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

High-accuracy SNV calling for bacterial isolates using deep learning with AccuSNV Accurate detection of mutations within bacterial species is critical for fundamental studies of microbial evolution, reconstructing transmission events, and identifying antimicrobial resistance mutati...

Precisely calling mutations across hundreds of bacterial isolates has been hard, requiring manual filtering and expertise.

Until now, using AccuSNV.

Herui Liao trained an ML model based on our previous meticulously called SNVs.
www.biorxiv.org/content/10.1...

Rational design of a hospital-specific phage cocktail to treat Enterobacter cloacae complex infections - Nature Microbiology The Entelli-02 phage product containing five phages has frontline potential to address infections caused by the multidrug-resistant Enterobacter cloacae complex.

Excited to annouce the latest research published by our lab, which is led by Dinesh Subedi and is out today in Nature Microbiology.

www.nature.com/articles/s41...

Phages with a broad host range are common across ecosystems - Nature Microbiology Proximity-ligation-based sequencing from 111 samples and 5 environments reveals that a substantial proportion of phages infect multiple species.

You like phages ? In this publication, we use metaHiC and our new version of the MetaTOR pipeline to challenge the traditional view of phages with a narrow host range.
@rkoszul.bsky.social @natmicrobiol.nature.com @cnrs.fr @institutpasteur.bsky.social

www.nature.com/articles/s41...

YprA family helicases provide the missing link between diverse prokaryotic immune systems https://www.biorxiv.org/content/10.1101/2025.09.15.676423v1

A widespread family of viral sponge proteins reveals specific inhibition of nucleotide signals in anti-phage defense Chang et al. discover anti-CBASS 4 (Acb4), a family of viral sponges that inhibits bacterial immunity by sequestering nucleotide immune signals. Acb4 homologs in phages that infect hosts across all ma...

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...

Divergent viral phosphodiesterases for immune signaling evasion Cyclic dinucleotides (CDNs) and other short oligonucleotides play fundamental roles in immune system activation in organisms ranging from bacteria to humans. In response, viruses use phosphodiesterase...

Excited to share our new preprint co-led by @jnoms.bsky.social!

Here we reveal an exceptional diversity of viral 2H phosphodiesterases (PDEs) that enable immune evasion by selectively degrading oligonucleotide-based messengers. This 2H PDE fold has evolved striking substrate breath & specificity.

The RecBCD complex interacts directly with the DNA sliding clamp in Escherichia coli https://www.biorxiv.org/content/10.1101/2025.08.20.671105v1

Synteny and linkage decay in bacteriophage pangenomes Bacteriophages are rich in genetic diversity, due to frequent horizontal transfer and recombination. This makes traditional microbial phylogenetic analyses, often based on the assumption of vertical i...

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

#phage #phagesky

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)

Recurrent acquisition of nuclease-protease pairs in antiviral immunity https://www.biorxiv.org/content/10.1101/2025.07.28.667249v1

Bacterial Schlafens mediate anti-phage defense Human Schlafen proteins restrict viral replication by cleaving tRNA, thereby suppressing protein synthesis. Although the ribonuclease domain of Schlafen proteins is conserved across all domains of lif...

First preprint from the Nemudryi Lab! 🍾

In this work, we link antiviral immunity in bacteria and humans by showing that homologs of human Schlafen nucleases protect bacteria from phages.

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

📢Preprint out!
Excited to share my final work from the @soreklab.bsky.social!

We mined phage dark matter using structural features shared by anti-defense proteins (viral tools that help phages bypass bacterial immunity) to guide discovery.

Found 3 new families targeting immune signaling!

Nuclease-NTPase systems use shared molecular features to controlbacterial anti-phage defense https://www.biorxiv.org/content/10.1101/2025.07.10.664194v1

Structural insights into type I and type II Lamassu anti-phage systems https://www.biorxiv.org/content/10.1101/2025.06.23.660979v1

New preprint: Modeling protein expression with explicit tRNA dynamics. We find that there's an optimum level of codon usage bias that maximizes expression. We also find charged rare tRNAs get fully depleted in late-stage bacteriophage T7 infection.
www.biorxiv.org/content/10.1...

Elucidating the mechanisms of action and evolutionary history of phage anti-defence proteins Phages and bacteria are locked in a molecular arms race, with phage anti-defence proteins (ADPs) enabling them to evade bacterial immune systems. To streamline access to information on ADPs, we develo...

Very excited to share our preprint on a new resource: the Encyclopaedia of Viral Anti-Defence Systems (EVADES)! This is the main result of my PhD at ‪EMBL-EBI (@ebi.embl.org)‬
and the University of Cambridge (@cam.ac.uk‬)! 🔗 www.biorxiv.org/content/10.1... 🧵1/n"

Really happy to see Julia Lopez-Perez's dissertation work on #phage defense systems in print:
mdpi.com/1422-0067/26...
🦠🔬
Check out a novel mechanism for #salmonella plasmid-mediated abortive infection
@mdpiopenaccess.bsky.social

A census of anti-CRISPR proteins reveals AcrIE9 as an inhibitor of Escherichia coli K12 Type IE CRISPR-Cas system CRISPR-Cas adaptive immunity systems provide defense against mobile genetic elements and are often countered by diverse anti-CRISPR (Acr) proteins. The Type IE CRISPR-Cas of Escherichia coli K12 has b...

We performed a dedicated search of anti-CRISPR proteins targeting the model E. coli Type IE CRISPR-Cas system and revealed AcrIE9 as a potent inhibitor and the most widespread anti-CRISPR protein in enteric bacteria.
www.biorxiv.org/content/10.1...

Cross-order detection of bacteriophage transduction in communities using ribosomal RNA barcoding Bacteriophages (phages) facilitate gene transfer and microbial evolution in all ecosystems and have applications as tools for engineering microbiomes and as antimicrobials. Historic efforts to map pha...

Very excited to share a manuscript at the heart of my PhD! We added an RNA-memory device (RAM) to phage P1 to identify transduction hosts in synthetic and wastewater microbial communities in high throughput. Also, I am on the post-doc market, so please reach out if interested! 1/6

t.ly/a8k9O

Target-induced Argonaute-HNH filaments confer bacterial immunity Argonaute proteins provide innate immunity in all domains of life through guide-dependent recognition of invader nucleic acids. While eukaryotic Argonautes (eAgos) act on RNA during RNA interference, ...

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

Previously characterized OLD family ATPases-nucleases participate in anti-virus defense (abortive infection, Gabija, retrons, PARIS). A new class of #archaeal OLD family enzymes is instead implicated in cell cycle control. New work from the group of Yulong Shen. www.biorxiv.org/content/10.1...

A minimal CRISPR polymerase produces decoy cyclic nucleotides to detect phage anti-defense proteins https://www.biorxiv.org/content/10.1101/2025.03.28.646047v1

Taxonomically different symbiotic communities of sympatric Arctic sponge species show functional similarity with specialization at species level Marine sponges harbor diverse communities of associated organisms, including eukaryotes, viruses, and bacteria. Sponge associated microbiomes contribute to the health of the host organisms by defendin...

Check it out! Three Arctic sponge species, six years of observation, and seven symbiotic bacteria—six of which belong to novel candidate genera. An odyssey that began in 2016 is now complete!
www.biorxiv.org/content/10.1...
#Sponges #Microbiome #Symbiosis #BacteriaSymbionts #Arctic

A new family of small ArdA proteins reveals an antirestriction activity. https://www.biorxiv.org/content/10.1101/2025.03.20.644391v1

Structure and Activation Mechanism of a Lamassu Phage Defence System https://www.biorxiv.org/content/10.1101/2025.03.14.643221v1

Molecular basis of foreign DNA recognition by BREX anti-phage immunity system - Nature Communications BrxX methylase in complex with SAM cofactor mediates foreign DNA recognition by the BREX system. BrxX can be engineered to modify BREX specificity and enhance defense. BREX defense and methylatio...

After many years in the making, this story is finally published! In the updated manuscript on BREX DNA recognition, we reveal that modifying the system's specificity can surprisingly enhance anti-phage defense.

www.nature.com/articles/s41...

Specificity and Mechanism of tRNA cleavage by the AriB Toprim nuclease of the PARIS bacterial immune system Transfer RNA molecules have been recently recognized as widespread targets of bacterial immune systems. Translation inhibition through tRNA cleavage or modification inhibits phage propagation, thereby...

First post here! Novel insights into the tRNA cleavage activity of the PARIS bacterial immunity system and the expansion of viral tRNAs enabling defense evasion.

Thanks to @rouillonchristophe.bsky.social and @dbikard.bsky.social for having us in this project!

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

Congratulations, Ilya!

A Class 1 OLD family nuclease encoded by Vibrio cholerae is countered by a vibriophage-encoded direct inhibitor https://www.biorxiv.org/content/10.1101/2025.01.06.631583v1