Simeon Nthuku

Diet outperforms microbial transplant to drive microbiome recovery in mice - Nature Experiments in mouse models show that proper recovery of the intestinal microbiota following depletion, with or without faecal microbiota transplant therapy, is dependent on syntrophic interactions th...

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...

30.04.2025 18:57 — 👍 306    🔁 71    💬 6    📌 5

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

broad spectrum antivenom

02.05.2025 15:34 — 👍 10    🔁 4    💬 0    📌 1

shifting from pip to uv feels revolutionary.

29.05.2025 12:03 — 👍 0    🔁 0    💬 0    📌 0

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.

09.05.2025 16:43 — 👍 2    🔁 1    💬 1    📌 0

Gut microbiome signatures of vegan, vegetarian and omnivore diets and associated health outcomes across 21,561 individuals - Nature Microbiology Using 21,561 individuals, the authors present a cross-sectional study of how gut microbiome signatures are associated with dietary intake patterns and with host health outcomes.

🧵 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...

07.01.2025 09:29 — 👍 77    🔁 30    💬 4    📌 4

GitHub - shandley/awesome-virome: A listing of software, tools and databases useful for virome analysis A listing of software, tools and databases useful for virome analysis - shandley/awesome-virome

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

github.com/shandley/awe...

#phagesky #microsky

12.03.2025 20:46 — 👍 52    🔁 31    💬 1    📌 0

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

13.03.2025 08:50 — 👍 20    🔁 16    💬 1    📌 1

Inferring replication states of bacteria and viruses in enrichment cultures via long-read sequencing Abstract. Most microorganisms cannot be cultured in isolation, necessitating sophisticated methods for studying their (eco)physiology. While numerous appro

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...

11.03.2025 08:15 — 👍 51    🔁 22    💬 1    📌 4

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

17.01.2025 12:33 — 👍 82    🔁 26    💬 4    📌 0

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

08.01.2025 22:49 — 👍 12    🔁 7    💬 0    📌 2