Osterman Ilya
@ostermanilya.bsky.social
📤 323
📥 324
📝 42
Senior Research Associate, microbiologist, biochemist, The Sorek lab, Weizmann Institute of Science
Potential metabolic symbiosis between bacteria and phages — very inspiring!
journals.asm.org/doi/10.1128/...
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Metagenomics reveals potential interactions between Patescibacteriota and their phages in groundwater ecosystems | mSystems
Here, we sought phages that were capable of infecting Patescibacteriota metagenome-assembled genomes (MAGs), and further explored the diversity and novelty of Patescibacteriota phages, as well as the mechanisms underlying phage-Patescibacteriota interactions in groundwater ecosystems. The abundance profiles of phage-Patescibacteriota interactions suggested that lysogenic infection may represent a mutually adapted strategy between Patescibacteriota and their phages in groundwater ecosystems. Furthermore, the groundwater Patescibacteriota phages possessed diverse auxiliary metabolic genes which might facilitate the symbiotic associations and metabolic exchange between host Patescibacteriota MAGs and other free-living microbes and expand the metabolic capabilities of host Patescibacteriota MAGs. This study elucidated the mechanisms of phage-Patescibacteriota interactions and the potential roles of phages in modulating the physiology and ecology of Patescibacteriota within groundwater ecosystems.
https://journals.asm.org/doi/10.1128/msystems.01204-25
10 days ago
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Jörg Vogel
15 days ago
Looking for a POSTDOC to work on jumbo phages (those with large genomes and fascinating cell biology), using our latest ASO technology (Gerovac M et al. 2025 Nature) to define RNA export mechanisms as well as to help to advance phage therapy. Here's the job ad.
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Nature Microbiology
15 days ago
Microbes weaponizing secondary metabolites to make rivals vulnerable to phage attack 🧪🦠
www.nature.com/articles/s41...
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Streptomyces secretes a siderophore that sensitizes competitor bacteria to phage infection - Nature Microbiology
A secondary metabolite sensitizes competitor Bacillus subtilis to a wide panel of lytic phages by sequestering iron and preventing the activation of Spo0A.
https://www.nature.com/articles/s41564-024-01910-8
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Olaya Rendueles
16 days ago
Preprint alert📢! Ever wondered how much bacterial parasites influence evolutionary outcomes of their host? ➡️ We co-evolved two bacterial strains in conditions in which the costs and benefits of prophage carriage varied Here is what we found.
www.biorxiv.org/content/10.6...
#MicroSky
#PhageSky
🧵
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Environment-dependent evolution drives divergent adaptive strategies and parasite dynamics in a minimal community
Prophages, phage genomes integrated into bacterial chromosomes, are widespread, yet, the extent to which these resident parasites contribute to host fitness and shape evolutionary trajectories, partic...
https://www.biorxiv.org/content/10.64898/2025.12.17.694638v1
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AI x Bio Discovery
16 days ago
AlphaFold 3-powered discovery of phage proteins that inhibit bacterial transcription
[new] Phage proteins inhibit bacterial transcription. Novel inhibitors binding RNA polymerase discovered via structural predictions.
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Phage-encoded small RNA hijacks host replication machinery to support the phage lytic cycle: Molecular Cell
www.cell.com/molecular-ce...
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Phage-encoded small RNA hijacks host replication machinery to support the phage lytic cycle
Using RIL-seq, Silverman et al. map the RNA interactome of E. coli during phage lambda infection and uncover a conserved phage-encoded sRNA that activates host replication machinery. Their findings re...
https://www.cell.com/molecular-cell/fulltext/S1097-2765%2825%2900936-0
16 days ago
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Martial Marbouty
17 days ago
💥 alert article 💥 New preprint from the lab !!! 🥳 In this work, we explore the 3D genome architecture of the virulent phage PAK_P3 during its infection cycle in P. Aeruginosa. We unveil a highly dynamic structuration as well as specific interactions patterns.
www.biorxiv.org/content/bior...
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https://www.biorxiv.org/content/biorxiv/early/2025/12/15/2025.12.15.694284.full.pdf
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Osterman Ilya
bioRxiv Evolutionary Biology
18 days ago
Closing the Loop on Phage-bacteria Coevolution
https://www.biorxiv.org/content/10.64898/2025.12.15.694372v1
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Osterman Ilya
bioRxiv Microbiology
18 days ago
A UG5 reverse transcriptase-nitrilase antiviral module confers phage immunity in the plant symbiont Sinorhizobium meliloti
https://www.biorxiv.org/content/10.64898/2025.12.16.694600v1
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Osterman Ilya
Tominaga K. (tomiken)
19 days ago
A synthetic cell phage cycle | Nature Communications
https://www.nature.com/articles/s41467-025-67249-8
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Osterman Ilya
Aude Bernheim
19 days ago
Bacterial genomes encode a rich repertoire of antiphage systems, but we still know surprisingly little about when these systems are actually expressed. In this preprint, Lucas Paoli et al, ask what shapes antiphage systems expression in native contexts.
www.biorxiv.org/content/10.6...
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Environment and physiology shape antiphage system expression
Bacteria and archaea encode on average ten antiphage systems. Quorum sensing, cellular, or transcription factors can regulate specific systems (CRISPR-Cas, CBASS). Yet, a systematic assessment of anti...
https://www.biorxiv.org/content/10.64898/2025.12.14.694197v1
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De novo origin of numerous microproteins in enterobacteria Igor Fesenko, Svetlana A Shabalina, Gisela Storz, Eugene V Koonin. Nucleic Acids Research, Volume 53, Issue 22, 11 December 2025
doi.org/10.1093/nar/...
19 days ago
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Osterman Ilya
New England Biolabs
19 days ago
Durham University (
@durham.ac.uk
) and NEB scientists described the first biochemical characterization of GmrSD Type IV restriction enzyme substrate specificity and inhibition by phage protein IP1*.
https://royalsocietypublishing.org/doi/10.1098/rstb.2024.0072
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Modified DNA substrate selectivity by GmrSD-family Type IV restriction enzyme BrxU
Abstract. Bacteriophages (phages), viral predators of bacteria, generate selection pressure that causes bacteria to evolve defence systems. Type I, II and
https://royalsocietypublishing.org/doi/10.1098/rstb.2024.0072
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Osterman Ilya
Emmanuele Severi
20 days ago
#microsky
#phagesky
Gut
#phage
biobank
www.nature.com/articles/s41...
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Gut Phage Biobank: a collection of bacteriophages targeting human commensal bacteria - Nature Communications
Here, the authors present Gut Phage Biobank (GPB), containing 104 isolates that target abundant or disease-associated gut bacteria, revealing extensive viral diversity, and provide in vivo evidence fo...
https://www.nature.com/articles/s41467-025-61946-0
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Osterman Ilya
Shai Zilberzwige Tal
25 days ago
Happy to share that I’m opening my lab at the Weizmann Institute of Science! We’ll study systems-level regulation of bacterial defense, driven by RNA-protein interactions shaping cell fate. Now recruiting PhD students & postdocs
tinyurl.com/4yfa55vd
Please reach out and share!
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Osterman Ilya
AI x Bio Discovery
24 days ago
PhaLP 2.0: extending the community-oriented phage lysin database with a SUBLYME pipeline for metagenomic discovery
[new] PhaLP 2.0: SUBLYME pipeline integrates new virome lysin sequences, improving discovery.
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Osterman Ilya
Kranzusch Lab
25 days ago
Exciting pre-print on new variants of anti-phage defense systems including CBASS, Pycsar, and Gabija!
www.biorxiv.org/content/10.6...
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Leveraging defense system modularity to discover anti-phage systems
Bacterial exposure to constant phage attack drives rapid diversification of anti-phage defense systems, often through the exchange of modular defensive domains. Here, we leverage this modularity signa...
https://www.biorxiv.org/content/10.64898/2025.12.08.692795v1
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Osterman Ilya
Doudna Lab
25 days ago
✨New preprint! 🧵1/4 Excited to share our work on AI-guided design of minimal RNA-guided nucleases. Amazing work by
@petrskopintsev.bsky.social
@isabelesain.bsky.social
@evandeturk.bsky.social
et al! Multi-lab collaboration
@banfieldlab.bsky.social
@jhdcate.bsky.social
@jacobsenucla.bsky.social
🧬 🔗👇
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Emmanuele Severi
26 days ago
#microsky
#phagesky
#phage
defence The different roles of the two glucosyltransferases of phage T4 in overcoming antiphage functions
www.biorxiv.org/content/10.6...
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A Pair of DNA Glucosyltransferases Elevate Counter-defense in Bacteriophage T4
Bacteriophages encode diverse pathways to modify their nucleobases. These modifications help phages to evade the host defense systems such as restriction-modification (RM), and type II and type V CRIS...
https://www.biorxiv.org/content/10.64898/2025.12.06.692756v1
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Osterman Ilya
Joe Bondy-Denomy
26 days ago
Phages are full of genes of unknown function that are likely adaptive in specific conditions. New preprint: Phage TnSeq identifies essential genes rapidly and knocks all non-essentials. We would like to send a pool of phiKZ mutants to anyone wanting it! Reach out
tinyurl.com/bdcfrejh
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Snorre Sulheim
about 1 month ago
Do you think transporters in E. coli contribute to metabolite release? No? Explore the effect of 66 different transporter knockout mutations on the exometabolome dynamics of ~300 metabolites yourself:
keio.unil.ch
Teaser: Increased proline in ΔputP
#microsky
#MEvoSky
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Osterman Ilya
bioRxivpreprint
29 days ago
Structural basis of Retron-Eco8-mediated anti-phage defense
https://www.biorxiv.org/content/10.64898/2025.12.04.692459v1
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Alberto Marin
30 days ago
Thrilled to share that my postdoc research is published today in
@science.org
! We found that DNA repair uses cohesin complexes to build new chromatin loops that guide the homology search and boost accurate repair! 1/n
www.science.org/doi/10.1126/...
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Cohesin drives chromatin scanning during the RAD51-mediated homology search
Cohesin folds genomes into chromatin loops, the roles of which are under debate. We found that double-strand breaks (DSBs) induce de novo formation of chromatin loops in human cells, with the loop bas...
https://www.science.org/doi/10.1126/science.adw1928
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New Thoeris systems and new bacterial TIRs, this time also producing plant and human immune signals 2'cADPR and cADPR!!! Congratulations to
@erezyirmiya.bsky.social
and Azita Leavitt! It was a pleasure to be involved in this project.
add a skeleton here at some point
about 1 month ago
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Osterman Ilya
Molecular Cell
about 1 month ago
Online Now: The Ppl protein senses 3′-hydroxyl DNA overhangs and NTP depletion to halt phage infection Online now:
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The Ppl protein senses 3′-hydroxyl DNA overhangs and NTP depletion to halt phage infection
Xu et al. reveal that the Ppl defense system protects bacteria from phages by acting as a “double-check” security system. It requires two simultaneous phage-induced stresses to activate, a sophisticated mechanism that ensures effective immunity while preventing premature abortive infection.
http://dlvr.it/TPcf14
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Osterman Ilya
Tominaga K. (tomiken)
about 1 month ago
Anti-phage defense mechanism involving phage-encoded DNA binding protein and bacterial reverse transcriptase DRT4 | Nature Communications
https://www.nature.com/articles/s41467-025-66997-x
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Osterman Ilya
Simon Roux
about 1 month ago
🦠🧪🧬🚨 New paper and database alert: the new IMG/VR release is now MetaVR ! We have a new website -
meta-virome.org
- with quick search capabilities for the >24M viruses, >12M vOTUs, and >42M protein clusters (including >790k with predicted structures !).
academic.oup.com/nar/advance-...
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Meta-virus resource (MetaVR): expanding the frontiers of viral diversity with 24 million uncultivated virus genomes
Abstract. Viruses are ubiquitous in all environments and impact host metabolism, evolution, and ecology, although our knowledge of their biodiversity is st
https://academic.oup.com/nar/advance-article/doi/10.1093/nar/gkaf1283/8349223
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Osterman Ilya
Anna Kanevskaya
about 1 month ago
Our SPARHA story is out in Nature Communications!
doi.org/10.1038/s414...
We investigated a new short pAgo-HNH defense system, showing that it assembles into filaments degrading cellular DNA, inducing abortive infection, resolved their structure, and uncovered the activation mechanism 🧵
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Osterman Ilya
bioRxiv Molecular Biology
about 1 month ago
An unprecedented DNA recognition-mimicry switch governs induction in arbitrium phages
https://www.biorxiv.org/content/10.1101/2025.11.27.690993v1
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Intron-rich viruses - WOW!
rdcu.be/eSfG2
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Widespread and intron-rich mirusviruses are predicted to reproduce in nuclei of unicellular eukaryotes - Nature Microbiology
Environmental metagenomic explorations show that Mirusviricota lineages lack essential replication and transcription genes and contain spliceosomal introns, suggesting nuclear reproduction.
https://www.nature.com/articles/s41564-025-02190-6?fbclid=IwdGRjcAOWf61jbGNrA5Z_qGV4dG4DYWVtAjExAHNydGMGYXBwX2lkDDM1MDY4NTUzMTcyOAABHvr8aAKgGFG5MQXni6Wtu9cbUr9wXwuZ8rR3oHq0K75CfdBJqK66NeKyPDYT_aem_mflTBIjhpkbBT4PfsXYCCQ
about 1 month ago
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Osterman Ilya
Aude Bernheim
about 1 month ago
🧬🛡️How are new immune mechanisms created? We show how Lamassu antiphage system, originated from a DNA-repair complex and evolved into a compact and modular immune machine, wt Dinshaw Patel lab in
@pnas.org
. 👏
@matthieu-haudiquet.bsky.social
, Arpita Chakravarti & all authors!
doi.org/10.1073/pnas...
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Osterman Ilya
Nucleic Acids Research
about 1 month ago
⭐ NAR Breakthrough! ⭐ 🦠 New study shows phage X1 hijacks Yersinia's enterocolitica flagellum to inject its DNA directly into the cytosol. Yersinia, though, strikes back! 🦠 A fascinating look at the
#dualrole
of
#flagella
in
#viralentry
and
#bacterialimmunity
. 🧬 Read more:
doi.org/10.1093/nar/...
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Osterman Ilya
Science Magazine
about 1 month ago
Some archaea—an ancient group of microorganisms—have an entirely novel genetic code, according to a new study in Science. The findings expand our understanding of how alternative genetic codes evolve and hint at new molecular tools for biotechnology applications.
https://scim.ag/4omApQ7
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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...
https://scim.ag/4omApQ7
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Osterman Ilya
Nucleic Acids Research
about 1 month ago
⭐ NAR Breakthrough! ⭐ 🔬 New study reveals how the Retron-Eco7 system helps bacteria sense and fight phage attacks, identifying a clever immune-sensing mechanism in the bacteria–phage arms race. 🧬 Read more:
doi.org/10.1093/nar/...
#NARBreakthrough
#Microbiology
#PhageBiology
#BacterialDefense
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Osterman Ilya
Stefaan Verwimp
about 1 month ago
Protein domains have no single definition, so why stick to one segmentation? 🧩 Instead of forcing structures into rigid classifications, we built AFragmenter. It uses AlphaFold PAE networks for a tuneable approach to domain parsing. You control the granularity. 👇 🔗
doi.org/10.1093/bioi...
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Osterman Ilya
Klebsiella Phage Collection
about 1 month ago
KlebPhaCol paper is now out! Go check it out and see all that we offer. And when ready, visit our website for more:
www.klebphacol.org
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Osterman Ilya
Emmanuele Severi
about 1 month ago
#microsky
#phagesky
#phage
Anyone who’s tried deleting prophages in the lab by HR knows the difficulties of the task. Here we have an example of how HR-mediated natural transformation might hit the same hurdle in a more native context.
academic.oup.com/mbe/article/...
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Chromosomal Curing Drives an Arms Race Between Bacterial Transformation and Prophage
Abstract. Transformation occurs when bacteria import exogenous DNA via the competence machinery and integrate it into their genome through homologous recom
https://academic.oup.com/mbe/article/42/11/msaf259/8339874
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Osterman Ilya
Karthik Anantharaman
about 1 month ago
Excited to share our new review article on Viral Dark Matter led by PhD student
@kosmopoulos.bsky.social
. We talk about what is known and unknown in the world of viruses (specifically phage), and highlight future opportunities for research and biotechnology.
pubs.acs.org/doi/10.1021/...
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Viral Dark Matter: Illuminating Protein Function, Ecology, and Biotechnological Promises
Viruses are the most abundant biological entities on Earth and play central roles in shaping microbiomes and influencing ecosystem functions. Yet, most viral genes remain uncharacterized, comprising w...
https://pubs.acs.org/doi/10.1021/acs.biochem.5c00349
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Osterman Ilya
Alexander Harms
about 1 month ago
🚨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
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Osterman Ilya
Dorentina Humolli
about 1 month ago
First the link to the preprint:
www.biorxiv.org/content/10.1...
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Systematic mapping of bacteriophage gene essentiality with HIDEN‑SEQ
The constant arms race of bacteriophages and their bacterial hosts has inspired major breakthroughs in biotechnology and shaped phages as fierce predators with great clinical potential to fight multid...
https://www.biorxiv.org/content/10.1101/2025.11.20.689424v1
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Osterman Ilya
Marcin J. Suskiewicz
about 2 months ago
Very happy to share our collaborative project on FAM118 proteins - noncanonical sirtuins that form filaments and process NAD in human and other vertebrate cells.
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Filament formation and NAD processing by noncanonical human FAM118 sirtuins
Nature Structural & Molecular Biology - Baretić and Missoury et al. identify vertebrate proteins FAM118B and FAM118A as sirtuins similar to bacterial antiphage enzymes and show that...
https://rdcu.be/eQjNK
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Osterman Ilya
Avery Noonan
about 2 months ago
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...
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https://www.biorxiv.org/content/10.1101/2025.11.15.688630v1
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Osterman Ilya
Owen Tuck
about 2 months ago
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...
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https://www.biorxiv.org/content/10.1101/2025.11.14.688446v1
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Osterman Ilya
Reid Oshiro
about 2 months ago
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.
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Osterman Ilya
Sternberg Lab
about 2 months ago
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/...
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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 ...
https://science.org/doi/10.1126/science.adx7604
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Osterman Ilya
Sorek Lab
about 2 months ago
Congratulations to Sorek lab alumnus Nitzan Tal, who won the prestigious 2025 Science & SciLifeLab prize for the best PhD thesis in Systems Biology! 💫 Read her Prize Assay, published in the journal Science today
www.science.org/doi/10.1126/...
@nitzantal.bsky.social
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Osterman Ilya
bioRxiv Microbiology
about 2 months ago
Cap1 forms a cyclic tetra-adenylate-induced membrane pore during the type III-A CRISPR-Cas immune response
https://www.biorxiv.org/content/10.1101/2025.11.13.688252v1
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Beautiful work, Congratulations! And bas63 is one of my favorite phages because it helped us to disciver NAD+ reconstitution pathway 1:)
add a skeleton here at some point
about 2 months ago
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Osterman Ilya
cryoEM papers
about 2 months ago
Cryo-EM structure of the bacterial anti-phage defense system DRT6
pubmed.ncbi.nlm.nih.gov/41223699/
#cryoem
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Fascinating discovery - anti-phage defense protein is a proenzyme that is cleaved by partner protease after phage infection and all three! products of cleavage form active nuclease.
add a skeleton here at some point
about 2 months ago
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