Michael Kuhn

Half of microbial eukaryote literature focuses on only 12 human parasites Abstract. Although microbial eukaryotes comprise the majority of eukaryotic phylogenetic diversity and inhabit nearly all ecosystems globally, most researc

Half of microbial eukaryote literature focuses on only twelve human parasites
#microbiology #protists #eukaryotes
@isme-microbes.bsky.social
academic.oup.com/ismej/articl...

What Rosalind Franklin truly contributed to the discovery of DNA’s structure Franklin was no victim in how the DNA double helix was solved. An overlooked letter and an unpublished news article, both written in 1953, reveal that she was an equal player.

What Rosalind Franklin truly contributed to the discovery of DNA’s structure. A really informative article, perfect for a weekend coffee read. www.nature.com/articles/d41...

🚨New preprint out!
We present a foundational genomic resource of human gut microbiome viruses. It delivers high-quality, deeply curated data spanning taxonomy, predicted hosts, structures, and functions, providing a reference for gut virome research. (1/8)
www.biorxiv.org/content/10.1...

We're up to 1000 studies in metalog.embl.de ! For the past year the focus was on finding inconsistencies in the data and creating the website, but now I have more time to go through the backlog of annotated issues to do QC and load them into the database.

Enabling options for review: from training and transparency to author-centered AI tools - openRxiv Peer review is widely viewed as a critical aspect of biomedical communication. Ideally, it provides authors with feedback so they can improve manuscripts and gives readers, particularly nonspecialists...

Excited to launch an openRxiv partnership with the scientist-run AI review service qed (@qedscience.bsky.social), the brainchild of @odedrechavi.bsky.social 1/n

openrxiv.org/enabling-rev...

I can scroll through the article with that link even without logging in. Not sure if that works for you as well and if you'd like to download it as PDF, or if you can't access it at all?

Metalog: curated and harmonised contextual data for global metagenomics samples Abstract. Metagenomic sequencing enables the in-depth study of microbes and their functions in humans, animals, and the environment. While sequencing data

Great to see this finally published!

Metalog: curated and harmonised contextual data for global metagenomics samples

now out in @narjournal.bsky.social

academic.oup.com/nar/advance-...

Untargeted longitudinal ultra deep metagenomic sequencing of wastewater provides a comprehensive readout of expected and unexpected viral pathogens Wastewater surveillance has become a powerful tool to monitor circulating viruses at a community level. Currently, most wastewater surveillance efforts use target-based approaches such as quantitative...

Can you take a quarter cup of composite sewage, simply ask ‘what’s in there?’, and find out all of the pathogens circulating in that community?

That is the question we asked in our latest pre-print.

Turns out you can.
1/
www.medrxiv.org/content/10.1...

🚨Our collaboration with @centriolelab.bsky.social & @gautamdey.bsky.social is out today in @cp-cell.bsky.social
We show that #Expansion #Microscopy is a broad-spectrum modality for Euks, enabling 3D phenotypic maps rooted to phylogeny.
#ProtistsOnSky #SciComm #SciSky

www.cell.com/cell/fulltex...

I wanted to offer some thoughts on the Gates climate memo that has been circulating this week. While I can't directly speak for others, I can say that my own response is one of dismay & deep frustration (and that this view is shared by many climate/Earth scientists). [1/n]

SARS-CoV-2 mRNA vaccines sensitize tumours to immune checkpoint blockade - Nature mRNA vaccines targeting SARS-CoV-2 also sensitize tumours to immune checkpoint inhibitors.

I've been asked about this paper (www.nature.com/articles/s41...) enough times that I finally had to read it.

The basic claim is that mRNA vaccines had huge synergistic benefit with checkpoint blockade against lung cancer melanoma.

tl;dr it's glam-slop & everyone involved should be embarrassed

Lab’s first paper is out!! We show the first structures of #Asgard #chromatin by #cryo-EM 🧬❄️
Asgard histones form closed and open hypernucleosomes. Closed are conserved across #Archaea, while open resemble eukaryotic H3–H4 octasomes and are Asgard-specific. More here: www.cell.com/molecular-ce...

Nature Communications will publish ~10K papers in 2025 pubmed.ncbi.nlm.nih.gov?term=%22Natu...

That's ~$70M in revenue, while many of the non-profit journals that used to occupy that slot in the journal hierarchy have seen a precipitous decline in submissions in the 15 years it's existed.

Deadline extension for #EMBLDataCarpentry! 📣 Apply by 10 November to save your spot in either Heidelberg or Barcelona: s.embl.org/dtc26-01-bl

This course teaches life science researchers essential skills in data management, R programming, genomics analysis, and more.

Ultra-deep long-read metagenomics captures diverse taxonomic and biosynthetic potential of soil microbes AbstractBackground. Soil ecosystems have long been recognised as hotspots of microbial diversity, but most estimates of their microbial and functional comp

Want to know how diverse soil really is?
Our ultra deep sequencing is now published in GigaScience: academic.oup.com/gigascience/...
Soil is wild! Thanks for leading the study @canerbagci.bsky.social
#secmet #soil #metagenomics #bacterialdiversity

Colonization, translocation, and evolution of opportunistic pathogens during hospital-associated infections Many commensal bacteria that peacefully reside in the human microbiome are also able to cause acute opportunistic infections. Emerging evidence suggests that within-host evolution contributes to infec...

Is the human microbiome a source for hospital-associated infections (HAI) and are any genetic changes associated with HAI? In our new preprint, we longitudinally reconstruct the evolutionary processes within the human microbiome leading up to HAI: doi.org/10.1101/2025...

First Shape Found That Can’t Pass Through Itself | Quanta Magazine After more than three centuries, a geometry problem that originated with a royal bet has been solved.

Petition for more counterexamples to plausible mathematical conjectures to contain the word "Nope". This is very cool in other ways too ofc.

www.quantamagazine.org/first-shape-...

We've all heard seminar speakers say (myself included), "I know this is too small for you to read, but..." This usually happens because people are repurposing panels from their papers without adjusting for the medium (1/20)

Predicting functions of uncharacterized gene products from microbial communities - Nature Biotechnology FUGAsseM predicts protein function in microbiomes using coexpression patterns from metatranscriptomes and diverse community-wide data.

NEW publication from our lab: One of the first methodologies (FUGAsseM) for gene function prediction from microbial community multi-omics data!

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

🧵⬇️

1/8

Long-read metagenomics for strain tracking after faecal microbiota transplant Nature Microbiology - A long-read metagenomics method empowers faecal microbiota transplantation studies by precisely tracking bacteria from donors to recipients, distinguishing co-existing strains...

Cool new method, LongTrack for long-read metagenomics, to accurately track high-resolution microbial strains after faecal microbiota transplant, revealing detailed, long-term engraftment patterns

rdcu.be/eMcNg

GTDB release 10: a complete and systematic taxonomy for 715 230 bacterial and 17 245 archaeal genomes Abstract. The Genome Taxonomy Database (GTDB; https://gtdb.ecogenomic.org) provides a phylogenetically consistent and rank normalized genome-based taxonomy

Our @narjournal.bsky.social manuscript is out! It explores the growth of the GTDB (gtdb.ecogenomic.org) since its inception, as well as updates to the website, methodology, policies, and major taxonomic and nomenclatural changes over the past three years.

academic.oup.com/nar/advance-...

This remains the funniest way to hear about an internet outage, though.

"New Far Side comics" was definitely not on my bingo card for this week. They're not bad!

www.thefarside.com/new-stuff/

Our newest preprint is the work of two talented PhD students: Dominic Eriksson (working in the labs of Meike Vogt, Nicolas Gruber & Shinichi Sunagawa @ethz.ch) and @jonas-bio.bsky.social from our group @embl.org, investigating latitudinal diversity gradients of the ocean microbiome (🧵 linked below)

Variations in the latitudinal diversity gradients of the ocean microbiome Latitudinal diversity gradients (LDGs), typically declining from the equator to the poles, are among the most pervasive macroecological patterns, yet their generality and underlying drivers in the oce...

Latitudinal diversity gradients (LDGs) are found across 🌱🐨🦠 but their underlying mechanisms remain unclear.

In this study, we highlight that LDGs are not universal in marine microbiomes but reflect lineage-specific ecological strategies and environmental responses.
doi.org/10.1101/2025...

Strainify: Strain-Level Microbiome Profiling for Low-Coverage Short-Read Metagenomic Datasets https://www.biorxiv.org/content/10.1101/2025.10.10.681738v1

Excited to share our preprint led by Carlos Voogdt et al

We developed new genetic tools & genome-wide libraries for species of the Bacteroidales order; constructed saturated barcoded transposon libraries in key representatives of three genera.
www.biorxiv.org/content/10.1...

A toolkit for transposon libraries and functional genomics in intestinal Bacteroidales https://www.biorxiv.org/content/10.1101/2025.10.10.681549v1

New paper out demonstrating how we can use strain-level analyses of soil metagenomes to investigate the biogeographical patterns exhibited by a dominant group of soil bacteria (Bradyrhizobium)
academic.oup.com/ismej/advanc...