✨New preprint! 🧵1/4 Excited to share our work on AI-guided design of minimal RNA-guided nucleases. Amazing work by @petrskopintsev.bsky.social @isabelesain.bsky.social @evandeturk.bsky.social et al! Multi-lab collaboration @banfieldlab.bsky.social @jhdcate.bsky.social @jacobsenucla.bsky.social🧬 🔗👇

Confused by all the histones that are cropping up in organisms that are decidedly NOT eukaryotes? check out our review - fantastic work by team NucEvo in the #Lugerlab The Expanding Histone Universe: Histone-Based DNA Organization in Noneukaryotic Organisms - www.annualreviews.org/content/jour...

I’m happy to share our new preprint! We uncovered the full diversity of bacterial TIR-based antiviral immune signaling, massively expanded the known diversity of Thoeris systems, and revealed conservation of TIR-derived immune signals across the tree of life. www.biorxiv.org/content/10.6...

📢 We have multiple open PhD positions to study bacterial immune systems using cutting-edge cryo-EM, microbiology, and biochemistry in our group! Join us and uncover how bacterial defenses eliminate predators and engineer next-gen biotech tools. 🔥 Apply by Jan 8, 2026 Details: phd.pages.ista.ac.at

Happy December! Join #MVIF 44 – we will discuss diverse #microbiome topics: human urinary, gut, oral and nasal microbiomes, extreme environments, and a new sequence alignment tool.

Are you a postdoc or 4-5th year grad student working on any problem in environmental microbiology and are interested in giving a virtual seminar (via zoom) on your hard work to a crowd of interested researchers at Montana State's Thermal Biology Institute in spring? Email/DM me!

Check out our latest paper on mirusviruses, one of the most remarkable new groups of protist viruses - extremely diverse, carry lots of spliceosomal introns (including new homing introns) and are at the evolutionary crossroads between tailed phages and herpesviruses! www.nature.com/articles/s41...

Officially out!

Now out in Science! Cyclin-dependent kinases (CDKs) are key regulators of the cell cycle. In @vcushing.bsky.social's magnum opus, we use #cryoEM to figure out how the CDK-activating kinase recognises CDKs to fully activate them - a key step in cell cycle control. www.science.org/doi/10.1126/...

omicsomics.blogspot.com/2025/10/pacb... $300 LongRead personal genome via PacBio

Most plasmids described in E. coli are small compared to the megaplasmids we identified here! Check out the preprint if you want to learn about these mysterious large elements and their potential functions 🧬. I’m very grateful to have had the opportunity to work on this in @banfieldlab.bsky.social

Now online at @nature.com we show how the Panoptes defense system protects against viruses that attempt immune evasion - and expands our understanding of the role of oligonucleotides in immunity. Check out this work co-led with @benadler.bsky.social here: www.nature.com/articles/s41...

New paper online at @nature.com from co-leads @erinedoherty.bsky.social + @benadler.bsky.social !

Our story describing the Panoptes bacterial immune defense system is now finally peer-reviewed and published today! www.nature.com/articles/s41...

Today in @nature.com , we highlight how a cousin of CRISPR-Cas10, mCpol, establishes an evolutionary trap in anti-phage immune systems. Check out @erinedoherty.bsky.social and my work from @doudna-lab.bsky.social lab here: www.nature.com/articles/s41...

Our Department of Microbiology & Immunology at UCSF is running a faculty search this year for a new Assistant Professor! Please see the ad below for details. Searching for a great colleague, mentor, and scientist! aprecruit.ucsf.edu/JPF05807

Join us tomorrow if you can. Link below to register.

New blog post! metaMDBG (@gaetanbenoit.bsky.social) and Myloasm (@jimshaw.bsky.social) have had recent releases, so I updated the benchmarks from the Autocycler paper: rrwick.github.io/2025/09/23/a... Both tools improved considerably! Time to update your conda environments 😄

The Department of Biology at Colorado State University is hiring an Assistant Professor in the area of plant-microbe interactions! Please spread the word! jobs.colostate.edu/postings/165...

❤️❤️❤️ CSU. Fort Collins is a lovely place to live, and students / faculty are awesome. I should know, I taught there for 15 years! Apply!

This is the dept where I got my PhD! Hiring for microbiology!

How can we understand the earliest events in evolution of eukaryotic immunity? @yao-li.bsky.social reports incredible molecular fossils of complete bacterial-like operons in eukaryotes that illuminate how animal immunity was first acquired from anti-phage defense www.biorxiv.org/content/10.1...

🦠Exciting PhD opportunity @ ETH Zürich! Our Environmental Microbiology group is looking for a motivated student to study microbial processes in peatland restoration — from fieldwork to metagenomics and lab experiments. 🗓 Start: Spring 2026 ⏳ Deadline: 3 Oct 2025 👉 Apply: lnkd.in/eSPiy6vQ Please 🔁

📢 🦠 A new methanotroph from Czech peat! Through an effort led by PhD student in my group Justus Nweze we isolated and describe a new CH4-muncher. Potential for a flexible (annaerobic) metabolisms and cool pH adaptations. www.biorxiv.org/content/10.1... #microbesky #microbiomesky

The beautiful, ever-expanding universe of viral proteins targeting nucleotide immune signals! Paper by @reneechang.bsky.social in @cp-molcell.bsky.social on a nucleotide sponge www.cell.com/molecular-ce... and preprint by @doudna-lab.bsky.social on viral nucleases www.biorxiv.org/content/10.1...

New pre-print from Doudna lab members @erinedoherty.bsky.social & @jnoms.bsky.social ✨ Here we explore how recurrent adaptation of a single anti-defense protein fold enables evasion of distinct immune systems.

At the request of @bradleyph.bsky.social, we have now added the Bacterial and Archaeal trees (credit to @aroneys.bsky.social) used to infer the GlobDB taxonomy to the website globdb.org Feel free to reach out if there's other resources you'd like to see added. No promises, but happy to chat 🖥️🧬🦠

Does sequence clustering confound AlphaFold2? www.sciencedirect.com/science/arti... From @hkws.bsky.social

New preprint up now! Interested in the evolution of halophily within DPANN archaea we decided to investigate the sister phylum to the Nanohaloarchaeota, GTDB phylum EX4484-52, for which we propose the name Caliditerrarchaeota www.biorxiv.org/content/10.1...

Excited to finally share this work! We noticed a pair of genes - a nuclease and a protease - shuffles between antiviral systems. We show how proteolysis activates the nuclease, triggering defense in known and unknown immune contexts. tinyurl.com/2uwwy4ty

‼️ New pre-print from co-leads @owentuck.bsky.social and Jason Hu! Check out this fascinating example of how coevolution enables defense system innovation.

Very proud to have our lab’s first work published in @cp-cellhostmicrobe.bsky.social! In this work, we use functional metagenomics to find phage defenses from human and soil microbiomes! Congrats to first author @luis840alberto.bsky.social ! www.cell.com/cell-host-mi... (1/3)

if i were a better person i would do a tweetorial on our recent paper - but, hey, read the paper. its right there, waiting for you. #Giantvirus #histones are cool! their #nucleosomes are cool. check it out.! thats the tweetorial. rdcu.be/exXBX

1. 🧵 New preprint out! WitChi: a fast, open-source Python tool to detect, quantify & prune compositional bias in MSAs. Lightweight, tree-free, scalable to 5k+ taxa... so we applied it to the GTDB archaea MSA. #ArchaeaSky #MEvoSky #MicroSky 🔗 doi.org/10.1101/2025... 💻 github.com/stephkoest/w...

Our latest work, driven by the fabulous @stephkoe.bsky.social! WitChi takes care of compositional bias in large phylogenomic datasets! WitChi is fast, efficient and free, try it out! With @kassipan.bsky.social and @danieltamarit.bsky.social

#Archaea #GRC folks, be sure to catch work by @oceancait.bsky.social representing our group this week in Switzerland. She'll talk about new Asgard archaea enrichments form the Oregon coast. Talk on Sunday, Poster during the week.

In a couple of days, my grad student Stavros Trimmer will present his new Asgard archaea culture at the GRC Archaea. He named it Skadiarchaeum after Skadi, the Norse goddess of skiing and hunting. Cartoon of Skadi based on cryoET, which was performed together with with @florianwollweber.bsky.social

Designed protein pockets recognize intrinsically disordered protein regions @science.org www.science.org/doi/10.1126/... www.science.org/doi/10.1126/... www.statnews.com/2025/07/17/n...

This #WorldZoonosesDay, learn five key facts about #zoonotic diseases and how we can prevent future outbreaks. Check out our infographic: onehealthtrust.org/publications...

🚨 Fresh from the press! We created and analyzed over 100 in vitro cyanobacterial consortia using well-characterized model cyanobacterial hosts to better understand how cyanobacteria recruit and interact with their microbiomes. Check it out: doi.org/10.1093/isme...

Structural motif search across the protein-universe with Folddisco www.biorxiv.org/content/10.1... Code: github.com/steineggerla... Web app: search.foldseek.com/folddisco

Franklin W. Stahl, 95, Dies; Helped Create a ‘Beautiful’ DNA Experiment. Gift article: www.nytimes.com/2025/07/07/s...

Lots of other fun Antarctic-themed things happening all week for the Family Fiesta too! www.monash.edu/performing-a...

📑 Programs? Printed. 🏛️ Venue? Looking amazing. 🧪 Energy? Building fast. We're almost ready to welcome the HFSP community to Melbourne for an unforgettable week of science and connection! Who's coming to the 24th HFSP Awardees Meeting? #HFSP #HFSPmtg2025

@science.org Zincore-coregulator dedicated to zinc🖐️ TFs essential in development www.science.org/doi/10.1126/... @rborza.bsky.social @sgregoricchio.bsky.social @amazouzi.bsky.social @zwartlab.bsky.social @lindersimon.bsky.social @tassosperrakis.bsky.social @thijnbrummel.bsky.social + al.

Beautiful work by Pam et al. !!

Congrats @sgribaldo.bsky.social !!

Bay Area friends! I’ll be around for the next few weeks. If you’re nearby and want to catch up - science chats, hikes, coffee, or just vibes — send me a message. Would love to reconnect

Our new consensus statement on reducing and reporting contamination in microbiome studies is the cover image of this month's Nature Microbiology: www.nature.com/articles/s41... In the cover photo, you can see our postdoc Sophie Holland in fully PPE sampling the atmosphere of terrestrial Antarctica.