Nanami Kubota

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

DYK 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...

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...

Faculty Professor Associate - Full-Time | Vaughn Cooper We are recruiting Faculty microbiologists in three (3) different, complementary, and collaborative areas at the University of Pittsburgh associated with the School of Medicine. 1) Fundamental researc...

🚨 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...

A reminder that the my department has an ongoing faculty search! Would love to have more colleagues here!

Phage susceptibility to a minimal, modular synthetic CRISPR-Cas system in Pseudomonas aeruginosa is nutrient dependent | Philosophical Transactions of the Royal Society B: Biological Sciences CRISPR-Cas systems can provide adaptive, heritable immunity to their prokaryotic hosts against invading genetic material such as phages. It is clear that the importance of acquiring CRISPR-Cas immunit...

Can 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...

STEPS To It Announcing a new program, called STEPS, to simulate the dynamics of evolving microbial populations.

Excited 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.

Research position in Microbial Pharmacology and Population Biology (282139) | UiT The Arctic University of Norway Job title: Research position in Microbial Pharmacology and Population Biology (282139), Employer: UiT The Arctic University of Norway, Deadline: Wednesday, August 27, 2025

Feels 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...

Evaluation of V3–V4 and FL-16S rRNA amplicon sequencing approach for microbiota community analysis of tracheostomy aspirates | mSphere The role of the respiratory microbiome in shaping outcomes for patients with chronic critical illness undergoing prolonged mechanical ventilation via a tracheostomy remains poorly understood, despite ...

Congratulations @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/...

graphical abstract of the article the extended mobility of plasmids

Here'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/...

New review article with @mmdesai.bsky.social is out today! Grateful for the opportunity to contribute something we hope will serve the community well

Prophages block cell surface receptors to preserve their viral progeny - Nature Zip promotes the accumulation of free phages in bacterial lysogen communities, safeguarding phage progeny.

Nature research paper: Prophages block cell surface receptors to preserve their viral progeny

go.nature.com/3IwINxb

POSTDOC🚨
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! 👇🏻

Junior, Assistant, or Associate Specialist – Xue Lab University of California, Irvine is hiring. Apply now!

The 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!! 💪🎉

Preprint: “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...

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.

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.

Can we add Becca @satterwhite.bsky.social onto the list too? Thanks!

This art is now immortalized on the Cooper lab slack group 👍

@satterwhite.bsky.social

Frog staring off into the distance

Picture of me digesting all the cool science discussions and suggestions at the GRC Micro Pop Bio

Simons Graduate Fellowships in Ecology and Evolution The purpose of these awards is to provide support for students entering U.S.-based Ph.D. programs with a plan to perform research in ecology and evolution. While we will consider all projects in ecolo...

There 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

Universal rules govern plasmid copy number - Nature Communications Plasmids exhibit a broad range of sizes and copies per cell, and these two parameters appear to be negatively correlated. Here, Ramiro-Martínez et al. analyse the copy number of thousands of diverse b...

🚨🚨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...

Looking forward to seeing everyone, new and old, at the Microbial Population Biology GRS + GRC in just a couple days!

go.bsky.app/GGxRjzC

Prevalent chromosome fusion in Vibrio cholerae O1 - Nature Communications The pathogenic bacterium Vibrio cholerae typically has two circular chromosomes. Here, Cuénod et al. analyse 467 clinical isolates and identify several independent chromosome fusion events that are li...

One 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)

1/27 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...

Come to my poster 🔬🦠
#ASMicrobe #ASMicrobe2025
#phage #phagesky

Come 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 :).

For #ASMicrobe folks - looking forward to a busy phage day on Sunday!