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Cress Lab

@cresslab.bsky.social
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The Cress Lab | Innovative Genomics Institute @ UC Berkeley | Microbiome Editing | Microbiome Delivery Technologies | Phage and MGE Functional Genomics | Hiring! www.cresslab.bio

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Saria McKeithen-Mead, PhD @sciria.bsky.social · 05/10/2026
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. 🧵
doi.org
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Uday Tak @nokaryote.bsky.social · 05/10/2026
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
apply.interfolio.com
Apply - Interfolio {{$ctrl.$state.data.pageTitle}} - Apply - Interfolio
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Sternberg Lab @sternberglab.bsky.social · 05/10/2026
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...
biorxiv.org
Arc represses gene expression in IS605-family transposons
Bacterial insertion sequences (IS) are compact transposable elements that encode proteins required for their mobility and maintenance, yet many also encode accessory proteins with poorly understood fu...
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UC Berkeley MCB @berkeleymcb.bsky.social · 05/10/2026
Reminder🎗️: MCB is hiring Assistant Professors across 3 divisions! 🗓️ Application Deadline: October 19, 2026
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James Gurney @jamesgurney.bsky.social · 02/10/2026
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
biorxiv.org
Robust Inference of Phage-Host Infection Dynamics from Sparse Single-Cell Transcriptomics Profiles in Pseudomonas aeruginosa
Phage therapy is providing a benefit to a limited number of people. To date those who have received phage therapy typically have done so via an IND expanded access mechanism, colloquially referred to ...
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Kranzusch Lab @kranzuschlab.bsky.social · 01/10/2026
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/...
science.org
Phage proteases activate CBASS antiphage immunity
Cyclic oligonucleotide–based antiphage signaling systems (CBASS) are bacterial immune pathways evolutionarily related to cGAS-STING (cyclic GMP-AMP synthase–stimulator of interferon genes) in humans. ...
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Maya Voichek @mayavoichek.bsky.social · 24/09/2026
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)
AI-generated illustration of the soma-to-germline transmission of retrotransposons described in our work
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Tominaga K. (tomiken) @pacyc184.bsky.social · 27/09/2026
Bacteriophages in Antarctic subglacial lakes reveal novel biodiversity and biogeochemical potential | ISME Communications | Oxford Academic
dx.doi.org
Bacteriophages in Antarctic subglacial lakes reveal novel biodiversity and biogeochemical potential
Abstract. Of the more than 600 subglacial lakes identified in Antarctica thus far, Whillans Subglacial Lake and Mercer Subglacial Lake are the only lakes t
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Alexander Harms @aharms485.bsky.social · 25/09/2026
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
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Tominaga K. (tomiken) @pacyc184.bsky.social · 25/09/2026
Defining the essential genome of diverse phages with phage Tn-seq | Nature Microbiology
nature.com
Defining the essential genome of diverse phages with phage Tn-seq - Nature Microbiology
Phage Tn-seq uses Tn5 transposon mutagenesis with anti-CRISPR-based selection and deep sequencing as a method to generate unbiased, genome-wide mutations across diverse phages
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Dorentina Humolli @humollidorentina.bsky.social · 25/09/2026
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...
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Noah Houpt @noahhoupt.bsky.social · 22/09/2026
*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...
grc.org
2027 Microbial Population Biology (GRS) Seminar GRC
The 2027 Gordon Research Seminar on Microbial Population Biology (GRS) will be held in Andover, New Hampshire. Apply today to reserve your spot.
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Amandine Maire @amandinemaire.bsky.social · 22/09/2026
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👇
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Thomas Gorochowski @chofski.bsky.social · 22/09/2026
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...
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New England Biolabs @nebiolabs.bsky.social · 21/09/2026
In our latest podcast (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.
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Malcolm White @mfwhite2.bsky.social · 21/09/2026
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...
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Martin Pacesa @martinpacesa.bsky.social · 21/09/2026
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...
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David Bikard @dbikard.bsky.social · 21/09/2026
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. doi.org/10.1038/s41564-026-02471-8
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bioRxivpreprint @biorxivpreprint.bsky.social · 21/09/2026
Language-Model-Based Detection of Genetic Editing in Bacteria www.biorxiv.org/content/10.64898/20…
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Iain Cheeseman @iaincheeseman.bsky.social · 20/09/2026
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!
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Alexis Verger 🧬🧫🧪 @alexis-verger.cpesr.fr · 20/09/2026
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 ! 🤯
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Jorge Moura de Sousa @jmouradesousa.bsky.social · 20/09/2026
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
doi.org
Shuttling, swapping, and mixing: the rapid modular evolution of antiviral repertoires in temperate phages and their satellites
Abstract. Interactions between bacteria, bacteriophages, and their satellites are shaped by a myriad of defence and counter-defence mechanisms. Here, we id
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Vivek Mutalik @vivekmutalik.bsky.social · 19/09/2026
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...
biorxiv.org
Genome-wide characterization of host factors involved in single-stranded RNA and DNA phage infection pathways
Single stranded RNA (ssRNA) and single stranded DNA (ssDNA) bacteriophages represent a key component of the global virome, yet the host genetic networks supporting their infection cycles remain poorly...
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Cress Lab @cresslab.bsky.social · 19/09/2026
Congrats Akos! Excited to read this.
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Akos Nyerges @akosnyerges.bsky.social · 19/09/2026
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
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bioRxiv Microbiology @biorxiv-microbiol.bsky.social · 19/09/2026
Genome-wide characterization of host factors involved in single-stranded RNA and DNA phage infection pathways www.biorxiv.org/content/10.64898/20…
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Kenneth Loi @kenjmloi.bsky.social · 18/09/2026
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...
nytimes.com
The Next Gene-Editing Technology May Also Be the Oldest (Gift Article)
Scientists have discovered a powerful gene-targeting system in viruses. Billions of years old, VIPR seems to predate CRISPR and may be even more effective.
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Kenneth Loi @kenjmloi.bsky.social · 18/09/2026
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 ↓
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Doudna Lab @doudna-lab.bsky.social · 19/09/2026
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
science.org
A noncontiguous code for RNA-guided DNA recognition at the origin of CRISPR-Cas
CRISPR-Cas provides RNA-mediated adaptive immunity, but how its first RNA-guided effector arose is unclear. In this study, we report the discovery of Viral Interference Programmable Repeat (VIPR) syst...
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PLOS Biology @plosbiology.org · 18/09/2026
#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
Left: Organisation and mechanism of the Panoptes System. In type I Panoptes systems, mCpol is constitutively active, generating signalling molecules that inactivate the cognate effector, 2TMβ. When an infecting phage expresses a sponge protein, the cyclic oligonucleotide pool is depleted. The Panoptes effector oligomerises, leading to membrane disruption and growth arrest or cell death. Right: CARF-TM model structure and cA3 binding. Alphafold3 model of CARF-TM in complex with cA3, including POPG molecules to simulate the membrane bilayer. The position mutated to generate the truncated CARF protein is shown by black arrows.
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Kranzusch Lab @kranzuschlab.bsky.social · 17/09/2026
New enzymes that create natural phosphorothioate modifications in RNA share homology with proteins in bacterial DndABCDE anti-phage defense! www.cell.com/cell/abstrac...
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Tatta Bio @tattabio.bsky.social · 15/09/2026
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... 🧵
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Yunha Hwang @microyunha.bsky.social · 15/09/2026
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.
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bioRxiv Molecular Biology @biorxiv-molbio.bsky.social · 13/09/2026
Temperature-Switchable Genome Editors from Extremophile-Derived Integrases www.biorxiv.org/content/10.64898/20…
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bioRxiv Molecular Biology @biorxiv-molbio.bsky.social · 12/09/2026
RNA-guided transcriptional repression by TIGR-Tas systems www.biorxiv.org/content/10.64898/20…
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Aditya Kunjapur @kunjapur.bsky.social · 11/09/2026
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/...
science.org
Robust cellular transformations of PET deconstruction products by import of glycol esters
Efforts to transform polyethylene terephthalate (PET) deconstruction products using live cells have been limited by terephthalic acid (TPA) uptake. Here, we used an intracellular carboxylate reduction...
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François Rousset @francoisrousset.bsky.social · 08/09/2026
🚨 We are excited to share the first preprint of our lab ! We discovered an NADase enzymatic domain in bacterial immunity and in the human protein TEP1. www.biorxiv.org/content/10.6...
biorxiv.org
A widespread NADase domain links bacterial immunity with human TEP1
Recent discoveries on bacterial immunity have revealed that several protein domains involved in anti-phage defense are conserved in eukaryotes, such as SIRim, TIR, PNP and gasdermin. Bacterial immune ...
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Conner Langeberg @clangeberg.bsky.social · 05/09/2026
RNA structure prediction lags behind proteins for lack of data. RNASSTR, our new dataset, offers millions of RNA sequence-secondary structure pairs, split structurally to avoid train/test leakage. 📄 doi.org/10.1261/rna.... 📰 innovativegenomics.org/news/ai-mode...
doi.org
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Rafal Mostowy @rafalmostowy.bsky.social · 04/09/2026
🧬 Postdoc ad is now live: evolutionary genomics of Klebsiella pneumoniae phages. How do prophage depolymerases vs SGNH-esterases shape phage host range? Krakow, Poland. Deadline 21 Sept: mostowylab.com/job-postdoc-...
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Filipa Trigo da Roza @filipatr.bsky.social · 03/09/2026
It’s out! 🥹🎉 We’re so incredibly happy and proud to see this work out in the world. And once again, a huge thank you to the great mastermind @jaescudero.bsky.social and all the co-authors; this wouldn’t have been possible without you! doi.org/10.1038/s415... @natmicrobiol.nature.com
doi.org
High-throughput recovery of integron cassettes for gene discovery screens - Nature Microbiology
Integron insertion sites engineered into counterselection markers allow large-scale and high-throughput capture of integron-encoded genes from genetically tractable bacteria or DNA samples.
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Patrick R. Secor @prsecor.bsky.social · 02/09/2026
This job ad is now live! Please share or apply here: jobs.montana.edu/postings/52780 Screening of applicants begins Sept 15, 2026 #MicroSky #PhageSky #ScienceJobs
jobs.montana.edu
Postdoctoral Researcher - Lyme Disease Bacteriophage Biology
The Secor Lab seeks a postdoctoral researcher to investigate bacteriophage biology in the Lyme disease spirochete Borrelia burgdorferi. The successful candidate will help define how phiBB-1 controls h...
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Erin Doherty @erinedoherty.bsky.social · 31/08/2026
I'm very excited to share that this January, I’ll be joining Columbia University’s Department of Biological Sciences as a tenure-track Assistant Professor 🏙️🦁🍎 @columbiauniversity.bsky.social 🧬 Learn more: dohertylab.org Thank you to all those who supported me along the way!
dohertylab.org
Doherty lab at Columbia University | immune signaling | Sherman Fairchild Center, 1212 Amsterdam Ave, New York, NY 10027, USA
We treat viral antagonism as a discovery tool for host biology to reveal fundamental mechanisms of immune signaling and new opportunities for therapeutic intervention.
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Nucleic Acids Research @narjournal.bsky.social · 28/08/2026
Congratulations to Edan Mortman and @sternberglab.bsky.social @shsternberg.bsky.social on this fascinating and important achievement! 🎉 Your work provides a compelling look at how selfish genetic elements balance their own propagation with the survival of their host. @columbiauniversity.bsky.social
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Nucleic Acids Research @narjournal.bsky.social · 28/08/2026
⭐ #NARBreakthrough ⭐ How do #IStrons juggle 3 competing functions from a single sequence? #Newstudy reveals an RNA-level #tug-of-war between #self-preservation and #hostprotection, shaped by #RNAfolding 🔬Read the article here: doi.org/10.1093/nar/...
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Hiten Madhani @hitenmadhani.bsky.social · 27/08/2026
Most basic science departments at UCSF are having faculty searches this year. Biochemistry & Biophysics, Microbiology & Immunology, Cellular and Molecular Pharmacology, Physiology and more. We're looking for new and exciting science and nice people. You'll find them all at aprecruit.ucsf.edu
aprecruit.ucsf.edu
Welcome - AP Recruit
University of California, San Francisco Online Faculty Recruitment
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Martin Steinegger 🇺🇦 @martinsteinegger.bsky.social · 26/08/2026
Foldseek-Interface enables fast search/clustering of the protein interface universe! We clustered 3.1M PDB dimers into 77,167 groups and found new interfaces keep appearing even as fold discovery plateaus. 🧵 📄 www.biorxiv.org/content/10.6... 🔎 search.foldseek.com/interface 🌐 interface.foldseek.com
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Patrick R. Secor @prsecor.bsky.social · 21/08/2026
I’ll soon be #Hiring a postdoc to join the Secor Lab at Montana State University. This NIH-funded position will investigate phage biology in Lyme disease spirochetes. The official ad will be available soon. Please share with anyone who might be interested! #MicroSky #PhageSky 🔬🦠🧪🧫
An engorged tick with fluorescent bacteria in its midgut
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Savitski Lab @savitski-lab.bsky.social · 20/08/2026
1/5 How much phosphorylation can a single kinase deposit? In our new study with @typaslab.bsky.social out in @nature.com, phage T7's kinase (T7K) modifies almost all the E. coli proteome + more densely than all ~500 kinases do our own proteomes 🤯 www.nature.com/articles/s41...
nature.com
Pervasive phosphorylation by phage T7 kinase disarms bacterial defences - Nature
The T7 bacteriophage deactivates bacterial defence systems through T7K phosphorylation of nearly all host and phage proteins during infection.
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Typas Lab @typaslab.bsky.social · 20/08/2026
Excited to share our paper with @savitski-lab.bsky.social, led by @tarabartolec.bsky.social, Karin Mitosch & Clément Potel, out now in @nature.com. We show that T7 phage broadly disables bacterial defenses using a unique ‘loose cannon’ protein kinase. www.nature.com/articles/s41...
nature.com
Pervasive phosphorylation by phage T7 kinase disarms bacterial defences - Nature
The T7 bacteriophage deactivates bacterial defence systems through T7K phosphorylation of nearly all host and phage proteins during infection.
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Trends in Microbiology @cp-trendsmicrobiol.bsky.social · 18/08/2026
Disarming a pathogen with programmable phage-derived particles
dlvr.it
Disarming a pathogen with programmable phage-derived particles
Shiga toxin-producing Escherichia coli (STEC) presents a therapeutic dilemma because antibiotic treatment induces prophage-encoded Shiga toxin expression. Galtier et al. engineer phage-derived particles with programmable cell specificity, genetic cargo, and CRISPR guide RNAs that destroy stx while killing STEC in animal models.
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