Simon Roux

Delighted to partner with @sullivan-lab.bsky.social & @labwilhelm.bsky.social on an exploration of the rhythms of viral life in the open ocean... led by Alfonso Carillo (OSU).

Bacterial Schlafen proteins mediate phage defence Nature Microbiology, Published online: 09 March 2026; doi:10.1038/s41564-026-02277-8This study highlights that Schlafens are ancient, mechanistically conserved immune effectors that mediate antiviral immunity in organisms ranging from humans to bacteria.

Out Now! Bacterial Schlafen proteins mediate phage defence #MicroSky

Sub-daily virus sampling at the Bermuda Atlantic Time Series reveals diel and depth-structured population dynamics without community-level shifts Viruses are often studied in disease settings, but in the ocean they outnumber cells and shape ecosystems, yet their dynamics remain poorly understood. In this study, high-resolution sampling of blue-...

Sub-daily virus sampling at the Bermuda Atlantic Time Series reveals diel and depth-structured population dynamics without community-level shifts journals.plos.org/plosbiology/... #jcampubs 🌊

🚨 𝗡𝗲𝘄 𝗽𝗿𝗲𝗽𝗿𝗶𝗻𝘁!

After years of work, I'm excited share our manuscript
"𝗣𝗿𝗲𝗴𝗻𝗮𝗻𝗰𝘆 𝗮𝗻𝗱 𝗘𝗮𝗿𝗹𝘆-𝗟𝗶𝗳𝗲 𝗚𝘂𝘁 𝗩𝗶𝗿𝗼𝗺𝗲 𝗶𝗻 𝘁𝗵𝗲 𝗟𝗶𝗳𝗲𝗹𝗶𝗻𝗲𝘀 𝗡𝗘𝗫𝗧 𝗰𝗼𝗵𝗼𝗿𝘁: 𝗢𝗿𝗶𝗴𝗶𝗻, 𝗣𝗲𝗿𝘀𝗶𝘀𝘁𝗲𝗻𝗰𝗲, 𝗜𝗻𝗳𝗹𝘂𝗲𝗻𝗰𝗶𝗻𝗴 𝗙𝗮𝗰𝘁𝗼𝗿𝘀 𝗮𝗻𝗱 𝗛𝗲𝗮𝗹𝘁𝗵 𝗜𝗺𝗽𝗹𝗶𝗰𝗮𝘁𝗶𝗼𝗻𝘀".

doi.org/10.64898/202...

A thread🧵👇 (1/11)

Carmen Sandiego from the 90s cartoon

Happy International Women's Day to the original International Woman

Vast scale of overseas human remains held in UK museums decried by MPs and experts Exclusive: Guardian study finds UK museums hold more than 260,000 items of remains, often in sacrilegious ways

'Lord Paul Boateng said the findings exposed UK museums and universities as “imperial charnel houses where the bones of Indigenous peoples torn from Britain’s empire in the past, with little or no regard...continue to be retained to this day in circumstances that beggar belief”.'

The School of Biosciences at University of Birmingham is recruiting FIVE Assistant/Associate Profs in areas including fungal biology, plant science and bioengineering. Full details below 🍄🌾🧬🧫

I've created this Starter Pack to help those with an interest in all things #soil find inspiring people, organisations, and platforms that regularly post content on #SoilScience, #SoilManagement, and #SoilGovernance. 🌱🧑🏻‍🌾🌾

Let me know if you wish to be added.

go.bsky.app/HADDT8P

Un poste MCF en génomique évolutive / écologie moléculaire à ECOBIOP - Université de Pau #PopGen 👇
urlr.me/rVQmN6

Viruses in marine sediments: a review of their effect on biogeochemistry and microbial interactions | Applied and Environmental Microbiology In the ocean, viruses are known to mediate the carbon cycle, keeping dissolved organic carbon (DOC) in the microbial loop and preventing its movement into secondary consumers (1). However, few direct ...

New paper out! We sat down and compiled all viral work in marine sediments. The water column has been getting a second look for viral interactions, its time for sediment to have the same!
journals.asm.org/doi/10.1128/...

🧫 Just out in Bioinformatics Advances: "AssiST: Convolutional neural network for analysis of antibiotic susceptibility testing" 

Read the full paper here:  https://doi.org/10.1093/bioadv/vbag063

Authors include: @carmenli.bsky.social, @amitchell.bsky.social

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.