Lukas Hafner

With AI getting better and better: will "taste" become the "key" human skill; e.g. the sense of knowing what is "good" and/or "true"?

Two intensive sampling periods of oyster-associated vibrio and their phage, 4 years apart, and many surprises. Despite being washed by the Atlantic, wide tides, and vibrio (almost?) disappearing most of the year, we can find the exact same virulent phages 4 years later (down to 0 SNP)! preprint👇

Mutational scanning by multiplexed genome editing of the essential transcription termination factor Nrd1. Proteins operate through a few critical residues, yet most proteins remain uncharacterized at the deep molecular resolution, particularly within essential genes, where functional dissection is obstructed by lethality. Here, we establish a platform for mutational scanning of essential genes at their endogenous locus, combining a repressible complementation system with multiplexed CRISPR-based genome editing in budding yeast. Our approach provides a generalizable framework for dissecting essential protein function in vivo, expanding the capacity to map critical residues underlying essential cellular processes. We applied this strategy to NRD1, encoding an essential RNA Polymerase II (RNAPII) termination factor and performed a systematic alanine scanning with near-saturation coverage. We discovered novel and unexpected lethal mutations in the CTD-interacting domain (CID), thus revealing an unanticipated importance for this domain. Overall, our results demonstrate the power of our mutation scanning platform to map critical residues underlying essential cellular processes. ### Competing Interest Statement The authors have declared no competing interest. European Molecular Biology Organization, https://ror.org/04wfr2810, ALTF 889-2022

1/ Do you have a favorite protein you wish you could dissect residue by residue? 🔬
Excited to share our platform for mutational scanning at endogenous loci in yeast (no ectopic expression needed!)
doi.org/10.1101/2025...

Microbial communities demonstrate robustness in stressful environments due to predictable composition shifts Environmental stress reduces species growth rates, but its impact on the function of microbial communities is less clear. Here, we experimentally demonstrate that increasing salinity stress shifts com...

Have you ever wondered what increasing environmental stress will do to microbial communities?

In our new preprint, @martinadalbello.bsky.social, Jeff Gore and I studied the impact of salinity on microbial community composition and function. 🧵 (1/5)
www.biorxiv.org/content/10.1...

Innovation is like falling asleep. You can create the right conditions for it, but you can’t force it to occur.

There’s a beautiful irony that all of our technologies rely on a phenomenon that fundamentally can’t be controlled.

A new version of gcplyr (1.12.0) has just been released and is available now from CRAN and github. This update fixes a handful of bugs along with some improvements to the documentation

mikeblazanin.github.io/gcplyr/

De novo mutations mediate phenotypic switching in an opportunistic human lung pathogen - Nature Communications Bacteria evolving within humans employ strategies to overcome trade-offs. Here, the authors report that the cystic fibrosis-associated pathogen Burkholderia dolosa alternates phenotypes in vivo by acc...

How likely are SNP-based phenotypic reversions during human infection/coloniziation?

Our latest paper on the rare CF pathogen B. dolosa -- a great collaboration with folks I've worked with since my PhD and led by Alex Poret -- adds to the evidence that reversions are likely in large populations.

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

Functional regimes define soil microbiome response to environmental change - Nature Experimental perturbation of soil pH leads to a generalizable model of the soil microcosm comprising three functional regimes with distinct mechanisms linking environmental change to metabolite dynami...

Published in Nature today! Here, we sought to systematically ask how natural community's metabolism changes with the environment. A simple consumer-resource model can predict N-cycle metabolism (nitrate use) and, more importantly, the mechanism behind its change.
www.nature.com/articles/s41...

Prophages block cell surface receptors to preserve their viral progeny - Nature Zip promotes the accumulation of free phages in bacterial lysogen communities, safeguarding phage progeny.

Prophages block cell surface receptors to preserve their viral progeny www.nature.com/articles/s41...

My quote of the day

As a consequence, geneticists described evolution simply as a change in gene frequencies in populations, totally ignoring the fact that evolution consists of the two simultaneous but quite separate phenomena of adaptation and diversification.

Ernst Mayr

When you still see microbial populations and communities everywhere after a week at the #GRCMicroPop

#JackWhitten #moma

The science was cutting edge, and the company was unparalleled- thank you everyone for such a welcoming and thrilling #GRCMicroPop! Looking forward to cyberstalking all your google scholar profiles ❤️

A celebratory cake at the 40th anniversary of the Gordon conference that says “ 40 years Micro Pop Bio Answering big questions with little things” .

This week I am at the #GRC meeting for Microbial Population Biology. It is my favourite meeting. There is nothing like these small meetings for gathering a community together, and I learn a huge amount here every time. Here is to 40 more years of this incredible conference!

Looking back to a fantastic microbial populations GRS&GRC - thanks to all the participants for providing so much food for thoughts!

An Artificial Intelligence system has learned how to cheat while playing chess. A good reminder of a universal law of evolving complex systems: cheaters are an expected outcome of complexity. Wonder how this will unfold. www.technologyreview.com/2025/03/05/1...

Listeria virulence: the key role of gene expression The bacterium Listeria monocytogenes can be pathogenic to humans and cause listeriosis, a potentially fatal infection. Until now, the variability in the pathogenicity of Listeria monocytogenes was not...

🧬 Listeria virulence: the key role of gene expression. @biupasteur.bsky.social team from the Institut Pasteur has recently shed new light on a new mechanism that determines virulence by regulating gene expression. ↘️ www.pasteur.fr/en/home/rese... #Listeria

45 days, 500 generations. Our first experimental evolution experiment using @atinygreencell.bsky.social chemistats. Crazy amount of spent media during the process.

This paper has been written by AI:
github.com/Technion-Kis...

To see how it works. check out our paper in NEJM AI, describing our "data-to-paper" platform: ai.nejm.org/doi/full/10....
#GenAI #LLMs #LLM

data to paper : Autonomous LLM-driven research from data to human-verifiable research papers YouTube video by Lukas Hafner

youtu.be/mHd7VOj7Q-g?...

Autonomous LLM-Driven Research — from Data to Human-Verifiable Research Papers Artificial intelligence (AI) promises to accelerate scientific discovery, but it remains unclear whether AI systems can perform fully autonomous research, and whether they can do so while adhering ...

Great way to continue here on 🦋: our data-to-paper framework is out in NEJM AI!

Autonomously analyzes data & writes human-verifiable papers.
+Fun AI-human copiloting!

with the amazing Tal Ifargan & Roy Kishony (not on 🦋 yet)

ai.nejm.org/doi/full/10....

Try it out:
github.com/Technion-Kis...

Systematic mapping of antibiotic cross-resistance and collateral sensitivity with chemical genetics - Nature Microbiology Resistance to one antibiotic can make bacteria resistant or sensitive to another antibiotic, opening paths for combinatorial treatments. This study presents an approach to systematically discover and ...

Excited to share our study led by @SakenovaNazgul! We used chemical genetics to identify and understand cross-resistance & collateral-sensitivity (CS) between antibiotics and reduced AMR development with CS drug pairs @embl.org with @camille_goemans @EPFL_en www.nature.com/articles/s41...

bsky.app/profile/biup...

How do the stressosome & stress responsiveness contribute to virulence heterogeneity in Listeria monocytogenes?

www.nature.com/articles/s41...

@biupasteur.bsky.social

Thanks a lot, Filipe!

Differential stress responsiveness determines intraspecies virulence heterogeneity and host adaptation in Listeria monocytogenes - Nature Microbiology Differences in virulence across the Listeria monocytogenes species are determined by the fine-tuning of SigB pathway responsiveness and reflect host adaptation.

1/6 Excited to share our new findings published today in
@naturemicrobiol.bsky.social, explaining what drives virulence heterogeneity in Listeria monocytogenes!
@lukashafner.bsky.social
@biupasteur.bsky.social
www.nature.com/articles/s41...

Differential stress responsiveness determines intraspecies virulence heterogeneity and host adaptation in Listeria monocytogenes - Nature Microbiology Differences in virulence across the Listeria monocytogenes species are determined by the fine-tuning of SigB pathway responsiveness and reflect host adaptation.

www.nature.com/articles/s41...

Good way to start here on bluesky: excited to share the latest contribution back from my PhD @biupasteur.bsky.social - and the end of a long standing chapter!

Many thanks to everyone involved!

We made a short video summarising our findings:
youtu.be/liJmZ51_Oxg