Adaptation in Real Time:
Evolution in Microbiomes
The gut microbiome is a amazing system to study interplay between evolutionary and ecological dymanic of complex microbial communities.
Microbiomes are highly complex ecosystems that exhibit rapid eco-evolutionary dynamics on human timescales. These attributes make them amazing model systems for the study of adaptation and evolutionary ecology. Additionally, evolutionary and ecological research in microbiomes has diverse applications, such as developing human gut microbiota therapeutics. Petrov Lab members who study evolution in microbiomes combine molecular population genetics, eco-evolutionary theory and systems microbiology to explore basic questions in evolutionary biology along with system specific questions. Evolution in microbiomes is a relatively new (but growing) topic in the Petrov lab and much of this work is done in collaboration with other labs, including the Good, Cremer, and Relman labs. Some of the big questions we are currently working on include:
How does ecological complexity modulate evolution at the single species level?
Natural populations evolve in the presence of many other species, but we lack a quantitative understanding of how this diversity will influence evolutionary dynamics of individual species. To explore this topic, members are conducting experiments using in vitro microbiomes, which allow us to perform controlled, high-throughput and replicated investigations of microbiome assembly and microbial evolution. Currently, we are working with both ex-vino communities composed of wine yeast and ex vivo communities from human stool samples.
How does within species genetic diversity translate to ecological specialization?
An example of change in microbiome dynamics after transient antibiotic exposure. A human subject had taken a course of low-dose antibiotics around day 0, which caused a drastic change in their microbiome composition. Each color represents a bacterial family. Adapted from Xue at al, 2023.
Recent work by lab members and others has illustrated that host-associated microbiomes often harbor high levels of within-species genetic diversity, due to multiple colonization events of genetically diverged strains of the same species. These populations exhibit rapid dynamics in response to perturbations, such as antibiotics, which suggests that they are significant for single species adaptation to transient perturbations. However, we lack an understanding of what ecological and evolutionary forces drive these strain dynamics and allow for long-term co-existence. To explore this topic, we analyze longitudinal metagenomic data from host-associated microbiomes, and we conduct experiments with ex vivo human gut microbiomes assembled from stool and work with communities that contain diverse yeast strains. This area of research has broader implications for understanding the dynamics of colliding populations after long periods of genetic isolation.
What are the ecological, evolutionary and genomic drivers of speciation in human gut bacteria?
Bacterial species are not obligately sexual, but they exhibit patterns of genetic exchange within species and limited genetic exchange between species like obligately sexual organisms. It is unclear whether this genetic isolation is driven by physical barriers to genetic exchange, such as limited homology or incompatible recombination machinery, or genetic factors, such as epistasis. To explore this topic, members are conducting molecular population genetics analyses of prominent human gut bacteria.