Actually, what is a gain-of-function mutation? Abstract. For more than a century, scientists have worked to characterize, understand, and predict the consequences of mutations. For almost as long, scien

academic.oup.com/genetics/adv...

Also thanks to Lyndall & @psarkies.bsky.social, @ahocher.bsky.social, and members of the lab for their comments and Francis Barr @oxfordbiochemistry.bsky.social for encouraging me to write down my thoughts. 2/2

Phage receptor prediction from genome sequencing alone. Bacterial receptor (blue) interacting with phage proteins (purple) is shown here

📣Huge preprint 🔔
Today we share something our group has been working toward for a long time, led by @lucasmoriniere.bsky.social We asked can we predict which receptor a phage targets from its genome sequence alone? For most phages, we couldn’t. So Lucas set out to do something I had only dreamed of.

Want to annotate a bacterial genome with structures?

@oschwengers.bsky.social bakta and @gbouras13.bsky.social phold got together, and the result is Baktfold: protein annotation across the microbial tree of life using structures

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

#phagesky #microsky #microbiomesky

Did you know?

🧵 1/3

Fantastic snow excursion of the lab together with our friends in Martin Loessner's group 🏔😁☀️

🚨Preprint! Happy to share the research from my PhD “Genome delivery of a contractile tailed phage and its superinfection exclusion mechanism”. We use cryoEM to study the genome ejection of the phage T4, revealing how the tape measure protein regulates the process.
www.biorxiv.org/content/10.6...

A small polymerase ribozyme that can synthesize itself and its complementary strand The emergence of a chemical system capable of self-replication and evolution is a critical event in the origin of life. RNA polymerase ribozymes can replicate RNA, but their large size and structural ...

Ooooh. Cool new paper on origins of life. A simple 45-nucleotide RNA molecule that can perfectly copy itself.

www.science.org/doi/10.1126/...

Excited to share first preprint from our lab! @giubotti.bsky.social found that antibiotic tolerance in multispecies biofilms follows a surprising spatial pattern: cells survive only at intermediate distances from a partner species. 🦠 Preprint: doi.org/10.64898/202...

It seems that NCBI GenBank is currently not active beyond the repository itself and has also been unresponsive to requests for a while already.

Do you think this may be a transient inconvenience or a sign that we should explore alternatives such as ENA at EMBL-EBI?

Life’s evil twins, called mirror cells, could wipe us out if scientists don’t stop them Researchers are close to making “reversed” cells that may wipe us off the planet

What could mirror bacteria do in nature if created? A story of these prospects and a plan to prevent them.

Titles aside, I hope you'll read it (the tech is NOT close). Thanks to Tom Freeman for writing help & @jfischman.bsky.social for ace editing! www.scientificamerican.com/article/life...

Phold's manuscript is now available @narjournal.bsky.social thanks to @susiegriggo.bsky.social @npbhavya.bsky.social @vijinim.bsky.social @linsalrob.bsky.social @martinsteinegger.bsky.social @milot.bsky.social @eunbelivable.bsky.social & others not on bsky #phagesky academic.oup.com/nar/article/...

We've got ISSUES. Literally.

We scraped >100k special issues & over 1 million articles to bring you a PISS-poor paper. We quantify just how many excess papers are published by guest editors abusing special issues to boost their CVs. How bad is it & what can we do?

arxiv.org/abs/2601.07563

A 🧵 1/n

And that's why mastermixes were invented 🤣 happy new year tho

As the year ends, we decided to select our favorite papers of 2025

Turns out, it is impossible as we love them all!

So, we picked 'some' that exhibit the range of microbiology highlighted through the columns of Nature Microbiology.

Here is a glimpse into #EditorPicks of 2025

#MicroSky 🦠

Do you relate to this as well?

Line chart showing the nuclear arsenals of Russia and the United States, plus all other nuclear powers, from 1945 to 2024. After a large build-up during the Cold War, nuclear arsenals in the US and Russia have decreased in the last decades. But both still have thousands of warheads. The data source is the federation of American Scientists (2024). The chart is licensed CC BY to Our World in Data.

During the Cold War, US President Reagan put nuclear war in clear words:

“A nuclear war cannot be won and must never be fought. The only value in our two nations possessing nuclear weapons is to make sure they will never be used. But then would it not be better to do away with them entirely?”

Persistent trade-offs balance competition and colonization across centuries Microbial competition drives rapid adaptation, often forcing organisms to specialize in new ecological niches. Adaptations that improve competitive ability can reduce performance in other environments...

ICYMI, this new preprint is just awesome.

"Here, we show that O-antigen–dependent trade-offs between pathogenicity and interbacterial competition have persisted for over two centuries in natural P. viridiflava populations."

www.biorxiv.org/content/10.1...

Graphic representation of the recombination events in the Sugarlandvirus I and J variants. Top left: Representation of the variants isolates in the different strains in the three lines. Genome fragments of each parent are represented in a different color. Regions with the most abundant recombination events are marked and associated with a schematic representation of the functional annotation and intergenomic similarity between the two parental phages. Bottom left: 3D folding of the RBPγ. The consensus recombinant region, which is associated with the infection of the K-type 47, is represented in light orange. Variable positions detected in the protein sequence alignment of the variants are represented as hot pink spheres. The table indicates the percentage of identity of the parental protein sequences in three protein regions limited by the amino acids indicated. Right: Transmission electron microscopy (TEM) image of Klebsiella myoviruses artificially coloured, showing their characteristic contractile tails and icosahedral capsids. Image acquired by the Environmental and Biomedical Virology group (Institute for Integrative Systems Biology, Universitat de València-CSIC).

Capsule diversity limits #phage host range by affecting receptor-binding protein (RBP) interactions in capsulated #bacteria. @pilardomingoc.bsky.social &co show that generalist phages evolve host range via RBP mutation & recombination, but specialists remain stable @plosbiology.org 🧪 plos.io/48nvOqY

KlebPhaCol paper is now out! Go check it out and see all that we offer.

And when ready, visit our website for more: www.klebphacol.org

An archaeal genetic code with all TAG codons as pyrrolysine Multiple genetic codes developed during the evolution of eukaryotes and bacteria, yet no alternative genetic code is known for archaea. We used proteomics to confirm our prediction that certain archae...

Some archaea—an ancient group of microorganisms—have an entirely novel genetic code, according to a new study in Science.

The findings expand our understanding of how alternative genetic codes evolve and hint at new molecular tools for biotechnology applications. https://scim.ag/4omApQ7

Benchmarking with synthetic communities provides a baseline for virus-host inferences from Hi-C proximity linking Virus discovery has accelerated but linking viruses to hosts remains challenging. This study uses synthetic microbiomes to optimize and benchmark Hi-C for virus-host linkage inference, and applies thi...

🚨NEW paper: Benchmarking Hi-C for virus–host inference
journals.plos.org/plosbiology/...

A clear baseline for anyone mapping virus–host interactions that establishes robust, benchmarked thresholds for Hi-C linkages.

Key results: 👇

In bacteria, TnSeq revolutionized genetics by linking genes to phenotypes at scale. But for phages nothing equivalent exists. So we built HIDEN-SEQ, the first TnSeq approach for phages, enabled by a hide-and-seek interplay between the host CRISPR-Cas13a and a phage anti-CRISPR protein.

🚨Preprint alert - this is a big one! We transfer the revolutionary power of TnSeq to bacteriophages.

Our HIDEN-SEQ links the "dark matter" genes of your favorite phage to any selectable phenotype, guiding the path from fun observations to molecular mechanisms.

A thread 1/8

🚀New preprint from our lab!
I am very excited to finally share what has been the main focus of my PhD for the past almost 3 years! It is about viral dark matter and a powerful tool we built to shed light on it. 🧬💡
Continue reading (🧵)

Strain displacement in microbiomes via ecological competition - Nature Microbiology Mathematical modelling and experimental tests reveal principles that govern displacement of a resident strain by an invader in microbial communities.

Can we leverage bacterial competition for targeted replacement of harmful strains? Maybe! Our recent piece in @natmicrobiol.nature.com provides a theoretical framework and a set of experiments to show what it might take: www.nature.com/articles/s41...

Genome-scale CRISPRi profiling reveals metabolic vulnerabilities of uropathogenic Escherichia coli in human urine www.biorxiv.org/content/10.1101/2025.10....

Rosalind Franklin and the damage of gender harassment Spurred by a recent report on sexual harassment in academia, our columnist revisits a historical case and reflects on what has changed—and what hasn’t

Thinking only of Rosalind Franklin today, and what was stolen from her (and so many other female scientists alongside her).

Multi-layered ecological interactions determine growth of clinical antibiotic-resistant strains within human microbiomes Nature Communications - The role of ecological factors in modulating the spread of antibiotic-resistance bacteria in the gut remains unclear. Here, the authors use anaerobic microcosms to study the...

🚨 Excited to share our new paper is out! 🎉
We show how interactions within gut microbiomes allow certain antibiotic-resistant E. coli strains to persist even without antibiotics, helping explain how resistance is maintained in the human gut.

Now published in @natcomms.nature.com rdcu.be/eOf63

Bacterial Halloween mask crafted by uniquely talented MSc student Dominic Spichtig - the team of Enea @phagemuffin.bsky.social is setting new standards in the lab! 🎃🔥🧬

Happy to see this hit the public! A story worth checking out that started back during my days as master student 🧑‍🔬🧬🦠