💻 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.

🚨 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...

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!🙌