Engineering Microbiomes to Improve Plant and Animal Health

Animal and plant microbiomes encompass diverse microbial communities that colonize every accessible host tissue. These microbiomes enhance host functions, contributing to host health and fitness. A novel approach to improve animal and plant fitness is to artificially select upon microbiomes, thus engineering evolved microbiomes with specific effects on host fitness. We call this engineering approach host-mediated microbiome selection, because this method selects upon microbial communities indirectly through the host and leverages host traits that evolved to influence microbiomes. In essence, host phenotypes are used as probes to gauge and manipulate those microbiome functions that impact host fitness. To facilitate research on host-mediated microbiome engineering, we explain and compare the principal methods to impose artificial selection on microbiomes; discuss advantages and potential challenges of each method; offer a skeptical appraisal of each method in light of these potential challenges; and outline experimental strategies to optimize microbiome engineering. Finally, we develop a predictive framework for microbiome engineering that organizes research around principles of artificial selection, quantitative genetics, and microbial community-ecology.

TrendsThe microbiome's evolutionary potential is often ignored in medical and agricultural research.Evolutionary engineering protocols can shape microbiomes that improve animal and plant health.Microbiome engineering leverages host traits that evolved to control associated microbes.Microbiome engineering employs basic principles of quantitative genetics and community ecology.Optimized microbiome engineering could revolutionize research on agriculturally and medically important microbiomes.