microbiome in obese and lean twins. Nature 457:480-484
90. Turnbaugh PJ, Quince C, Faith JJ et al. (2010) Organismal, genetic, and transcriptional variation in the deeply sequenced gut microbiomes of identical twins. In: Proceedings of National Academy of Science, U S A 107:7503-7508
91. Van Soest PJ (1984) Some physical characteristics of dietary fibres and their influence on the microbial ecology of the human colon. Proc Nutr Soc 43:25-33
92. Variyam EP, Hoskins LC (1981) Mucin degradation in human colon ecosystems: degradation of hog gastric mucin by fecal extracts and fecal cultures. Gastroenterology 81:751-758
93. Vervaeke IJ, Van Nevel CJ, Decuypere JA et al (1973) A comparison of two methods for obtaining anaerobic counts in different segments of the gastro-intestinal tract of piglets. J Appl Bacteriol 36:397-405
94. Wells JM, Rossi O, Meijerink M et al. (2011) Epithelial crosstalk at the microbiota-mucosal interface. In: Proceedings of National Academy of Science, U S A 1:4607-4614 (108 Supplementary)
95. Woese CR (1987) Bacterial evolution. Microbiol. Rev. 51:221-271
96. Wolin MJ, Miller TL (1983) Carbohydrate fermentation. In: Hentges DJ (ed) Human intestinal microflora in health and disease. Academic Press, New York, p 19
97. Woting A, Clavel T, Loh G et al (2010) Bacterial transformation of dietary lignans in gnotobiotic rats. FEMS Microbiol Ecol 72:507-514
98. Xu J, Bjursell MK, Himrod J et al (2003) A genomic view of the human Bacteroides thetaiotaomicron symbiosis. Science 299:2074-2076