Table 1.

In vitro and in vivo models of the human gut microbiota and their potentials and limitations

Models	Description	Main use	Limitations	References
In vitro
Static batch system	Fresh feces or colonic contents suspended in buffer solution	Short-term metabolic and enzymatic studies	Rapid change in ecosystem composition	7
Semicontinuous batch system	Chemostat culture system of semicontinuous flow Inoculated with defined bacteria, feces, or colonic content	Long-term studies on metabolic, ecologic, and dietary fermentation	Host factors are ignored Stability of ecosystem is assumed	7
Continuous batch system	Chemostat culture system of continuous flow Inoculated with defined bacteria, feces, or colonic content	Long-term studies on metabolic, ecologic, and dietary features of GI microbiota	Host factors are ignored Complex system to set up Stability of ecosystem is assumed	7,105,106
In vivo
Laboratory animals	Fresh feces or colonic contents from conventional microbiota animals	Metabolic, ecological, and preclinical studies	Differences between animals and humans gut microbiota composition	7,109,112
Gnobiotic animals	Germ-free laboratory animals colonized with defined organisms or transferred microbiota from a laboratory animal or a human volunteer	Host-bacterial and bacterial-bacterial interaction studies	Alteration of bacterial interactions	7,10,49
Human volunteers	Fresh feces or colonic contents from human volunteers	Metabolic, ecological, chemical, and clinical studies	Ethical issues Relevance of feces/colonic contents to represent the overall GI microbiota	7,36,42

Abbreviation: GI, gastrointestinal.