Westermann Lab

Scientific Advisory Board Meets at the Helmholtz Institute Würzburg Two days of intensive scientific exchange

Two days of inspiring exchange 🧬🤝✨

On February 10 and 11, our Scientific Advisory Board came together to review the scientific orientation and performance of #HIRI. We are grateful for the insightful discussions and valuable feedback.

👉 Read more: www.helmholtz-hiri.de/en/newsroom/...

Thrilled to announce that I’ve just opened my research lab at @helmholtz-hiri.bsky.social !
A huge thank you to my mentor Roi Avraham (and lab members!) for the incredible training and support that made this possible.

Do you want to understand how RNA #splicing decisions are made? We‘ve got a PhD position open for you (see 👇👇)!!
Please share #RNAsky and RT!

tinyurl.com/4ztu9cb9

📢 We are hiring 📢 1st round of recruiting for our ERC project BacImmune-Decode! @erc.europa.eu
We are looking for a postdoc for wet-lab work on regulation of phage defence systems in bacteria using high-throughput microbial genetics. Check it out: lnkd.in/es7AE968
#Hiring #Postdoc #Microbiology

Uropathogenic Escherichia coli invade luminal prostate cells via FimH–PPAP receptor binding - Nature Microbiology Uropathogenic Escherichia coli infection of a murine prostate organoid model reveals a bacterial FimH–host prostatic acid phosphatase adhesin-receptor interaction enabling invasion and replication wit...

Our first paper is out today in @natmicrobiol.nature.com!

We introduce a prostate organoid model and show that UPEC invades prostate cells via FimH binding to the prostate-specific protein PAPP. A step toward targeted therapies against bacterial prostatitis. 🎉

#UTI #UPEC #Organoids #AMR

3′UTR-derived small RNA couples acid resistance to metabolic reprogramming of Salmonella within macrophages Abstract. Acid resistance is crucial for enterobacteria to withstand host acidic environments during infection, including the gastrointestinal tract and ma

3′UTR-derived small RNA couples acid resistance to metabolic reprogramming of Salmonella within macrophages url: academic.oup.com/nar/article/...

Intramacrophage RIL-seq uncovers an RNA antagonist of the Salmonella virulence-associated small RNA PinT Abstract. Salmonella virulence chiefly relies upon two major pathogenicity islands, SPI-1 and SPI-2, which enable host cell invasion and intracellular surv

RIL-seq boosts the study of sRNAs. Here comes its first application to intracellular bacteria. Plus, 10 years after its characterization, we now present an RNA sponge of Salmonella PinT.
Congrats to @kooshapour.bsky.social & great collaboration w/ @jorg-vogel-lab.bsky.social!
doi.org/10.1093/nar/...

🎓 Congrats to Elise Bornet, who completed her PhD this week! Her courageous work dissected morphological heterogeneity in predominant human gut commensals, and yielded an ultra-sensitive transcriptomics pipeline to sequence the RNA content of single Bacteroides cells. doi.org/10.1016/j.ce...

Grateful to be among the 25 inspiring women featured in @zeit.de as part of the #Zia fellowship for Visible Women in Science. Thanks to @uni-wuerzburg.de for their support and to everyone involved for making scientific work by women more visible. Honored and proud to be part of this initiative ☺️.

Biased sampling driven by bacterial population structure confounds machine learning prediction of antimicrobial resistance Machine learning methods have emerged as promising tools to predict antimicrobial resistance (AMR) and uncover resistance determinants from genomic data. This study shows that sampling biases driven b...

Our new paper from my PhD work is online. It shows how bacterial population structure can trick machine learning—sampling matters! Many thanks to @lbarquist.bsky.social for the support and guidance! dx.plos.org/10.1371/jour...

How does a bacterial small RNA evolve new functions?

Our new study reveals the stepwise evolutionary journey of UhpU, a 3′UTR-derived sRNA in E. coli and relatives. It evolved from a metabolically-focused regulator to one with expanded targets and biogenesis manner.

www.pnas.org/doi/10.1073/...

🔊 Interested in doing a PhD on RNA-binding proteins in an abundant microbiota species and becoming a member of the German Priority Programme “Illuminating Gene Functions in the Human Gut Microbiome”? Apply here: www.uni-wuerzburg.de/karriere/sin...

De-DUFing the DUFs 🧩 @franznarberhaus.bsky.social lab uncovers how small DUF1127 proteins regulate #phosphate uptake by binding the sensor kinase PhoR. Their conserved role from Agrobacterium to E. coli highlights how even small DUFs can shape bacterial physiology 🦠
buff.ly/jJd9Eho

Excited to share our preprint led by Carlos Voogdt et al

We developed new genetic tools & genome-wide libraries for species of the Bacteroidales order; constructed saturated barcoded transposon libraries in key representatives of three genera.
www.biorxiv.org/content/10.1...

RAPDOR: Using Jensen-Shannon Distance for the computational analysis of complex proteomics datasets Nature Communications - RNA-binding proteins play key roles in post-transcriptional gene regulation. Here, Hemm et al. developed RAPDOR, a widely applicable tool based on Jensen-Shannon Distance...

How to search for unknown RNA-binding proteins? We did GradR in the cyanobacterium Synechocystis 6803. And now our paper „RAPDOR: Using Jensen-Shannon Distance for the computational analysis of complex proteomics dataset“ is finally out in Nature Communications, here: rdcu.be/eImcr .

Congrats to Ann-Sophie Rüttiger who successfully defended her PhD this week! 🎓
She focused on global RNA-binding proteins in Bacteroides—bacteria lacking Hfq, ProQ, CsrA, Khp—culminating in the discovery of a post-transcriptional network governed by RbpB (www.nature.com/articles/s41467-024-55383-8).

Looking for a new approach to studying or eliminating phages? Check out our study introducing anti-phage ASOs (antisense oligos) out in @Nature today. nature.com/articles/s4158…

An RNA regulates iron homeostasis and host mucus colonization in Bacteroides thetaiotaomicron Symbiotic bacteria in the human intestinal microbiota provide many pivotal functions to human health and occupy distinct biogeographic niches within the gut. Yet the molecular basis underlying niche-s...

New preprint from the lab, in collaboration with Wenhan Zhu (U Vanderbilt): using dual RNA-seq during B. theta colonization of the host mucous layer, we identify IroR--an iron-response sRNA that tunes capsule expression and facilitates adaptation to iron limitation.
doi.org/10.1101/2025.09.08.672848

Starting the meeting microbes and RNA- Gerhart on stage - lifetime achievement Lecture - congrats Gerhart!

A Salmonella T3SS-2 mutant grows fine in spleen macrophages, contradicting tissue culture dogma (PMID: 23236281). This observation was largely ignored, but adding certain carbon sources rescues growth in cultured macrophages, hinting that T3SS-2 may be doing something entirely different in vivo.

Ablation of polysaccharide breakdown in Bacteroides thetaiotaomicron prevents cross-feeding and growth of Salmonella Typhimurium in the mouse gut Pathogens invading the intestine compete for nutrients with the resident microbiota. However, there is evidence that commensal members of the gut also provide nutritional resources to enteropathogens ...

Latest preprint from the lab: doi.org/10.1101/2025...
In this study lead by @lenaamend.bsky.social from the group, we explore carbon cross-feeding between a gut commensal and an enteropathogen. Can we counter infection by cutting sugar supply to pathogens?

Convergent evolution of distinct D-ribulose utilisation pathways in attaching and effacing pathogens - Nature Communications Cottam et al. identify distinct pathways for D-ribulose utilisation in pathogenic Escherichia coli and Citrobacter rodentium, providing mechanistic details and suggesting convergent evolution towards ...

Absolutely delighted to share the labs latest work. We identify and characterise two pathways for D-ribulose utilisation in pathogenic EHEC and Citrobacter.

Non-antibiotics disrupt colonization resistance against enteropathogens Nature - Non-antibiotic drugs from a wide range of therapeutic classes can alter the ability of gut commensals to resist invasion by enteropathogens, a previously underappreciated side effect of...

Finally online!
Our latest research is out @nature.com: We show that non-antibiotic drugs can disrupt colonization resistance, raising the risk of enteric infections.
rdcu.be/ewwrG

Left: Compound-promoter interaction network. Fifty-three significant compound-promoter interactions are shown as edges in a Sankey diagram connecting the compounds (left, source nodes) to the promoters (right, target nodes). Edge thickness represents mean Z-scores (n = 8), while node size represents the total number of interactions. Right: Proposed model for the molecular mechanism of caffeine-ciprofloxacin antagonism. Caffeine triggers expression of MicF small RNA in a Rob-dependent manner, which then binds to the 5′-UTR of ompF mRNA to inhibit and decrease OmpF protein levels. This ultimately prevents ciprofloxacin from entering the cell, resulting in caffeine-ciprofloxacin antagonism

How are bacterial transport machineries regulated by external cues? @brochadolab.bsky.social &co identify environmental chemicals that regulate #transporter transcription, identifying the TF Rob as a key modulator of #EffluxPump expression in #Ecoli #AMR @plosbiology.org 🧪 plos.io/46pUM9Q

New preprint! We characterise the small, regulatory RNA Arp which controls DNA uptake and twitching motilty in A. baumannii. Led by our Dr Fergal Hamrock @hamrockfergal.bsky.social and in collaboration with @westermannlab.bsky.social and Mike Gebhardt's lab!

Congrats to Gianluca Prezza (@gprezza.bsky.social) for reveiving the 2025 PhD Award from the Friends of the Helmholtz Centre for Infection Research (HZI)!👏 The award honours excellent PhD theses from the field of life sciences at HZI partner universities. His thesis focused Bacteroides' RNA biology.

Low biomass bacterial transcriptomics takes shape Bornet et al. apply a low-input bacterial RNA-seq pipeline to transcriptionally profile small, medium, and large cell populations of the human gut symbiont Bacteroides thetaiotaomicron separated by fl...

Very honored that our recent study on Bacteroides morphotypes was spotlighted 🔦 in Trends in Microbiology by Eric Martens & Qinnan Yang: www.cell.com/trends/micro....

Thank you to all students and to the GSLS for this award! It means a lot to me! (-AW)

𝔟α𝐜𝐓𝕖Ř𝒾ⒶĹ ＳＨⓐ𝓹Ẹ 丂ħ𝓲ƒ𝓉ⒺⓇร 🦠

Ultra-sensitive RNA-seq and FISH show 𝘉𝘢𝘤𝘵𝘦𝘳𝘰𝘪𝘥𝘦𝘴 𝘵𝘩𝘦𝘵𝘢𝘪𝘰𝘵𝘢𝘰𝘮𝘪𝘤𝘳𝘰𝘯 cells adopt different shapes reflecting distinct gene expression profiles and metabolic specializations

A deliberate survival strategy for the ever-changing gut environment?

www.cell.com/cell-reports...