Simon Roux

CRISPR targeting seems to suggest it's definitely not as "rare" as we may have thought, especially in situations like micro-aggregates, etc

➡️ preprint from the lab! Bacteria have loads of antiviral defences in their mobile genetic elements (MGEs). So when MGEs move between bacteria, the defences move with them, generating a fast turnover of defences in bacteria. But what about the antiviral defence turnover in the MGEs themselves? 🤔

🧵👇

This scalability unlocks extensive cross-proteome discovery. By querying viral proteomes against host genomes, FlashPPI identifies host-virus interactions involving previously uncharacterized proteins. 6/

Predicting protein-protein interactions (PPIs) at proteome scale can take months with co-folding models due to the massive all-vs-all comparisons required.

We are excited to announce FlashPPI, a contrastive learning framework that predicts proteome wide physical interfaces in minutes. 1/🧵

With Eugene Koonin, we propose a concept of “the selfish ribosome”, under which evolution of life is viewed as a ribosomal takeover, where the ribosome evolved to consume most of the cell’s resources, while other cellular componentry ensures the propagation of the ribosome. arxiv.org/abs/2602.23268

The Voyageurs Wolf Project of Northern Minnesota tags & documents grey wolf ecology & behavior: www.voyageurswolfproject.org

The video you see here is confirmatory proof:
Wolves. Love. Blueberries.

As much as 83% of a wolf's calories in summer months comes from eating berries.

🔔Seminar Opportunity🔔

We're looking for (self)recommendations for a Postdoc who is working in the area of AMR (any area, any discipline) to give an online seminar in May.

Reply, DM or email me, there will more opportunities in the future as well so will be good to have a list.

#MicroSky #AMR

Posting again!

Given that clonal biofilms of single bacterial species rapidly diversify into niche specialists, how do biofilms of multiple species evolve?
A 🧵 featuring new collaborative pubs:
1. www.biorxiv.org/content/10.6...
2. www.nature.com/articles/s41...

This is brilliant

So I pleased to announce the conceptual spawn of FigTree: PearTree (acronym still to be finalised). If you want to dive right in it is hosted as a web app here: artic-network.github.io/peartree (click the “Example...” button for immediate candy and then click every button you can find).

These wee birds are just zen

Post a pic you took, no context, to bring some zen to the feed.

Post a pic you took, no context, to bring some zen to the feed.

I have the same cat

Post a pic you took, no context, to bring some zen to the feed.

But this is so new that we 100% need more perspective and "cautionary tales" from people who have looked at these data in detail and thought deeply about these questions !!

"not perfect" for prophages either, "very not perfect" for lytic viruses 😁
We touch on this a bit in our "host prediction" review www.sciencedirect.com/science/arti...
and the Sullivan lab has done benchmarking that highlights the potential noise in these data
journals.plos.org/plosbiology/...

Also, g’damnit I need to write up the “Hi-C is not perfect when identifying plasmids and host cells” paper

New @plosbiology.org code sharing policy. In this Editorial, @npariente.bsky.social and Lauren Cadwallader explain the policy and offer guidance on compliance, noting that code sharing remains less well understood than equivalent requirements for data and ethics.

journals.plos.org/plosbiology/...

We’re recruiting new Research Group Leaders!
We offer:
🔬 Core funding
💻 Access to world-leading infrastructure
👩🏽‍🔬A network of world-leading scientists
…and much more.
Apply by 11 April: embl.wd103.myworkdayjobs.com/en-US/EMBL/j...
#ResearchCareers #Bioinformatics @timcoorens.bsky.social @embl.org

On this day on February 26, 1948, the Max Planck Society was formally founded in Göttingen as the successor organization to the Kaiser Wilhelm Society, in the cafeteria of the KWS's aerodynamic testing facility in Göttingen.

Happy birthday to....well, to us, actually! 😉🎂🥳 On this day on February 26, 1948, the Max Planck Society was formally founded in Göttingen as the successor organization to the Kaiser Wilhelm Society, in the cafeteria of the KWS's aerodynamic testing facility in Göttingen.

Courtesy of @martibartfast.bsky.social , we have a new release of AllTheBacteria which adds another 322,920 assemblies, covering all ENA (illumina, isolate) prokaryotes to May 2025.
allthebacteria.readthedocs.io/en/latest/ov...

Protease-Controlled Prophage Activation in Staphylococcus aureus: New Mechanisms Driving Antimicrobial Resistance and Virulence at University of St Andrews on FindAPhD.com PhD Project - Protease-Controlled Prophage Activation in Staphylococcus aureus: New Mechanisms Driving Antimicrobial Resistance and Virulence at University of St Andrews, listed on FindAPhD.com

📢 Funded PhD in molecular microbiology & phage biology

How do bacterial stress responses control prophage activation and horizontal gene transfer?

Join us at St Andrews to dissect Clp protease–mediated regulation in Staphylococcus aureus.

Apply:
www.findaphd.com/phds/project...

Reflections on MVIF #46 (Feb. 9-11)

We brought together researchers across continents for an inspiring exploration of microbiome science. Whether joining from the Atlantic (ATL) or Pacific (PAC) regions, our community connected to advance knowledge that transcends borders.

1/10

The MicrobeAtlas database: Global trends and insights into Earth’s microbial ecosystems MicrobeAtlas (www.microbeatlas.org) is an integrated, reference-based resource for truly planet-wide microbiomics, analyzing hundreds of thousands of microbial lineages across diverse environments, co...

MicrobeAtlas is now published in Cell. 🌐🌎🦠

Explore the paper and resource to see what large-scale microbiome data reveal about global ecological patterns:
www.cell.com/cell/fulltex...

For a concrete application, see our recent work on “Community conservatism”:
www.nature.com/articles/s41...

Scientists: for a new story, I have one big question—>

What is a “good day” in the lab?

I’m looking for epic examples of the best day ever to general criteria for what constitutes a “good day” compared to a nothing-burger day.

Ping me if you have examples to share!

Re-posts appreciated!