Iris Irby

A graphic showing E. coli and T7 bacteriophage floating in space. Image credit: C. Chitboonthavisuk.

Phage-host interactions have a role shaping microbial ecosystems, but what happens in #microgravity? Experiments aboard the #ISS reveal distinct evolutionary adaptations in T7 bacteriophage & #Ecoli, revealing #phage variants effective against resistant pathogens @plosbiology.org 🧪 plos.io/3LtKOfs

Our new review highlights that ants, cockroaches, and flies carry antimicrobial-resistant bacteria and fungi in hospitals. Better pest management is key to infection prevention. #ASHEJournal #microsky www.cambridge.org/core/journal...

The distinction between virulent & temperate phages gets fuzzier if one can find so many virulent phages in the sequences of bacterial genomes coming from standard lab "pure" cultures. Check Peter's thread on our work and the N&V by Carson & Hynes: doi.org/10.1038/s415...
#phagesky #microsky

A family of linear plasmid phages that detect a quorum-sensing autoinducer exists in multiple bacterial species | mBio The discovery of quorum-sensing responsive linear plasmid phages has transformed understanding of phage-bacterial interactions by demonstrating inter-domain chemical communication. To date, however, e...

The final form of my 2nd postdoc paper with the Bassler Lab! Turns out our favorite quorum-sensing phage isn’t a one-off, but rather a member of a globally dispersed family of phages that sense a universal autoinducer.

#phagesky #microsky

journals.asm.org/doi/10.1128/...

Congrats!!! 🎉

Bacterial immune systems as causes and consequences of microbiome structure Bacterial immune systems have evolved in response to diverse molecular "parasites", yet their ecological roles remain poorly understood. This Essay explores how interactions between mobile genetic ele...

Very happy to see this piece out in @plosbiology.org, on the bacterial immune systems and microbial communities. It was a great team effort with Rafael Custodio, @brockhurstlab.bsky.social , @brownlab.bsky.social, and Edze Westra! 🦠🧫 #phagesky #mevosky

journals.plos.org/plosbiology/...

Phage diversity mirrors bacterial strain diversity in the honey bee gut microbiota - Nature Communications Authors analyse paired viral and bacterial shotgun metagenomics data from individual honeybee guts, revealing modular, nested phage–bacteria networks, with viral diversity mirroring bacterial strain c...

🐝🦠 New paper: rdcu.be/eOf7A
Phages may drive microbial diversity, yet we often don’t even know how phages & bacteria correlate in nature. Our new study tackles this in the honeybee gut, thanks to the great work of PhD student @malickndiaye.bsky.social at @dmf-unil.bsky.social @fbm-unil.bsky.social

Genomic characterization of Microbacterium meiriae sp. nov., a novel bacterium isolated from the International Space Station - Scientific Reports Scientific Reports - Genomic characterization of Microbacterium meiriae sp. nov., a novel bacterium isolated from the International Space Station

New species from space 🦠💫Genomic characterization of Microbacterium meiriae sp. nov., a novel bacterium isolated from the International Space Station www.nature.com/articles/s41...

Ecological constraints foster both extreme viral-host lineage stability and mobile element diversity in a marine community Phages are typically viewed as very rapidly evolving biological entities. Little is known, however, about whether and how phages can establish long-term genetic stability. We addressed this eco-evolut...

Phages evolve fast, or do they?
In oysters, some stay identical for years.
With >1,200 phages & 600 Vibrio genomes, we reveal long-term stability and new mobile elements.
Proud of this collaborative work across our teams (Roscoff-UdeM and @epcrocha.bsky.social www.biorxiv.org/cgi/content/...

Trade-offs between phage resistance and conjugative ability shape the ecological and evolutionary response of a multidrug resistance plasmid to plasmid-dependent phage Phage therapy is a promising alternative to antibiotics to treat multidrug resistant infections. Plasmid dependent phages (PDPs) are particularly attractive as therapeutics because they can both kill ...

New pre-print www.biorxiv.org/content/10.1...
Plasmid-dependent phage (PDPs) are ubiquitous, but the selective pressures that they impose on plasmids are not well understood. Project led by Daniel Cazares in collaboration with @brockhurstlab.bsky.social!
#phagesky#microsky

Resistance mutation supply modulates the benefit of CRISPR immunity against virulent phages Only a fraction of bacterial genomes encode CRISPR-Cas systems but the selective causes of this variation are unexplained. How naturally virulent bacteriophages (phages) select for CRISPR immunity has...

New preprint!

Ever wondered why only a fraction of genomes encode CRISPR immunity? 🧬 🦠

Turns out CRISPR is rarely beneficial against virulent phages, being most beneficial against those for which resistance mutations are rare!

An epic effort by Rosanna Wright

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

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...

I use lysogens with mitomycin C!

Plasmid prevalence is independent of antibiotic resistance in environmental Enterobacteriaceae The rapid rise of antibiotic-resistant pathogens poses a critical threat to the treatment of infectious diseases. While the spread of antibiotic resistance genes (ARGs) via plasmid conjugation has bee...

If you ever find yourself needing evidence for ‘Plasmids are just as common in microbes without resistance genes,’ we’ve got you covered! Check our new paper, out today:

www.microbiologyresearch.org/content/jour...

Protein Structure Informed Bacteriophage Genome Annotation with Phold Bacteriophage (phage) genome annotation is essential for understanding their functional potential and suitability for use as therapeutic agents. Here we introduce Phold, an annotation framework utilis...

Stoked to finally have a preprint out for Phold, our tool that uses protein structural information to enhance phage genome annotation #phagesky 1/n

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

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...