The use of non-laboratory animals in gut microbiome studies

The gut microbiota plays an important role in host health and host-parasite interactions. The composition of the enteric microbiome is influenced by host characteristics; for instance age and genetics, as well as environmental factors such as diet. Much of the information gained on the gut microbiome has been achieved from human studies and laboratory models. However there is still much that can be learnt regarding the enteric microbiota, in particular the interactions that may occur with the parasitic helminth community of the gut. Non-laboratory animals have much to offer the scientific community in terms of how the natural gut microbiota is structured and influenced by interacting factors. Aside from representing greater genetic variation and a natural diet, wild animals exhibit intuitive behaviours. Furthermore non-laboratory species are more likely to possess natural helminth populations in the gut, which is of particular interest when investigating the effect of parasites on gut microbiota. Here, we review the literature to provide an overview of the current research on the microbiota of non-laboratory animals and the driving force behind the choice of certain animal species for study. We describe the variation found between wildlife species in terms of their microbial community and the underlying factors that cause this variation, the role of parasitism in shaping the microbiota and the insight that can be gained from a community ecology style analysis