How is the gut microbiome community assembled in wild rodents?

The bacterial gut microbiome has a profound impact on the biology of its host. But, how this microbiome is assembled and maintained, and the dynamics of changes in its composition, is unknown. Many factors may affect the microbiome's assembly - an animal's diet, its immune responses, and the bacteria an individual is exposed to its environment, which includes bacteria from other individuals with whom it interacts. But, the relative roles of these different factors is unknown.

The aim of this project is to investigate the relative importance of diet, immune responses, and bacterial exposure in assembling and maintaining the bacterial gut microbiome in wild rodents. The work will use a combination of field observation studies and controlled experiments where various factors pertaining to microbiome assembly will be manipulated

The gut microbiome is of enormous importance and research effort but, to date, this has almost exclusively been studied in laboratory rodents. Laboratory rodents have less diverse microbiomes than wild animals. Also, laboratory animals' microbiomes are artefactual - for example, which company has supplied the animals, and in which laboratories they are kept, are dominant factors affecting their microbiome's composition. The novelty of this proposed project is that (i) we will study the composition, assembly and dynamics of the microbiome of wild rodents and (ii) consider the relative role of different factors in controlling its assembly. This multifactorial approach has not been used before, which contributes to the project's novelty.

This work is timely because by studying wild systems it will contribute to validating (or not) microbiome research in laboratory animals, for which there is a pressing need. The work is also timely, building on Viney and Pocock's recent work on the immune function and microbiome of wild mice, which is further complemented by Hurst's expertise in wild rodent systems.