I’m thrilled to share that our paper on the Evolutionary dynamics of bacteria in the gut microbiome within and across hosts is now published in PLoS Biology!

What is the paper about?

The human gut microbiome is comprised of a complex ecosystem of microbes that reside inside of us and play an important role in our health. With as many as a billion new mutations entering our microbiomes per day, bacterial genomes inside us have a great opportunity to evolve rapidly, unlike our own genomes, which change very little throughout our lifetimes. For us humans, this genetic dynamism is both an opportunity (e.g., enabling digestion of new foods) and a challenge (e.g. the evolution of drug resistance). Despite the potential importance of these effects, we currently know very little about if and how bacteria living in us evolve. In our recent work, we quantify the evolutionary dynamics of ~40 prevalent species of gut bacteria. We find that gut bacteria can evolve within humans on short timescales (~6 months), but over our lifetimes resident bacteria are typically replaced by distantly related strains. These results suggest that gut bacteria can evolve on human-relevant timescales, but that there are limits to the extent of local adaptation.

Isabel Gordo wrote a very nice perspective featuring our work.

Happy to share that I have revised my manuscript on the Evolutionary dynamics of bacteria in the gut microbiome within and across hosts with my colleagues Benjamin Good, Oskar Hallatschek, and Katherine Pollard. Please see the latest on bioRxiv.

My talented colleague, Alison Feder, drew a graphical abstract of my paper!

I will be presenting my latest paper on the evolution of bacteria in the gut microbiome at the New York Area Population Genomics Meeting at Cold Spring Harbor.

Bacteria in the microbiome can potentially respond to selective pressures in many ways. One possible mechanism could be via a change in the relative abundances of species. Alternatively, a better fit strain could invade the population. Or, a pre-existing strain could evolve an adaptive mutation. Although differences in species abundances and the genetic composition between samples has been well-studied, little is known about whether lineages within a healthy host can evolve. Here is a preview of the hypotheses I will be addressing in my talk!

 

I recently posted a preprint of my work with Benjamin Good, Oskar Hallatschek, and Katherine Pollard on the evolutionary dynamics of bacteria in the gut microbiome within and across hosts on BioRxiv. In this paper, we use a model-based approach to analyze shotgun metagenomic data to reveal evolutionary forces that operate in the gut microbiome. We offer empirical evidence that gut bacteria evolve within healthy human hosts, and we find that between-host genealogical patterns challenge existing population genetic models of quasi-sexual evolution.

We welcome your feedback on the paper.

I will be co-chairing a symposium at the 2017 Society for Molecular Biology and Evolution in Austin TX with my colleague, Sharon Greenblum, on ‘Probing microbiome dynamics.’ We look forward to receiving abstracts on how evolutionary and ecological forces have shaped diversity in the microbiome.

Symposium abstract:

Microbiomes are comprised of many bacterial species with complex interactions and dependencies between community members. Adaptation of microbiomes to rapidly fluctuating environments can result in changes in species diversity and composition, as has been observed in patients with Crohn’s disease and asthma. Individual species within the microbiome experience adaptation too, as evidenced by single-species studies of adaptation in response to specific conditions, for example the evolution of Burkholderia dolosa over the course of an outbreak, or the virulent transformations of E. coli in response to nutrient limi-tation. How these strain-level dynamics play out in a community setting, and what the strain-level signatures of adaptation are in the microbiome, remain open questions. Only recent technological breakthroughs have provided the means to leverage metagenomic data to understand signatures of adaptation at the strain level, such as single nucleotide polymorphisms and gene copy number variants. Such information will illuminate the evolutionary forces shaping microbiome diversity, transforming in turn our ability to manipulate the microbiome to benefit host health. This symposium will focus on probing signatures of adaptation in the microbiome, with special attention paid to novel data sources, statistical methodology, and biological examples.