Most of the genetic and metabolic diversity that exists on earth – and has existed for billions of years – is microbial.

Arguably more impressive than the sheer quantity of microbial diversity is its dynamic nature: microbes are constantly evolving and adapting.

Our ongoing research tracks evolving microbial populations in real time, using whole-genome and whole-community DNA sequencing to understand their evolution and predict how they adapt to changing environments. For example:

  1. freshwaters subject to seasonal cyanobacterial blooms,
  2. the human gut, focusing on cholera infections,
  3. the evolution and ecology of antibiotic resistance,
  4. ​semi-natural mesocosms at LEAP,
  5. ​genomic epidemiology and pandemic reponse with CoVaRR-Net.

    ​Illustration of bacterial speciation with gene flow, modified from Shapiro et al. 2012