STRAIN VARIATION IN MICROBIAL COMMUNITIES

Small genomic differences between closely related microbial strains are thought to play important roles in maintaining community resilience and in the evolution of new species. Multiple examples now exist for the impact of these variations on community outcome and its environment as in the cases of methicillin resistant Staphylococcus aureus (MRSA) and pathogenic Escherichia coli. Despite the importance of strain-level genomic variations and their prevalence in most microbial communities, very little is known about the scale and dynamics of these variations in natural environments.

Here I will discuss strain variation in natural microbial communities. Using new methods for the recovery of genomes from metagenomics data and an analysis of synthetic long reads we were able to thoroughly describe systems of strain variation in different environments. These include strain-specific phage predation during infant gut colonization, and also complex populations of dozens of species and strains in terrestrial sediments. Our results provide insights about the roles of deterministic and stochastic factors in determining the dynamics of strain populations.