Kotaro Chihara
Molecular biology in phage-bacteria interactions | Postdoc in the phage engineering group at NIID, Japan
- Reposted by Kotaro ChiharaMy first paper from my undergraduate work is out today :)
- Chemical inhibition of a bacterial immune system Small molecules inhibit type II Thoeris anti-phage systems from diverse bacteria. One compound, IP6C, improves phage-therapy against P. aeruginosa & is effective against Thoeris in polymicrobial communities www.cell.com/cell-host-mi...
- Reposted by Kotaro ChiharaOut Now! A phage protein screen identifies triggers of the bacterial innate immune system #MicroSky
- Reposted by Kotaro ChiharaHappy to share our recent preprint: "DNA-intercalating antiphage molecules trigger abortive infection through mutual destruction and synergize with bacterial immunity" www.biorxiv.org/content/10.6... @spp2330.bsky.social, @mibinet.bsky.social, @dfg.de @hhu.de @fzj.bsky.social
- Reposted by Kotaro ChiharaPhold's manuscript is now available @narjournal.bsky.social thanks to @susiegriggo.bsky.social @npbhavya.bsky.social @vijinim.bsky.social @linsalrob.bsky.social @martinsteinegger.bsky.social @milot.bsky.social @eunbelivable.bsky.social & others not on bsky #phagesky academic.oup.com/nar/article/...
- Stoked to finally have a preprint out for Phold, our tool that uses protein structural information to enhance phage genome annotation #phagesky 1/n www.biorxiv.org/content/10.1...
- Reposted by Kotaro ChiharaSecret life of prophages: template-directed synthesis of DNA superstructures via prophage activation and rolling circle replication in bacterial biofilms bioRxiv by Gabriel Antonio S. Minero et al with @thethormannden.bsky.social, Rikke Louise Meyer www.biorxiv.org/content/10.6...
- Reposted by Kotaro ChiharaOnly in Shenzhen: Science Nature coffee bar. If you’ve published in @science.org or @nature.com, they give you coffee for free. 100% real!
- Very fascinating! can’t help wondering whether mimivirus tRNAs — together with its local translation compartment — might play a failsafe role against host immunity. www.nature.com/articles/s41564-025-02234-x
- Reposted by Kotaro ChiharaOur paper is out! Hiding in plain sight among Cas12a nucleases, Cas12a3 cleaves not its RNA target but the 3′ ends of tRNA. Huge thanks to all who made this possible, especially the Beisel lab, Biao & Dirk for the structure, & @sebastianglatt.bsky.social for all things tRNA. doi.org/10.1038/s415...
- Reposted by Kotaro ChiharaA systematic analysis of STAND NTPases and their associated sensor domains in bacterial immunity 🤯 Mind-blowing work !
- Reposted by Kotaro ChiharaDo viruses use RNA to rewire bacteria? Yes! In our paper in @cp-molcell.bsky.social RIL-seq reveals interkingdom RNA interactions during λ infection. Phages don’t just encode proteins, they use small RNAs to hijack bacterial replication and fine-tune infection. #RNA #Phage doi.org/10.1016/j.mo...
- Reposted by Kotaro ChiharaPhages 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
- Reposted by Kotaro Chihara💾 ABRicate 1.2.0 has been released! This 'oversight' lasted 6 years, but with help from @finlaym.bsky.social we got CI working and updated all the databases. #bioconda #conda #bioinformatics #microbiology #genomics github.com/tseemann/abr...
- Reposted by Kotaro ChiharaThrilled 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/...
- Reposted by Kotaro Chihara[This post could not be retrieved]
- www.nature.com/articles/s41... Structural mechanism of the Retron-Eco7 anti-phage defense system
- Reposted by Kotaro ChiharaCheck this out for the 2026 SISB (phage defense) meeting in NYC. Mark your calendar! (and note the Zoom option, if needed) sisb2026.rockefeller.edu
- Reposted by Kotaro ChiharaOur 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 🧵
- Reposted by Kotaro Chihara🧬🛡️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...
- Reposted by Kotaro Chihara⭐ 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
- Reposted by Kotaro ChiharaKlebPhaCol 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
- ⭐ NAR Breakthrough! ⭐ A community-driven collection uniting 52 phages, 74 Klebsiella isolates, and extensive genomic + phenotypic data — all freely available at klebphacol.org. 🧬 Learn more: doi.org/10.1093/nar/... @fnobrega.bsky.social @danielarothschild.bsky.social #antimicrobialresistance
- Reposted by Kotaro Chihara#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/...
- Reposted by Kotaro ChiharaExcited to share our new study! Great fun working again with my good friend @stephenrgarrett.bsky.social — always a highlight! Huge thanks to fantastic co-authors @samkaytucker.bsky.social, @drandyjroe.bsky.social and our star technician Vojtech Pavelka. academic.oup.com/nargab/artic...
- Reposted by Kotaro Chihara🚀New preprint from our lab! I am very excited to finally share what has been the main focus of my PhD for the past almost 3 years! It is about viral dark matter and a powerful tool we built to shed light on it. 🧬💡 Continue reading (🧵)
- Reposted by Kotaro Chihara🚨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
- Reposted by Kotaro ChiharaOur nuclease-protease story is out! We explored a fascinating case of coevolution and modularity in prokaryotic immune systems: www.science.org/doi/10.1126/... Thanks to wonderful coauthors/collaborators/friends, the whole @doudna-lab.bsky.social and everyone at @innovativegenomics.bsky.social
- Reposted by Kotaro ChiharaI am so excited to share our project with you! We find prokaryotic proteases activate toxic enzymes and pores as a modular strategy in phage defense. We studied four fascinating protease-toxin pairs that are abundant across bacterial genomes: www.biorxiv.org/content/10.1...
- Reposted by Kotaro ChiharaA phage-derived reconfigurable effector associated with an actinobacterial contractile nanomachine tailors bacterial responses to competition | bioRxiv biorxiv.org/content/10.1101/202…
- Reposted by Kotaro Chihara#microsky #phagesky #phage defence Novel bacterial ubiquitination-like pathway! www.nature.com/articles/s41...
- Reposted by Kotaro ChiharaThe Wilkinson Lab is open for science! @mskcancercenter.bsky.social 🧬We'll be finding funky new RNA biology, mainly by looking at reverse transcriptases (i.e. the Best Enzymes In The World)🧬 annnd: I'm hiring - come join! Especially postdocs and PhD students - please get in touch (NYC is great)
- Reposted by Kotaro ChiharaUse antisense oligomers to silence phage genes and discover new biology. @jorg-vogel-lab.bsky.social @helmholtz-hiri.bsky.social @helmholtzhzi.bsky.social @uni-wuerzburg.de print: www.nature.com/articles/s41... highlight: www.nature.com/articles/s41... briefing: www.nature.com/articles/d41...
- Reposted by Kotaro ChiharaI’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...
- Reposted by Kotaro Chihara@prczhaoyansong.bsky.social’s deep dive into the dark matter of compost communities is now out 🎉 Genomic islands hijack jumbo phages—whose capsids enable transfer of large tracts of DNA—shedding new light on the scale & scope of phage-mediated gene flow 😎 www.pnas.org/doi/10.1073/...
- Reposted by Kotaro ChiharaNew retron systems from environmental bacteria identify triggers of anti-phage defense and expand tools for genome editing | PLOS Biology journals.plos.org/plosbiology/article…
- Reposted by Kotaro ChiharaBeen 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.
- Reposted by Kotaro Chihara1/10 Genome maintenance by telomerase is a fundamental process in nearly all eukaryotes. But where does it come from? Today, we report the discovery of telomerase homologs in a family of antiviral RTs, revealing an unexpected evolutionary origin in bacteria. www.biorxiv.org/content/10.1...
- Reposted by Kotaro Chiharawww.science.org/doi/10.1126/... Another breakthrough work on the fascinating biology of Diversity Generating Retroelements by Jeff Miller’s team
- Reposted by Kotaro ChiharaViral AlphaFold Database (VAD) is live in Science Advances ~27,000 predicted viral protein monomers & homodimers Conserved folds across bacteria, archaea & eukaryotic viruses New toxin–antitoxin system KreTA uncovered Vast “functional darkness” remains uncharted www.science.org/doi/10.1126/...
- Reposted by Kotaro ChiharaOur story describing the Panoptes bacterial immune defense system is now finally peer-reviewed and published today! www.nature.com/articles/s41...
- Reposted by Kotaro ChiharaToday in @nature.com , we highlight how a cousin of CRISPR-Cas10, mCpol, establishes an evolutionary trap in anti-phage immune systems. Check out @erinedoherty.bsky.social and my work from @doudna-lab.bsky.social lab here: www.nature.com/articles/s41...
- Reposted by Kotaro ChiharaYou’ve heard of ubiquitination, meet deazaguanylation: Doug Wassarman in our lab discovered phage defense pathways have co-opted Q nucleobase biosynthetic enzymes to catalyze a new form of protein conjugation chemistry @science.org www.science.org/doi/10.1126/...
- Reposted by Kotaro ChiharaExcited 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...
- Reposted by Kotaro Chihara
- Reposted by Kotaro ChiharaNo Genetics? Try ASOs – A non-genetic approach to silence genes at the phage-host interface. We use it to study jumbo phage biology and anti-phage defence. @jorg-vogel-lab.bsky.social @helmholtz-hiri.bsky.social @uni-wuerzburg.de @helmholtzhzi.bsky.social published now in @nature.com
- Reposted by Kotaro ChiharaLooking for a new approach to studying or eliminating phages? Check out our study introducing anti-phage ASOs (antisense oligos) out in @Nature today. nature.com/articles/s4158…
- Reposted by Kotaro ChiharaA new theme issue of #PhilTransB examines the evolutionary history of bacterial immune systems, their modes of action, and the patterns how different bacterial immune systems are distributed across different ecosystems. Read: buff.ly/Z4qdxY1
- Reposted by Kotaro ChiharaMicrocolony-seq reveals inherited phenotypic diversity directly from infected human samples, revealing that bacteria can retain long-term genetic and nongenetic memory from the host environment @cellcellpress.bsky.social www.cell.com/cell/fulltex...
- Reposted by Kotaro ChiharaCongratulations Rotem Sorek @soreklab.bsky.social on receiving the Gruber prize today in Stockholm
- Reposted by Kotaro ChiharaIn a multi-CRISPR-Cas system host, @peterfineran.bsky.social & I found that type I priming promotes spacer 🧬 uptake & maintenance by a type III system & that multiple systems minimize phage escape ⬇️ @cp-cellhostmicrobe.bsky.social @otagomicroimmuno.bsky.social www.sciencedirect.com/science/arti...
- Reposted by Kotaro Chihara
