Transmission ecology of the gut microbiota in wild mice

Gut microbiota forms an influential part of its host animal’s phenotype, but how variation in gut microbiota arises is poorly understood. Attempts to explain microbiota variation with traits of the host individual, such as physiology or genetics, have had limited success, and an emerging view is that microbiota is greatly shaped by processes operating between individuals, such as transmission of microbes among hosts. Parallel lines of research have shown that both transmission through social contacts and contacts with the natural environment can shape microbiota, but the relative importance of these transmission processes remains unclear. In this thesis, I use novel RFID-tracking technology and molecular microbiota profiling to study microbiota transmission in populations of wild wood mice. Combining methods from network theory and metacommunity theory I study how gut microbiota is transmitted through social contact networks among mice as well as through exposure to broader living environment and other sympatric species therein. I show that social contact networks strongly predict the microbiota composition independent of kinship and shared exposure to the same space and that transmission of microbes from the environment likewise shapes microbiota independently of social relationships, but far less so than social transmission. Further, these two transmission routes seem to transmit different sets of gut microbes, with environmental transmission being influential for aerotolerant bacteria while social networks functioning as a transmission pathway specifically for anaerobic microbes. Finally, I show that social contacts and space-sharing between individuals of different sympatric species can spread gut microbes across species boundaries within a mixed-species rodent community. The key findings are verified with alternative statistical frameworks and replicated in two separate study populations. These findings provide striking evidence for transmission processes in shaping the gut microbiota of wild mammals and emphasize the importance of considering contexts beyond individuals in explaining microbiota variation