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Eugen Pfeifer

@eugenpfeifer.bsky.social
191 followers 141 following 17 posts

Junior Professor @ MICALIS, Jouy-en-Josas, INRAE (France) Passionated about gut phages, especially the temperate and episomal ones (phage-plasmids).

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Eugen Pfeifer @eugenpfeifer.bsky.social · 10/07/2026
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!
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Reposted by Eugen Pfeifer
Julia Frunzke @frunzkelab.bsky.social · 06/05/2026
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
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Julia Frunzke @frunzkelab.bsky.social · 06/05/2026
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!
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Manuel Ares-Arroyo @aresarroyom.bsky.social · 14/01/2026
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...
biorxiv.org
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Olaya Rendueles @olayarendueles.bsky.social · 18/12/2025
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 🧵
biorxiv.org
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...
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Chloé Feltin @chloe-feltin.bsky.social · 12/01/2026
🚨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!)
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Milan Gerovac @gerovac.bsky.social · 11/09/2025
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
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...
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Eduardo Rocha @epcrocha.bsky.social · 03/09/2025
At last ! A tool specifically for phage-plasmid hunters. Check tyPPing by @karinailchenko.bsky.social and @eugenpfeifer.bsky.social
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Eugen Pfeifer @eugenpfeifer.bsky.social · 04/09/2025
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.
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Karina Ilchenko @karinailchenko.bsky.social · 03/09/2025
🚨 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...
biorxiv.org
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 ...
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Chloé Feltin @chloe-feltin.bsky.social · 11/08/2025
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 👇
biorxiv.org
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...
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Clara Torres-Barceló @clara-inrae.bsky.social · 28/07/2025
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:
onlinelibrary.wiley.com
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...
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Eloi Littner @eloilittner.bsky.social · 09/05/2025
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...
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Eugen Pfeifer @eugenpfeifer.bsky.social · 28/07/2025
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 🤓
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Eduardo Rocha @epcrocha.bsky.social · 23/07/2025
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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Eugen Pfeifer @eugenpfeifer.bsky.social · 10/02/2025
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!🙌
doi.org
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...
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Eduardo Rocha @epcrocha.bsky.social · 01/01/2025
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.
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