We built GenoPHI: a machine learning workflow that predicts phage-host interactions at strain level. This could help rapidly select phages to treat drug-resistant bacterial infections or for microbiome engineering without exhaustive lab testing. www.biorxiv.org/content/10.1...

📣 New preprint from us at phagefoundry.org 📣 A solid machine learning framework & to predict strain-level phage-host interactions across diverse bacterial genera from genome sequences alone. Avery Noonan from the Arkin Lab led this massive effort www.biorxiv.org/content/10.1...

I am so excited to share our project with you! We find prokaryotic proteases activate toxic enzymes and pores as a modular strategy in phage defense. We studied four fascinating protease-toxin pairs that are abundant across bacterial genomes: www.biorxiv.org/content/10.1...

I’m excited to share my recent postdoc work. Here, we interrogate how different phage infection outcomes (productive vs. restrictive) affect the expression of phage defense systems. We find that a restricted infection not only inhibits the phage but also induces increased immune protein abundance.

Beautiful preprint from Simone Evans et al. in Alex Gao's group looking at MBL/nuclease and other cool zymogens (pepco, EACC1) in antiphage defense systems. Great to see this paradigm extended - probably many more proteolytically activated effectors out there... www.biorxiv.org/content/10.1...

Amazing piece of work from @rtoshiro.bsky.social & Kim Seed at UC Berkeley. 🙌 Played a tiny role in this work. Surviving phage attack dynamically regulates bacterial immunity to defeat counterdefenses www.biorxiv.org/content/10.1...

Very excited to share our latest work in Science on metagenomic editing (MetaEdit) of the gut microbiome in vivo & directly modifying unculturable immune-modulatory SFB bug in the small intestine. 🦠🧬🛠️ www.science.org/doi/10.1126/...

#microsky #phagesky #phage defence Thanks, @crypticprophage.bsky.social for pointing it out on “the other side” www.science.org/doi/10.1126/...

A mysterious lactamase-nuclease module found in multiple defense systems finally solved ! Congrats @owentuck.bsky.social et al. !

Fascinating discovery - anti-phage defense protein is a proenzyme that is cleaved by partner protease after phage infection and all three! products of cleavage form active nuclease.

Huge congrats to Owen, Jason, and team! Such a fun story

1/9 Metagenomics lets us read microbiomes in nature without cultivation, but writing (editing) them in their native context is still a major challenge. Meet MetaEdit: a platform for pathway-scale metagenomic editing inside the gut microbiome. science.org/doi/10.1126/...

Our nuclease-protease story is out! We explored a fascinating case of coevolution and modularity in prokaryotic immune systems: www.science.org/doi/10.1126/... Thanks to wonderful coauthors/collaborators/friends, the whole @doudna-lab.bsky.social and everyone at @innovativegenomics.bsky.social

🚨vConTACT3 preprint live!🚨(Peer Review soon...!) vConTACT3 delivers a unified, scalable, and transparent framework for genome-based virus taxonomy — helping translate big viral data into systematic classification. 🔗 Read the preprint: doi.org/10.1101/2025... Improvements details below 👇

Preprint: Bacteria sense virus-induced genome degradation via methylated mononucleotides tinyurl.com/ch3damp We show how molecular byproducts released during virus-induced cell exploitation are used as signals to trigger host immunity Revealed by the amazing Ilya Osterman. See his thread below👇

Bacteria can sense when a virus starts shredding their genome — by detecting methylated mononucleotides. Here’s the story of how we discovered the Metis defense system 👇 www.biorxiv.org/content/10.1...

After 5 years of waiting, the new #CRISPR classification by Makarova et al. is out @natmicrobiol.nature.com www.nature.com/articles/s41...

"We need more institutional experiments for science" makes sense to me @seemaychou.bsky.social. We might not like some of 'em and some'll fail, but given academic science often looks like a feudal system needing an industrial revolution trying things can't hurt.. seemay.substack.com/p/big-experi...

🚨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...

#microsky #phagesky CRISPR-cas galore www.nature.com/articles/s41...

The Wilkinson Lab is open for science! @mskcancercenter.bsky.social 🧬We'll be finding funky new RNA biology, mainly by looking at reverse transcriptases (i.e. the Best Enzymes In The World)🧬 annnd: I'm hiring - come join! Especially postdocs and PhD students - please get in touch (NYC is great)

From @plos.org #Computational #Biology | Ten rules for a structural bioinformatic analysis | i like Recommendation #10: Visualize everything! | #Bioinformatics #Education #Recommendations #NotSimpleRules 🧬 🖥️ 🧪 🔓 CC/ @ppalagi.bsky.social ⬇️ journals.plos.org/ploscompbiol...

The Python Software Foundation won a $1.5m grant from the US government National Science Foundation. Turned it down because required to affirm that we "will not... operate any programs that advance or promote DEI" simonwillison.net/2025/Oct/27/...

Excited to share: DNA glycosylases are diverse antiviral effectors. They recognize phage base modifications and initiate genome destruction. A structure‑guided approach made the scope of this discovery possible! 🧪 #phagesky doi.org/10.1101/2025... #phage #microbiology

Our @narjournal.bsky.social manuscript is out! It explores the growth of the GTDB (gtdb.ecogenomic.org) since its inception, as well as updates to the website, methodology, policies, and major taxonomic and nomenclatural changes over the past three years. academic.oup.com/nar/advance-...

Excited to share some new work from the lab, led by @shelbyeandersen.bsky.social where we developed a method and computational pipeline to identify antiphage defenses across diverse bacterial phyla.

1/10 Genome maintenance by telomerase is a fundamental process in nearly all eukaryotes. But where does it come from? Today, we report the discovery of telomerase homologs in a family of antiviral RTs, revealing an unexpected evolutionary origin in bacteria. www.biorxiv.org/content/10.1...

US Academia Be Like

The latest preprint from the lab is out! Here we used structural clustering and immunoprecipitations to uncover some networks in our knowledge of giant virons proteomes. An interesting story by Hela Safi and @ambsch.bsky.social. www.biorxiv.org/content/10.1...

www.science.org/doi/10.1126/... #phagesky #phage

Panoptes guards the CBASS pathway (bacterial cGAS-STING). One facet of this work that I find particularly exciting is the genetic linkage between Panoptes and CBASS, which significantly co-occur in bacterial genomes. What other phage defense systems may be genetically (and functionally) linked?

Our work on the Panoptes antiphage system is published! Here we find that Panoptes "watches" the cytosol for phage immune evasion proteins–captured in this illustration by Clair Huffine of Insight Illustrations. A beautiful example of the effector triggered immunity paradigm.

Check out the complementary story from @doudna-lab.bsky.social led by @erinedoherty.bsky.social and @benadler.bsky.social Their work on OptE oligomerization is particularly crucial to completing our understanding of Panoptes. www.nature.com/articles/s41...

This is how the Craspedochiton zefranki do.

New preprint! Ever wondered why only a fraction of genomes encode CRISPR immunity? 🧬 🦠 Turns out CRISPR is rarely beneficial against virulent phages, being most beneficial against those for which resistance mutations are rare! An epic effort by Rosanna Wright www.biorxiv.org/content/10.1...

Job alert ‼️ UChicago Micro is hiring! Open to tenured/tenure track faculty at all levels in any area of microbiology. Come join our amazing and growing department. apply.interfolio.com/174404

The Peters lab is looking for a new team member! The role transposons play in evolution, basic mechanisms regulating transposition, and applying transposons as tools for genome modification with a special focus on guide RNA-directed transposition. cornell.wd1.myworkdayjobs.com/CornellCaree...

A little late to the Panoptes party, but I’m delighted to share that our paper is published! 👁️ www.nature.com/articles/s41...

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

Droplet-based Random Barcode Transposon-site Sequencing (Droplet RB-TnSeq) to characterize phage-host interactions https://www.biorxiv.org/content/10.1101/2025.09.29.679331v1

My pleasure @erinedoherty.bsky.social and @benmorehouse.bsky.social - for me this was the stand-out discovery of the last year in the field

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

This also leads to a major constraint for the evolution of viral proteins that inhibit immune signaling, which we explored in recent pre-print co-led with @jnoms.bsky.social www.biorxiv.org/content/10.1...

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...

Huge congrats for such an amazing story, @benadler.bsky.social and @erinedoherty.bsky.social!!

Super cool paper by @benadler.bsky.social @erinedoherty.bsky.social #phage #phagesky

Out today in @nature.com, a new paper from @doudna-lab.bsky.social lab, co-first authors @erinedoherty.bsky.social + @benadler.bsky.social and collaborators at @ucsandiego.bsky.social unveils a powerful new defense strategy in the arms war between viruses + microbes. Read here: ow.ly/mPQI50X5g68

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