Single-cell approaches in microbial ecology

Illuminating the microbial world using genome-based fluorescence microscopy

Our understanding of microbial diversity on Earth has been fundamentally changed by metagenomic characterisation of natural ecosystems. However, traditional approaches for visualising microbial communities are time consuming and provide limited information about the identity of specific microorganisms.

We have developed novel approaches that combine single-cell genomics and super resolution microscopy to provide high-throughput, genome-based techniques to visualise microorganisms, along with their plasmids and viruses, with strain-level specificity. The application of these approaches will provide comprehensive and unprecedented insight into the fine-scale dynamics and evolution of microbial communities from a range of environmental and host-associated ecosystems. Our understanding of such communities, and our consequent ability to manipulate them, will be essential for addressing some of the most critical global challenges today, such as climate change, human health, sustainable agriculture and energy (e.g., biogas).

Chief Investigators


  • Allison McInnes
  • Eilish McMaster

Funding / Grants

  • Australian Research Council Discovery Project #DP200102310