Metagenomic approaches are currently being used to decipher the genome of the 
microbiota (microbiome), and, in parallel, functional studies are being 
performed to analyze the effects of the microbiota on the host. Gnotobiological 
methods are an indispensable tool for studying the consequences of bacterial 
colonization. Animals used as models of human diseases can be maintained in 
sterile conditions (isolators used for germ-free rearing) and specifically 
colonized with defined microbes (including non-cultivable commensal bacteria). 
The effects of the germ-free state or the effects of colonization on disease 
initiation and maintenance can be observed in these models. Using this approach 
we demonstrated direct involvement of components of the microbiota in chronic 
intestinal inflammation and development of colonic neoplasia (i.e., using models 
of human inflammatory bowel disease and colorectal carcinoma). In contrast, a 
protective effect of microbiota colonization was demonstrated for the 
development of autoimmune diabetes in non-obese diabetic (NOD) mice. 
Interestingly, the development of atherosclerosis in germ-free apolipoprotein E 
(ApoE)-deficient mice fed by a standard low-cholesterol diet is accelerated 
compared with conventionally reared animals. Mucosal induction of tolerance to 
allergen Bet v1 was not influenced by the presence or absence of microbiota. 
Identification of components of the microbiota and elucidation of the molecular 
mechanisms of their action in inducing pathological changes or exerting 
beneficial, disease-protective activities could aid in our ability to influence 
the composition of the microbiota and to find bacterial strains and components 
(e.g., probiotics and prebiotics) whose administration may aid in disease 
prevention and treatment.