The complex microbial community in the gastrointestinal (GI) tract consists of different
groups of microbes including bacteria, archaea, ciliate and flagellate protozoa, anaerobic
phycomycete fungi and bacteriophages. Bacteria are the most abundant and studied microbes
in this community. They are provided with substrates from the diet as well as components
deriving from the host such as mucopolysaccharides, mucins, epithelial cells and enzymes
[45]. With the introduction of molecular techniques to indentify the microbiota it has become
apparent that only a minority of the GI microbes have been isolated by culture based methods
[46] and consequently the knowledge we have today most likely needs to be revised in the
future (Figure 3).