PhD position available in Mostowy Lab!

We are inviting applications for a research technician (with an option of becoming a PhD student) in the area of computational biology and genomics of bacteria-phage interactions. The successful candidate will join Dr Rafał Mostowy’s Microbial Genomics Group ( at the Malopolska Centre of Biotechnology in Krakow. The position is available from September 2019 and funded by the Polish National Agency of Academic Exchange.

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Why are bacterial capsules so diverse?

Biology is full of complex problems to solve. One of these problems is the remarkable diversity of some bacterial capsules, like in Streptococcus pneumoniae, Klebsiella pneumoniae or Escherichia coli (100 or more types in each species alone). It's not merely a philosophical question: capsules, so ubiquitous in the bacterial world, are highly medically relevant being the target of polysaccharide conjugate vaccines, and they are more and more often mentioned in the context of phage therapy as phages recognise specific capsule types. As large antigenic diversity poses a problem for eradication of a bacterial disease, it is important to understand what drives it in the first place.

So what drives capsule diversity in bacteria?

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Pneumococcal capsule: evolution on steroids

I remember it was Andrew Read who first sparked my interest in Streptococcus pneumoniae. During my visit at Penn State in 2011, he told me that Marc Lipsitch had been working on 'serotype switching', whereby pneumococcal bacteria using recombination were swapping surface structures – capsules – thus escaping vaccines. Eventually this persuaded me to come to Imperial College London to work on S. pneumoniae with Christophe Fraser.

Not that long after I'd arrived, I had a discussion with Christophe about pneumococcal capsules. He then told me about the fascinating problem of capsule diversity. There's around 100 of different pneumococcal serotypes, and they are generated by different combinations of genes – a bit like Lego bricks. Christophe suggested that they could be evolving to form new serotypes, and that this would be interesting from a medical point of view. He then said: "Could we build a tree of all these serotypes to reconstruct how they evolved? If I were you, I'd take scissors, glue and get to work."

Now, over four years later, the results of this complex work have been published in Molecular Biology and Evolution [1]. Turns out that scissors and glue didn't quite help, but instead I used a number of other tools. So here's a summary of what capsules are, what I found and why it's important.

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fastGEAR: detecting mosaicism in bacterial genomes

This month I had a paper accepted on a project I had done in collaboration with Pekka Marttinen at Aalto University in Finland, and several other colleagues. The paper introduces a new method for the analysis of bacterial genomes called fastGEAR [1]. There are so many new methods being published these days. That's why I thought it would be useful to write a short article about what fastGEAR is, how it works, and how to use it. Ok, here we go!

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