Fantastic dental calculus and where to find it! Now published (not quite with this title) @ecol-evol.bsky.social doi.org/10.1002/ece3... @johnlrichards.bsky.social uncovers general rules for the formation of preserved oral microbiomes in mammals. With @markella-morait.bsky.social and many others

Dental Calculus Formation Is Linked to Diet and Phylogeny in Mammals

In a survey of > 1600 specimens across all mammalian orders, we found that most species present dental calculus. We found calculus production to be strongly associated with herbivory, and we provide ...

doi.org

Katerina Guschanski@kguschan.bsky.social · 11mo ago

Fantastic dental calculus and where to find it Johnny Richards and team (@markella-morait.bsky.social + curators from 5 museums) survey >140 mammalian species with >1,600 specimens to understand what factors determine dental calculus formation. #aDNA #museomics www.biorxiv.org/content/10.1...

Starting with the DNA sequence of a #phage genome, #PholdAPhage will create a 3D reconstruction of the complete phage, almost like you did cryoEM on it! Check out Renee's awesome software github.com/reneegreen81... to assemble unknown phage particles one protein at a time

My main PhD paper is out on bioRxiv! 🎉 The microbiomes of wild animals, besides the gut, remain unexplored. To help remedy this, we used museum-preserved dental calculus to characterise the oral microbiome of 34 diverse mammal species. 💀🦠🦷 Read here: www.biorxiv.org/content/10.6...

Out Now! A phage takes the wheel #MicroSky

A phage takes the wheel

Nature Microbiology, Published online: 19 June 2026; doi:10.1038/s41564-026-02405-4Prophage FRφ rewires the flagellar apparatus of its Enterobacter sp. host through RNA-guided repression of native flagellin, favouring its own phage-encoded isoform. This enhances host motility and reduces immune recognition, boosting bacterial fitness in mice.

go.nature.com

Hey Hey, a few weeks ago, we released quicksand version v2.6 github.com/mpieva/quick... This version allows the `--taxlvl g` flag to obtain summary statistics and output-files on the genus level. Especially for multi-genus families (e.g. Bovidae or Cervidae), this is much more informative 🐂

GitHub - mpieva/quicksand: A pipeline for the analysis of sedimentary ancient mtDNA.

A pipeline for the analysis of sedimentary ancient mtDNA. - mpieva/quicksand

github.com

I am hiring a Data Curator in my group nikolay-oskolkov.com/metabolic-re...! This is an excellent opportunity for anyone interested in multi-omics data analysis, exploratory (unsupervised) machine learning, and data management/curation. Apply here: euraxess.ec.europa.eu/jobs/443793. Appreciate RT!

🌎 🧬 🖥️ logan-search.org the tool to query all SRA sequences (Dec 2023 snapshot) — just got major updates. Here's what's new. 🧵 1/12

Pleased to see this beautiful paper out. Kudos to @jeroenmeijer.bsky.social who took @stevenquistad.bsky.social data and dug deep, revealing a new phage that erupts to astonishing abundance. As theory predicts, the life of SGEs is fuelled by encounters with new hosts www.science.org/doi/10.1126/...

Eco-evolutionary dynamics of massive, parallel bacteriophage outbreaks in compost communities

A single bacteriophage can dominate microbial communities yet only evolves when migration changes its ecological context.

science.org

Viruses are highly abundant in the oceans, but there is one place you won't typically find them: in global ocean ecosystem models... until now. Introducing "vDarwin", an explicit integration of viruses into the MITgcm/Darwin global ecosystem framework: www.biorxiv.org/content/10.6... a 🧵

New preprint! 🚨 Phage proteins don't act alone. Phages rely on homooligomerisation to assemble identical protein subunits into functional forms. But figuring out those exact configurations experimentally is tough. Learn about our approach in our new preprint! 👇 (1/n) www.biorxiv.org/content/10.6...

Like a prophage being awakened from its slumber, the phage field has seen a lot of renewed activity during the last decade. Check out our new @natrevmicro.nature.com review on the temperate phage life cycle here to stay up-to-date 🧫🦠 www.nature.com/articles/s41...

Revisiting the life cycle of temperate phages - Nature Reviews Microbiology

The life cycle of temperate bacteriophages involves lytic or lysogenic cycles and has historically served as a model for studying genetic regulation. This Review provides an updated overview of these ...

nature.com

Beyond thrilled that our paper ‘Co-migration of hundreds of microbial species over metres drives selection and promotes non-motile hitchhikers’ has been accepted in Nature Communications! 🎉🦠 (1/n) www.nature.com/articles/s41...

I had fun writing a short commentary on the importance of integrating prophage biology into microbiome research 🦠 Now out in @cp-cellhostmicrobe.bsky.social #microbiomesky #phagesky www.cell.com/cell-host-mi...

Making room for gut prophages in human health

Prophages are pervasive in the human gut yet largely overlooked in microbiome research, despite substantial functional potential. Emerging evidence indicates that prophages regulate bacterial fitness,...

cell.com

Are gut phages friends or foes? A nice "forum" in Cell Host&Microbe by @naamagz.bsky.social discussing it's all about context. Depending on host inflammation and ecology, phages can shift between stabilizing and destabilizing our microbiome. www.cell.com/cell-host-mi... #phagesky

The gut phageome: Friend or foe?

Gut bacteriophages defy simple classification as beneficial or harmful, instead shifting between roles that stabilize or destabilize microbial communities depending on phage lifestyle dynamics, host i...

cell.com

Mushuvirus is the most widespread phage genus in the human gut. 🌍 Together with other family members, these viruses occur in 89% of humans worldwide, including the Iceman Ötzi! How is it possible that they were hidden in previous metagenomic analyses? [1/7] Read: doi.org/10.64898/202...

@xavierdidelot.bsky.social et al. present the R package DiagnoDating for diagnosing issues in a reconstructed dated phylogeny, including outlier detection, posterior predictive checking, and residual analysis. 🔗 doi.org/10.1093/molbev/msag093 #evobio #molbio #compbio #phylogeny

DiagnoDating: diagnostics for dated phylogenies in microbial population genetics

Abstract. Microbial population genetic studies often involve the use of a dated phylogeny to show how the genomes are related over a relevant timescale. Ma

doi.org

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

Phage host range: determinants, dynamics and applications - Nature Reviews Microbiology

Comprehensive assessment of the host range of phages is a prerequisite for their safe and effective use in multiple applications but is rarely undertaken. This Review outlines the molecular and ecolog...

nature.com

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

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.

go.nature.com

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...

Fast and accurate multiple-protein-sequence alignment at scale with FAMSA2 - Nature Biotechnology

FAMSA2 accurately aligns millions of protein sequences at high speed.

nature.com

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

High-resolution metagenome assembly for modern long reads with myloasm

Nature Biotechnology - A long-read metagenome assembly method recovers circular and complete genomes better than existing tools.

rdcu.be

Nature Biotechnology@natbiotech.nature.com · 4mo ago

High-resolution metagenome assembly for modern long reads with myloasm - @lh3lh3.bsky.social @jimshaw.bsky.social @danafarber.bsky.social @harvardmed.bsky.social go.nature.com/3PBEwvR

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!

bioRxiv Bioinfo@biorxiv-bioinfo.bsky.social · 5mo ago

Sassy2: Batch Searching of Short DNA Patterns https://www.biorxiv.org/content/10.64898/2026.03.10.710811v1

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...

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

academic.oup.com

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, #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...

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–...

nature.com