Microbial Genomics Group travelled to Guimaraes, Portugal, to attend Viruses of Microbes 2022. It was an incredible conference, with almost 700 participants. We presented 4 posters, received tons of useful feedback and spoke to dozens of incredible phage biologists. We are very grateful to the organisers for making this happen, this being our first group conference ever. See you next year in Georgia!
Joint EMBO meeting with Karnkowska Lab and Dunin-Horkawicz Lab in Chęciny
Microbial Genomics Group attends the ”Meeting of the EMBO Young Investigator Network on computational methods in ecology and evolutionary biology of microbes”, between 7-9 of July 2022 in Chęciny in Poland, held together with the labs of Ania Karnkowska and Staszek Dunin-Horkawicz. We had a wonderful time presenting research results as well as discussing science and potential areas to collaborate.
Successful MSc defence by Jan Havránek
Our MSc student, Jan Havránek, has successfully defended his MSc thesis at Jagiellonian University in Krakow. His thesis, entitled Average nucleotide identity and its applications beyond prokaryotic species delineation, received 5, the highest grade in the Polish academic system, and a distinction. Jan is soon leaving us to pursue an an exciting opportunity in Paris. Janek, it was a pleasure to have you as part of Mostowy Lab. We wish you all the best!
(Polish) Jak w Polsce idzie nam zaszczepianie populacji?
Problem z danymi
Od kilku miesięcy regularnie i z zainteresowaniem czytam dziennik pandemiczny Marcina Kędzierskiego “w poszukiwaniu nowej normalności”, jako że pojawiają się tam bardzo trafne analizy, spostrzeżenia i przemyślenia odnośnie pandemii COVID-19 w Polsce. W jednym z ostatnich wpisów przeczytałem tam zdanie, które szczególnie mnie zmartwiło, bo autor sugerował w nim, że słabo idzie nam ze szczepieniami seniorów w Polsce:
“Zważywszy, że po ostatnich dostawach problemy z dostępnością szczepionki nie występują – ba, mamy nawet 2 mln niewykorzystanych dawek ‒ można założyć, że zaszczepili się prawie wszyscy, którzy chcieli. To zaś oznacza, że prawie połowa seniorów zaszczepić się nie chce.”
(źródło: Marcin Kędzierski, komentarz z 17.04.2021)
Zmartwiło mnie, bo – jeżeli to prawda – oznacza to duży problem. Osoby powyżej 70ego roku życia są najbardziej zdrowotnie narażoną grupą na COVID-19, a zakażenia w tej grupie wiekowej charakteryzują się wysoką śmiertelnością. Nawet jeżeli szczepionki nie chronią perfekcyjnie przed zakażeniem, to jak pokazują dane są one bardzo skuteczne w zapobieganiu hospitalizacji i śmierci, już nawet po pierwszej dawce. Dlatego podczas gdy kolejnej fali epidemicznej na jesień 2021 możemy nie uniknąć, nadzieja leży w tym, że przy wysokim odsetku zaszczepienia populacji możemy dramatycznie zredukować umieralność na COVID-19, dzięki czemu nie tylko ocalimy życie tysięcy ludzi ale miejmy nadzieję unikniemy też najbardziej bolesnych obostrzeń mających na celu zatrzymanie zapaści służby zdrowia. Jeżeli jednak prawdą jest to, co pisze Kędzierski, jest spora szansa, że kolejna fala po raz kolejny zbierze śmiertelne żniwo a my zostaniemy znowu zamknięci w domach.
Read moreWe are recruiting!
We are currently looking for a postdoc and a PhD student as part of the NCN OPUS 19 grant. Please see here for more details.
NCN Sonata Bis grant for Microbial Genomics Group!
Another successful week for the Microbial Genomics Group. We have just received a 3.8M PLN (~1M USD) collaborative grant with the Zuzanna Drulis-Kawa lab in Wrocław to study interactions and specificity of tail fibre proteins against bacterial surface polysaccharides in Klebsiella. We will be recruiting people soon so please watch this space!
Rafal in EMBO Encounters
Rafal has featured in the latest issue of EMBO Encounters, the official newsletter of European Molecular Biology Organization. The photo below, and the full issue can be found here.
(Polish) Jak zaczynają i kończą się pandemie?
Choroby zakaźne podlegają pewnym regułom, które można opisać matematycznie. Czy te reguły mogą nam podpowiedzieć, co czeka nas w najbliższych miesiącach?
Read moreNCN OPUS grant for Microbial Genomics Group!
Our group has received almost 2 000 000 PLN of funding in the latest OPUS 19 competition, funded by the National Science Centre. The plan of the proposed research is to develop a new bioinformatic methodology to study evolution of tailed bacteriophages. The lay summary can be accessed here (in Polish only). We will soon be recruiting new people to join the group, so please watch this space!
New student, Dana Pikulska, to join the group
Our group welcomes a new member: Dana Pikulska. Dana is a BSc student at the Department of Biochemistry, Biophysics and Biotechnology of Jagiellonian University. She joins our group as an intern and will be learning about the biology and bioinformatics of transposable elements in bacterial genomes.
Evolutionary Purpose of bacterial Sex
If there is one thing we learned from over 150 years of studies on the evolution of sex it is that more sex is not always better. So why some bacteria exchange genetic material more frequently than others?
Read moreWhy 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?
Read morePneumococcal 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.
Read morefastGEAR: 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!
Read more