Nanami Kubota
PhD student in the Cooper Lab, University of Pittsburgh. Research on bacteria/phage cheater evolution. Ruth L. Kirschstein Predoctoral Fellow. New Yorker, first-gen US immigrant, & cat lady. she/her
🔗 nanamikubota.com
- Reposted by Nanami KubotaInterested in eco-evolutionary feedbacks? Microbial experimental evolution? Pleiotropy? Filamentous phages?? Check out our latest preprint, now up on BioRxiv! biorxiv.org/content/10.6... For a quick summary, peep the thread below...🧵 (1/10)
- Reposted by Nanami Kubota
- Reposted by Nanami KubotaLooking for a paid summer research experience? Apply to MSU’s Extreme Biofilms REU and work on cutting-edge biofilm science in extreme environments. No prior research experience needed. #MicroSky #PhageSky
- Reposted by Nanami KubotaCongratulations Nanami on your PhD thesis and defense, a tour de force! Deepest thanks for leading our lab into the wonders of phage biology 🧪 🧬🦠
- Happy to announce that I successfully defended my PhD thesis today! Thank you those who attended in person and virtually.
- I need to give my biggest thanks to my thesis advisor, Vaughn Cooper ( @vscooper.micropopbio.org ) and my committee members Will DePas , Daria Van Tyne ( @dariavantyne.bsky.social ), Pat Secor ( @prsecor.bsky.social ), and Graham Hatfull.
- Reposted by Nanami KubotaExcellent defense by @nanamikubota.bsky.social ! And I’m proud to see her love of integrating viruses even when working in a bacteria lab. 😉
- A wonderful commentary by @asherleeks.bsky.social and @sociovirology.bsky.social on our recent work with P. aeruginosa filamentous cheater miniphages! @vscooper.micropopbio.org @shellyscrib.bsky.social
- It was great to write a brief commentary with @sociovirology.bsky.social on @nanamikubota.bsky.social and @vscooper.micropopbio.org's recent discovery of cheat-driven cycles in Pseudomonas (www.cell.com/current-biol... - amazing example of the tragedy of the commons! 🧪 #socialviruses #evosky
- Reposted by Nanami KubotaCongratulations to @nanamikubota.bsky.social in the @vscooper.micropopbio.org lab on her upcoming thesis defense! 👏
- Reposted by Nanami KubotaWhat is the best strategy to win any contest? Eliminate your opponents of course. Recently, my friend @fernpizza.bsky.social showed how plasmids compete intracellularly (check out his paper published in Science today!). With @baym.lol, we now know they can fight. www.biorxiv.org/content/10.1...
- Reposted by Nanami KubotaHot off the press! Our latest paper led by @fernpizza.bsky.social, understanding how plasmids evolve inside cells. These small, self-replicating DNA circles live inside bacteria and carry antibiotic resistance genes, but also compete with one another to replicate. 1/ www.science.org/doi/10.1126/...
- I will be defending on Dec 8th at 1pm Eastern Time! I will be sharing both published and new work. If filamentous phages, Pseudomonas aeruginosa, evolution, and active lysogeny sound cool: It is hybrid, and the zoom link info can be found on the webpage. 🔗 calendar.pitt.edu/event/filame...
- Reposted by Nanami KubotaI am so excited to have this published today detailing a new system for growing biofilms and observing the resulting populations (stress on the plural!) in chemostats! A chemostat-based model for growing bacterial biofilms | Microbiology Spectrum journals.asm.org/doi/10.1128/...
- Reposted by Nanami Kubota@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 Nanami KubotaI am super excited to announce that we have a tenure-track faculty position in biophysics open in the Department of Physics at Carnegie Mellon! 🧪 Interfolio link: apply.interfolio.com/174360 PLEASE, share widely across the blue skies! Let me briefly explain what we're looking for: 1/10
- Reposted by Nanami KubotaTwo tenure-track faculty positions open in our department: 1) Microbial Ecology and Evolution careers.rpi.edu/en-us/job/49... 2) Cellular Neuroscience careers.rpi.edu/en-us/job/49... Join our collaborative, interdisciplinary community, which has proved to be a fantastic place to start a lab!
- Reposted by Nanami KubotaDo plasmids really move around that much? Well, maybe not always Thrilled to have contributed to this story with two of my favourite microbiologists: @jrpenades.bsky.social & @sanmillan.bsky.social This great work was led by Akshay Sabnis & @wfigueroac3.bsky.social www.cell.com/cell-reports...
- Reposted by Nanami Kubota#PhD Position: Interested in the evolutionary and ecological impacts of whole genome duplication? Join Dr. Tia-Lynn Ashman @drtialynn.bsky.social and I at the U. of Pittsburgh, to test what drives the competitive outcomes between diploids and #polyploids Details: shorturl.at/nQ8UW
- Excited to see our recent paper get covered by Pitt media!
- Terrific writeup of our new paper led by @nanamikubota.bsky.social, thanks Pitt media! www.medschool.pitt.edu/news/bacteri...
- Reposted by Nanami KubotaVery happy to share that I will be starting as an Assistant Professor in the department of Biological Sciences at the University of South Carolina in January! My group will be working on environmental phage ecology and evolution, and I am recruiting for the upcoming year (more info below).
- Published in Current Biology! P. aeruginosa can use its filamentous phage to inhibit competitors but high phage production is susceptible to cheater miniphage invasion. Subsequent phage tragedy of the commons can lower bacteria and phage fitness. Link: authors.elsevier.com/c/1lt5I3QW8S...
- Preprint out! Bacteria w/ hyper-replicative filamentous phage lead to overnight emergence of cheater phages. Bacteria w/ both phages can outcompete wildtype, then rapidly lose phage via a phage Tragedy of the Commons @shellyscrib.bsky.social @vscooper.micropopbio.org www.biorxiv.org/content/10.1...
- Thanks to @vscooper.micropopbio.org, @shellyscrib.bsky.social, Cooper Lab members, my committee, and everyone who helped get this to the finish line! #MicroSky #phagesky #VirEvol
- Reposted by Nanami KubotaDYK most P. aeruginosa carry filamentous phage(s) that don't need to kill the cell to reproduce? We 👉🏻@nanamikubota.bsky.social show that these Pf phages can go ROGUE. "Filamentous cheater phages drive bacterial and phage populations to lower fitness" 🔗 authors.elsevier.com/c/1lt5I3QW8S...
- Reposted by Nanami Kubota🚨 Microbiologists! We are recruiting Assistant / Associate Professors in 3 collaborative areas of our U. Pittsburgh School of Medicine. 1) MMG (my dept): fundamental research in med micro 2) Peds ID / I4Kids institute 3) Center for Vaccine Research 🔗 to all 3 w/info: www.linkedin.com/posts/vaughn...
- Reposted by Nanami KubotaA reminder that the my department has an ongoing faculty search! Would love to have more colleagues here!
- Reposted by Nanami KubotaCan CRISPR-Cas systems target any phage? Yes, no, it depends? What does it depend on? The second paper from my PhD came out today in a special issue of Phil Trans B on the ecology and evolution of bacterial immune systems doi.org/10.1098/rstb...
- Reposted by Nanami KubotaExcited to share new #program, STEPS, which can simulate #dynamics of the E. coli Long-Term Evolution Experiment (#LTEE) or other microbes in serial transfer regime. telliamedrevisited.wordpress.com/2025/08/12/s... STEPS developed by @devinmlake.bsky.social, Zachary Matson, Minako Izutsu, and me.
- Reposted by Nanami KubotaFeels surreal to say but: I'm hiring! If you are or know anyone interested in looking at the evolution of phage resistance using A. baumannii and natural transformation, then this might be for you www.jobbnorge.no/en/available...
- Reposted by Nanami KubotaCongratulations @anshika22.bsky.social and Anna Zemke on this useful paper demonstrating superiority of full length 16S sequencing for profiling respiratory samples from tracheostomy patients. h/t @seqcoast.bsky.social journals.asm.org/doi/10.1128/...
- Reposted by Nanami KubotaHere's our new broad review on the extended mobility of plasmids, about all mechanisms driving and limiting their transfer. From conjugation to conduction, phage-plasmids to hitchers, molecular to evolutionary dynamics, ecology to biotech. The state of affairs. 1/9 academic.oup.com/nar/article/...
- Reposted by Nanami KubotaNew review article with @mmdesai.bsky.social is out today! Grateful for the opportunity to contribute something we hope will serve the community well
- Reposted by Nanami KubotaNature research paper: Prophages block cell surface receptors to preserve their viral progeny go.nature.com/3IwINxb
- Reposted by Nanami KubotaPOSTDOC🚨 With the excellent @anshika22.bsky.social moving to UCI 🥲Anna Zemke and I are again recruiting a postdoc on the HOST-PATHOGEN BIOLOGY of TRACHEOBRONCHITIS. This is a microbiome-device-host immunity problem of broad significance. Contact Dr. Zemke (zemkea at upmc dot edu) if interested! 👇🏻
- Reposted by Nanami KubotaThe Xue lab at UC Irvine is looking for a staff scientist to support our work investigating how microbes interact and evolve in the gut microbiome! Open to a wide range of previous experience levels, see ad for more. recruit.ap.uci.edu/JPF09601
- Fellow Cooper lab member, Alecia will be defending next week! Go Alecia!! 💪🎉
- Congratulations to @aleciarokes.bsky.social from the @vscooper.micropopbio.org lab on her thesis defense next week! Way to go, Alecia!
- Reposted by Nanami KubotaPreprint: “Structural modeling reveals viral proteins that manipulate host immune signaling” Using AI-guided structural modeling, we find new families of viral proteins that sequester or cleave host immune signaling molecules Congrats Nitzan Tal! www.biorxiv.org/content/10.1...
- GRC Micro Pop Bio is one of my favorite meetings. I had a blast! Met some awesome people (+ wildlife) and had many engaging conversations. Definitely would like to return in the future. Shoutout to Pia for being an awesome roommate and for taking a photo of me catching grasshoppers during the break.
- Now I'm off to Edmonton for SMB 2025! Honored to be invited to give a talk at the minisymposium. Excited/nervous to present my project with an evo game theory angle since this will be the first time talking to a math-focused audience.
- This art is now immortalized on the Cooper lab slack group 👍 @satterwhite.bsky.social
- Not everyone gets to meet their hero’s… but there is a lucky few @vscooper.micropopbio.org @emmajoycarlson.bsky.social @asm.org #GRCMicroPop
- Picture of me digesting all the cool science discussions and suggestions at the GRC Micro Pop Bio
- Reposted by Nanami KubotaThere is one month left to apply for our Simons Graduate Fellowships in Ecology and Evolution! These awards provide support for students entering U.S.-based Ph.D. programs with a plan to perform research in #ecology and #evolution. www.simonsfoundation.org/grant/simons... #science
- Reposted by Nanami Kubota🚨🚨New paper out in @natcomms.nature.com!! Come for the first large-scale analysis of plasmid copy number across species, stay for one of the most intriguing results of my lab: universal scaling laws in plasmid biology! 📈🧬 👉 www.nature.com/articles/s41...
- Reposted by Nanami KubotaLooking forward to seeing everyone, new and old, at the Microbial Population Biology GRS + GRC in just a couple days! go.bsky.app/GGxRjzCat://did:plc:biu33qzl4taulu3ns5vkitw4/app.bsky.graph.starterpack/3lt3c5yncqg2l
- Reposted by Nanami KubotaOne of my favourite serendipitous results from the lab came about because we were long-read sequencing bacterial: Vibrio cholerae, which is "supposed to" have TWO circular chromosomes (3 + 1 million base pairs) often has just ONE fused chromosome (4 Mbp). www.nature.com/articles/s41... (1/n)
- Reposted by Nanami Kubota1/27 We have a new paper out! Turns out that snowflake yeast have been hiding a secret from us - they've evolved a (very!) crude circulatory system. Not with blood vessels or a heart, but through spontaneous fluid flows powered by their metabolism. 🧪🔬 www.science.org/doi/full/10....
- Got to grab lunch with a dear phage friend, Tiffany, at ASM Microbe today! @scientiff.bsky.social She had an awesome rapid fire poster talk about phage therapy against P. aeruginosa infection in an elderly person with CF Read the preprint here!: doi.org/10.1101/2025...
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- Reposted by Nanami KubotaCome check out my poster tomorrow at #ASMicrobe in the E&EB section! We found that repressor mutations in Pf prophages sparked a coevolutionary dynamic that resulted in loss of twitch motility and susceptibility to virulent pilus-targeting phage. Would love to chat about all things phage :).
- Reposted by Nanami KubotaFor #ASMicrobe folks - looking forward to a busy phage day on Sunday!
- Reposted by Nanami KubotaTurner Lab representation at #ASMicrobe #ASMicrobe2025 (1/5) Postbac Matthew Davidson will present a poster about phage Woody 🪵 #newPhageAlert Matthew will be applying for grad school soon!
- Congrats @drjdennehy.bsky.social on becoming a fellow!!
- Cooper lab is at #ASMicrobe ! See the thread for a list of all our presentations. Interested in filamentous cheater phages of P. aeruginosa? I'll be talking about them tomorrow Friday from 9:45-10am at the "Who Runs the World? Phage" session (408B, LACC)
- Welcome to all attending @asm.org #Microbe2025 and to all following here. Looking forward to a great meeting! Delighted that many labmates & colleagues are presenting, as follows, and to celebrate the publication of the Academy's Early Microbial Life report, which I co-chaired. Check these out!🧵
- Reposted by Nanami KubotaOur paper in @science.org 👉🏽 www.science.org/doi/10.1126/... is accompanied by an especially thoughtful perspective by Carey Nadell and Chris Marx 👉🏽 www.science.org/doi/10.1126/...
- Reposted by Nanami KubotaAre you a recent PhD (or soon to be PhD) from outside Canada looking to do a postdoc in Quebec? Get in touch if you are excited about microbes, evolution, ecology, genomics (or all of the above!) and I'd be happy to help develop a project together! www.mcgill.ca/gps/funding/...
- Reposted by Nanami KubotaNow published and improved thanks to peer review in Microbiology @microbiologysociety.org, who were awesome to work with. Super work by @aleciarokes.bsky.social @asantoslopez.bsky.social! Thanks Editor @brockhurstlab.bsky.social 👀Final version here: www.microbiologyresearch.org/content/jour...
- What influence does evolutionary history have on basal transcriptomes? On transcriptomic response to drug? On genetic paths for drug resistance? On fitness tradeoffs? Check out our latest preprint to find out! By @aleciarokes.bsky.social @asantoslopez.bsky.social www.biorxiv.org/content/10.1...
- Reposted by Nanami KubotaSharing the most significant work from my group, led by the @evolvingstem.bsky.social team. Come for the discoveries of how Pseudomonas adapts in biofilms, stay for the story of how they were discovered by thousands of young scientists in grades 9-12. 🧪🧫🧬🧵 www.biorxiv.org/content/10.1...
- Reposted by Nanami KubotaThe Wadsworth Center is expanding it's research focus on #virology /vector-borne diseases! www.asmcareerconnections.org/job/research-scientist-5-g-31/78488664/ This is a unicorn assistant prof equivalent position with 12-month hard money salary and no teaching commitments (!) Reposts appreciated 🙏
- Reposted by Nanami KubotaCheck out this brand new fellowship from the Simon’s Foundation in Ecology and Evolution. Incoming grad students this year are eligible to apply. No citizenship restrictions. www.simonsfoundation.org/grant/simons...
- Reposted by Nanami KubotaThe latest work from my lab, Phage Disco, a method @ellie-rand.bsky.social developed for targeted discovery of bacteriophages based on the bacterial receptor, defense system, or other component they interact with, is now live in mSystems journals.asm.org/doi/10.1128/...
- Reposted by Nanami KubotaOur NSF HSI STEM grant w/ @drmtrujillo.bsky.social & Dr. Olga Calderon was terminated today. The goal was to help community college students transition to 4 yr schools and train them in wastewater epidemiology. We had an amazing 1st cohort and had a strong positive impact on their lives.
- Reposted by Nanami KubotaThe “who” is impacted by cancellation of NIH “diversity” awards is much broader than “not white.” Eligibility criteria included individuals who are disabled, economically disadvantaged, grew up in rural communities, first generation college students, homeless… grants.nih.gov/grants/guide...
- The combination of Pf repressor mutation happening spontaneously + virome diversification means what you thought were bacterial clones might not be clones, and every colony/overnight might be different! A nightmare when doing experiments but very cool!
- TLDR: most P. aeruginosa cells have active, diverse viromes that affect host-pathogen interactions. ➡️ Pf interact with host cells, interfere w/ antibiotics as @prsecor.bsky.social et al have shown. Dynamics can be FAST! If you don't look carefully, you'll miss it! www.biorxiv.org/content/10.1...
- Reposted by Nanami KubotaOur new preprint by @nanamikubota.bsky.social shows that P. aeruginosa, and likely many other bacteria carrying filamentous prophages (like V. parahaemolyticus), risk being exploited by these phages in a runaway process that reduces fitness of both host and virus. www.biorxiv.org/content/10.1... 🧵
- Preprint out! Bacteria w/ hyper-replicative filamentous phage lead to overnight emergence of cheater phages. Bacteria w/ both phages can outcompete wildtype, then rapidly lose phage via a phage Tragedy of the Commons @shellyscrib.bsky.social @vscooper.micropopbio.org www.biorxiv.org/content/10.1...
- Reposted by Nanami KubotaExcited to share our latest, out today in @naturemicrobiol.bsky.social Bacteriocin production facilitates nosocomial emergence of vancomycin-resistant Enterococcus faecium www.nature.com/articles/s41... @idpittstop.bsky.social
- Excited to see a project I started back in high school finally published! Relative changes in precipitation drive global patterns of bird beta diversity. Huge thanks to Pedro, Mario, and José—couldn't have done it without you!
- Very happy to see this paper finally out in Global Ecology and Biogeography. "Precipitation Steepness Drives Global Patterns of Changes in Bird Community Composition Without Major Phylogenetic Signal". @unisevilla.bsky.social @queenscollegecuny.bsky.social onlinelibrary.wiley.com/doi/10.1111/...
- Reposted by Nanami KubotaA small moment of science in the world of the very small... announcing calls for applications from MS + PhD students + postdocs for a Summer School on Quantitative Phage-Bacteria Dynamics Across Scales U of Maryland, College Park, June 23-27, 2025 Apply by 3/21/25: bit.ly/phageschool2...
- Reposted by Nanami KubotaWhat influence does evolutionary history have on basal transcriptomes? On transcriptomic response to drug? On genetic paths for drug resistance? On fitness tradeoffs? Check out our latest preprint to find out! By @aleciarokes.bsky.social @asantoslopez.bsky.social www.biorxiv.org/content/10.1...
