Cress Lab

Our lab is proud to present our latest work harnessing Bridge Recombinase for genome-scale editing in diverse bacteria, microbiome editing, and programmable horizontal gene transfer.

🚨 New preprint 🚨 We’ve discovered millions of viruses from sequencing data but we don’t always know who they infect. Our new tool, VHAMSTeR generates broad virus host predictions across the tree of life (prokaryote, plant, animal, fungi and protist hosts) A thread 🧵👇 www.biorxiv.org/content/10.6...

www.biorxiv.org/content/10.6...

1/4 Bacterial immunity with “two-factor authentication”? Our new preprint by @monikajasnauskaite.bsky.social et al. reveals how DRT4 combines DNA synthesis with recognition of a phage protein to activate antiviral defense - a short thread below 🧵 BioRxiv: www.biorxiv.org/content/10.6...

Viruses have parasites too. Our new preprint shows how phages use VIPR to silence parasitic satellites, and how the satellites fight back with its own decoy VIPR RNAs that redirect VIPR to DNA REP elements in the host genome!! www.biorxiv.org/content/10.6...

LoL-align is out in @natmethods.nature.com! It aligns protein structures without superposition. More sensitive than TM-align and DALI, producing better alignments 5–20× faster. Now available in Foldseek! 📄 www.nature.com/articles/s41... 💾 github.com/steineggerlab/foldseek 🌐 search.foldseek.com

Want to run targeted hypermutation in E. coli? You can now order our DGRec plasmids from Addgene: www.addgene.org/browse/artic... We recommend using them in a strain with sbcB and recJ deletions such as this one: www.addgene.org/220588/

Forgot to tag #phage #phagesky #AMR

This work was possible 🙏 because of U.S. Department of Energy Office of Science BRaVE phagefoundry.org at Biosciences Area at Berkeley Lab. 🎨 Illustration by me 🎨

Huge thanks to my PI @vivekmutalik.bsky.social, Alexey Kazakov, @igmurray.bsky.social , and our collaborators Graham Hatfull, Michael Niederweis, Adam Deutschbauer, Katie S. Wetzel, Colin Lewis and Deborah Jacobs-Sera 🎉

What does it take for a mycobacteriophage to infect M. smegmatis mc² 155? 🦠🗺️ We mapped it for 70 phages using genome-wide CRISPRi. Our new preprint from the Phage Foundry is out! (phagefoundry.org) 🥳🧵 Read the preprint here: www.biorxiv.org/content/10.6...

Funded by the DOE for BRaVE Phage Foundry at @berkeleylab.lbl.gov @biosci.lbl.gov Thanks 🙏🏽 to Graham Hatfull, Katherine S. Wetzel and Michael Niederweis teams & Phage Foundry teams

A new preprint 🎉 from phagefoundry.org Mycobacteriophages are candidate therapies for drug-resistant mycobacterial infections, but we still don't know how most of them get into their hosts. Our new preprint tackles this challenge 👉🏽 www.biorxiv.org/content/10.6...

#plasmidbiology #plasmid Just out! 🚀 Thrilled by our discovery: the function of the C-terminal domain of MOBH1 relaxases! We uncovered this thanks to a fertility inhibitor encoded by a parasitic mobile genetic element. Congrats to Florence on a great piece of work! 👏 academic.oup.com/nar/article/...

Excited to share our work on bacterial immune signaling! Our preprint reveals how RNA-guided Cas13 cleaves host tRNAs to generate small-molecule messengers that activate 2TMβ, linking RNA recognition to membrane damage and phage defense. 1/11

Pleased to share my first preprint from my postdoc, where I ask what drives mobile DNA movement between bacterial cells in complex communities like the gut microbiome. To answer this, we built a way to capture mobile DNA in the act of moving between cells, using short-read metagenomics. 🧵

JOB ALERT: University of Virginia School of Medicine, Department of Microbiology, Immunology, and Cancer Biology is recruiting a virologist (open rank). Please share and forward to anyone who may be interested! More information and link to application: apply.interfolio.com/191946

1/2 Here we report the activity of Arc, a 50-aa DNA-binding protein encoded within IS605-family transposons. www.biorxiv.org/content/10.6...

Reminder🎗️: MCB is hiring Assistant Professors across 3 divisions! 🗓️ Application Deadline: October 19, 2026

www.biorxiv.org/content/10.6... New preprint from the lab. We tried to capture phage infection using scRNAseq. With admittedly mixed results. Importantly our reads weren’t random and we see predicted biological patterns. Phage gene expression along the genome for one 1/3

Our story with @hobbslabutah.bsky.social discovering CBASS sensing of phage proteases out now in @science.org New data include CBASS recognition of diverse proteases beyond T4, and verifying CD-NTase activation loop cleavage as the trigger for defense in vivo www.science.org/doi/10.1126/...

Super excited to share my postdoctoral work at @imbavienna.bsky.social @viennabiocenter.bsky.social - We discovered that some retrotransposons, or "jumping genes" 🧬, are able to spread from cell to cell via a new viral infectivity route. A short thread: 🧵👇 (1/7)

Bacteriophages in Antarctic subglacial lakes reveal novel biodiversity and biogeochemical potential | ISME Communications | Oxford Academic

The final version of our manuscript on TnSeq in bacteriophages (“HIDEN-SEQ”) is out today – if you have an interesting phage phenotype and want to know the underlying genetic basis, this one is for you! 1/4

Defining the essential genome of diverse phages with phage Tn-seq | Nature Microbiology

Very happy to share that HIDEN-SEQ is now out in @natmicrobiol.nature.com! Using this technique, we recapitulated decades of established phage genetics and uncovered new gene functions, including previously unknown anti-defense factors against several defense systems. www.nature.com/articles/s41...

*PLEASE RE-POST* Applications for the trainee-focussed GRS immediately preceding this meeting are also now open! We will begin accepting applicants on *January 15th, 2027*. We will expedite our review for applicants requiring Visas, so please submit ASAP. www.grc.org/microbial-po...

Happy to share the core work of my PhD! Our CRISPRi screens revealed key genes for E. coli survival in a gut environment shaped by diet and inflammation. Many thanks to my co-supervisors @dbikard.bsky.social and @nathalierolhion.bsky.social, and to all co-authors! Details in David's thread👇

Using recombinases to build robust cross-kingdom genetic circuits? 🧬 Need to know what they are *actually* doing? We got you covered! In the latest from the lab, we show the power of nanopore sequencing for unraveling the inner workings of these circuits. doi.org/10.1038/s414...

In our latest podcast (https://nebiolabs.com/4yJC1c3), microbiologist and virologist Dr. Paul Turner, from Yale School of Medicine, joins us to explain how bacteriophage can be used to treat and kill bacterial infections, and what the future of this technology looks like.

New preprint from PhD student Yu Sun. TSR1 is a TIR effector specialised for CRISPR defence. It is an obligate dimer activated by cA3 and degrades its own activator using a ring nuclease domain. Perhaps the first confirmed dimeric TIR effector? www.biorxiv.org/content/10.6...

ʙɪɴᴅᴄʀᴀꜰᴛ2 is out, and we're not waiting for the paper. The full code drops today, free for academic and industry use. We're releasing it early so you can start designing right now, and bring its full power to the current Adaptyv competition. github.com/PacesaLab/Bi...

New paper from the lab, out in Nature Microbiology. We ran CRISPRi screens to ask what genes E. coli needs in order to live in a gut and what this can tell us about the gut environment itself. https://doi.org/10.1038/s41564-026-02471-8

Language-Model-Based Detection of Genetic Editing in Bacteria https://www.biorxiv.org/content/10.64898/2026.09.17.751846v1

We built this tool and resource to share. These systematic gene functional annotations have been critical for our own work and we hope that they are widely useful for everyone. Enjoy!

Affinage: Genome-Scale Mechanistic Gene Annotation from the Published Literature arxiv.org/html/2607.02... affinage.wi.mit.edu this tool looks fantastic @iaincheeseman.bsky.social ! 🤯

Happy to see our work on the evolution of antiviral repertoires in P4-like satellites and their P2-like helper phages (check out the 🧵 👇) out in @narjournal.bsky.social 🔗 doi.org/10.1093/nar/... #phagesky #MicroSky #evosky

Preprint here: Please let us know if we have missed any references to cite. This is like looking at past 60 years of work with a small window. www.biorxiv.org/content/10.6...

Proud and excited to share our first preprint 🚀 in which we • create a high-fitness firewalled organism, • that stably colonizes the mouse gut for >100 days, • resists all tested phages in the gut, • and blocks horizontal gene transfer. + A new method: Chimera genomes to tailor existing synthetic

Genome-wide characterization of host factors involved in single-stranded RNA and DNA phage infection pathways https://www.biorxiv.org/content/10.64898/2026.09.17.752499v1

Pretty surreal to see our work in The New York Times. Thank you, Carl Zimmer, for sharing the story of VIPR! www.nytimes.com/2026/09/17/s...

VIPR is now out in Science! What started with a mysterious RNA led us to an unexpected way of recognizing DNA, as well as some clues to CRISPR’s origins. So happy to share these two papers with an incredible team. Links below; original discovery thread here ↓

Out now in Science: Two papers from our lab reveal VIPR, an RNA-guided DNA-targeting system in bacteriophages, providing clues to the origins of CRISPR www.science.org/doi/10.1126/... www.science.org/doi/10.1126/... Congrats to Peter Yoon, @kenjmloi.bsky.social @terryzzy.bsky.social, T.Docter & team

#Phages can evade #bacterial #immunity by disrupting #antiviral signals like cA3, triggering Panoptes defense systems. @mfwhite2.bsky.social &co show that Type II Panoptes detects cA3 loss and activates a CARF-TM effector to disrupt membranes & stop infection @plosbiology.org 🧪 buff.ly/1ixwg9v

New enzymes that create natural phosphorothioate modifications in RNA share homology with proteins in bacterial DndABCDE anti-phage defense! www.cell.com/cell/abstrac...

Microbial intergenic regions encode much of the regulatory and functional logic of the genome, but they remain systematically difficult to discover and annotate. We trained a sparse autoencoder on gLM2 to identify recurring patterns across hundreds of millions of microbial intergenic regions... 🧵

Microbial genomes have been extensively mined for new proteins, but the noncoding sequences between genes remain largely unexplored despite encoding important regulatory and functional information. In our new work, we asked whether gLM2 could help systematically discover these intergenic features.

Temperature-Switchable Genome Editors from Extremophile-Derived Integrases https://www.biorxiv.org/content/10.64898/2026.09.10.749218v1

RNA-guided transcriptional repression by TIGR-Tas systems https://www.biorxiv.org/content/10.64898/2026.09.09.750476v1

New PET upcycling work in Science Advances: BHET/MHET readily enter E. coli, letting us directly couple PET glycolysis to whole-cell biocatalysis. Fun collaboration with Dion Vlachos, and congrats to first author Roman Dickey! www.science.org/doi/10.1126/...