🎉🎉🎉 New preprint to start the new year 🎉🎉🎉 Patients recovering from bowel surgery may have stomas formed to divert the flow of faeces to the opening on the skin, away from healing intestinal tissue. The visible sign of this process is an ileostomy or colostomy bag. /1 #surgerysky #medsky

We found: - High-dose VOWST enabled rapid, durable engraftment and rescued efficacy in phase 3 vs phase 2 - VOWST shifted the gut toward a healthy-like community, reducing Proteobacteria and C. diff - Engrafted Firmicutes restored key metabolites (secondary bile acids, SCFAs) that inhibit C. diff

Revising a large grant for the last time before submission, and all means are fair

Fascinating read on the immunological origins of endometriosis - with insights into improved diagnostics and treatment www.science.org/content/arti...

We concluded that plasmids evolve through a birth-death process, involving fusion (birth of a new "species"), but also fragmentation (by many processes, such as MGE-mediated recombination). Fusions mostly are removed by selection, but sometimes they survive 16/n

Delighted to see our paper studying the evolution of plasmids over the last 100 years, now out! Years of work by Adrian Cazares, also Nick Thomson @sangerinstitute.bsky.social - this version much improved over the preprint. Final version should be open access, apols. Thread 1/n

3/ Bioinformatics is not just about the data. It’s about the biology behind the data. Without that, your code is just noise in a terminal.

Glad to have been a tiny part in this consortium!

I have 44 students enrolled in this course. Class officially started two minutes ago. They have an exam next week. Thoughts and prayers.

About fifteen months ago, someone handed me a bad study. Today it was retracted. So far, so normal. But do I just want to yell at journals and publishers again? Hell no. What could they actually DO to be better at handling this sort of nonsense? open.substack.com/pub/jamescla...

The Nordic medical and drug registries are amazing because you not only can tell RFK to fuck off and start making some sense, you have the numbers to back it up www.dn.se/sverige/sven...

Finally, the results of my postdoc at the @bigdatabiology.bsky.social lab in Shanghai see the light! The work includes my three favorite things research-wise: 🦠 microbiome, 🧬 long-reads, and 🐶 dogs. See our new preprint: www.biorxiv.org/content/10.1...

Fusobacterium nucleatum, a common mouth bacterium, may worsen oral cancer by using waste and changing cell behavior. This study offers clues for better oral cancer prevention！👇 #oral #cancer @ijosjournal.bsky.social www.nature.com/articles/s41...

This is a major issue is that the incentives are to output false positives in your tools If you need to survive on having many citations to your tools, it is better if your tool gives users lots of results so that they cite it! open.substack.com/pub/luispedr...

The legs-up-in-stirrups position sometimes used in birth or gynaecological procedures is called the lithotomy position. Etymology fans among you might note that this derives from the Greek for "stone cut". Let's explain why...

FANTASIA's paper is finally out! Check it out if you're interested in alternative methods to homology for functional annotation in nonmodel organisms 🦐🐙🪱🧬🐝🪲 @gemmaeling.bsky.social @amrojasm.bsky.social @ibe-barcelona.bsky.social @cabd-upo-csic.bsky.social @csic.es www.nature.com/articles/s42...

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/... 🧵

Anyone know what happened to hmpdacc.org? More importantly, does anyone know how to apply for HMP participant data nowadays?

Practice-engaged and practice-critical philosophy of science is needed now more than ever in light of widespread AI-integration into science and its oversight mechanisms.

I do miss when things were called "neural networks" and "principal components analysis" etc instead of lumping everything as "ML" and then "AI"

The @scilifelab.se ancient DNA unit is looking for an bioinformatician placed at Uppsala University. This is a great way to be part of diverse #aDNA research projects as a staff scientist with permanent (!!) employment: www.uu.se/en/about-uu/...

Best comment on Jay Bhattacharya that I've read to date.

My PhD student @leonielorenz.bsky.social (with Eva Geissen) has made this nice (free) online course to introduce mathematical modelling for biology: www.ebi.ac.uk/training/onl... Including both molecular and epidemiological examples

Niche bloop but: The endocrine system is the original object-oriented program.

NIH Director say journals "bully scientists into paying large fees". No. Academia is a prestige economy in which scientific leadership chose to make journals the currency & Gold OA was deemed 'the way'. Publishers just cashed in; you don't have to pay $10K www.insidehighered.com/news/governm...

Mixed feelings when a question I've been musing about for a long time gets answered in a paper. Yes, we have an answer! But also oh no, I wanted to study that!

Out now in @natcomms.nature.com: we show how wastewater surveillance identifies viral strains several weeks before the clinics, and study the trade-offs between the size of the catchment area for the sewer and the number of unique variants identified www.nature.com/articles/s41...

Why is germ theory in the same air quotes as "miasma theory," I ask as a historian of medicine who is very very tired

New in @plosone.org : Amplicon sequencing of pasteurized retail dairy reveals H5N1 avian influenza virus in U.S. cattle milk. Tiled-amplicon NGS achieved >90% genome coverage from pasteurized milk samples, enabling genomic surveillance of H5N1 spillover in cattle. journals.plos.org/plosone/arti...

One simple way for people who are not well-versed in machine learning to evaluate the use of ML in clinical research: Replace "ML" with "logistic regression." If your reaction is: 1. Oh, that's confounded -> it's still confounded 2. Wow, how can you do that with logistic regression? -> keep reading

Gearing up for an exciting talk by @jfcryan.bsky.social! He started in the brain and ended up in the gut, so opposite trajectory from mine. But as Hippocrates say, everything starts in the gut - or more accurately, in the evolution of the holobiont.

Sharing the most significant work from my group, led by the @evolvingstem.bsky.social team. Come for the discoveries of how Pseudomonas adapts in biofilms, stay for the story of how they were discovered by thousands of young scientists in grades 9-12. 🧪🧫🧬🧵 www.biorxiv.org/content/10.1...

So the random groupings...may not actually be random at all. If only we could speak fungus and ask them. "EXCUSE ME! YES YOU MAKING THE MUSHROOM! WHY DO YOU STORE YOUR GENETIC MATERIAL THE WAY YOU DO?" The End.

This paper makes me CACKLE. Every so often a fungus comes along that is like "oh, you think you understand genetics? lol. You're cute." and completely upends everything we thought we knew. Distribution of haploid chromosomes into separate nuclei in two pathogenic fungi | Science 🧪 #academicsky 🧵

A gift from a student 😂

One day, when I'm old and wise, I'm gonna understand the logic behind ggplot and stop embarrassing myself in front of the students.

How did I miss this paper? @ronanmccarthy.bsky.social lab screened nosocomial bugs for plastic-degrading enzymes, reasoning that they've been selected for this ability. They found a P. aeruginosa enzyme that efficiently degrades plastic #Biofilms11 #MicroSky (Image: www.cell.com/cell-reports...

📣 Junior PI Opportunity Join CNRS Strasbourg to lead cutting-edge research on host-pathogen interactions in insects 🪰 450k€ package | Drosophila, RNA, immunity IBMC + Labex NetRNA network 📅 Apply by June 30, 2025 🔗 ibmc.cnrs.fr/en/laboratoi... #RNA #Insects #Drosophila #NetRNA #Immunity #JobAlert

New vacancy in my team! PhD student position on microbial genome evolution, focusing on the evolutionary principles underlying bacterial genome architecture. Please repost and share with talented MSc students in #evobio, bioinformatics or related :) www.uu.nl/en/organisat... #MEvoSky #MicroSky

*pronouncing leo XIV like arXIV*

I'm semi-manually harmonising patient-level data for 9198 metagenomes from 29 separate projects and I just need someone 6o feel sorry for me at the moment

New paper out! We discovered a tiny archaeon with the smallest known archaeal genome — only 238 kbp! Candidatus Sukunaarchaeum mirabile has almost no recognizable metabolic pathways and may rely heavily on a host to survive. It also represents a novel, deep-branching lineage in the archaeal tree.

Not my usual line of research, but a fun night project - and important, too!

A huge new NIH-funded clinical trial of 20,000 girls has shown that a single dose of HPV vaccine yields the same response as two doses after 4.5 years. This is critical to public health efforts to save lives with this vaccine. Yes. We still have to battle RFK Jr. to ensure access to HPV vaccine.

Small update from AllTheBacteria (allthebacteria.org). Assemblies can be bulk downloaded from OSF as before, or you can now get individual assemblies from AWS. We now also have a LexicMap index on AWS, so you can align your favourite gene against 2.4million bacteria (next post for price estimates)

BaCon = bacteriophage-conditional mouse Gut phages deleted in conventionally reared mice & then reconstituted, allowing study of phage function. Using BaCon, authors show phages have minimal impact during equilibrium, but increase potency of ampicillin www.cell.com/cell-host-mi...

Finally a group picture I can use!

Turning a Technology into a concrete thing that does something requires a lot of decisions, and most of those decisions are about what NOT to do. This is not solely a commercial pressure, but the nature of the game - the ways scientists package their own tools is often extremely limited.

Algorithms are especially valuable for the evocation of science based neutrality, because it's really just math. Silly liberals saying 2+2 isn't 4. This conversation is so Orwellian. Numbers don't actually exist in the world. Quantifying is a thing *we do to something* - and we choose how to do it.

I keep catching strays from "technology is neutral" people, so let's set things straight. 1) Technology is not neutral, especially the subset of technology called "algorithms" 2) The form-factor that makes a technology into a tool is not neutral 3) How tools are productized is not neutral [rant]