Role of Intestinal Microbiota in Ulcerative Colitis

Theoretical part
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2. The colonic environment
2.2. The luminal environment
The high content and the long transit time of nutrients in the colon allow a sufficient reproduction
rate and avoid wash out of the luminal bacteria; hence a high number of bacteria are able to
colonize the lumen (10 10 ‐ 10 11 CFU/ ml). These bacteria are either facultative or strict anaerobic
and live in mutual relationship with their host helping extract energy by digesting indigestible
polysaccharides (Holzapfel et al., 1998;Backhed et al., 2005). The range of indigestible dietary
carbohydrates that reaches the colon include polysaccharides from components of plant cell walls
(including cellulose, xylan, and pectin), as well as storage polysaccharides such as inulin and
resistant starch (Hooper et al., 2002). Recent metagenomic studies have revealed that the
microbiome in the human gut is one of the richest sources of carbohydrate active enzymes with at
least 81 families of glycoside‐hydrolases (GH) with endo‐ and exo‐activities (Gill et al.,
2006;Turnbaugh et al., 2010). Of these families, GH13 (20%), GH3 (11%), GH2 (9%), GH1 (7%), and
GH31 (5%) are the most abundant in the gut microbiome of human beings (Gill et al., 2006;Li et
al., 2009). The main saccharolytic species in the colon belong to the genera Bacteroides,
Bifidobacterium, Ruminococcus, Eubacterium, Lactobacillus, and Clostridium (Vernazza et al.,
2006).
Bacteroides, the most abundant genus in the colon (section 1.1), has shown to be able to degrade
and ferment a wide variety of plant polysaccharides (Hooper et al., 2002). A study by Tasse and
colleagues (2010) demonstrated that Bacteroides has genes coding for glycosidic enzymes such as
β‐glucanases, xylanases, galactanases, and amylases. Additionally, the study showed that some of
the genes coding for the carbohydrate active enzymes in Bacteroides were found in multiple
clusters and could be involved in carbohydrate degradation, transport and/or binding. The high
saccharolytic capacity of Bacteroides could partly explain why this genus is so abundant in the
colon.
Bifidobacterium is another dominant genus in the human colon (section 1.1). To this date,
nineteen genomes of strains from this genus have been completely sequenced. These include
strains of B. adolescentis, B. animalis subsp. lactis, B. angulatum, B. bifidum, B. breve, B. longum
subsp. longum, B. longum subsp. infantis, B. pseudocatenulatum, B. catenulatum, and B. gallicum
(Pokusaeva et al., 2011). Large numbers of the genes found in the Bifidobacterium genom have
shown to encode proteins which are involved in carbohydrate metabolism and transport, such as
GH, and sugar ABC transporters (Ventura et al., 2007;Ventura et al., 2010;Pokusaeva et al., 2011).