Nanami Kubota

Ad for Postdoctoral Scientist Position in Burmeister Lab on Bacteria-Phage Coevolution. Full document available here: https://arburmeister.weebly.com/uploads/1/9/9/9/19990727/burmeister_lab_postdoc_position_2026.pdf

Postdoc position on phage-bacteria coevolution available in the @aburmeister.bsky.social lab at University of Wisconsin - Milwaukee #phage #evosky #MicroSky #VirEvol 🦠 🔬 #microbiology

arburmeister.weebly.com/join-the-lab...

We’re hiring a Microscopy Core Director at the Wadsworth Center!
It's a state position (job stability & PENSION!) in a uniquely academic, research-driven environment 😎
Please share 🙏
statejobs.ny.gov/public/vacan...

Excited to share a preprint of work from my postdoc with @paulturnerlab.bsky.social exploring how prophages can impact host thermal ecology and evolution. www.biorxiv.org/content/10.6...

Adaptation without Dominance in Pseudomonas syringae Pathovars - Microbial Ecology Understanding local adaptation of phytopathogens has significant practical and economic implications. The opportunistic pathogen Pseudomonas syringae exemplifies this challenge, causing regular epidem...

My PhD work with the inimitable Joy Bergelson looking at local adaptation in a super-cool generalist pathogen that nucleates ice and decimates your favorite crop plant 🌱 👾 🧬 Thrilled to see this out (& reminded by @vscooper.micropopbio.org to celebrate each win)!
link.springer.com/article/10.1...

If you have an interest in mixing computation and experiments to understand microbial evolution (for example antibiotic resistance) and you think you might be a good fit for a postdoc in my lab, reach out. If it seems it might be a fit I’m happy to help you frame it as AI for Biology per this call

Interested 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)

Now published in PLoS Pathogens! #microsky #phagesky
journals.plos.org/plospathogen...

Looking 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

Congratulations Nanami on your PhD thesis and defense, a tour de force!
Deepest thanks for leading our lab into the wonders of phage biology 🧪 🧬🦠

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.

Thanks Pat for being in my committee and for being the Pf phage expert! 🦠

Happy to announce that I successfully defended my PhD thesis today! Thank you those who attended in person and virtually.

Thank you for coming! Integrating viruses are the best

Nanami’s description of herself

Excellent defense by @nanamikubota.bsky.social ! And I’m proud to see her love of integrating viruses even when working in a bacteria lab. 😉

I want to selfishly plug that there's more to this story that we hope to share soon! (Wildtype phage has a way to "fight back" cheater miniphage invasion.) We're currently working on the paper so stay tuned 😎

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

Nanami Kubota's defense will be held on Monday, December 8, 2025 and is titled "Filamentous prophage as drivers of rapid bacterial and phage evolution."

Congratulations to @nanamikubota.bsky.social in the @vscooper.micropopbio.org lab on her upcoming thesis defense! 👏

What 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...

Intracellular competition shapes plasmid population dynamics From populations of multicellular organisms to selfish genetic elements, conflicts between levels of biological organization are central to evolution. Plasmids are extrachromosomal, self-replicating g...

Hot 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/...

Filamentous Prophage as Drivers of Rapid Bacterial and Phage Evolution

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...

Congrats on the paper, Fab!

A chemostat-based model for growing bacterial biofilms | Microbiology Spectrum Biofilms are the predominant way that bacteria live in natural environments and are characterized by three emergent properties: ubiquity, resilience, and impact. They can be found across all environme...

I 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/...

Jumbo phage–mediated transduction of genomic islands | PNAS Bacteria acquire new genes by horizontal gene transfer, typically mediated by mobile genetic elements (MGEs). While plasmids, bacteriophages, and c...

@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/...

Tenure-track Position in Biophysics at Carnegie Mellon University, Department of Physics Location: Pittsburgh, PA Open Date: Sep 19, 2025 Description The Department of Physics at Carnegie Mellon University invites applications for a tenure-track faculty position in biophysics. The appointment is intended to be at the Assistant Professor level, but exceptional candidates at a higher level may also be considered. We seek outstanding candidates with a strong record in cellular and subcellular biophysics. Topics of particular interest include, but are not limited to, uncovering how key characteristics of living systems arise from the interplay between supramolecular cellular structures, how the emergent cellular circuitry defines goals and enables robust decision making, and how metabolic resources are allocated. This encompasses understanding of how information is learned, stored, transduced, and processed across subcellular structures. Applicants with theoretical, data science, or experimental backgrounds within biological physics are encouraged to apply. The ideal candidate will strengthen and extend research programs of current biophysics faculty in the Department of Physics and collaborate with broader life science activities across many departments at CMU and the wider Pittsburgh area. More details on Interfolio: https://apply.interfolio.com/174360

I 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

Two 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!

Non-conjugative plasmids limit their mobility to persist in nature Sabnis et al. explain why non-conjugative plasmids move at a low rate in nature. While increased mobility can easily evolve by incorporating phage DNA into plasmids, this is disadvantageous because it...

Do 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...

#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!

A graphic advertising phage ecology and evolution research at the University of South Carolina, showing a central image of a tide pool flanked by a photo of an agar plate containing diverse microbes and a TEM image of a virus particle.

Very 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).

Congrats!! 🎉