Shaw Lab

Research

Applying to them Darwin’s theory of evolution, there was nothing strange in the idea that the ordinary organisms found in wounds might change their normal character and become infective… It was said that bacteria doubled themselves in twenty minutes, and that in a fortnight they had a thousand successive generations, which was equivalent to a thousand years in the life of the wheat plant and 30,000 in the life of man. — W. Roberts, 1881

Bacteria have been evolving for billions of years and continue to do so today. They are fascinating organisms to study: they can swap genes, have genetic parasites, and live in complex communities almost everywhere on earth.

The recent availability of thousands (and now millions) of genome sequences has provided new ways to explore bacterial evolution, but these datasets are often challenging to analyse. In extreme cases, even two strains within the same species may share only a minority of their genes in common. And many genomes also contain mobile genetic elements that can move between bacteria, making it important to consider how natural selection acts at multiple levels.

Bearing these challenges in mind, we use genomic data to better understand how bacteria evolve. Although the organisms we study are often important for human disease we are interested in broad patterns of bacterial evolution — we care about non-pathogenic bacteria too. When we need new tools we develop them, but in general we are driven by fundamental questions rather than technical challenges.

Research areas

Our work spans several overlapping areas, with the below giving some indication of the types of questions we work on in collaboration with colleagues. If you’re interested in collaborating in the future, please get in touch!

Antibiotic resistance

Antibiotic resistance, also known as antimicrobial resistance (AMR), is a natural consequence of bacterial evolution. As well as being an important challenge for public health, it offers a perfect opportunity to study the fundamental mechanisms that allow bacteria to evolve rapidly: horizontal gene transfer, the ‘domestication’ of new genes, interactions between genes, and the amelioration of fitness costs. Coupled with this, many of the bacteria that have been sequenced are often clinical strains that carry resistance genes, so there is usually no shortage of data.

Previous papers:


Plasmid evolution

Plasmids are autonomous genetic elements that can replicate by themselves and are often capable of independent transfer between bacteria. They can be studied as evolutionary individuals that are subject to natural selection. That opens up a whole host of questions. Some of our current work draws on approaches from host-pathogen evolution to study the adaptation of plasmids to their bacterial hosts.

Previous papers:

  • finding evidence that plasmids are under selective pressure from restriction-modification systems (Shaw et al. 2023)
  • exploring plasmid sharing between bacterial populations in humans and livestock (led by Will Matlock and Sam Lipworth) (Matlock and Lipworth et al. 2023)

Genome structure

As the quality of bacterial genomes keeps getting better, it’s now possible to analyse the structure of genomes — how genes are arranged and ordered within them. However, this means our models of evolutionary change need to catch up with the quality of the data that’s now available.

Previous papers:


Bacterial populations and communities

Bacteria never live in isolation. Thinking about them in their ecological context, statistical approaches from macro-ecology and elsewhere can be used to explore how these communities are structured and change over time.

Previous papers:

  • modelling microbiome recovery after antibiotics (Shaw et al. 2019)
  • exploring how geography shapes the pangenome of bacterial species within a 30km radius (Shaw et al. 2021)