Juken Hong

eLife Assessment This manuscript offers valuable theoretical predictions on how horizontal gene transfer (HGT) can lead to alternative stable states in microbial communities. Using a modeling framework, solid theoretical evidence is provided to support the claimed role of HGT. However, given that the model has many degrees of freedom, a more comprehensive analysis of the role of different parameters could strengthen the study.

Abstract The balance between chromosomal and plasmid DNAs determines the genomic plasticity of prokaryotes. Natural selections, acting on the level of organisms or plasmids, shape the abundances of plasmid DNAs in prokaryotic genomes. Despite the importance of plasmids in health and engineering, there have been rare systematic attempts to quantitatively model and predict the determinants underlying the strength of different selection forces.

Abstract 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.