Karina Ilchenko

🚨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!)

💻 Code: github.com/EpfeiferNutri/Phage-plasmids
📦 Data: doi.org/10.5281/zenodo.16616313

Huge thanks to my co-authors 🙌
@epcrocha.bsky.social, Remy A. Bonnin, and especially to my supervisor @eugenpfeifer.bsky.social!
Special thanks to Marie-Agnes Petit & her team at MICALIS for deep discussions💡

Many P-P types remain unknown and/or difficult to identify.

🪄 The real power comes from combining 𝐭𝐲𝐏𝐏𝐢𝐧𝐠 with other methods (𝐯𝐂𝐨𝐧𝐓𝐀𝐂𝐓, 𝐌𝐌-𝐆𝐑𝐂, 𝐠𝐞𝐍𝐨𝐦𝐚𝐝) → also enables systematic discovery of 𝐡𝐢𝐠𝐡𝐥𝐲 𝐝𝐢𝐯𝐞𝐫𝐬𝐞 𝐚𝐧𝐝 𝐧𝐨𝐯𝐞𝐥 𝐭𝐲𝐩𝐞𝐬 𝐨𝐟 𝐏-𝐏𝐬.

📊 What did we find?

👉 Applied to 𝐜𝐨𝐦𝐩𝐥𝐞𝐭𝐞 + 𝐝𝐫𝐚𝐟𝐭 bacterial genomes → many new high-confidence P-Ps 🎯
👉 Large plasmid dataset (>38k plasmids) processed in just ~8 minutes ⏱️
👉 New P-Ps detected in draft genomes of carbapenem-resistant strains→ confirmed as active by experiments 🧪

📌 𝐭𝐲𝐏𝐏𝐢𝐧𝐠'𝐬 workflow:

1️⃣ Compare proteins to 763 signature profiles
2️⃣ Process via two analytical branches
3️⃣ Assign 𝐜𝐨𝐧𝐟𝐢𝐝𝐞𝐧𝐜𝐞 𝐥𝐞𝐯𝐞𝐥𝐬 (High / Medium / Low) for simple interpretation.

✨ Currently covers the most prevalent groups (with experimentally proven members).
🚀 𝐍𝐞𝐰 𝐠𝐫𝐨𝐮𝐩𝐬 𝐜𝐚𝐧 & 𝐰𝐢𝐥𝐥 𝐛𝐞 𝐚𝐝𝐝𝐞𝐝!

We generated 763 𝐬𝐩𝐞𝐜𝐢𝐟𝐢𝐜 𝐩𝐫𝐨𝐭𝐞𝐢𝐧 𝐩𝐫𝐨𝐟𝐢𝐥𝐞𝐬 for most 𝐩𝐫𝐞𝐯𝐚𝐥𝐞𝐧𝐭 𝐏-𝐏 groups and described their properties:

👉 They cover both phage and plasmid functions
👉 And distinguish #P-Ps from #plasmids & #phages with high accuracy.

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...

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!🙌