Models of microbiome evolution incorporating environmental microbial selection

The environment plays a crucial role in shaping the microbial composition of hosts. Different environments harbor distinct microbial communities, leading to variation in the availability of different microbes to potential hosts. Over the past few decades, human activities have significantly altered the environment, resulting in a decline in microbial diversity. Currently, the impact of this environmentally-induced reduction in microbial diversity on environmental microbial communities, host-microbiome interactions, and their evolutionary implications remains unclear. In this paper, we simulated how environmental microbial selection can lead to decreasing microbial diversity, using a previously-developed selection model. Our results indicate that microbial communities are influenced by both environmental conditions and host preferences. The diversity of the microbiome carried by hosts is impacted by the environment, with stronger environmental microbial selection reducing microbial diversity in the hosts, while at the same time, facilitating the emergence of mutually beneficial symbioses between microorganisms and hosts. Environmental microbial selection (EMS) leads to the survival of highly fit microorganisms in the environment, while the fitnesses of hosts and microbes within hosts remain relatively unaffected by environmental microbial selection.