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).