Studying the Mammalian Intestinal Microbiome Using Animal Models

The gastrointestinal (GI) tract of humans and animals is colonized by microorganisms immediately after birth. The composition of the GI tract microbiota undergoes remarkable alterations during early age, reaches a relative stable status in adulthood, and is driven by external factors such as habitual diet, location along the intestine, antibiotic therapy and maternal microbiota, and intrinsic factors such as host species and genotype. Whereas usually faecal samples are used for assessing the impact on the microbiota in human intervention studies, in vitro and animal models provide an easier way to collect many (invasive) samples, have multiple comparisons and regulating the genotype background. Animal models, and in particular mammalian models, provide an alternative way to study the in vivo responses to beneficial, commensal and pathogenic microorganisms in the GI tract, including studies that aim to see the impact of the host system as well. The main animals used to study the mammalian GI tract are rodents (mainly mice and rats) and pigs. Rodent and pig models, including gnotobiotic and humanized rodents and pigs and minipigs, have been extensively employed in gut microbiota studies, and especially the piglet model has been suggested as an appropriate model for human infant studies. With pig models, several intestinal sampling techniques can be applied in kinetic microbiota studies, including small intestinal segment perfusion and cannulation. In many cases, to test a certain treatment, a tiered approach consisting of complementary methods is employed, comprising in vitro, in vivo animal models, eventually leading towards human intervention studies.