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Reposted by Nanami Kubota

Cathy Hernandez @cathyhernandez.bsky.social · 17h

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).

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.

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Nanami Kubota @nanamikubota.bsky.social · 17h

Congrats!! 🎉

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Nanami Kubota @nanamikubota.bsky.social · 6d

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

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Reposted by Nanami Kubota

Vaughn Cooper @vscooper.micropopbio.org · 6d

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...

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Nanami Kubota @nanamikubota.bsky.social · 6d

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...

Nanami Kubota @nanamikubota.bsky.social · Apr 2

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...

Filamentous cheater phages drive bacterial and phage populations to lower fitness

Many bacteria carry phage genome(s) in their chromosome (i.e., prophage), and this intertwines the fitness of the bacterium and the phage. Most Pseudomonas aeruginosa strains carry filamentous phages ...

www.biorxiv.org

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Reposted by Nanami Kubota

Vaughn Cooper @vscooper.micropopbio.org · 15d

🚨 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...

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...

www.linkedin.com

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Reposted by Nanami Kubota

Zandrea Ambrose, Ph.D. @zandrea.bsky.social · 15d

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

Joanne Flynn @joanneflynn19.bsky.social · Aug 20

We are hiring! The Dept of Microbiology and Molecular Genetics is looking for faculty at the Assistant or Associate professor level (tenure track). Please consider joining our vibrant microbiology and immunology community at the University of Pittsburgh School of medicine

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Josie Elliott @josie-e.bsky.social · Sep 4

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...

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...

doi.org

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Reposted by Nanami Kubota

Richard Lenski @relenski.bsky.social · Aug 12

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.

STEPS To It

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

telliamedrevisited.wordpress.com

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Reposted by Nanami Kubota

Ellinor Alseth @ellinoralseth.bsky.social · Aug 8

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...

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

www.jobbnorge.no

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Reposted by Nanami Kubota

Vaughn Cooper @vscooper.micropopbio.org · Jul 24

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/...

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 ...

journals.asm.org

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Reposted by Nanami Kubota

Eduardo Rocha @epcrocha.bsky.social · Jul 23

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/...

graphical abstract of the article the extended mobility of plasmids

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Joao Ascensao @joaoascensao.bsky.social · Jul 21

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

Nature Reviews Genetics @natrevgenet.nature.com · Jul 21

New online! Experimental evolution in an era of molecular manipulation

Experimental evolution in an era of molecular manipulation

Nature Reviews Genetics, Published online: 21 July 2025; doi:10.1038/s41576-025-00867-6In this Review, Ascensao and Desai discuss how methodological advances in genotype and phenotype manipulation are transforming experimental evolution approaches and providing new insights into the underlying genetics and forces that shape phenotypic evolution.

www.nature.com

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Nature @nature.com · Jul 18

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

go.nature.com/3IwINxb

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.

go.nature.com

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Vaughn Cooper @vscooper.micropopbio.org · Jul 17

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! 👇🏻

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Reposted by Nanami Kubota

Katherine Xue @ksxue.bsky.social · Jul 17

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

Junior, Assistant, or Associate Specialist – Xue Lab

University of California, Irvine is hiring. Apply now!

recruit.ap.uci.edu

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Nanami Kubota @nanamikubota.bsky.social · Jul 16

Fellow Cooper lab member, Alecia will be defending next week!

Go Alecia!! 💪🎉

Pitt Program in Microbiology & Immunology @pitt-pmi.bsky.social · Jul 16

Congratulations to @aleciarokes.bsky.social from the @vscooper.micropopbio.org lab on her thesis defense next week! Way to go, Alecia!

Thesis defense announcement for Alecia Rokes to be held on July 24, 2025 and entitled “Evolutionary history constrains paths of adaptation in Acinetobacter baumannii”

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Sorek Lab @soreklab.bsky.social · Jul 14

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...

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Nanami Kubota @nanamikubota.bsky.social · Jul 13

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.

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Nanami Kubota @nanamikubota.bsky.social · Jul 13

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.

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Nanami Kubota @nanamikubota.bsky.social · Jul 11

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

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Nanami Kubota @nanamikubota.bsky.social · Jul 11

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

@satterwhite.bsky.social

Kendal Tinney @kendalt.bsky.social · Jul 11

Not everyone gets to meet their hero’s… but there is a lucky few @vscooper.micropopbio.org @emmajoycarlson.bsky.social @asm.org #GRCMicroPop

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Nanami Kubota @nanamikubota.bsky.social · Jul 10

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

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Reposted by Nanami Kubota

Simons Foundation @simonsfoundation.org · Jul 2

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

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...

www.simonsfoundation.org

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Jerónimo Rodríguez-Beltrán @jerorb.bsky.social · Jul 2

🚨🚨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...

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...

www.nature.com

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