We are looking for a motivated PhD student in phage genomics! Please find the details attached. Application deadline 24/07. Don't hesitate to spread the word!

Very happy to share our recent preprint: “An Lsr2-like xenogeneic silencer confers immunity against AT-rich bacteriophage infection” www.researchsquare.com/article/rs-9... @fz-juelich.de; @hhu.de; @spp2330.bsky.social

Fantastic collaboration with @eugenpfeifer.bsky.social, Stan Brouns, and @pozhydaieva.bsky.social. Thanks to students @parissaclay.bsky.social an @ombelinerossier.bsky.social d we finally had the right phage for the experiments!

Bacteria chromosomes contain Genomic Islands that provide virulence, antibiotic resistance, MGE-defence,... They transfer between cells, but the mechanism of most remains elusive. Here we explore the conjugative capacity of these mysterious Genomic Islands. www.biorxiv.org/content/10.6...

Preprint alert📢! 
Ever wondered how much bacterial parasites influence evolutionary outcomes of their host? ➡️ We co-evolved two bacterial strains in conditions in which the costs and benefits of prophage carriage varied Here is what we found. 
www.biorxiv.org/content/10.6... 
#MicroSky #PhageSky 🧵

Environment-dependent evolution drives divergent adaptive strategies and parasite dynamics in a minimal community

Prophages, phage genomes integrated into bacterial chromosomes, are widespread, yet, the extent to which these resident parasites contribute to host fitness and shape evolutionary trajectories, partic...

biorxiv.org

🚨Our new article is out in #PLOS Pathogens! What drives nestedness in phages–bacteria interactions network in an agro-ecosystem? 🌱 📖 journals.plos.org/plospathogen... #Phagesky @inrae-pv.bsky.social @phimresearch.bsky.social @phagedirectory.bsky.social (Yes, that's a phage in those kinetics!)

No Genetics? Try ASOs – A non-genetic approach to silence genes at the phage-host interface. We use it to study jumbo phage biology and anti-phage defence. @jorg-vogel-lab.bsky.social @helmholtz-hiri.bsky.social @uni-wuerzburg.de @helmholtzhzi.bsky.social published now in @nature.com

Programmable antisense oligomers for phage functional genomics - Nature

Establishing antisense oligomers as versatile, non-genetic tools to silence phage mRNAs opens applications in basic research and biotechnology, as shown by identifying essential factors for propagatio...

nature.com

At last ! A tool specifically for phage-plasmid hunters. Check tyPPing by @karinailchenko.bsky.social and @eugenpfeifer.bsky.social

Karina Ilchenko@karinailchenko.bsky.social · 11mo ago

🚨 New preprint! 🧬 𝐏𝐡𝐚𝐠𝐞-𝐩𝐥𝐚𝐬𝐦𝐢𝐝𝐬 (𝐏-𝐏𝐬) are fascinating elements: both 𝐭𝐞𝐦𝐩𝐞𝐫𝐚𝐭𝐞 𝐩𝐡𝐚𝐠𝐞𝐬 and 𝐩𝐥𝐚𝐬𝐦𝐢𝐝𝐬 ➡️ tricky to detect. We present 𝐭𝐲𝐏𝐏𝐢𝐧𝐠 — the first 𝐢𝐝𝐞𝐧𝐭𝐢𝐟𝐢𝐜𝐚𝐭𝐢𝐨𝐧 𝐚𝐧𝐝 𝐜𝐥𝐚𝐬𝐬𝐢𝐟𝐢𝐜𝐚𝐭𝐢𝐨𝐧 𝐭𝐨𝐨𝐥 🛠️designed specifically for P-Ps: ✅ Accurate ✅ Sensitive ✅ Easy to use 📖 www.biorxiv.org/content/10.1...

If you look for phage-plasmids, you absolutely have to try tyPPing! Results and user guide on bioRxiv, GitHub+Zenodo Check out: bsky.app/profile/kari... Super proud (!) of the work by @karinailchenko.bsky.social & happy + many thanks to awesome collaboration with @epcrocha.bsky.social and R Bonnin.

Karina Ilchenko@karinailchenko.bsky.social · 11mo ago

🚨 New preprint! 🧬 𝐏𝐡𝐚𝐠𝐞-𝐩𝐥𝐚𝐬𝐦𝐢𝐝𝐬 (𝐏-𝐏𝐬) are fascinating elements: both 𝐭𝐞𝐦𝐩𝐞𝐫𝐚𝐭𝐞 𝐩𝐡𝐚𝐠𝐞𝐬 and 𝐩𝐥𝐚𝐬𝐦𝐢𝐝𝐬 ➡️ tricky to detect. We present 𝐭𝐲𝐏𝐏𝐢𝐧𝐠 — the first 𝐢𝐝𝐞𝐧𝐭𝐢𝐟𝐢𝐜𝐚𝐭𝐢𝐨𝐧 𝐚𝐧𝐝 𝐜𝐥𝐚𝐬𝐬𝐢𝐟𝐢𝐜𝐚𝐭𝐢𝐨𝐧 𝐭𝐨𝐨𝐥 🛠️designed specifically for P-Ps: ✅ Accurate ✅ Sensitive ✅ Easy to use 📖 www.biorxiv.org/content/10.1...

🚨 New preprint! 🧬 𝐏𝐡𝐚𝐠𝐞-𝐩𝐥𝐚𝐬𝐦𝐢𝐝𝐬 (𝐏-𝐏𝐬) are fascinating elements: both 𝐭𝐞𝐦𝐩𝐞𝐫𝐚𝐭𝐞 𝐩𝐡𝐚𝐠𝐞𝐬 and 𝐩𝐥𝐚𝐬𝐦𝐢𝐝𝐬 ➡️ tricky to detect. We present 𝐭𝐲𝐏𝐏𝐢𝐧𝐠 — the first 𝐢𝐝𝐞𝐧𝐭𝐢𝐟𝐢𝐜𝐚𝐭𝐢𝐨𝐧 𝐚𝐧𝐝 𝐜𝐥𝐚𝐬𝐬𝐢𝐟𝐢𝐜𝐚𝐭𝐢𝐨𝐧 𝐭𝐨𝐨𝐥 🛠️designed specifically for P-Ps: ✅ Accurate ✅ Sensitive ✅ Easy to use 📖 www.biorxiv.org/content/10.1...

Efficient detection and typing of phage-plasmids

Phage-plasmids are temperate phages that replicate as plasmids during lysogeny. Despite their high diversity, they carry genes similar to phages and plasmids. This leads to gene exchanges, and to the ...

biorxiv.org

New preprint out! 🧬🦠🌱 What shapes #phage–bacteria #networks in #plant environments? - Ecological origins of bacteria and phages? - Phage taxonomy? - Bacterial phylogeny? - #Prophages? #Defence-systems? 📖 here: www.biorxiv.org/content/10.1... Discover which of these actually shape the network 👇

Ecological ubiquity and phylogeny drive nestedness in phages–bacteria networks and shape the bacterial defensome

Identifying the ecological and evolutionary factors that shape phage–bacterial interactions is key to understanding their dynamics in microbial communities. Yet, such interactions remain poorly charac...

biorxiv.org

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:

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...

onlinelibrary.wiley.com

Habemus paper! Our story on integron-encoded anti-phage defenses is now out in @science.org! 16 new systems, small versions of known ones, and a lot more in this highly-collaborative study. Many thanks to everyone involved, especially my supervisor @epcrocha.bsky.social bsky.app/profile/bapt...

Baptiste Darracq@baptistedarracq.bsky.social · last yr.

White smoke, we have a new pope and also 16 new anti-phages systems in sedentary integrons (SCIs) ! In collaboration with the Rocha lab, we show in our new paper that cassettes of these large platforms encode many known anti-phage defenses, and uncovered 16 new ones. www.science.org/doi/10.1126/...

Excited 🥳 to share our latest work on gut phages! Big thanks to @epcrocha.bsky.social, Erick D, Camille d'H, @fplazaonate.bsky.social, Quentin LB, and all others involved for support and contributions! 🙌 Out in Cell Reports @cp-cellreports.bsky.social doi.org/10.1016/j.ce... Here's what we found 🤓

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/...

Excited🚨to share our first work on the human gut phageome doi.org/10.1101/2025... Always inspiring to work with @epcrocha.bsky.social , Erick D, Camille d'H and everyone else within this super dynamic consortium @inrae-france.bsky.social+@pasteur.fr+@inserm.fr! Many thanks for this great journey!🙌

Third-generation cephalosporin antibiotics induce phage bursts in the human gut microbiome.

The use of antibiotics disrupts the gut microbiota, potentially leading to long-term health issues and the spread of resistance. To investigate the impact of antibiotics on phage populations, we follo...

doi.org

New preprint. Large genomes vibriophages have it all: multiple functions, autonomy (full set of tRNA genes!), anti-defenses, broad host range. Yet, they remain rare, pinpointing the limits of generalists. Great collaboration with @fredoleroux.bsky.social led by Charles Bernard in our lab.

Frédérique Le Roux@fredoleroux.bsky.social · 2y ago

Excited to share our latest preprint on the genetic and evolutionary mechanisms behind the generalism of the Schizotequatrovirus (T4 giant vibriophage). Another great collaboration with @epcrocha.bsky.social and a relay effort from my lab in Roscoff to Montreal University biorxiv.org/cgi/content/...