Eugen Pfeifer
@eugenpfeifer.bsky.social
Junior Professor @
MICALIS, Jouy-en-Josas, INRAE (France)
Passionated about gut phages, especially the temperate and episomal ones (phage-plasmids).
MICALIS, Jouy-en-Josas, INRAE (France)
Passionated about gut phages, especially the temperate and episomal ones (phage-plasmids).
Reposted by Eugen Pfeifer
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
@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...
www.nature.com
September 11, 2025 at 9:10 AM
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
@jorg-vogel-lab.bsky.social @helmholtz-hiri.bsky.social
@uni-wuerzburg.de @helmholtzhzi.bsky.social
published now in @nature.com
Reposted by Eugen Pfeifer
At last ! A tool specifically for phage-plasmid hunters. Check tyPPing by @karinailchenko.bsky.social and @eugenpfeifer.bsky.social
🚨 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...
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 ...
www.biorxiv.org
September 3, 2025 at 2:00 PM
At last ! A tool specifically for phage-plasmid hunters. Check tyPPing by @karinailchenko.bsky.social and @eugenpfeifer.bsky.social
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.
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.
🚨 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...
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 ...
www.biorxiv.org
September 4, 2025 at 8:19 AM
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.
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.
Reposted by Eugen Pfeifer
🚨 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...
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 ...
www.biorxiv.org
September 3, 2025 at 1:03 PM
🚨 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...
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...
Reposted by Eugen Pfeifer
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 👇
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...
www.biorxiv.org
August 11, 2025 at 7:46 AM
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 👇
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 👇
Reposted by Eugen Pfeifer
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:
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
July 28, 2025 at 11:13 AM
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:
These are our key findings:
Reposted by Eugen Pfeifer
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...
Many thanks to everyone involved, especially my supervisor @epcrocha.bsky.social
bsky.app/profile/bapt...
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/...
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/...
Sedentary chromosomal integrons as biobanks of bacterial antiphage defense systems
Integrons are genetic systems that drive bacterial adaptation by acquiring, expressing, and shuffling gene cassettes. While mobile integrons are well known for spreading antibiotic resistance genes, t...
www.science.org
May 9, 2025 at 11:51 AM
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...
Many thanks to everyone involved, especially my supervisor @epcrocha.bsky.social
bsky.app/profile/bapt...
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 🤓
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 🤓
July 28, 2025 at 8:41 AM
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 🤓
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 🤓
Reposted by Eugen Pfeifer
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/...
July 23, 2025 at 7:35 AM
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[email protected][email protected]! Many thanks for this great journey!🙌
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[email protected][email protected]! 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
February 10, 2025 at 9:55 AM
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[email protected][email protected]! Many thanks for this great journey!🙌
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[email protected][email protected]! Many thanks for this great journey!🙌
Reposted by Eugen Pfeifer
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.
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/...
biorxiv.org/cgi/content/...
Generalists in a Specialist World: Vibrio-Phages with Broad Host Range
The host range of a bacteriophage, the diversity of hosts it can infect, is central to understanding phage ecology and applications. While most well-characterized phages have narrow host ranges, broad...
biorxiv.org
January 1, 2025 at 3:07 PM
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.