A trait-based framework to identify microbial keystone taxa for microbiome engineering

Defining simplified microbial consortia and harnessing their functional potential holds promise for microbe-based solutions in agriculture, biotechnology, and medicine. However, defining their optimal composition remains challenging, primarily due to the vast taxonomic and functional diversity of natural microbiomes. Implementing the “keystone taxa” concept into microbiome research may help to define simplified consortia and prioritize microorganisms that drive essential ecosystem functions. The idea was developed in the 1960s to describe organisms with disproportionate ecological influence. Despite its potential, a systematic workflow for the identification of microbial keystone taxa has remained elusive. Here, we propose a trait-based 8-component framework that characterizes the ecological significance of microbial keystone taxa, and an operational 4-step approach to recover “keystone taxa candidates” from complex omics data and propose strategies for their in vitro and in vivo empirical assessments. This approach may facilitate the rational design of simplified microbial consortia with enhanced functional performance in both applied and natural contexts.