Iris Irby

New short story from my postdoc in the Bassler lab is up on bioRxiv!

Turns out our favorite quorum sensing responsive phage VP882 is a member of a larger family of phages that is distributed across multiple bacterial species and can eavesdrop on a universally conserved autoinducer.

#PhageSky 🦠🧫

Plasmids link antibiotic resistance genes and phage defense systems in E. coli Phage therapy has been proposed as an alternative to antibiotics to treat resistant infections. However, we have a limited understanding of how antibiotic resistance genes (ARGs) associate with bacter...

New pre-print from my lab!
Plasmids link antibiotic resistance and phage defense.

E.coli plasmids are hotspots for both antibiotic resistance and phage defense. Phage therapy has the potential to accidentally select for antibiotic resistance!!!
#microsky#AMR#phage

www.biorxiv.org/content/10.1....

A Phylogenetic Host‐Range Index Reveals Ecological Constraints in Phage Specialisation and Virulence Phages are typically known for having a limited host range, targeting particular strains within a bacterial species, but accurately measuring their specificity remains challenging. Factors like the g...

After many years in the making, here is our host range #phage paper with #ecology, #evolution and #biocontrol perspectives published in Molecular Ecology! @phimresearch.bsky.social‬ @inrae-pv.bsky.social‬ #PVBMT #JulianGarneau onlinelibrary.wiley.com/doi/10.1111/...
These are our key findings:

GitHub - mujiezhang/PSOSP: PSOSP (Prophage SOS dependency Predictor) is a novel bioinformatics tool to predict prophage induction modes by analyzing the heterology index (HI) of LexA protein binding t... PSOSP (Prophage SOS dependency Predictor) is a novel bioinformatics tool to predict prophage induction modes by analyzing the heterology index (HI) of LexA protein binding to target DNA, classifyin...

🧪Struggling to induce #prophage?
🧬 Meet PSOSP, a tool to predict prophage induction mode!
🚀Distinguishes SOS-dependent vs independent prophages.
🖥️Available on web server: vee-lab.sjtu.edu.cn/PSOSP and Github: github.com/mujiezhang/P...
#Bioinformatics #phage #viruse #microbiome #GutHealth

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/...

Do plasmids evolve faster 🐇, slower 🐢, or just like chromosomes 🧬?

In our new paper, we tackled this question using theory, simulations, bioinformatics, and experiments!

👇 Check out all the details in Paula’s thread!

Hint: 🐇 (most of the time)

We made structural predictions of representatives of each #PHROG from #phage genomes, and put the whole lot online. You can browse through montages or go to your favourite phrog directly and download its PDB.

💻🧬 #phagesky

linsalrob.github.io/PHROG_struct...

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...

Curious about plasmid biology? Our latest paper is out now in Nature Communications! 🚨

doi.org/10.1038/s414...

We analyzed thousands of diverse bacterial plasmids to shed light for the first time on a key aspect of plasmid biology: plasmid copy number. 1/7 👇

New pre-print out \o/ All about CRISPR, metagenomes, and what you learn when you collect (a lot of) spacers from natural communities, with @apcamargo.bsky.social @urineri.bsky.social @lhug.bsky.social but also Uri Gophna, Nikhil George (not on Bsky I think) & others at JGI doi.org/10.1101/2025...

Big day for the Gurney lab, first paper from the lab is now published. @sczerwinski.bsky.social led this work and answered a simple question does phage steering work when other bacteria are around? Tldr: yes! journals.asm.org/doi/epub/10....

Pseudomonas aeruginosa: ecology, evolution, pathogenesis and antimicrobial susceptibility - Nature Reviews Microbiology Pseudomonas aeruginosa is a functionally versatile bacterium, a leading opportunistic human pathogen and a model organism in microbiology. In this Review, Letizia, Diggle and Whiteley discuss P. aerug...

Our new big review on Pseudomonas aeruginosa. Hope you enjoy reading it. www.nature.com/articles/s41...

Through the new PLASFIGHTER project, we drive significant advances in unravelling and fighting AMR.
We study plasmid-bacteria interactions to answer important questions about their role in generating and maintaining superbugs.

Discover the project ➡️ plasmidlab.es/project/ 

#AntibioticResistance

Quantifying phage infectivity from characteristics of bacterial population dynamics A frequent goal of phage biology is to quantify how well a phage kills a population of host bacteria. Unfortunately, traditional methods to quantify phage success can be time-consuming, limiting the t...

Excited to see this new, and extensively-rewritten, version of our preprint up now! With @paulturnerlab.bsky.social we show how bacterial population dynamics (e.g. growth curves) can be used to accurately quantify bacteriophage infectivity

🦠 🧫🔬 #microbiology #VirEvol

doi.org/10.1101/2023...

Defence systems drive accessory genome interactions in Pseudomonas aeruginosa As well as undergoing mutational selection, bacterial genomes are shaped by a complex evolutionary interplay among diverse accessory genome elements (AGEs). In this study we define AGEs as encompassin...

Defence Systems are so hot right now 🔥 🔥 🔥 so check out our latest preprint to see how DSes contribute to niche adaptation, interact with each other, and drive accessory genome interactions in Pseudomonas aeruginosa 1/n
www.biorxiv.org/content/10.1...

Conjugative transfer inhibition of IncA and IncC plasmids by pervasive SGI1-like elements via relaxosome assembly interference Broad-host-range IncA and IncC conjugative plasmids propagate multidrug resistance in bacteria and mobilize chromosomal resistance islands, including Salmonella Genomic Island 1 (SGI1) across genera. ...

Preprint: Conjugative transfer inhibition of IncA and IncC plasmids by pervasive SGI1-like elements via relaxosome assembly interference
#plasmid #relaxase #bacteria #parasite #MGE #plasmidbiology
www.biorxiv.org/content/10.1...

argnorm

Hey #AMR people,
the argNorm preprint is now available on #QUT ePrints: eprints.qut.edu.au/252448

We* designed a tool for normalizing ARG annotations across currently popular tools & dbs.

*@svetlanaup.bsky.social
Vedanth Ramji
Hui Chong
Yiqian Duan
Finlay Maguire
@luispedrocoelho.bsky.social

1/6

morphological and genomic distinctions of the phage

New paper @isme-microbes.bsky.social : Among a sample of 1044 vibrio phages, we found 17 new Schizotequatrovirus with large genomes (>250kb), a broad host range, and yet a low frequency in our samples (?!). #MicroSky #PhageSky

So excited to be able to introduce Mystique to the world! Had such a great time working with @ellinoralseth.bsky.social, @phagephan.bsky.social, and the rest of the team!

Congrats!!

Congrats!!

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 ...

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...

Congrats!! Such interesting work!

Can we use social evolution to fight pathogens? @asgriffin.bsky.social and I review the evidence for 'cheat therapy' in bacteria and viruses...

🧪🦠 #socialviruses #evosky #virosky

1/3

At #standupforscience Atlanta!

R-pyocins as targeted antimicrobials against Pseudomonas aeruginosa - npj Antimicrobials and Resistance npj Antimicrobials and Resistance - R-pyocins as targeted antimicrobials against Pseudomonas aeruginosa

Delighted to be able to share our new review on R-pyocins produced by Pseudomonas aeruginosa. It covers genetics, regulation, killing mechanisms and therapeutic potential amongst other things. #MicroSky www.nature.com/articles/s44...

Header: "ASM Action Alert" and "ASM Advocacy" next to image of bacteria Text: Urge the Trump Administration to Restore Normal Federal Grant Operations

Kudos to @asm.org I have never in my nearly 25yrs as a member been sent an "ASM Action Alert" asking me to contact my members of Congress. Make those calls. Write those emails.

There are extraordinary times and we must make ourselves heard

Vaughn Cooper, Ph.D.; Joanna Goldberg, Ph.D.; Michael Johnson, Ph.D.

We’re thrilled to announce the election of Vaughn Cooper, Ph.D., as the new ASM President-Elect & the newly elected At-Large Board Directors Joanna Goldberg, Ph.D., & Michael Johnson, Ph.D. Congrats to our elected officers! Read more: asm.social/2fU @vscooper.micropopbio.org @copperbae.bsky.social

Hello world! I'm starting out on bluesky with a job posting - we're looking for lab research tech who shares our love of bugs. More info here brownlab.biology.gatech.edu/opportunities/