I am absolutely thrilled to have received a Robert Austrian Research Award at this year’s ISPPD meeting. Seeing all the great science being done, but especially the community around it, has been amazing and very inspiring. See you all soon👋🏽 #ISPPD14 #ISPPD2026 #pneumonia #pneumococcalresearch

Our lab's website has a summary of what we have done: www.microbial-pangenomes-lab.org/2026/05/04/T...

Are you frustrated by how arbitrary fixed SNPs thresholds "feel"? Are you wondering if there are genetic differences between "promiscuous" and "shy" pathogens? If yes, then read our latest preprint to see what @jburgaya.bsky.social has been up to! www.medrxiv.org/content/10.6...

Excited to share our discovery of a new programmable RNA-guided DNA-targeting system hiding inside bacteriophages that predates CRISPR. We call it VIPR (Viral Interference Programmable Repeat), and it uses an entirely new logic to find its targets. Thread + link below.

ggCallaroo v0.1.0 is now out! This snakemake pipeline predicts, clusters and annotates bacterial genes using ggCaller, Panaroo and Bakta. It generates Panaroo files with functional annotations already integrated, which can then be used with the usual downstream tools. github.com/samhorsfield...

Protein–protein interactions (PPIs) are key to discovering and interpreting new biological functions. We’re excited to introduce 𝑭𝒍𝒂𝒔𝒉𝑷𝑷𝑰: a new application of gLM2 that uses genomic language modeling to predict proteome-wide PPIs in microbial genomes in minutes.

💾 Shovill 1.4.1 has been released! The best way to de novo assemble microbial genomes from Illumina FASTQ. Major fixes to the SKESA module, plasmid mode for the Spades module, and more error checking. #bioinformatiocs #genomics #microbiology github.com/tseemann/sho...

On Wednesday I started my postdoc at the Institut für Infektionskrankheiten (IFIK) @unibe.ch 🧬💻 Excited to get started on my project exploring Streptococcus pneumoniae virulence and all the science ahead!

Delighted to see our paper studying the evolution of plasmids over the last 100 years, now out! Years of work by Adrian Cazares, also Nick Thomson @sangerinstitute.bsky.social - this version much improved over the preprint. Final version should be open access, apols. Thread 1/n

Awesome to see the transparent, systematic, and evidence-based approach behind the WHO Bacterial Priority Pathogens List 2024 out in the Lancet Infectious Diseases www.thelancet.com/journals/lan...

Truly honored to receive the Infection Biology PhD Prize. Grateful for the support @resist-cluster.bsky.social

PhD, done 🥹🥂 Massive thanks to my brilliant supervisor @mgalactus.bsky.social and amazing colleagues!

Are you interested what proportion of differentially expressed genes in bacteria can be explained by cis non-coding variants? Then head over to our latest preprint, in which Bamu used her dry- and wet-lab skills to answer this and other related questions! www.biorxiv.org/content/10.1...

We are very happy to report that the 3rd and 4th PhD theses from the lab have been submitted! This time we had a “tale of two theses”: @jburgaya.bsky.social had her thesis 99% ready more than a week before the deadline (!), while Hannes preferred to wait until just before it was due ☕ Congrats!

New opinion paper from the lab! www.cell.com/trends/micro...

And this only the beginning! I’m glad we did that collaboration with the Maric lab. ASOs for the people!

Do people in the same household share strains when they have the same species? How many cells transmit when a strain is shared? Can strain composition be dynamic when species composition is stable? We answer these and related questions for the facial skin microbiome in our latest paper. 🧵[1/10]

This is fascinating, but also terrible news regarding antimicrobial resistance in multidrug-resistant Gram-positives 'Emergence of transferable daptomycin resistance in Gram-positive bacteria' www.nature.com/articles/s44...

New paper: long-term trends in antibiotic resistance show signs of stabilisation (thread). journals.plos.org/plospathogen...

Properties of bacteria are constantly changing. @mgalactus.bsky.social is developing methods to better predict the properties. His team has now developed software that facilitates genome-wide association studies #GWAS Congratulations to all 🧫🦠😊 www.resist-cluster.de/en/better-pr...

We even got the press office to take this lovely photo of the three main authors :) Quite nice that we got it published on the International Day of Women and Girls in Science!

Our paper describing the microGWAS pipeline was published yesterday in Microbial Genomics. Lots of fixes and additions to the code/documentation since the preprint, including a hard to reproduce bug that only showed up in a specific HPC 🥵 www.microbiologyresearch.org/content/jour...