Faecalibacterium prausnitzii enzyme reprograms PD-L1 trafficking and sensitizes colorectal cancer to immunotherapy in mice Nature Microbiology, Published online: 17 April 2026; doi:10.1038/s41564-026-02326-2Phosphoribosyl pyrophosphate synthetase from Faecalibacterium prausnitzii inhibits PD-L1 trafficking to boost anti-tumour immunity and potentiate anti-PD-1 immune checkpoint inhibitor therapy during colorectal cancer.

Out Now! Faecalibacterium prausnitzii enzyme reprograms PD-L1 trafficking and sensitizes colorectal cancer to immunotherapy in mice #MicroSky

Fast and accurate multiple-protein-sequence alignment at scale with FAMSA2 - Nature Biotechnology FAMSA2 accurately aligns millions of protein sequences at high speed.

10 years after the first FAMSA paper, its successor is now published in Nat Biotech! We believe that FAMSA2 can enable analyses of large protein collections that were previously unattainable. Thank you, Andrzej and Cedric, for great collaboration
www.nature.com/articles/s41...

Alex Kramer, Alan Zhang and friends posted our preprint today. In it, we introduce Panmap, a tool for phylogenetic placement, assembly, lineage abundance estimation, and eDNA assignment using phylogenetic pangenomes.

www.biorxiv.org/content/10.6...

Myloasm, our long-read metagenome assembler, is now published! w/ @mgmarin.bsky.social and @lh3lh3.bsky.social

Very rewarding after > a year of development and countless hours thinking about assembly. Thanks to beta testers, Li lab, and reviewers who gave very helpful feedback.

rdcu.be/famFj

First page of the article

Excert of the text mentioniing Vera Aldeias

part of the text mentioning Vera Aldeias

The latest issue of Nature features a deep dive into sedimentary ancient DNA, with insights from our Matrix ERC-StG PI, @veraaldeias.bsky.social highlighting some of the big challenges shaping the field right now.

It's a good day when the first item in your feed is your own work :)

@rickbitloo.bsky.social was annoyed that scanning reads for all 96 rapid kit barcodes is bottleneck in Barbell, so he made Sassy2: 13x (150bp) to 4.6x (8kbp) faster than v1 by batch-searching patterns, and >100Gbp/s on 16 threads!

Spatial structure: Shaping the ecology and evolution of microbial communities Abstract. Most microbes grow in spatially structured communities, and this profoundly shapes their ecology and evolution. At the microscale, short interact

Spatial structure: Shaping the ecology and evolution of microbial communities

@femsjournals.bsky.social Microbiology Review by @marcelbaecker.bsky.social et al
from @bedutilh.bsky.social @bramvandijk.bsky.social

academic.oup.com/femsre/advan...

PhD position in Jena! Unique German-French collaboration to work on integrating phage genomic modules into VirJenDB.org - make sense of #phages, #big_data, #front_end, #back_end, #database. Please apply here 👇
jobs.uni-jena.de/jobposting/c...

If you ever need to fuzzy search some DNA, sassy is your tool.

Please spread the word; I think many people just outside my own circle could benefit from this :)

cc @rickbitloo.bsky.social

github.com/RagnarGrootK...

📣Excited to share our (first) VirJenDB publication!
🎁Check it out to see how your #virus database supports #metadata #biocuration and #bioinformatics integration.
🎶Stay tuned for collaboration opportunities in 2026, including a hackathon at #ViBioM2026!
📃 doi.org/10.1093/nar/...
💻 www.virjendb.org

Check out our new ancient DNA article on the deep time evolution of antimicrobial peptides in the oral microbiome! Learn more about actifensins and test out our new software tool, AMPcombi! A big congratulations especially to Anan and Rosa for all their hard work on this!
doi.org/10.1021/jacs...

We worked hard in 2025, will be super busy in 2026 and you will hear all about it.

For now, we are ready for a break and wish you all the best of holidays!

#MatrixERC #ICArEHB #Neanderthal #Paleolithic #HumanEvolution #Prehistory #AncientDNA #Biomolecules #SedimentDNA #Geoarchaeology

Long-read metagenomics reveals phage dynamics in the human gut microbiome - Nature Complex prophage integration dynamics, including low-level induction, cross-family host range and transposase-mediated mobilization, challenge existing paradigms and deepen our understanding of phage–...

Long read Metagenomics, #phage and #prophage in the gut by Ami Bhatt's group. Beautiful data showing changes in phages over two years

#phagesky

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

Scalable and systematic hierarchical virus taxonomy with vConTACT3 Viruses are key players in diverse ecosystems, but studying their impacts is technically and taxonomically challenging. Taxonomic complexities derive from undersampling, diverse DNA and RNA genomes wi...

🚨vConTACT3 preprint live!🚨(Peer Review soon...!)

vConTACT3 delivers a unified, scalable, and transparent framework for genome-based virus taxonomy — helping translate big viral data into systematic classification.

🔗 Read the preprint: doi.org/10.1101/2025...

Improvements details below 👇

🚨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...

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-...

Fantastic resource! Do you know when we can expect a preprint about vire db?

Selection and transmission of the gut microbiome alone can shift mammalian behavior Nature Communications - Here, the authors present evidence that the gut microbiome alone, without changes in the host genome, can shape how animals respond to selection, identifying a bacterium and...

We selected the laziest mouse at each round to inoculate the next batch of germfree mice: over rounds of selection and passaging, behavior shifted without changes to the mouse genome: rdcu.be/eM3rO
🦠🧫

Isolation, engineering and ecology of temperate phages from the human gut - Nature Human host-associated cellular products may act as induction agents for bacteriophages.

Very cool phage study from @jeremyjbarr.bsky.social's lab.

Isolation, engineering and ecology of temperate phages from the human gut
#microbiomesky #phagesky

Ecological constraints foster both extreme viral-host lineage stability and mobile element diversity in a marine community Phages are typically viewed as very rapidly evolving biological entities. Little is known, however, about whether and how phages can establish long-term genetic stability. We addressed this eco-evolut...

Phages evolve fast, or do they?
In oysters, some stay identical for years.
With >1,200 phages & 600 Vibrio genomes, we reveal long-term stability and new mobile elements.
Proud of this collaborative work across our teams (Roscoff-UdeM and @epcrocha.bsky.social www.biorxiv.org/cgi/content/...

Imagem with the 6 team members altogether. There is also the name of the porject and its logo and institutional logos. The color is light red.

The ERC Project MATRIX explores one of the big questions in our past: how Neanderthals disappeared as modern humans spread across Europe. Meet the team behind it and learn more about our research on sediments, ancient DNA, proteins, lipids & human evolution
👉 matrix.icarehb.com

Phages with a broad host range are common across ecosystems - Nature Microbiology Proximity-ligation-based sequencing from 111 samples and 5 environments reveals that a substantial proportion of phages infect multiple species.

You like phages ? In this publication, we use metaHiC and our new version of the MetaTOR pipeline to challenge the traditional view of phages with a narrow host range.
@rkoszul.bsky.social @natmicrobiol.nature.com @cnrs.fr @institutpasteur.bsky.social

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

Bacterial community adaptation after freshwater and seawater coalescence Microbial community coalescence, the merging of entire microbial communities, is common across ecosystems, particularly in estuaries where freshwater and seawater mix. The complexity of these habitats...

💧🌊 What happens when freshwater bacteria meet their salty counterparts?
Our new preprint explores the ecological factors driving community coalescence 👉www.biorxiv.org/content/10.1101/2025.09.... @bedutilh.bsky.social @microverse.bsky.social

Happy Birthday, Goethe! 🌿
Though he never saw microbes under a microscope, his holistic view of nature still inspires us today. At the #Microverse, we explore how microbial worlds shape life’s balance – just as Goethe imagined nature as one interconnected whole.
Illustration: AI-generated

Rapid species-level metagenome profiling and containment estimation with sylph - Nature Biotechnology The microbial composition of metagenomes is identified in seconds by profiling against large databases.

The microbial composition of metagenomes is identified in seconds by profiling against large databases go.nature.com/3BBVqDC
rdcu.be/eCbj4

Synteny-aware functional annotation of bacteriophage genomes with Phynteny Accurate genome annotation is fundamental to decoding viral diversity and understanding bacteriophage biology; yet, the majority of bacteriophage genes remain functionally uncharacterised. Bacteriopha...

Plus, it's heaps good timing with preprints for our phage annotation tools Phynteny and Phold coming out in the past few weeks! www.biorxiv.org/content/10.1... www.biorxiv.org/content/10.1...

Protein Structure Informed Bacteriophage Genome Annotation with Phold Bacteriophage (phage) genome annotation is essential for understanding their functional potential and suitability for use as therapeutic agents. Here we introduce Phold, an annotation framework utilis...

Stoked to finally have a preprint out for Phold, our tool that uses protein structural information to enhance phage genome annotation #phagesky 1/n

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

Synteny-aware functional annotation of bacteriophage genomes with Phynteny Accurate genome annotation is fundamental to decoding viral diversity and understanding bacteriophage biology; yet, the majority of bacteriophage genes remain functionally uncharacterised. Bacteriopha...

🚨 New preprint 🚨

My phage annotation tool, Phynteny, finally has a preprint and a brand new version powered by a cool AI transformer architecture and protein language models! #phagesky

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/...

We (with Clement Coclet, not on Bsky) had the chance to work on a broad "state of viromics" review. We tried to use this to give an overview of how the field changed over the last ~ 15 years, and also what we think are some of the major remaining challenges. Full-text access at -> rdcu.be/excHt