Role of Intestinal Microbiota in Ulcerative Colitis

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1. Firmicutes phylum 2. Bacteroidetes phylum 3. Akkermansia muciniphila 4. Prevotella spp. 5. Bacteroides spp. 6. Alistipes spp. 7. Clostridium coccoides group 8. Clostridium leptum subgroup 9. Desulfovibrio spp. 10. Roseburia spp. 11. Lactobacillus spp. 12. Bifidobacterium spp. 13. Bacteroides uniformis 14. Bacteroides vulgatus 15. Bacteroides fragilis group 16. Bacteroides thetaiotaomicron 17. Bacteroides distasonis 18. Faecalibacterium prausnitzii Figure 1. Principal component analysis of the quantitative PCR measurements using the first and second principal component (PC1and PC2). The sources of the communities are indicated by diamond for healthy subjects, open circles for UC patients in remission, and closed circles for UC patients in relapse. Numbers in the loading plot indicate the listed bacterial taxa used in this analysis. 18
Figure 2: Principal component analysis of the quantitative PCR measurements for Gram‐negative bacteria. The amount of variability accounted for by PC136.22% and PC2 22.20%. The sources of the communities are indicated by diamond for healthy subjects, open circles for UC patients in remission, and closed circles for UC patients in relapse. Numbers in the loading plot indicate the bacterial taxa listed in Figure 1. Individual (N/6) 6 4 2 0 Genus B. bifidum B. adolescentis B. catenulatum B. breve B. angulatum B. longum Figure 3: Prevalence of six selected Bifidobacterium species in the individual faecal samples from healthy controls (white), UC patients in remission (light grey) and UC patients in relapse (dark grey). B. catenulatum is both B. catenulatum and B. pseudocatenulatum 19
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Role of Intestinal Microbiota in Ul
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Role of Intestinal Microbiota in Ul
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Preface Preface This thesis present
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Summary Summary The microbiota of t
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Dansk sammendrag Dansk sammendrag M
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Introduction and objectives Introdu
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List of Manuscripts Not included in
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List of contents List of Centents P
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List of Centents Methodology append
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1. The intestinal environment Theor
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Theoretical part 5 1. The intestina
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2. The colonic environment Theoreti
Page 27 and 28: Theoretical part 9 2. The colonic e
Page 29 and 30: Table 1: The presence of glycoside
Page 31 and 32: Theoretical part Figure 3: The colo
Page 33 and 34: 3. Inflammatory Bowel disease Theor
Page 35 and 36: Theoretical part 17 3. Inflammatory
Page 37 and 38: Theoretical part 19 4. Modulation o
Page 43 and 44: Table 4: Clinical trials on the pre
Page 45 and 46: Theoretical part 5. Production of p
Page 51: Methodology part
Page 54 and 55: Methodology part 6. Methodology, co
Page 60 and 61: Introduction Methodology part 42 Pa
Page 62 and 63: Abstract Background Detailed knowle
Page 64 and 65: depending the level of disease acti
Page 66 and 67: in 1 x TAE at 60 °C for 16 h at 36
Page 68 and 69: Statistics PCA were generated by SA
Page 70 and 71: The PCA of the Gram‐positive bact
Page 72 and 73: layer of UC patients and found that
Page 74 and 75: Acknowledgements The authors thank
Page 76 and 77: Table 2 ‐ 16S rRNA gene and 16S
Page 80 and 81: Supplementary Figure S1. Dice clust
Page 82 and 83: Reference List 1. Ahmed S, Macfarla
Page 84 and 85: 32. Matsuki T, Watanabe K, Fujimoto
Page 87 and 88: Methodology part Paper 2 Fecal lact
Page 89 and 90: Fecal lactobacilli and bifidobacter
Page 91 and 92: Introduction The mucus layer lining
Page 93 and 94: efore enrolment and there was no si
Page 95 and 96: (Bio‐Rad Labs, Hercules, Californ
Page 97 and 98: Microbial community analysis using
Page 99 and 100: difference from the luminal microbi
Page 101 and 102: that C. coccoides group and C. lept
Page 103 and 104: Table 1 ‐ 16S rRNA gene of phylum
Page 105 and 106: Table 2 ‐ Preference of bacterial
Page 107 and 108: Figure 1. A) Schematic overview of
Page 109 and 110: A. B. Figure 3. Principal component
Page 111 and 112: 15. Fooks LJ, Gibson GR. (2002) In
Page 113 and 114: 47. Ouwehand AC, Suomalainen T, Tol
Page 115 and 116: Methodology part Paper 3 Paper 3 In
Page 117 and 118: APPLIED AND ENVIRONMENTAL MICROBIOL
Page 119 and 120: 8338 VIGSNÆS ET AL. APPL. ENVIRON.
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Methodology part Introduction The a
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Journal of Agricultural and Food Ch
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Methodology part Paper 5 Paper 5 Ma
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Appl Microbiol Biotechnol (2011) 90
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Methodology part Paper 6 Tailored e
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Process Biochemistry 46 (2011) 1039
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Table 1 List of enzymes. Enzyme Sou
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J. Holck et al. / Process Biochemis
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Intensity 50 0 C1 175.05 J. Holck e
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J. Holck et al. / Process Biochemis
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[29] Bauer S, Vasu P, Persson S, Mo
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Methodology part 150
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Methodology part 152 Appendix 1 hor
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Appendix 3 Methodology part Appendi
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Methodology part 156 Appendix 3
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7. Discussion and perspectives Disc
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Discussion and conclusion 161 7. Di
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References References Abreu,M.T., V
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References Derrien,M., Vaughan,E.E.
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References Haarman,M. and Knol,J. (
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References Lantz,P.G., Matsson,M.,
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References Matsuki,T., Watanabe,K.,
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References Pullan,R.D., Thomas,G.A.
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References Tannock,G.W. (2010). Ana
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National Food Institute Technical U
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Role of Intestinal Microbiota in Ulcerative Colitis

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