Table 1 Advantages and disadvantages of different animal models commonly used for studying host-microbe interactions

• Transparent until adulthood allowing real-time visualization of fluorescently labeled microbes throughout the gut [44].

• GIT is homologous to that of mammals but not identical (reviewed in [45]).

• Chemical screens and forward genetic tests can be performed to investigate host genetic factors or signaling pathways regulated by microbes [46].

• Diet and living environment strongly differs from humans

• Relatively short generation time (3 to 4 months) with a progeny size of about 100 to 200 eggs/female [46].

• Aging differs strongly from humans

• 3 to 4 cm long as an adult allowing storage of a large number in laboratory facilities [46].

• Zebrafish and their natural pathogens exist at a temperature of 28°C, while most human-relevant pathogens are only infectious at 37°C [47].

• Genome fully sequenced (http://www.sanger.ac.uk/Projects/D_rerio/).

• Zebrafish do not have distinguishable lymph nodes, Peyer’s patches, or splenic germinal centers [48].

• Well characterized mutant strains [46].

• Gastrointestinal tract (GIT) is homologous to that of mammals, containing a liver, pancreas, gall bladder, and a linearly segmented intestinal tract with absorptive and secretory functions. The intestinal epithelium forms tight junctions and microvilli. Displays absorptive enterocytes, goblet cells, and enteroendocrine cells (reviewed in [45]).

• Numerous mouse specific disease models or genetically altered mice are available [49].

• Marked differences in the immune system [50]

• Well characterized model; genome fully sequenced (http://www.sanger.ac.uk/resources/mouse/genomes/) and virtually all mouse genes have human homologues.

• Marked differences in microbiota composition between mice and humans have been noted [51].

• Relatively small and thus can be easily maintained.

• Diet and living environment differs from human.

• Reproduction rather quick so that several generations can be observed in a relatively short period of time, generally a mouse can live 2 to 3 years.

• Mice present the same organs as humans but in different proportions

• A lot of rat-specific disease models or genetically altered rats are available (http://rgd.mcw.edu/wg/physiology).

• Diet and living environment differs from human.

• Genome fully sequenced (http://rgd.mcw.edu/).

• Relatively small and thus can be easily maintained.

• Reproduction rather quick so that several generations can be observed in a relatively short period of time,

• Generally a rat can live 2 to 3 years.

• Omnivore.

• Reproduction rather slow (4 months gestation), generally a pig can live 10 to 15 years.

• Physiology of digestion, digestate transit times and associated metabolic processes are very similar between humans and pigs (reviewed in [52]).

• Important in size and thus expensive and complicated to maintain in laboratory conditions.

• Digestive tract shares many anatomical and physiological traits with that of humans.

• Immune system similar to humans.

• Genome fully sequenced (http://www.sanger.ac.uk/resources/downloads/othervertebrates/pig.html).

• Conserved homology between human and pig genomes.