Cedric Laczny 🖥️🦠💡

Highly accurate prophage island detection with PIDE - Genome Biology As important mobile elements in prokaryotes, prophages shape the genomic context of their hosts and regulate the structure of bacterial populations. However, it is challenging to precisely identify pr...

Highly accurate prophage island detection with PIDE genomebiology.biomedcentral.com/articles/10.... #jcampubs

🚨New paper 🚨

Can protein language models help us fight viral outbreaks? Not yet. Here’s why 🧵👇
1/12

📉Despite the hype, protein language models trained across the “protein universe” are outperformed by even the simplest, site-independent alignment-based model.
5/12

Our high-precision metagenomic strain caller, PHLAME, is now published in Cell Reports!! www.cell.com/cell-reports...

PHLAME works on tough sample types -- including those with coexisting strains of a species and low depth.

This is v cool

Archaea produce peptidoglycan hydrolases that kill bacteria Archaea regularly interact with bacteria but reports of archaea killing bacteria are very rare. This study shows that many archaea encode peptidoglycan hydrolases, which specifically target bacterial ...

Archaea are often surrounded by bacteria. But is there ever active conflict between the two? Can archaea kill bacteria? If so, how do they do it?

Work by @romainstrock.bsky.social shows that some archaea can kill bacteria by secreting peptidoglycan hydrolases. journals.plos.org/plosbiology/...

New preprint from lab: www.biorxiv.org/content/10.1... describing the Metalog database of manually annotated contextual data for >110k metagenomics samples around the globe metalog.embl.de

See the thread below from @biocs.bsky.social for more info!

If you are interested in learning more about Clinical Methods for Nutrition and Obesity Research - I strongly recommend you apply for this course - it's free and they provide a $500 travel stipend to offset costs of attendance.

www.pbrc.edu/training-and...

We just bumped into something very preliminary… but very exciting:

AF2.3 and AF3.0 distograms may potentially reproduce MD-like behavior.

Until we do further tests, you can reach our early insights at www.biorxiv.org/content/10.1...

FAMSA2 enables accurate multiple sequence alignment at protein-universe scale We introduce FAMSA2, an algorithm that produces high-accuracy multiple protein sequence alignments with unprecedented speed. Across structural, phylogenetic, and functional benchmarks, FAMSA2 matches ...

Interested in a tool that aligns millions of proteins in minutes with quality similar to or better than the state-of-the-art utilities? Please take a look at our FAMSA2 paper: www.biorxiv.org/content/10.1...
and GH repo: github.com/refresh-bio/...

"Arbuscular mycorrhizal fungal hotspots and global protected areas: Predicted richness and endemism hotspots (95th percentile of predictions) for AM fungi. Coloured areas on the map show richness hotspots (green), rarity hotspots (purple) and the overlap of richness and rarity hotspots (yellow). Black areas indicate non-hotspots. Bar graphs show the total hotspot size and percentage overlap with protected areas by biome, and grey bars reflect different IUCN management categories (I, most strictly preserved habitats; NA, unassigned category). The dashed line at 30% hotspot area protected reflects the ambitions of 30 × 30 target goals under the Kunming–Montreal Global Biodiversity Framework. ND, no data." -- Source: Nature | ISSN 1476-4687 (online). Van Nuland, M.E., Averill, C., Stewart, J.D. et al. Global hotspots of mycorrhizal fungal richness are poorly protected. Nature (2025).

The new paper published in @nature.com reveals that 90% of mycorrhizal fungal biodiversity hotspots lie outside protected areas.

Details ➡️ www.avcr.cz/en/media/pre... #SoilHealth #CarbonStorage

Research by @spun.earth, @ethz.ch, @stanford.edu, @biologylu.bsky.social, @mbuavcr.bsky.social et al.

The attribution of human health outcomes to climate change: transdisciplinary practical guidance - Climatic Change For over 30 years, detection and attribution (D&A) studies have informed key conclusions in international and national assessments of climate science, providing compelling evidence for the reality and...

New workshop paper out today with 60 of our closest friends, providing guidance on how to design a study attributing health impacts to climate change. Hopefully this helps expand the field and start closing the representation gaps we discuss in our forthcoming work link.springer.com/article/10.1...

An Asgard archaeon from a modern analog of ancient microbial mats It has been proposed that eukaryotic cells evolved via symbiosis between sulfate-reducing bacteria and hydrogen-producing archaea. Here we describe a highly enriched culture of a novel Asgard archaeon...

📣 New paper alert!
One of the most exciting projects we've done in recent years is now out on BioRxiv: "An Asgard archaeon from a modern analog of ancient microbial mats".

Glimpse into early complex life! ❄️🦠 🔬🧬

www.biorxiv.org/content/10.1.... A thread...

ATP synthesis driven by atmospheric hydrogen concentrations | PNAS All cells require a continuous supply of the universal energy currency, adenosine triphosphate (ATP), to drive countless cellular reactions. The un...

Our article showing energy production from air alone is in PNAS today. This paper provides an ultimate biochemical proof that microbes can survive simply by 'making' energy from air (making two ATP per molecule atmospheric H2 consumed) and has biotech applications. www.pnas.org/doi/10.1073/...

🦠🧍‍♀️From bacterial to human immunity.

We report in @science.org the discovery of a human homolog of SIR2 antiphage proteins that participates in the TLR pathway of animal innate immunity.
Co-led wt @enzopoirier.bsky.social by D. Bonhomme and @hugovaysset.bsky.social

www.science.org/doi/10.1126/...

🎧 New SciLux episode!

Professor Elisabeth Letellier (@uni.lu) and Dr. Mina Tsenkova (@amgen.bsky.social) discuss how diet and gut microbiome influence colorectal cancer development.

🎙️Listen now.

Powered by @researchluxembourg.org

#ColorectalCancer #GutHealth #SciLux #SciencePodcast

Gut microbiome evolution from infancy to 8 years of age - Nature Medicine In a unique cohort of twins followed from birth to 8 years of age, shotgun sequencing of stool samples reveals that the transmission, persistence and evolutionary adaptation of bacterial strains are s...

#NatMicroPicks

Tracking the gut microbiome evolution 🦠

A big data analysis of gut microbiome of kids from infancy to 8 years of age.

#MicroSky #MicrobiomeSky
www.nature.com/articles/s41...

Preprint alert! 🦌
Our new abundance index, REINDEER2, is out!
It's cheap to build and update, offers tunable abundance precision at kmer level, and delivers very high query throughput.

Short thread!

www.biorxiv.org/content/10.1...

github.com/Yohan-Hernan...

Quantum algorithms unlock tomorrow's impossible problems Imagine a world where quantum computing solves problems that even our most powerful supercomputers can't handle today. This technology could help design

🟣 Quantum algorithms aren’t science fiction anymore. They’re shaping the future, right here in #Luxembourg.

At our first #QuantumBreakfast, experts explored how quantum tech could revolutionise AI, medicine, security, and more.

#QuantumAtUniLu

For those at the #ASMicrobe @asm.org conference this weekend, my PhD student Alejandro De Santiago (a bioinformatics ninja) is presenting his poster on a new nematode-bacterial symbiosis we’ve recently discovered! TODAY in the poster hall www.abstractsonline.com/pp8/#!/20974...

A short preprint describing the GlobDB is now on arXiv: arxiv.org/abs/2506.11896

If you find the resource useful, please also check globdb.org for info on how to cite the underlying resources and tools.

Klimaschutz trifft Darmgesundheit: Unsere Mikrobiomexpertin Christine Moissl-Eichinger erhält den prestigeträchtigen Advanced Grant (2,5 Mio. €) des für ihre Forschung zu Methanobrevibacter – einem winzigen Mikroorganismus mit großem Potenzial ➡ https://bit.ly/3FDDJpO.

#ERCAdG

🥳 Important + positive changes to the @erc.europa.eu program:
- PhD age eligibility up to 10 years (starting) and 15 years (consolidator
- Application Part I focuses on the aim + strategy
- Application Part II restricted to 7 pages

Bacteria break through one-micrometer-square passages by flagellar wrapping Confined spaces are omnipresent in the micro-environments, including soil aggregates and intestinal crypts, yet little is known about how bacteria behave under such conditions where movement is challe...

This is cool - bacteria wrap their flagella to propel themselves through narrow passages www.biorxiv.org/content/10.1...

Ambitious project to develop low-cost genome sequencing for pathogens known and unknown - University of Birmingham Project will build on research that helped diagnostic labs to adopt sequencing capacity for COVID-19 and permit characterisation of future infectious threats

Absolutely thrilled to announce the launch of ARTIC2 - a £5.5M 5 year project funded by @wellcometrust.bsky.social to build on the ARTIC approach of low-cost, globally accessible genome sequencing for surveillance of outbreaks, epidemics and endemic diseases: www.birmingham.ac.uk/news/2025/am...

**NEW Doctoral Training Programme just launched!!** This exciting programme on Microbial Genomics for Health Protection is joint between @imibirmingham.bsky.social and UKHSA @ukhsa.bsky.social. 9 brilliant projects available!!

Phylogenomic analyses reveal that Panguiarchaeum is a clade of genome-reduced Asgard archaea within the Njordarchaeia The Asgard archaea are a diverse archaeal phylum important for our understanding of cellular evolution because they include the lineage that gave rise to eukaryotes. Recent phylogenomic work has focus...

#Asgard,#phylogeny
1/ 🧵 Does MAGs contamination affect the placement of Njord as suggested by Zhang et al, 2025? www.nature.com/articles/s41...
Our updated analysis suggests instead... www.biorxiv.org/content/10.1...

Nobel Prize winner inspires young minds It’s not every day that high school students get to ask questions to a Nobel Prize laureate—let alone witness a physics demonstration that ends in a loud, crowd-startling explosion. But that’s exactly...

"There is a certain class of people who don’t lose that curiosity. And those people are called scientists."
— Prof. William D. Phillips, #Nobel Laureate

📸 One unforgettable night at #PhysicsForFuture, Luxembourg.

👇 (Thread)

#uni_lu

Autocycler: long-read consensus assembly for bacterial genomes Motivation: Long-read sequencing enables complete bacterial genome assemblies, but individual assemblers are imperfect and often produce sequence-level and structural errors. Consensus assembly using ...

www.biorxiv.org/content/10.1...

Autocycler, the automated successor to Trycycler from @rrwick.bsky.social has a pre-print out - overall, pretty awesome performance (and is very easy to use)

github.com/rrwick/Autoc...

Quite satisfied with my new #archlinux "modern" setup, Secure Boot, Unified Kernel Images, systemd-boot, disk encryption with luks (using the TPM for unlocking), btrfs (with compression and snapper for the snapshotting policy), apparmor... Install notes here: hcartiaux.github.io/posts/2025-0...