This looks really promising! It’s a step in the right direction to drill down to a more function based microbiome analysis while still maintaining taxonomic information.

New paper out: Subspecies of the human gut microbiota carry implicit information for in-depth microbiome research.

What do you think about our latest pre-print? 1/3 of human microbioal species have, mostly neglected, subspecies. Human gut microbiota subspecies carry implicit information for in-depth microbiome research doi.org/10.1101/2025...

My supervisor finally agreed to post a preprint, but he said I should not publicize it on social media.. sad it is revolutionary...

Google voice typing needed 2y to be on the same level as Whisper, but it still cannot distinguish if I speak french or english ,🙄

That will be the future?

I worry less about AI taking my job and more about how much of my job becomes 1) verifying AI-generated claims and 2) figuring out where the AI went wrong and fixing it.

10 INCREDIBLE ways to BOOST your immune system: The Measles vaccine The Mumps vaccine The Rubella vaccine The Tetanus vaccine The Diphtheria vaccine The Polio vaccine The HPV vaccine The Pneumonia vaccine The Hepatitis B vaccine The Covid-19 vaccine

There’s an open postdoc position in our EIC funded project FIBRE-MATCH at the University of Helsinki, Finland. Further information in the ad. jobs.helsinki.fi/job-invite/3...

J’ai regroupé dans ce stack les outils #IA que j’utilise ou que je trouve dignes d’intérêt. 🤖 Cette liste est vouée à évoluer chaque semaine, vu les évolutions incessantes dans le domaine. N'hésitez pas à me dire s'il manque quelque chose 🙂 reymondin.notion.site/144643c1f676...

Vaccines work.

I didn't know ncbi actually made a CLI to download genomes and gene sets github.com/ncbi/datasets

Reading "A realistic benchmark for differential abundance testing and confounder adjustment in human microbiome studies" from our friends in Berlin and in Leiden Quotes are from the paper (minor edits for space), non quoted text is me link.springer.com/article/10.1...

African elephants address one another with individually specific name-like calls www.nature.com/articles/s41...

"A random half of panelists were shown a CV and only a one-paragraph summary of the proposed research, while the other half were shown a CV and a full proposal. We find that withholding proposal texts from panelists did not detectibly impact their proposal rankings" link.springer.com/article/10.1...

Who had thought that something as basic as sequence alignment can still be improved www.research-collection.ethz.ch/handle/20.50...

And I complain, when my ssh connection is delayed for halve a second. What about coding with 22h delay blogs.nasa.gov/voyager/2024...

Now published: "Phage predation, disease severity, and pathogen genetic diversity in cholera patients" www.science.org/doi/10.1126/... Check out the podcast to hear co-senior author Eric Nelson talk about the twists and turns of our study (around 18:25): www.science.org/content/podc...

Inspiring! German state ditches Microsoft for Linux and LibreOffice

Some exciting GLP-1 drug new randomized trial evidence for potential disease-modifying impact on Parkinson's disease (there are none). No progression of motor disability in the Rx group for 12 months. nejm.org/doi/full/10....

Excited to share our latest preprint on a novel computational tool to predict fecal microbial load solely from relative species profiles! Our study revealed that fecal microbial load is a substantial confounder in microbiome-disease association studies. www.biorxiv.org/content/10.1...

A fantastic postdoc position in bioinformatic microbiome research is available in Justin Sonnenburg's lab at Stanford! I'm leaving after 4 great years to start my lab at Boulder, and Justin is looking to fill my position. DM me or email Justin ([email protected]) for questions

Expanding the human gut microbiome atlas of Africa https://www.biorxiv.org/content/10.1101/2024.03.13.584859v1

I thought the Biodynamic farm at EPFL was as low as it gets @skepteis.bsky.social www.science.org/doi/abs/10.1...

When stress goes viral... Delighted to have this collaboration with Colin Hill's lab out in Nature Microbiology. Led by PhD student Nate Ritz we show that the gut virome plays a key role in the modulation of the microbiota–gut–brain axis during stress rdcu.be/dxP4s

Postdoc afraid of 'how much the personal brand vibe has already infected my mind'

We updated our metagenomic profiling + detection tool sylph to v0.5.1 (github.com/bluenote-157...). Sensitivity for low-abund species is much improved for Illumina now (thanks @fplazaonate for showing issue). bioRxiv updated with a few new benchmarks too.

Through homology search & pLMs, we identified an effective kynureninase that degrades a key immunosuppressor in cancer, reducing tumor weight in mice by 3.4x. 📄 www.biorxiv.org/content/10.1... Seek & rank your own protein based on only a handful of measures. ⛵ seekrank.steineggerlab.com

Effective binning of metagenomic contigs using contrastive multi-view representation learning www.nature.com/articles/s41... #jcampubs

Interesting PhD position eth-gethired.ch/en/jobs/deta...

This is why I enjoy coffee breaks so much www.nature.com/articles/s41...

We are recruiting a postdoctoral researcher 👩🏼‍💻🔬to join our research group at @VIB_microbes in Jeroen Raes lab 🇧🇪, focusing on studying human-associated microbial communities in health and disease. Please apply here ⬇️ www.nature.com/naturecareer...

Are you running antiSMASH across many genomes? Check out multiSMASH, my simple wrapper that streamlines comparative BGC analyses by parallelizing antiSMASH runs and tabulating the results. Runs BiG-SCAPE too! WIP, so feedback and bug reports appreciated. github.com/zreitz/multi...

"...fermentation products cover between 1.8% and 12.1% of the daily energy demand of human hosts, substantially less than the 21% estimated for laboratory mice."

I will start a new position at the Geneva University Hospital working on microbiome and Alzheimer's. Stay tuned for some posts on the subject..

Seems I am already late to the party. This place looks like a good place for science. 👋 to all the old and new friends.