Horizontal Gene Transfer and Mobile Elements in Microbial Ecology and Evolution

Coordinators: Allison Carey, Ben Good, Honour McCann, Katie Pollard, and Julia Salzman

Horizontal transfer plays a critical role in accelerating adaptive and evolutionary dynamics in many microbes, yet the mechanism, ecological context, frequency and impact of recombination remain a mystery outside a handful of model organisms. The violation of laws of vertical inheritance is frequently acknowledged during the analysis of sequence data, yet the absence of more accurate methods of identifying, modeling and visualizing horizontal transfer hinders greater understanding and discovery. This program will bring together researchers using statistical bioinformatic, theoretical and experimental approaches to identify and model the dynamics of Mobile Genetic Elements (MGEs) and bacterial immune systems; their impact on the structure and function of microbial populations and communities, and their role in antimicrobial resistance and pathogen evolution.

The program seeks to unite researchers studying a broad range of systems across environmental, agricultural and clinical niches. There will be a strong focus on open problems for methods development, including bioinformatics needed to advance discovery in the field, and how these methods can both inform and learn from new experiments. Program participants will engage with critical questions, including:

  • How do MGEs spread in complex communities, across spatially heterogeneous environments? 
  • How can we quantify rates of transfer in complex systems?
  • How do viruses structure bacterial populations within individual hosts and across broad landscapes?
  • What impacts do MGEs have on infection dynamics and pathogen evolution?
  • How do microbial interactions impact the transfer and maintenance of mobile elements?
  • How can we improve computational methods of MGE prediction, phylogenetic reconstruction and visualization to better understand the evolution of mobile elements and their hosts?
  • Can a unifying statistical genomic theory of phage and mobilome identification be developed?
  • What are the most rigorous methods of evaluating statistical bioinformatic approaches?
  • Can statistical bioinformatics determine what is upstream of the initiation of transfer and downstream of DNA receipt in bacterial genomes?
  • How will these predicted mechanisms be tested?
  • What general principles are emerging in the study of mobile elements?

"QBio" summer research course for graduate students and postdocs will run concurrently with the program. Admitted summer course students will attend morning lectures and discussions with program participants and spend their afternoons taking part in team-taught lab experiments. The summer course application deadline is March 3, 2024.