Understanding microbiomes through trait-based ecology

Abstract

Ecology is the study of the interactions amongst organisms and their environment1. In microbial ecology, a major goal is to understand how environmental microbiomes impact ecosystem health and function. This desire to mechanistically link micro and macro processes is increasingly highlighting the importance of functional ecology, which aims to develop an understanding of relationships using functional traits, as opposed to species names. A functional trait may be any morphological or physiological trait that influences the performance or fitness of an individual in a given environment, such as regeneration time, size, antibiotic production or motility2. Although it is not possible to measure a given trait for each individual within an environmental microbiome, community-level functional traits can be derived from the community metagenome either directly via shotgun sequencing or predictively (for bacteria) from 16S rRNA profiles3. In understanding environmental microbiomes, functional traits have unique properties that can be utilised to (1) compare microbiomes using an ecological framework, (2) understand processes governing community assembly, and (3) build predictive ecological models.