New preprint from the lab!

We developed a new tool to identify prokaryotic species (down to the strain level) directly from mass spectrometry-based bottom up proteomics data.

#teammassspec #microsky

www.biorxiv.org/content/10.6...

We’re still doing some final improvements, but the whole NovoTax pipeline should be available soon. We use GTDB which only includes bacteria and archaea, but it should be possible to implement a similar strategy for a wider genome database. Just less efficient…

So happy to have been part of the @savitski-lab.bsky.social! I also want the sweater!

The secrets of Archaea could provide new keys to our health | Knut and Alice Wallenberg Foundation Our intestines teem with life. Billions of bacteria are already known and play a crucial role in our health – but there is also an almost invisible neighboring group: the Archaea. These are ancient mi...

Billions of bacteria are already known and play a crucial role in our #health – but there is also an almost invisible neighboring group: the #Archaea. These are ancient microorganisms whose function in the human body remains something of a mystery @umeauniversitet.bsky.social tinyurl.com/yhr9yjsm

Our new preprint is out 🥳🥳🥳

Henipaviruses, like Nipah and Hendra, package their genomes inside helical shells built by thousands of nucleoproteins. These nucleocapsids are essential to protect the viral RNA, but how do they ever let the polymerase in to read the sequence?

👇

Mosquitoes like Aedes aegypti spread viruses that cause major global diseases. We decided to have a closer look at a family of mosquito carbohydrate-binding proteins involved in infecting these vector species. We found some unexpected things 😁

Preprint out now 🦟🦟🦟

www.biorxiv.org/content/10.6...

ICYMI during the holidays. I am really proud of Bolor's efforts and the first work coming out of the lab!

Read it here: www.biorxiv.org/content/10.6...

Pili are essential for conjugation also in many Gram-positive bacteria Type IV secretion systems (T4SS) enable the spread of antibiotic resistance and other virulence factors. In Gram-positive bacteria, T4SSs have long been thought to lack VirB2-like proteins that form c...

📣New preprint with @rberntsson.bsky.social👇We overturn the long-standing view that Gram-positive bacteria lack conjugative pili! We identify pili-forming proteins in a wide range of bacteria and show they're essential for the spread of #antibioticresistance #AMR 🧵1/6
www.biorxiv.org/content/10.6...

New paper from the lab!
Led by Patrick Müller: we show that non-antibiotic compounds — but not macrolide antibiotics — can induce an efflux pump that protects Bacteroidaceae from macrolides.
A neat twist on drug–microbe interactions... www.tandfonline.com/doi/full/10....

Discovering Glycosylation-Dependent Protein Function by Thermal Proteome Profiling Protein glycosylation regulates essential cellular processes including protein folding, stability, and cell-cell interactions; however, how aberrant glycosylation impacts protein function and interact...

Congratulations former postdoc @jfhevler.bsky.social (in transit to Roche) and the team on their work using thermal proteome profiling along with glycosylation perturbagens to discover glycan-dependent protein functions at the proteome scale 👏

www.biorxiv.org/content/10.6...

The pcnB gene sustains Shigella flexneri virulence Author summary Bacterial infections represent a major global threat. Understanding the genetic determinants promoting infections is crucial to overcome this threat. Shigella is an intracellular bacter...

Thrilled to share that our study on how the pcnB gene sustains Shigella virulence is now published in PLOS Pathogens: journals.plos.org/plospathogen...

In short: pcnB ➝increased virulence-plasmid replication ➝ elevated T3SS expression ➝ enhanced invasion/spread within the intestinal epithelium.

Systematic screen uncovers regulator contributions to chemical cues in Escherichia coli Transport machineries are crucial for antibiotic resistance, but their regulation by external cues is poorly understood. This study identifies environmental chemicals that regulate transporter transcr...

Finally out! A small screen helps understand a little more about how E. coli regulates major transporters, and reveals how caffeine induces phenotypical antibiotic resistance. Huge thanks to collab @andrenmateus.bsky.social (Umeå) and Christian L. Müller (Munich)!
journals.plos.org/plosbiology/...

#ProudPI

New preprint out: www.biorxiv.org/content/10.1...
We followed up on our recent Nature Genetics paper mapping Shigella colonization in intestinal organoids with a deep dive into one of the screen hits: pcnB.

#Shigella #virulence #microsky

A scalable gut epithelial organoid model reveals the genome-wide colonization landscape of a human-adapted pathogen Nature Genetics - A genome-wide screen using human gut epithelial organoids combined with transposon-directed insertion sequencing identifies over 100 Shigella flexneri genes required for...

Our latest work combines human gut epithelial #organoid culture with experimental #Shigella #infections, transposon mutagenesis, and statistical modeling. This has led to the mapping of the comprehensive geneset that drives Shigella epithelial colonization.

Out @natgenet.nature.com:

rdcu.be/eqGgf

Do we really know the antibiotics that we already have?

Check out our story on 60y old drug nitroxoline and its new tricks!
@goetheuni.bsky.social @embl.org
www.nature.com/articles/s41...

+ great piece from the synchrotron @esrf.fr where we chased nx effects on metals
www.esrf.fr/home/news/ge...

Looking forward to speaking in this webinar series next Wednesday.

So happy to see the first paper on research from the lab out! Just a review for now, but it gives an idea of the avenues we are exploring.

PhD position in Chemistry, with a specialization in biochemistry The Department of Chemistry is opening a PhD position in Chemistry with a specialization in biochemistry. The thesis project will focus on drug resistance mechanisms in microbiome species, and is part

We have a PhD student position open in the context of the ENDAMR doctoral network. Deadline is 31/May. Apply here: umu.varbi.com/en/what:job/...

Looking forward to sharing with this community what our lab is doing