At long last, my final PhD chapter is out: we developed a novel evolutionary simulator of bacterial pangenomes, Pansim, fitting it to data from >600K genomes using a likelihood-free framework, PopPUNK-mod, to explore neutral and adaptive pangenome dynamics www.biorxiv.org/content/10.6...
The Carney speech is worth reading in full: globalnews.ca/news/1162087...
Merry X-SMASH!
My first first author paper is out on bioRxiv! 🖥
We present epsSMASH, a comprehensive and high-throughput tool for predicting exopolysaccharide (exoPS) biosynthetic gene clusters (BGCs) in bacterial genomes 🦠🧬🧫
1/8
💾 Prokka 1.15.6 is released!
This is the last major release of Prokka. But don't be sad, because @oschwengers.bsky.social already has an excellent replacement called Bakta you can migrate to.
#bioinformatics #microbiology #genomics
github.com/tseemann/pro...
Huge preprint if you are interested in bacterial strain taxonomy! The why and how of cgMLST LIN codes: An extensively revised and expanded version doi.org/10.1101/2024... I will summarize it for you in this thread 👇
Thrilled to share our new review online with
@scottvedwards.bsky.social in @Trends Ecol & Evo! “pangenomics is rapidly transforming our ability to dissect the genetic basis of ecological and evolutionary change in natural systems.”
Our Pectobacterium story continues. This one shows the conservation of tailocin and localized HGT of the tail fiber locus across the Pectobacterium genus.
A new paper from the lab on virus-like particles called eCISs www.nature.com/articles/s41...
How bacteria evolved thousands of precision nanoinjectors?
Some bacteria don’t secrete toxins — they inject them using phage-derived machines called extracellular contractile injection systems (eCISs).
Aude Bernheim @audeber.bsky.social and Eugene Koonin discuss one of most interesting questions in the field connecting bacterial and animal immunity!
www.nature.com/articles/s41...
Fantastic talk by @vikramshivakumar.bsky.social Mumemto—Scalable multi-MUM finding for pangenomes
Papers biorxiv.org/content/10.1101/2025.05.20.654611 & doi.org/10.1186/s13059-025-03644-0
Code: github.com/vikshiv/mume...
Very efficient pangenome visualization tool, revealing synteny and variations!
www.biorxiv.org
Prime Minister Mark Carney gave a forceful speech in Davos, Switzerland, on the 'new world order' and how middle powers like Canada can benefit by working together.
The future
This is probably the last release of Prokka. I won't be making any code changes except bug fixes. I will update the databases occasionally. I strongly recommend you use Bakta by @oschwen...
Unified strain taxonomies are needed for the epidemiological surveillance of bacterial pathogens and international communication in microbiological research. Core genome multilocus sequence typing (cg...
Extracellular contractile injection systems (eCISs) are bacteriophage tail-derived toxin delivery complexes that are present in many prokaryotes. Here, the authors present an analysis of eCIS tail fib...
www.nature.com
The widespread prokaryotic immune systems, in particular restriction–modification, CRISPR–Cas and defensive toxin–antitoxin systems, are absent in eukaryotes, whereas relatively rare ones, such as Arg...
@lakhanp01.bsky.social @annecmg.bsky.social et al. characterized the genomic diversity of a tailocin and discovered that diversity is maintained through exchange of the tail fiber locus DNA across Pectobacterium, a pathogen causing soft rot.
🔗 doi.org/10.1093/gbe/evag106
#genome #evolution
epsSMASH uncovers exopolysaccharide biosynthetic gene clusters in environmental and human microbiomes https://www.biorxiv.org/content/10.64898/2025.12.21.693542v1
