@artemisaev.bsky.social
Everything phage biology and bacterial immunity
Assistant professor at Skoltech, Russia
Assistant professor at Skoltech, Russia
Reposted
🚨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 👇
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 👇
Scalable and systematic hierarchical virus taxonomy with vConTACT3
Viruses are key players in diverse ecosystems, but studying their impacts is technically and taxonomically challenging. Taxonomic complexities derive from undersampling, diverse DNA and RNA genomes wi...
doi.org
November 7, 2025 at 4:36 PM
🚨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 👇
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 👇
Reposted
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...
Here’s the story of how we discovered the Metis defense system 👇
www.biorxiv.org/content/10.1...
November 6, 2025 at 5:00 AM
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...
Here’s the story of how we discovered the Metis defense system 👇
www.biorxiv.org/content/10.1...
Reposted
A membrane-bound nuclease directly cleaves phage DNA during genome injection https://www.biorxiv.org/content/10.1101/2025.11.03.685801v1
November 3, 2025 at 4:16 PM
A membrane-bound nuclease directly cleaves phage DNA during genome injection https://www.biorxiv.org/content/10.1101/2025.11.03.685801v1
Reposted
I’m thrilled to share our Retron Eco8 paper published in Molecular Cell today. Thanks all Fu lab members and our collaborators.
👉Phage SSB detection by retron Eco8 msDNA unleashes nuclease-mediated immunity. www.cell.com/molecular-ce...
👉Phage SSB detection by retron Eco8 msDNA unleashes nuclease-mediated immunity. www.cell.com/molecular-ce...
Phage SSB detection by retron Eco8 msDNA unleashes nuclease-mediated immunity
The cryo-EM structure of the retron Eco8 system reveals an autoinhibited 4:4:4 complex
of RT, msDNA, and OLD nuclease. Phage SSB binding to msdDNA unleashes non-specific
nuclease activity to restrict ...
www.cell.com
October 30, 2025 at 3:06 PM
I’m thrilled to share our Retron Eco8 paper published in Molecular Cell today. Thanks all Fu lab members and our collaborators.
👉Phage SSB detection by retron Eco8 msDNA unleashes nuclease-mediated immunity. www.cell.com/molecular-ce...
👉Phage SSB detection by retron Eco8 msDNA unleashes nuclease-mediated immunity. www.cell.com/molecular-ce...
Reposted
Been working on a really strange retron bacterial immune system, here's the preprint: www.biorxiv.org/content/10.1...
Type VI retrons are unlike any other. Phage infection triggers reverse transcription of a DNA fragment that activates translation of a toxin to kill the infected cell.
Type VI retrons are unlike any other. Phage infection triggers reverse transcription of a DNA fragment that activates translation of a toxin to kill the infected cell.
October 23, 2025 at 6:49 PM
Been working on a really strange retron bacterial immune system, here's the preprint: www.biorxiv.org/content/10.1...
Type VI retrons are unlike any other. Phage infection triggers reverse transcription of a DNA fragment that activates translation of a toxin to kill the infected cell.
Type VI retrons are unlike any other. Phage infection triggers reverse transcription of a DNA fragment that activates translation of a toxin to kill the infected cell.
Reposted
It’s finally out!
Our paper on the bacterial symbionts of three White Sea sponges is here.
A story that began in 2016 has reached its last chapter… or has it? We hope that by the time you finish our hefty tome — maybe around 2034 — we’ll release the sequel.
journals.asm.org/doi/10.1128/...
Our paper on the bacterial symbionts of three White Sea sponges is here.
A story that began in 2016 has reached its last chapter… or has it? We hope that by the time you finish our hefty tome — maybe around 2034 — we’ll release the sequel.
journals.asm.org/doi/10.1128/...
Taxonomically different symbiotic communities of sympatric Arctic sponge species show functional similarity with specialization at species level | mSystems
Sponges are regarded among the earliest multicellular organisms and the most ancient
examples of animal-bacterial symbiosis. The study of host-microbe interactions in
sponges has advanced rapidly due ...
journals.asm.org
October 20, 2025 at 8:48 PM
It’s finally out!
Our paper on the bacterial symbionts of three White Sea sponges is here.
A story that began in 2016 has reached its last chapter… or has it? We hope that by the time you finish our hefty tome — maybe around 2034 — we’ll release the sequel.
journals.asm.org/doi/10.1128/...
Our paper on the bacterial symbionts of three White Sea sponges is here.
A story that began in 2016 has reached its last chapter… or has it? We hope that by the time you finish our hefty tome — maybe around 2034 — we’ll release the sequel.
journals.asm.org/doi/10.1128/...
Reposted
Two intensive sampling periods of oyster-associated vibrio and their phage, 4 years apart, and many surprises. Despite being washed by the Atlantic, wide tides, and vibrio (almost?) disappearing most of the year, we can find the exact same virulent phages 4 years later (down to 0 SNP)! preprint👇
October 14, 2025 at 4:08 PM
Two intensive sampling periods of oyster-associated vibrio and their phage, 4 years apart, and many surprises. Despite being washed by the Atlantic, wide tides, and vibrio (almost?) disappearing most of the year, we can find the exact same virulent phages 4 years later (down to 0 SNP)! preprint👇
Reposted
Happy that the final version of our Lamassu work @yli18smc.bsky.social is now out:
www.nature.com/articles/s41...
Thanks again to our awesome collaborators @mblokesch.bsky.social and David and co and Mark Szczelkun and @steven-shaw.bsky.social and the DCI Lausanne @fbm-unil.bsky.social
www.nature.com/articles/s41...
Thanks again to our awesome collaborators @mblokesch.bsky.social and David and co and Mark Szczelkun and @steven-shaw.bsky.social and the DCI Lausanne @fbm-unil.bsky.social
Glad to share the work of @yli18smc.bsky.social and co on Lamassu, a bacterial defense system related to Rad50/Mre11 (RM). While RM carefully trims DNA ends for repair, Lamassu chops up the host chromosome. Our study reveals how it is regulated to minimize damage, activating only during infection.
October 14, 2025 at 9:28 AM
Happy that the final version of our Lamassu work @yli18smc.bsky.social is now out:
www.nature.com/articles/s41...
Thanks again to our awesome collaborators @mblokesch.bsky.social and David and co and Mark Szczelkun and @steven-shaw.bsky.social and the DCI Lausanne @fbm-unil.bsky.social
www.nature.com/articles/s41...
Thanks again to our awesome collaborators @mblokesch.bsky.social and David and co and Mark Szczelkun and @steven-shaw.bsky.social and the DCI Lausanne @fbm-unil.bsky.social
Reposted
Phages evolve fast, or do they?
In oysters, some stay identical for years.
With >1,200 phages & 600 Vibrio genomes, we reveal long-term stability and new mobile elements.
Proud of this collaborative work across our teams (Roscoff-UdeM and @epcrocha.bsky.social www.biorxiv.org/cgi/content/...
In oysters, some stay identical for years.
With >1,200 phages & 600 Vibrio genomes, we reveal long-term stability and new mobile elements.
Proud of this collaborative work across our teams (Roscoff-UdeM and @epcrocha.bsky.social www.biorxiv.org/cgi/content/...
Ecological constraints foster both extreme viral-host lineage stability and mobile element diversity in a marine community
Phages are typically viewed as very rapidly evolving biological entities. Little is known, however, about whether and how phages can establish long-term genetic stability. We addressed this eco-evolut...
www.biorxiv.org
October 12, 2025 at 9:16 PM
Phages evolve fast, or do they?
In oysters, some stay identical for years.
With >1,200 phages & 600 Vibrio genomes, we reveal long-term stability and new mobile elements.
Proud of this collaborative work across our teams (Roscoff-UdeM and @epcrocha.bsky.social www.biorxiv.org/cgi/content/...
In oysters, some stay identical for years.
With >1,200 phages & 600 Vibrio genomes, we reveal long-term stability and new mobile elements.
Proud of this collaborative work across our teams (Roscoff-UdeM and @epcrocha.bsky.social www.biorxiv.org/cgi/content/...
Reposted
How do SMC complexes load onto DNA to get ready for loop extrusion?
@roisnehamelinf.bsky.social & co discovered that Wadjet, an SMC complex involved in bacterial DNA immunity, performs some impressive molecular gymnastics 🤸♂️🤸♂️🤸♂️.
Check out the new paper: www.cell.com/molecular-ce...
@roisnehamelinf.bsky.social & co discovered that Wadjet, an SMC complex involved in bacterial DNA immunity, performs some impressive molecular gymnastics 🤸♂️🤸♂️🤸♂️.
Check out the new paper: www.cell.com/molecular-ce...
October 9, 2025 at 2:43 PM
How do SMC complexes load onto DNA to get ready for loop extrusion?
@roisnehamelinf.bsky.social & co discovered that Wadjet, an SMC complex involved in bacterial DNA immunity, performs some impressive molecular gymnastics 🤸♂️🤸♂️🤸♂️.
Check out the new paper: www.cell.com/molecular-ce...
@roisnehamelinf.bsky.social & co discovered that Wadjet, an SMC complex involved in bacterial DNA immunity, performs some impressive molecular gymnastics 🤸♂️🤸♂️🤸♂️.
Check out the new paper: www.cell.com/molecular-ce...
Reposted
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
September 30, 2025 at 4:17 AM
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
Reposted
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...
Until now, using AccuSNV.
Herui Liao trained an ML model based on our previous meticulously called SNVs.
www.biorxiv.org/content/10.1...
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...
www.biorxiv.org
September 29, 2025 at 7:45 PM
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...
Until now, using AccuSNV.
Herui Liao trained an ML model based on our previous meticulously called SNVs.
www.biorxiv.org/content/10.1...
Reposted
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...
www.nature.com/articles/s41...
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.
www.nature.com
September 24, 2025 at 12:20 PM
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...
www.nature.com/articles/s41...
Reposted
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...
@rkoszul.bsky.social @natmicrobiol.nature.com @cnrs.fr @institutpasteur.bsky.social
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.
www.nature.com
September 19, 2025 at 9:32 AM
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...
@rkoszul.bsky.social @natmicrobiol.nature.com @cnrs.fr @institutpasteur.bsky.social
www.nature.com/articles/s41...
Reposted
YprA family helicases provide the missing link between diverse prokaryotic immune systems https://www.biorxiv.org/content/10.1101/2025.09.15.676423v1
September 16, 2025 at 6:17 AM
YprA family helicases provide the missing link between diverse prokaryotic immune systems https://www.biorxiv.org/content/10.1101/2025.09.15.676423v1
Reposted
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...
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...
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...
www.cell.com
August 22, 2025 at 9:02 PM
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...
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...
Reposted
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.
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.
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...
www.biorxiv.org
August 22, 2025 at 7:02 PM
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.
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.
Reposted
The RecBCD complex interacts directly with the DNA sliding clamp in Escherichia coli https://www.biorxiv.org/content/10.1101/2025.08.20.671105v1
August 21, 2025 at 4:16 AM
The RecBCD complex interacts directly with the DNA sliding clamp in Escherichia coli https://www.biorxiv.org/content/10.1101/2025.08.20.671105v1
Reposted
Reposted
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)
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)
July 29, 2025 at 2:53 PM
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)
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)
Reposted
Recurrent acquisition of nuclease-protease pairs in antiviral immunity https://www.biorxiv.org/content/10.1101/2025.07.28.667249v1
July 29, 2025 at 4:17 AM
Recurrent acquisition of nuclease-protease pairs in antiviral immunity https://www.biorxiv.org/content/10.1101/2025.07.28.667249v1
Reposted
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...
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...
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...
www.biorxiv.org
July 25, 2025 at 2:52 PM
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...
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...
Reposted
📢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!
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!
July 13, 2025 at 7:49 AM
📢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!
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!
Reposted
Nuclease-NTPase systems use shared molecular features to controlbacterial anti-phage defense https://www.biorxiv.org/content/10.1101/2025.07.10.664194v1
July 11, 2025 at 3:18 AM
Nuclease-NTPase systems use shared molecular features to controlbacterial anti-phage defense https://www.biorxiv.org/content/10.1101/2025.07.10.664194v1