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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...

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...

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).

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

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.”

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 👇

💾 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...

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!

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...

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...

Unified strain taxonomies are needed for the epidemiological surveillance of bacterial pathogens and international communication in microbiological research. Core genome multilocus sequence typing (cg...

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...

@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

Genomic structural variation is an important component of genetic variation in natural populations. By assembling and analyzing multiple high-quality genomes within a species or clade, pangenomes capture variation that can be missed by reference-based genomics at both the sequence and the genic levels. Although pangenomes are nascent tools for animals compared with other taxa, they have already unveiled novel insights into genome evolution, adaptation, the genomic basis of organismal traits, and conservation genomics. We highlight the rapid progress and unique ecological and evolutionary discoveries emerging from applying pangenome tools to diverse natural populations. We conclude that pangenomes are fundamentally shifting the field by revealing structural variants as a key source of adaptive potential and genomic diversity previously missed by single-reference methods.