Alvaro Sanchez, Djordje Bajic, Juan Diaz-Colunga, Abigail Skwara, Jean C. C. Vila, Seppe Kuehn

Quantitatively and predictively linking the composition and function of microbial communities is a major aspiration of microbial ecology. It is also a critical step in the path toward engineering synthetic consortia and manipulating natural microbiomes. The functions of microbial communities are collective properties that emerge from a complex web of molecular interactions between individual cells, which in turn lead to population-level interactions among strains and species. Incorporating this complexity into predictive models has been highly challenging. A similar problem of predicting phenotype from genotype has been addressed for decades in the field of quantitative genetics, leading to advances in the fields of protein and molecular engineering. By analogy to the genotype-phenotype landscape, an ecological community-function (or structure-function) landscape could be defined that maps community composition and function. In this piece, we present an overview of our current understanding of these community landscapes, their uses, limitations, and open questions. We argue that exploiting the parallels between both landscapes could bring powerful predictive methodologies from evolution and genetics into ecology, providing a boost to our ability to engineer and optimize microbial consortia.