Cress Lab

An archaeal genetic code with all TAG codons as pyrrolysine Multiple genetic codes developed during the evolution of eukaryotes and bacteria, yet no alternative genetic code is known for archaea. We used proteomics to confirm our prediction that certain archae...

New paper out: An archaeal genetic code with all TAG codons as pyrrolysine: www.science.org/doi/10.1126/...

Thrilled to share the core of my PhD work, now published in NAR!

This project was a true collaborative effort across multiple teams, and it was a joy to bring it to life.

Huge thanks to everyone involved, and especially to @fnobrega.bsky.social for the incredible support and guidance 🙏🏻

🧵1/5

⭐ NAR Breakthrough! ⭐

A community-driven collection uniting 52 phages, 74 Klebsiella isolates, and extensive genomic + phenotypic data — all freely available at klebphacol.org.
🧬 Learn more: doi.org/10.1093/nar/...
@fnobrega.bsky.social @danielarothschild.bsky.social #antimicrobialresistance

Summer Undergraduate Research Experience | HHMI The Cech Fellows Program is a paid, nine-week summer research experience empowering the next generation of scientific leaders.

Calling all rising juniors & seniors: Interested in biological or biomedical research? Applications for our ’26 Summer Undergraduate Research Experience Program are now open! Nine weeks, hands-on research, & mentorship from some of the nation’s top scientists — learn more: bit.ly/CechFellows

What is the best strategy to win any contest?

Eliminate your opponents of course.

Recently, my friend @fernpizza.bsky.social showed how plasmids compete intracellularly (check out his paper published in Science today!). With @baym.lol, we now know they can fight.

www.biorxiv.org/content/10.1...

When different kinds of mobile genetic elements get together, they become even more powerful catalysts for microbial evolution! In this work we discovered a mechanism by which Insertion Sequences drive their spread across Plasmids, which helps explain this evolutionary potential!

Intracellular competition shapes plasmid population dynamics From populations of multicellular organisms to selfish genetic elements, conflicts between levels of biological organization are central to evolution. Plasmids are extrachromosomal, self-replicating g...

Hot off the press! Our latest paper led by @fernpizza.bsky.social, understanding how plasmids evolve inside cells. These small, self-replicating DNA circles live inside bacteria and carry antibiotic resistance genes, but also compete with one another to replicate. 1/
www.science.org/doi/10.1126/...

🚀New preprint from our lab!
I am very excited to finally share what has been the main focus of my PhD for the past almost 3 years! It is about viral dark matter and a powerful tool we built to shed light on it. 🧬💡
Continue reading (🧵)

🚨Preprint alert - this is a big one! We transfer the revolutionary power of TnSeq to bacteriophages.

Our HIDEN-SEQ links the "dark matter" genes of your favorite phage to any selectable phenotype, guiding the path from fun observations to molecular mechanisms.

A thread 1/8

The best group of lab Minions out there 🥸🧪

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...

Phylogeny-agnostic strain-level prediction of phage-host interactions from genomes Bacteriophages offer promising alternatives to antibiotics for treating drug-resistant infections and engineering microbiomes, but applications are limited by inability to select phages infecting spec...

#microsky #phagesky

Predicting host- #phage interactions from genomics.

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...

Programmable DNA insertion in native gut bacteria A gene-editing approach enables modification of bacteria within the mouse gut

also, an excellent perspective by @dbikard.bsky.social summarizing the work! 🙏
www.science.org/doi/10.1126/...

Congrats all!

We are hiring PhD & Postdocs in this space so please reach out if interested. Also check out the Gordon Research Conference on Microbiome Editing in Jan 11-16, 2026.
www.grc.org/microbiome-e...

Metagenomic editing of commensal bacteria in vivo using CRISPR-associated transposases Although metagenomic sequencing has revealed a rich microbial biodiversity in the mammalian gut, methods to genetically alter specific species in the microbiome are highly limited. Here, we introduce ...

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/...

🚀 PhD opportunity

The Dept of Biological and Environmental Science, University of Jyväskylä, is recruiting 1–4 new PhD candidates.

One of the positions is potentially in my lab, focusing on megaphages and their hosts.

Details and apply here 👇
bit.ly/48eqYNB

#phage

Congrats Diego, Carlotta, and all!

Metagenomic editing of commensal bacteria in vivo using CRISPR-associated transposases Although metagenomic sequencing has revealed a rich microbial biodiversity in the mammalian gut, methods to genetically alter specific species in the microbiome are highly limited. Here, we introduce ...

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/...

🔬 Interested in bacterial immune systems & AMR, or how antibiotics affect phage infectivity?

Three SWBio DTP PhD project opportunities linked to the MultiDefence consortium are now open (1/4)

#PhD #DoctoralTraining #ResearchCarrers #LifeSciences #phagesky #AMR #microsky #PhDPositions

We’re a bit late, but better late than never (bi do)! Happy Belated Halloween from the Cress and @therubinlab.bsky.social Labs!

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

Congrats!!!

Recurrent acquisition of nuclease-protease pairs in antiviral immunity Antiviral immune systems diversify by integrating new genes into existing pathways, creating new mechanisms of viral resistance. We identified genes encoding a predicted nuclease paired with a trypsin...

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

Congrats Alex, excited to read this!

Very happy to share our recent work @cultivarium.bsky.social on genetic tools for Ideonella sakaiensis, a (Betaproteo-)bacterium that degrades PET plastic.

We identified a plasmid vector for the strain and generated a large RB-TnSeq library, screening for genes impacting plastic degradation.

Figure 3. Conjugation tractability mutant screen results.

We also performed a neat screen where you deliver a plasmid to the RB-TnSeq library, and select to enrich gene mutants with improved transformation efficiency. This is kind of similar to a recent approach by @cresslab.bsky.social and colleagues (www.biorxiv.org/content/10.1...)