Annual conference, Microbiology Society (2023, Birmingham)

This week was time for the Annual Conference of the Microbiology Society. This was my second time at this meeting, and I enjoyed it once again. There’s a committed core of attendees which gives a good community spirit, and the society is openly very keen on supporting PhD students attending.

Favourite session – plasmids

There was a great block of talks in the Genetics and Genomics session on plasmids that I thought fit together really nicely. I only have a bit of knowledge about them, and I think the talks covered a good range of questions on these charismatic genome elements:

• Paidraic Heneghan gave an entertaining talk about toxin/antitoxin systems in yeast which cleave tRNAs. I didn’t know that some yeasts have an alterative coding table which causes a non-synonymous changes (which was pointed to be high cost, as it leads to reading the ancestral proteome incorrectly). Paidraic used bioinformatic searches to find more of these toxins, which he is now characterising.
• Liam Shaw gave a (multi-font) overview of his recent preprint proposing that small plasmids may be more common as restriction sites (6mers) can be avoided by SNPs, whereas longer plasmids contain a methylase to avoid being cleaved by the host – overall making mid-length plasmids less common.
• Victoria Orr told us about her PhD work to understand the interaction between plasmids and smaller mobile genetic elements, which can integrate in either the chromosome or the plasmid. She’d developed an agent-based model (with some fun orange-slice outputs) to predict interactions in different conditions, and is also combining this with lab work to study the system in vitro.
• Adrian Cazares told us about their use of the ‘Murray collection’ of pre-antibiotic era isolates which have recently been sequenced. Bacteria are very adaptable and have plastic genomes, and the plasmids that have been kicking around forever were an efficient way to respond to the development of antibiotics.
• Jacob Wildfire is addressing why S. aureus has not become fully resistant to antibiotics. By screening a transposon mutant library in USA300 (which seemed like a lot of work!) he had identified a region of the chromosome lowering horizontal gene transfer rates, which he is now characterising in more detail.

Other talks I liked

Again, a non-exhaustive list, but some other talks I enjoyed:

• Matthew Barber taught me about the battle between bacteria and fungi on our skin, and how the stringent response of Staphylcocci gives resistance against their eukaryotic enemies.
• Angelika Kiepas showed us the challenges of typing the Streptomyces genus, extending previous work. rRNA typing doesn’t work well due to all the copies. The MLST scheme doesn’t work well either, giving too many clusters in some parts of the taxonomy, and not enough in others. Perhaps a k-mer based method could work better?
• Emma Waters told us about genome rearrangements in Salmonella. Seven rRNAs throughout the genome mean different rearrangements are possible, which cause slower growth and gene dosage effects due to the imbalance in ori-ter. I saw Gemma Langridge’s talk on this topic last year, so it was nice to see the work progressing, particularly answering the question of why and what adaptive effects these rearrangements might have.
• Anna Dewar used datasets from around 120 bacteria species to ask why some pangenomes are more fluid than others. By looking at pairwise gene differences then using causal associations to search for links with lifestyle traits, finding that ecology likely causes variation in pangenome ’type’. I asked Anna afterwards whether she could fit gene gain and loss rates too, but she pointed out that doing this accurately for so many species would be a challenge, especially on commensals with sparse data!
• Jan Kosincki told us about new work imaging the nuclear pore complex in flu-A infected cells, showing it dilating. By increasing the resolution of the imaging, they’ll eventually be able to use AlphaFold2 protein structures and integrative modelling to pin down the protein(s) responsible for this conformational change.
• Tim Russell gave a tour of his work on COVID-19 transmission and testing. A lot to like, but I particularly enjoyed the extension to previous work on testing to hierarchical modelling of Ct trajectories for different variants and clinical presentations. The talk included some memorable reflections on working at speed with constantly changing goalposts (bad and stressful) compared to working closely with collaborators with a range of expertise on a carefully designed dataset (good). Tim is going to be visiting EBI for a few months, which is very exciting for us!