As my time as a researcher at FSU Jena and @microverse.bsky.social in the group of Rosalind Allen comes to an end, I warmly thank all collaborators and colleagues for the excellent science and discussions! 🚨I am (yes, again...) on the job market, looking for higher positions -->

"Planten kunnen niet poepen; daar hebben ze dieren voor nodig."

Welcome to Bluesky, @pieterhart.bsky.social! Pieter just joined my group as a PhD student studying bacterial genome evolution—exciting years ahead! Here he is enjoying a chat about his MSc work (w/ @kassipan.bsky.social & @ettema.bsky.social) at Science4Life @utrechtuniversity.bsky.social 🧬🦠✨

🧬🦠🚨 Another new paper alert, this time led by @maureenbug.bsky.social ! In collaboration with the Emerson lab and @titus.idyll.org lab (@taylorreiter.bsky.social), both at UC Davis. Asking the question: what are we missing in short-read metagenome assembly, and why ? doi.org/10.1093/narg...

Now officially published in Current Biology 🥳🥳 @mfseidl.bsky.social @binfutrecht.bsky.social www.cell.com/current-biol...

I am very excited to announce that a fully funded PhD position is available in my group. Topic: Synergistic coevolution in mono-specific and multi-species microbial consortia Please RT or forward this information to interested candidates. Deadline: 11.01.26 More info: shorturl.at/f1TuF

Very happy to see this piece out in @plosbiology.org, on the bacterial immune systems and microbial communities. It was a great team effort with Rafael Custodio, @brockhurstlab.bsky.social , @brownlab.bsky.social, and Edze Westra! 🦠🧫 #phagesky #mevosky journals.plos.org/plosbiology/...

🚨New preprint out! We present a foundational genomic resource of human gut microbiome viruses. It delivers high-quality, deeply curated data spanning taxonomy, predicted hosts, structures, and functions, providing a reference for gut virome research. (1/8) www.biorxiv.org/content/10.1...

Issuing a tentative but hopeful “holy shit” www.hollywoodreporter.com/movies/movie...

#microsky #mevosky @spp2389.bsky.social A PhD position is available in my lab to work on: Emergence and self-organisation of bacterial metabolism in consortia of cross-feeding bacteria. Please RT Deadline: 12.11.25 More infos 👇 shorturl.at/rAKAT

@prczhaoyansong.bsky.social’s deep dive into the dark matter of compost communities is now out 🎉 Genomic islands hijack jumbo phages—whose capsids enable transfer of large tracts of DNA—shedding new light on the scale & scope of phage-mediated gene flow 😎 www.pnas.org/doi/10.1073/...

Happy to announce that our comparative metagenomic analysis of the gut microbiota of five honeybee species - spearheaded by @aiswarya.bsky.social - is finally published in a peer-reviewed journal! rdcu.be/eKMCs @fbm-unil.bsky.social @dmf-unil.bsky.social 🧵👇

Very excited to share the latest work from our lab, which was published today in Nature! nature.com/articles/s41... PhD graduate and now post-doc Sofia Dahlman, along with co-senior author Sam Forster from The Hudson and other researchers from our lab and others.

Phages evolve fast, or do they? In oysters, some stay identical for years. With >1,200 phages & 600 Vibrio genomes, we reveal long-term stability and new mobile elements. Proud of this collaborative work across our teams (Roscoff-UdeM and @epcrocha.bsky.social www.biorxiv.org/cgi/content/...

Is a healthy microbiome one that is rich in phages? 🦠 Excited to share our paper out in Lancet Microbe with @bkoskella.bsky.social & @dholtappels.bsky.social where we test whether virome diversity can be used a broad signature of microbiome health 📈

Very nice documentary about the origins of complex life with my PhD advisor Berend Snel @binfutrecht.bsky.social!

Wetsvoorstel! Elke keer als een dichtgetikte boomer iets zegt dat dichtgetikte boomers al decennia roepen én daar aan toevoegt "dat je dit niet mag zeggen", krijgen ze daadwerkelijk een boete. Met je malle censuur-fetish.

Leuk interview met voormalig PhD student Lars Zandbergen over zijn promotie onderzoek in NRC. www.nrc.nl/nieuws/2025/...

How much of selection in human microbiomes is driven by phage? Excited to share our latest, led by A. Delphine Tripp, showing a case where phage is just not that important: Phage-mediated lysis does not determine Cutibacterium acnes colonization on human skin www.biorxiv.org/content/10.1... 🧵

Drop your backbone! Close your eyes! Focus on your science! Don’t talk politics!!

jeetje de fascisten hebben gefascist hoe kan dat nou (vanaf morgen in alle media: -boze burgers -zorgen serieus nemen -links begrijpt hen niet -links is eigenlijk erger -je moet trans ideologie niet opdringen -en de vluchtelingen dan -ja die zijn ook erg -misschien wel erger -PVV 42 zetels?)

www.biorxiv.org/content/10.1... #phagesky #phage Anecdotally, a few years ago a very trigger-happy temperate had infected a strain of E. coli of mine and caused significant lysis. The release of enzymes in the medium degraded a sugar into a different form which could be used by the other cells.

💧🌊 What happens when freshwater bacteria meet their salty counterparts? Our new preprint explores the ecological factors driving community coalescence 👉https://www.biorxiv.org/content/10.1101/2025.09.09.675091v1 @bedutilh.bsky.social @microverse.bsky.social

📢Join us for the next ECR #Viromics Webinar: "Chronotyping the #Ocean Virome: Fine-Scale Temporal Clustering Reveals Viral Ecological and Evolutionary Patterns" ‍🎙️Luis Bolaños Avellaneda, Exeter, UK 🗓️10 Sep 2025, 4 PM CEST 📍Online, Zoom (register for login details) 🔗 evbc.uni-jena.de/events/ecr-v...

At last ! A tool specifically for phage-plasmid hunters. Check tyPPing by @karinailchenko.bsky.social and @eugenpfeifer.bsky.social

Really appreciated how @sethf.bsky.social described using AI in the evolution class that we co- teach: “ it’s like paying for a gym membership and then using a forklift to raise and lower your weights.”

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...

Stoked to finally have a preprint out for Phold, our tool that uses protein structural information to enhance phage genome annotation #phagesky 1/n www.biorxiv.org/content/10.1...

📝New preprint! We investigated how spatial structure affects cooperation between phages, combining mathematical modelling and experiments. A short thread 🧶

Protein Structure Informed Bacteriophage Genome Annotation with Phold https://www.biorxiv.org/content/10.1101/2025.08.05.668817v1

In the arms race between viruses and their hosts, viruses have found a dependable ally..

Our new paper on experimental evolution in wild tree-holes -Eco-evolutionary robustness of wild bacterial communities to experimental perturbation #ISMEJournal @duhitasant.bsky.social Tom Smith Edgar Wong Juli Cohen @kayla-king.bsky.social Tom Bell academic.oup.com/ismej/advanc...

🚨 New preprint 🚨 My phage annotation tool, Phynteny, finally has a preprint and a brand new version powered by a cool AI transformer architecture and protein language models! #phagesky www.biorxiv.org/content/10.1...

We (with Clement Coclet, not on Bsky) had the chance to work on a broad "state of viromics" review. We tried to use this to give an overview of how the field changed over the last ~ 15 years, and also what we think are some of the major remaining challenges. Full-text access at -> rdcu.be/excHt

New online! Viromics approaches for the study of viral diversity and ecology in microbiomes

Er is altijd wel een overtreffende trap. En in een tijd dat steeds duidelijker is dat mensen zich als stripboekslechterik gedragen, moet de journalistiek daar in meegaan, denk ik. "Ah, dus je neukt twaalfjarige kinderen, maar je eet ze daarna niet op? Beetje brave Hendrik bent je wel hè? Loser!"

Dear Blue-Sky-verse, I have a question: On which platform did you advertise a position for a postdoctoral position (field: computational/ evolutionary biology) and made good experiences? The site could be paid or free. Thank you very much for your help.

We've folded a lot of proteins! You can see some of them here @linsalrob.bsky.social @gbouras13.bsky.social

❤️ www.uu.nl/en/news/paul...

Our paper demonstrating that within-species warfare interactions are ecologically important on human skin is now published in Nature Micro! www.nature.com/articles/s41...

Cycling along the Saale, I report with mixed feelings that the #insectapocalypse hasn’t reached Jena yet

🚨 Join us at TBB Utrecht by applying for this evo-devo PhD position! 🚨 www.uu.nl/en/organisat...

1/6 Today, Jared Kushner spoke via @euronews.com Albania about the sprawling luxury resort he plans to build on the Vjosa-Narta Protected Area, key habitat for millions of migratory birds & other wildlife. His greenwashing of the project is unconscionable.

Uptake and leakage rates differentially shape community arrangement and composition of microbial consortia academic.oup.com/ismej/advanc... #jcampubs

New pre-print out \o/ All about CRISPR, metagenomes, and what you learn when you collect (a lot of) spacers from natural communities, with @apcamargo.bsky.social @urineri.bsky.social @lhug.bsky.social but also Uri Gophna, Nikhil George (not on Bsky I think) & others at JGI doi.org/10.1101/2025...

Today we celebrate over 40 years of research of Rob de Boer, chair Professor of Theoretical Biology. Rob complemented his tremendous scientific career with a deep impact in multiple roles, as a dedicated teacher, an inspiring mentor, and a kind and generous colleague. Thank you, Rob!

Excited to share our new work! We found that bacteria can turn antagonism into a foraging strategy - by killing their neighbours, and eating their remains 🧫🔬💥

Thrilled to share our new paper in @science.org describing our discovery that bacteria can switch from competitors to bonafide predators when resources run dry—arming nanoscale “spears” (T6SS) to stab & consume neighbours. www.science.org/doi/10.1126/... #MicroSKy #Microbiology

This is still open for another week or so! Please apply :)

Researchers led by @bedutilh.bsky.social at the Cluster of Excellence @microverse.bsky.social investigate #phages, showing how viruses not only cause harm but also create the basis for diversity & balance. Read more in the #UniJena research magazine. ➡️ www.lichtgedanken.uni-jena.de/en/3157/smal...