Hong, J.; Xue, W.; Wang, T.

Microbial communities living in the same environment often display multiple alternative stable states, each characterized by a unique composition of species. Understanding the origin and determinants of microbiome multistability has broad implications in environments, human health and microbiome engineering. However, despite its conceptual importance, how multistability emerges in complex communities remains largely unknown. Here, we focused on the role of horizontal gene transfer (HGT), one important aspect mostly overlooked in previous theories, on the stability landscape of competing microbial populations. Combining theoretical derivation and numerical simulations, we demonstrated that in many scenarios increasing gene transfer rate could promote the emergence of many alternative stable states in complex microbiota. In metacommunities composed of multiple local patches, such multistability enabled by HGT allows the regional coexistence of diverse microbes which would otherwise outcompete each other. We further discussed the effects of different complicating factors on the role of HGT in mediating microbiome stability. Our results provide key insights for the predictive control and engineering of complex microbiota.