Identifying fundamental principles of evolutionary dynamics in multispecies microbiomes

About This Grant

PROJECT SUMMARY This research program will elucidate the causes and consequences of evolution in multispecies microbiomes, leveraging experimental evolution in synthetic systems. The human microbiome modulates key components of health and its disruption and has been linked to diseases including inflammatory bowel disease, allergies, and inflammatory skin conditions. Research on microbiomes is shifting from describing diversity to developing a framework of how stable microbiomes are assembled, and what mechanisms underlie shifts to dysbiosis. However, such efforts have mostly focused on the ecological forces that operate within microbiomes, and much less is known about the consequences of evolutionary processes. The work proposed here will shed light on the evolutionary dynamics within multispecies consortia, by quantifying the consequences of evolutionary processes, such as intraspecies strain diversification following rapid adaptation and horizontal gene transfer, on microbiome assembly and function. Here we propose an innovative strategy to study evolution in complex communities using synthetic consortia from fermented foods, including sourdough starter that the PI has already established as a model microbiome. This proposal combines existing genetic variation from a global collection of fermented food microbiomes and experimental evolution based on manipulations of community members. We use an integrative toolkit, including long-read sequencing, comparative genomics and transcriptomics, genetic screens, and model testing to link evolutionary processes to assembly and function. Fermented food microbiomes are a powerful model system: they are easily manipulated in the lab and exhibit dynamics representative of natural microbiomes (e.g. succession, species interactions, adaptation). The synthetic consortia we have developed contain many microbial species that are directly relevant to human health, including Levilactobacillus brevis and Limosilactobacillus reuteri which are considered probiotic species and may aid in the maintenance of a stable microbiome. More broadly, we will determine generalizable principles that are applicable to human gut, skin, and oral microbiomes.