Host control and species interactions jointly determine microbiome community structure

Abstract

The host microbiome can be considered as an ecological community where microbial species interact with each other in a highly complex and dynamic host environment. The host is under selective pressure to ensure the microbiome remains beneficial. Hosts can impose a range of ecological filters including host immune response that can influence the assembly and composition of the microbial community. How the host immune control and its interactions with the intrinsic within-microbiome community dynamics affect the assembly of the microbiome has been largely unexplored. We present a mathematical framework to elucidate the role of host immune control and its interaction with the balance of ecological interactions types within the microbiome community. We find that highly mutualistic microbial communities characteristic of high community population sizes are most susceptible to changes in immune control. Such communities can become invasion prone as host immune control strength is increased whereas communities prevalent with competitive interactions remain relatively stable in resisting invasion to changing host immune control. Our model reveals that the host immune control can interact in unexpected ways with a microbial community depending on the prevalent ecological interactions types for that community. We stress that understanding microbial community assembly and stability is incomplete without considering the role of host-control mechanisms on the microbial community.