Role of Intestinal Microbiota in Ulcerative Colitis

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Theoretical part 10 2. The colonic environment As for Bacteroides, it has been shown that many of these genes are located in clusters (Schell et al., 2002;Ventura et al., 2007;Tasse et al., 2010;Pokusaeva et al., 2011). Genome sequencing of the different Bifidobacterium species has revealed that carbohydrate modifying enzymes can vary among species. Additionally, the affinity of the enzymes may vary depending on the length and complexity of the substrate (Warchol et al., 2002;Margolles and de los Reyes‐Gavilan, 2003;Janer et al., 2004). Table 1 lists some of the GH found in Bifidobacterium spp. Most of the biochemical characterized GH from Bifidobacterium spp. have shown to be active towards oligosaccharides, but only some GH are active towards polysaccharides (Van Den Broek and Voragen, 2008). Van Laere and colleagues (2000) studied the ability of four Bifidobacterium species (B. breve, B. longum, B. infantis and B. adolescentis) to ferment plant polysaccharides and their corresponding oligosaccharides in vitro. The results showed that the ability to ferment plant cell wall derived polysaccharides varied depending on Bifidobacterium species, but most of the species were able to ferment oligosaccharides. B. breve could ferment arabinogalactan, but not arabinan and arabinoxylan. This was in line with results from genome sequencing that has revealed the absence of arabinan‐ and arabinoxylan degrading enzymes in B. breve (Table 1). B. infantis was not able to ferment any of the polysaccharides even though genome sequencing has revealed that it may contain α‐L‐arabinofuranosidase (Table 1). Additionally, B. infantis was only able to utilize arabino‐galactooligosaccharides. These results could indicate that the α‐L‐ arabinofuranosidase found in B. infantis has a low affinity for plant polysaccharides but specificity for certain oligosaccharides. B. longum was able to utilize arabinogalactan, arabinan, and arabinoxylan. This is in agreement with previous work by Gueimonde et al. (2007), which showed that α‐L‐arabinofuranosidase activity in B. longum could be induced by arabinose‐ and/or xylose‐ containing polymers and/or their related oligosaccharides. Genome sequencing of B. longum has revealed that more than 8% of the genome is related to the catabolism of oligo‐ and polysaccharides. Among these genes, many were predicted to encode proteins involved in catalyzing the degradation of arabinose‐containing saccharides such as intra‐ and extracellular α‐L‐ arabinofuranosidases (Schell et al., 2002). This provides B. longum with a competitive advantage in the utilization of different substrates in the gut (Van Den Broek and Voragen, 2008).
Table 1: The presence of glycoside‐hydrolases in bifidobacteria. Catalyze reaction Bifidobacterium Species* Glycoside hydrolase family Glycoside hydrolase (GH) Hydrolysis of terminal, non‐reducing 2,1‐ B. animalis subsp. lactis GH32 Fructan β‐(2,1)‐fructosidase linked β‐D‐fructofuranose residues in B. longum subsp. longum (EC 3.2.1.153) fructans. Hydrolysis of terminal non‐reducing 1,3‐ or 1,5‐ B. adolescentis B. animalis subsp. lactis GH3, GH43, GH51 α‐L‐arabinofuranosidase linked α‐L‐arabinofuranoside residues in B. longum subsp. longum (EC 3.2.1.55) arabinan, arabinoxylan and arabinogalactan. B. adolescentis B. longum subsp. infantis Hydrolysis of (1→4)‐β‐D‐galactosidic linkages B. longum subsp. longum GH53 Endo‐β‐(1,4)‐galactanase in arabinogalactans. B. breve (EC 3.2.1.89) Theoretical part Hydrolysis of (1→4)‐β‐D‐xylosidic linkages in B. bifidum B. animalis subsp. lactis GH5, GH8, GH43 Endo‐β‐(1,4)‐xylanase xylans. B. longum subsp. longum (EC 3.2.1.8) 11 B. adolescentis B. longum subsp. infantis Hydrolysis of (1→6)‐α‐D‐glucosidic linkages in B. bifidum B. animalis subsp. lactis GH13, GH31 Oligo‐α‐(1,6)‐glucosidase some oligosaccharides produced from starch B. longum subsp. longum (EC 3.2.1.10) 2. The colonic environment and glycogen. Hydrolysis of β‐D‐glucose units from the non‐ B. adolescentis B. longum subsp. longum GH3, GH5 Glucan‐β‐(1,3)‐glucosidase reducing ends of (1→3)‐β‐D‐glucans. B. longum subsp. infantis (EC 3.2.1.58) Hydrolysis of (1→6)‐α‐D‐glucosidic linkages in B. animalis subsp. lactis GH13 Pullulanase pullulan, amylopectin and glycogen. B. longum subsp. longum (EC 3.2.1.41) B. dentium B. adolescentis Data is based on database search (http://www.uniprot.org/uniprot and http://www.cazy.org, 2011‐09‐25) *All bifidobacterial species listed have been detected in human feces (Turroni et al., 2009;Tannock, 2010).
Page 1: Role of Intestinal Microbiota in Ul
Page 4 and 5: Role of Intestinal Microbiota in Ul
Page 6 and 7: Preface Preface This thesis present
Page 8 and 9: Summary Summary The microbiota of t
Page 10 and 11: Dansk sammendrag Dansk sammendrag M
Page 12 and 13: Introduction and objectives Introdu
Page 14 and 15: List of Manuscripts Not included in
Page 16 and 17: List of contents List of Centents P
Page 18 and 19: List of Centents Methodology append
Page 21 and 22: 1. The intestinal environment Theor
Page 23 and 24: Theoretical part 5 1. The intestina
Page 25 and 26: 2. The colonic environment Theoreti
Page 27: Theoretical part 9 2. The colonic e
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
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1. Firmicutes phylum 2. Bacteroidet
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Supplementary Figure S1. Dice clust
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Reference List 1. Ahmed S, Macfarla
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32. Matsuki T, Watanabe K, Fujimoto
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Methodology part Paper 2 Fecal lact
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Fecal lactobacilli and bifidobacter
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Introduction The mucus layer lining
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efore enrolment and there was no si
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(Bio‐Rad Labs, Hercules, Californ
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Microbial community analysis using
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difference from the luminal microbi
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that C. coccoides group and C. lept
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Table 1 ‐ 16S rRNA gene of phylum
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Table 2 ‐ Preference of bacterial
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Figure 1. A) Schematic overview of
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A. B. Figure 3. Principal component
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15. Fooks LJ, Gibson GR. (2002) In
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47. Ouwehand AC, Suomalainen T, Tol
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Methodology part Paper 3 Paper 3 In
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APPLIED AND ENVIRONMENTAL MICROBIOL
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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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