Eugen Pfeifer

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...

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

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.

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 ...

🚨 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...

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...

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 👇

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:

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...

Overall, our findings underscore the complex interplay within the gut microbiome, where antibiotics not only affect bacteria but also reshape the associated phage communities, and in turn again influence the bacterial populations.
We look forward to get further interesting insights in future works!

We believe that its phages are the key players!
By targeting these dominant bacteria, these phages create opportunities for other bacterial species to re-colonize, ultimately helping to regain diversity in the gut!

We believe that "Kill-the-Winner" dynamics are at play: Antibiotics create a disturbance allowing certain bacteria to flourish.
Parabacteroides distasonis is one of those, and typically thrives after cephalosporin treatment.
What wasn't fully understood was why it loses its dominance.

3rd: Despite the initial loss of some phage species, we saw a temporary and significant increase in the number of dominant, virulent phages. But why?

2nd: Gut phages are unique to each individual (nothing new) and here we show that your unique phage "fingerprint" largely persists even after strong perturbations. So, in a way, your phages remain truly yours!

We studied the dynamics of gut phage populations in healthy individuals who received antibiotic treatment: 3rd Gen Cephalosporins.
1st: Antibiotics💊do not only just affect bacteria🦠 but also their viruses. We observed a 20% decrease in the richness+diversity, but (lucky us) it recovers over time!

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 🤓

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/...

GitHub - EpfeiferNutri/PrediRes Contribute to EpfeiferNutri/PrediRes development by creating an account on GitHub.

This work sheds light on the underappreciated role of phages in post-antibiotic gut microbiome recovery. We think this is just the beginning!

More infos here: github.com/EpfeiferNutr...
and👇
doi.org/10.5281/zeno...

A great example:
Parabacteroides distasonis known to bloom after treatment🦠➡️🔋and only when its phages were absent.
But when they (phages) were around and burst 📈 P. distasonis bacteria were hardly detectable 🦠➡️🪫

🧐We believe these phages help gut recovery! 🛡️
They prevent bacterial blooms of (e.g., antibiotic-resistant) species that would otherwise dominate the gut.

💥 Most surprising: some phages thrived the day after treatment! More than on any other day.
🚀 BUT: these phages were virulentand NOT induced prophages. So, what is their role 🤔?

So, what happens to gut phages after antibiotics?🤔 20% of them vanished after treatment 📉, but over time, recovery occurred
📌The response was highly individual-specific, reinforcing the uniqueness of each person’s microbio- and phageome!

We found >6400 phage species🧮, lots of high quality🌟, most predicted to be temperate, ca. 1900🆕 ones, and (super exciting!) a lot are also phage-plasmids!

🧐We fine-tuned the analysis of the phageome part taken from the CEREMI trial🔍
Briefly: 22 volunteers (healthy background) received antibiotic treatment💊 typical for a clinical setting. Their 💩 were analyzed over a period up to 180 days after treatment for phages and bacteria

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...

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!🙌

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.