Michael Kuhn

This surprisingly relaxing footage is from SIX MILES under the ocean – and it’s the deepest ecosystem yet discovered

Very excited to host the GRS Marine Microbes next year, which we are centering on three key themes: diversification, adaptation and resilience! Applications are now open - www.grc.org/marine-micro...

Metagenomic estimation of absolute bacterial biomass in the mammalian gut through host-derived read normalization | mSystems In this study, we asked whether normalization by host reads alone was sufficient to estimate absolute bacterial biomass directly from stool metagenomic data, without the need for synthetic spike-ins, ...

You can get an accurate estimate of total bacterial biomass from stool metagenomes by simply normalizing by host read count, without needing any additional measurements.

Excellent work by UW Master's student Gechlang Tang in @asm.org #mSystems Journal.

journals.asm.org/doi/10.1128/...
🧵

Group Leader - Genome Biology Unit Are you ready to lead groundbreaking research in Genome Biology? Join us at EMBL! We are seeking a motivated scientist to lead an independent research group addressing exciting and original biological...

To all post-docs: The Genome Biology dept ‪@embl.org
has an Independent faculty position. Fantastic place to set up your lab –great package: core funding, fantastic Ph.D. students, cutting edge core facilities & great colleagues. Closing date Sept 19th
embl.wd103.myworkdayjobs.com/en-US/EMBL/j...

Just out: metagenomics with internal standards yields phylogenetically resolved genome ("~cell") counts of bacteria, archaea, and photosynthetic eukaryotes per L of seawater, over the AMT29 Atlantic transect, via "single copy" genes (recA, radA, psbO). Compares with microscopy and flow cytometry.

Group Leader – Molecular Systems Biology Unit Are you ready to lead groundbreaking research in Molecular Systems Biology? Join us at EMBL! We are seeking a motivated scientist to lead an independent research group, addressing original biological ...

Ready to lead pioneering research that bridges systems-level investigations of biological systems to molecular mechanism? The EMBL Molecular Systems Biology Unit in Heidelberg is hiring a Group Leader!

Genome-resolved long-read sequencing expands known microbial diversity across terrestrial habitats - Nature Microbiology Nanopore sequencing of Danish soils and sediments yields genomes from over 15,000 microbial species, expanding the phylogenetic diversity of prokaryotes by 8%.

Genome-resolved long-read sequencing expands known microbial diversity across terrestrial habitats www.nature.com/articles/s41... #jcampubs

Alcohol-related liver disease disrupts bile acid synthesis and is associated with compensatory gut microbiota changes Background: Alcohol overuse disrupts liver function and alters microbial gut communities, with alcohol-related liver disease (ALD) accounting for half of all liver-related deaths worldwide. Bile acids...

Super happy to share our latest preprint in #liverdisease & #gut microbiota mechanisms.

www.medrxiv.org/content/10.1...

Postdoctoral position in human gut microbiome and bioinformatics - VIB About the Lab Thelab of JeroenRaes(VIB, KU Leuven) is home to a vibrant, dynamic and international group of researchers in the field of gut microbial ecology and its

We're hiring a postdoc!🚨

Study human-associated microbial communities in health & disease.

🔬Requirements:
- PhD in bioinformatics, microbiology, or related field
- Expertise in omics data analysis
- Micro & molecular bio techniques are a plus!

Apply now!🌟
jobs.vib.be/j/119682/pos...

TIL the EBV genome is *included in the hg38 assembly* so that EBV reads are not erroneously mapped elsewhere to the human genome. That's certainly .... an interesting solution ... 🤯

But it enabled this extremely cool work:

The MicrobeAtlas database: Global trends and insights into Earth’s microbial ecosystems www.biorxiv.org/content/10.1... #jcampubs

New preprint from the lab: "Planetary microbiome structure and generalist-driven gene flow across disparate habitats" analysing 85k metagenomes across the world, e.g. looking into generalism across habitats www.biorxiv.org/content/10.1... – see the thread below for more details!

#MicroSky 🖥️🧬🦠

Spending some time in Germany at my parents' place after moving to Bio2Q / Keio University in Tokyo at the beginning of the year. Feels good to contemplate and find that's it was an awesome move.

We have a few open positions at Postdoc level with lots of freedom and resources. DM if interested

Last year, I joined a brilliant group of researchers for a 3-week deep dive into host–microbe systems. Each week explored a different theme, led by inspiring lecturers.

I’m excited to share that videos of their talks — along with presentations by several team members — are now on YouTube:

Comprehensive taxonomic identification of microbial species in metagenomic data using SingleM and Sandpiper - Nature Biotechnology Novel microbial species in metagenomes are identified using conserved regions within universal marker genes.

Comprehensive taxonomic identification of microbial species in metagenomic data using SingleM and Sandpiper www.nature.com/articles/s41... #jcampubs

It's finally out!🎉

We known that the #microbiome confers colonization resistance against #pathogens, we know that some meds 💊 affect gut microbes 🦠

So, do 💊 alter colonization resistance? It turns out that some do! If you wanna know more, check out our latest work www.nature.com/articles/s41...

Systematic pairwise co-cultures uncover predominant negative interactions among human gut bacteria - Microbiome Background Understanding pairwise bacterial interactions in the human gut is crucial for deciphering the complex networks of bacterial interactions and their contributions to host health. However, the...

Very cool. Here, authors did pairwise co-culturing (mGAM/anaerobiosis) of 97 gut microbial species (113 strains) to infer ecological interactions (n=3233). Most negative were between distant taxa & positive were more among low-abundance taxa.
🔗 microbiomejournal.biomedcentral.com/articles/10....

Is the deuterostome clade an artifact? There is a long-standing consensus that the animal phyla closest to our own phylum of Chordata are the Echinodermata and Hemichordata. These three phy…

Fresh off the presses in @currentbiology.bsky.social : Is the deuterostome clade an artefact? www.sciencedirect.com/science/arti...

We (yours truly, Paschalis Natsidis, Laura Piovani and co-leads Paschalia Kapli and @maxjtelford.bsky.social) set out to try to answer this question.

Why? (1/12)

The "reproducibility crisis" in science constantly makes headlines. Repro efforts are often limited. What if you could assess reproducibility of an entire field?

That's what @brunolemaitre.bsky.social et al. have done. Fly immunity is highly replicable & offers lessons for #metascience

A 🧵 1/n

Maybe not the most beautiful experiment in biology but certainly top ten.

What are your nominees?
1/

The team's first preprint is out!

Led by ‪
‪@vishnuprasoodanan.bsky.social‬‬ & @omaistrenko.bsky.social , we asked a question (almost) as old as microbiology: how many prokaryotic species exist on Earth? More specifically, how much diversity is "hiding" in existing metagenomic data?

A 🧵.

📢 REMINDER ‼️ AMC - Abstract submission deadline: June 30, 2025

The Aging and Microbiome Conference 2025 #AMC2025 will take place from October 28-29, 2025 in #Jena. Join us for the latest developments and exciting discussions on #microbiome & #aging.

📅 amc25.leibniz-fli.de/registration/

Novel Research in Biological Artificial Intelligence Expressions of interest and nominations for a Max Planck Director to lead research in the field of Biological Artificial Intelligence.

Novel Research in Biological Artificial Intelligence: Expressions of interest and nominations for a Max Planck Director to lead research in the field of Biological Artificial Intelligence @mpi-cbg.de and @csbdresden.bsky.social. More information: www.mpi-cbg.de/news-outreac...

After a long silence on X (for obvious reasons), the Zeller Lab is now on Bluesky! We’ll post updates soon on what’s been happening in the lab over the past few months. For the future, we promise to share our News in a more timely manner here on this channel.
#Microbiome #Bioinformatics #ZellerLab

Congrats! Unfortunately the link doesn't work, looks like the URL is cut off

The rare microbial biosphere harbors many chemosensitive microorganisms undetectable by regular shotgun metagenomics. We can now explore them using our custom target-capture sequencing approach. Impressive work by
Claudia Sanchis, part of her PhD thesis!
www.biorxiv.org/content/10.1...

1/27 We have a new paper out! Turns out that snowflake yeast have been hiding a secret from us - they've evolved a (very!) crude circulatory system. Not with blood vessels or a heart, but through spontaneous fluid flows powered by their metabolism. 🧪🔬

www.science.org/doi/full/10....

Powerful stuff from @juliosaezrod.bsky.social who found himself on the other end of the process - as a patient not a computational biology researcher - giving him insight into both research and patient perspectives. Huge credit to Julio for talking about his experiences here

Proton-pump inhibitors increase C. difficile infection risk by altering pH rather than by affecting the gut microbiome based on a bioreactor model Clostridioides difficile infections often occur after antibiotic use, but they have also been linked to proton-pump inhibitor (PPI) therapy. The underlying mechanism – whether infection risk is due...

Ever wondered why proton pump inhibitors raise the risk of C. diff infections? Is it due to pH shifts or direct antibacterial effects on the gut microbiome? We think it’s the pH. 🧪💡 Dive into Julia & Patrick’s new paper for the full story! 📖👇 #Microbiome #PPI
doi.org/10.1080/1949...

There Were Still Old People When Life Expectancy Was 35. A demography myth that won't die

“Historically, no one lived past age 35”

"I’ve heard *so* many versions of this claim, including recently from a menopause doctor (implying menopause is not “natural” because noone lived long enough to go through it). Every time someone states this “fact,” a demographer loses a piece of their soul"