Excited to share our new preprint on bioRxiv where we show that gut health isn’t just about which microbes are present—it’s about how the immune system interacts with them.

Link: www.biorxiv.org/content/10.6...

Thread:

Functional Immuno-metagenomics Seizes the Alteration of Microbiota-Immune Interactions at the Early Onset of Multiple Sclerosis https://www.biorxiv.org/content/10.64898/2026.01.13.699307v1

I am very happy (and anxious) to share with you our most recent work in which we evaluated four of the most popular long-read assemblers,

www.biorxiv.org/content/10.1...

and tell you just a little bit about it in the following 🧵

To restore the gut microbiome after antibiotics, the right diet (rich in carbohydrates, low in fat) was a better approach than fecal microbial transplants (in the experimental model)
www.nature.com/articles/s41...
www.nature.com/articles/d41...

Snake venom protection by a cocktail of varespladib and broadly neutralizing human antibodies
www.cell.com/cell/fulltex...

broad spectrum antivenom

shifting from pip to uv feels revolutionary.

Pretty excited to be part of the team offering an Introduction to R course at the Centre of Immunology and Infectious Diseases in Paris.
Feel free to reach out if you are interested and know someone who might find the course useful.

🧵 How does being a #vegan, #vegetarian or omnivore impact your gut #microbiome? 🥦 Find out in our new paper on gut microbiome signatures of vegan, vegetarian & omnivore diets & associated health outcomes across 21,561 individuals in @naturemicrobiol.bsky.social!🎉 1/10

www.nature.com/articles/s41...

Check out this list of awesome #virome tools and be sure to add yours!

github.com/shandley/awe...

#phagesky #microsky

Metabuli App preprint is out!
💻Taxonomic classification & interactive visualization—right on your laptop
🛠️Create new databases or update existing ones with new sequences. 🧵1/5
github.com/steineggerla...
www.biorxiv.org/content/10.1101/2025.03.10.642298v1

Want to know who’s replicating and who’s just hanging out in your enrichment cultures? Our new study led by @soansi.bsky.social shows how @nanoporetech.com long-read sequencing can reveal replication states, shedding light on microbial growth. 🦠🧬

See our latest publication: doi.org/10.1093/isme...

The Foldseek webserver for fast protein structure searches now features a Sankey tree taxonomy visualization and filter, allowing to subset hits by clades. Developed by my talented student @sunjaelee.bsky.social. Try it out!
🌐 search.foldseek.com

Guide: Switching from Conda/Mamba to Pixi. Near instant environments, better HPC compatibility and reproducibility. But really, it's the speed!

josephguhlin.com/pixi-uv-bioi...

#bioinformatics #genomics #python