Distinguishing among evolutionary and ecological processes shaping microbiome dynamics

Evolution is defined as the change in allele frequency over time as a result of either neutral processes, such as genetic drift, or as an adaptive process in response to selection. In contrast, ecological dynamics describe changes in population densities, species distributions, species interactions, and/or relative abundances within communities, all of which can also be the result of either stochastic or deterministic processes. Although the distinction between these patterns has long held for plants and animals, microbial community dynamics can blur the line between ecological and evolutionary processes, especially as they can occur on very similar timescales. Despite the importance of differentiating changes occurring within a population or strain from those occurring among populations, many common methodologies used to study microbiomes are not able to differentiate among them. In this review, we summarize the forces known to generate genetic diversity in bacterial genomes and describe the approaches used to study bacterial evolution from simple to more complex systems. We then explore how current methodologies and conceptual understanding can be applied to both understand and differentiate between the ecological and evolutionary processes in microbial communities. By highlighting lessons from longitudinal microbiome studies and experimental evolution, we explore the unique opportunities afforded by newer sequencing approaches and better sequencing resolution. Throughout, we identify the unique and outstanding challenges in studying these processes in microbiome systems and emphasize the great benefits in doing so to move forward our ability to better predict and manipulate microbiomes.