Databases may contain lots of misannotated 16S rRNA sequences, which can hinder accurate taxonomic assignment in metabarcoding and metagenomic analyses. We have addressed this issue for Asgard archaea and generated a curated set of high-quality 16S rRNA sequences: academic.oup.com/ismecommun/a...

Bats’ remarkable longevity and immunity are linked through pleiotropic adaptations to viruses and ageing-related disease @nature.com @psudmant.bsky.social @ucberkeleyofficial.bsky.social @lucievirevolte.bsky.social www.nature.com/articles/s41...

Happy to see the last parts of my PhD with @milja001.bsky.social now published in @microbiomej.bsky.social (many thanks to all involved!) link.springer.com/article/10.1...

Distinct gut viral communities across life stages in dairy cattle - Microbiome

Background Ruminant gut microbial communities influence host health, productivity, and methane emissions, yet viral communities across life stages remain uncharacterized. Whilst bacteriophages shape m...

link.springer.com

Ryan Cook@ryancook94.bsky.social · last yr.

🧬🐄 NEW PREPRINT: Really happy to finally share the last big piece of work from my PhD! Spoiler: Cows are great and so are their viromes 🧵1/13 www.biorxiv.org/content/10.1...

📢 We are excited to announce that the new SILVA 144 Release is now live! See more details here: www.arb-silva.de/news/item/si...

SILVA Release 144 is here

arb-silva.de

The narrowing prokaryote–eukaryote divide reveals a complexity spectrum #microbiology #eukaryote #prokaryote #evolution #MicroSky @cp-trendsmicrobiol.bsky.social www.sciencedirect.com/science/arti...

Molecular architecture of colossal surface layers from hyperthermophilic archaea Led by @idocaspy.bsky.social (Ido) In collaboration with @mkrupovic.bsky.social and @vikramalva.bsky.social labs doi.org/10.64898/202...

Nature research paper: Diverse bacterial pattern recognition receptors sense the core phage proteome go.nature.com/45fpXCZ

Diverse bacterial pattern recognition receptors sense the core phage proteome - Nature

Systematic analysis of prokaryotic STAND NTPases — relatives of animal and plant immune receptors — uncovers diverse antiviral sensors that detect most of the core structural and replicative proteins of bacteriophages.

go.nature.com

Viruses, Proviruses and Satellites from Asgard Archaea Enrichments www.biorxiv.org/content/10.6...

Viruses, Proviruses and Satellites from Asgard Archaea Enrichments Reveal Complex Microbial Interactions

Asgard archaea are the closest known relatives of eukaryotes and are central to models of eukaryogenesis involving archaeal bacterial symbiosis, yet the contribution of viruses remains unexplored. Her...

biorxiv.org

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

Do biofilms give an ecological advantage? Yes! A fantastic follow-up to our previous biofilm work in ammonia-oxidizing archaea: "Biofilm Lifestyle Drives Ecophysiological Niche Expansion in an Archaeal Soil Nitrifier" www.biorxiv.org/content/10.6... Congratulations to all authors! #archaea

With Eugene Koonin, we wrote a rather comprehensive review on the origin, evolution and organization of the #virosphere. We describe all 10 viral realms and the logic behind them, and so much more. Check it out! comptes-rendus.academie-sciences.fr/biologies/ar...

Absolutely extraordinary work from Hui Gao, John Briggs and co @mpibiochem.bsky.social on the structure of the influenza matrix protein in situ, particularly in filamentous virions. It's beautiful, and answers questions I've been wondering about for twenty years www.biorxiv.org/content/10.6...

Want to annotate a bacterial genome with structures? @oschwengers.bsky.social bakta and @gbouras13.bsky.social phold got together, and the result is Baktfold: protein annotation across the microbial tree of life using structures www.biorxiv.org/content/10.6... #phagesky #microsky #microbiomesky

With Eugene Koonin, we propose a concept of “the selfish ribosome”, under which evolution of life is viewed as a ribosomal takeover, where the ribosome evolved to consume most of the cell’s resources, while other cellular componentry ensures the propagation of the ribosome. arxiv.org/abs/2602.23268

Out today: We discovered new viral proteins that target immune signaling molecules, solely based on their AlphaFold-predicted shapes www.science.org/doi/10.1126/... Congrats Nitzan Tal and coauthors! Thank you Kranzusch lab for the fun collaboration! Linking below previous thread on our findings

Structural modeling reveals phage proteins that manipulate bacterial immune signaling

Immune systems in animals, plants, and bacteria often rely on intracellular nucleotide signaling, which viruses can block by sequestering or degrading these signals. We identified structural and bioph...

science.org

Nitzan Tal@nitzantal.bsky.social · last yr.

📢Preprint out! Excited to share my final work from the @soreklab.bsky.social! We mined phage dark matter using structural features shared by anti-defense proteins (viral tools that help phages bypass bacterial immunity) to guide discovery. Found 3 new families targeting immune signaling!

Big update for #gbdraw! - Multi-record circular plots: Genomes with multiple replicons can now be displayed in a single view! - Advanced linear plots: Focus on regions of interest with granular control over feature selection and color-coding! Try now: gbdraw.app #microbiology #bioinformatics

Life's a continuum of organisms - from independently mobile bits of genomes, through viruses, to organelles, to barely non-organellar symbiotes, to cells. That are mostly not independent either.

Zamin Iqbal@zaminiqbal.bsky.social · 6mo ago

Madness. A bacterium with a 10kb genome, lost replication initiation, translation.., relies on symbiotic host. www.nature.com/articles/s41...

Beyond thrilled to share that our study has been published! This project encompasses years of work, including my thesis research on Asgard archaea in the @archaeal.bsky.social lab at @utmsi.bsky.social and @texasscience.bsky.social!!! #MicroSky #ArchaeaSky 1/12

Are you a long-time fan of Archaea, an extremophile-phile, or are you simply curious? Either way, we have good news. We’re delighted to announce the 2026 EMBO Workshop on Archaea, 6–10 July. Sign up: meetings.embo.org/event/26-arc... We look forward to seeing you in Cambridge, UK. Please repost!

gcMeta 2025: a global repository of metagenome-assembled genomes enabling cross-ecosystem microbial discovery and function research. DOI: 10.1093/nar/gkaf1115 https://pubmed.ncbi.nlm.nih.gov/41171134/

gcMeta 2025: a global repository of metagenome-assembled genomes enabling cross-ecosystem microbial discovery and function research - PubMed

The rapid growth of metagenomic sequencing has generated an unprecedented wealth of metagenome-assembled genomes (MAGs), transforming opportunities for microbial discovery and functional characterization. Yet, full utilization of these resources has been constrained by heterogeneous data generation …

pubmed.ncbi.nlm.nih.gov

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

Phylogenetic reconciliation supports a methanogenic ancestor of the Archaea and a derived origin for host-associated lineages

The phylogeny of the Archaea continues to be revisited and revised as new groups are discovered and phylogenetic methods improve, but key questions about their early evolution remain. It has been sugg...

biorxiv.org

This paper has been a must! Great collaboration with @mkrupovic.bsky.social and @yifanzhou.bsky.social, a N&V by a legend of halophilic archaea tinyurl.com/yc3dcv72, and one picture of one of our expeditions to Dallol making the cover of the November issue of @natmicrobiol.nature.com rdcu.be/eLtCH

Glad to share our paper out today @NatureEcoEvo: “Serial innovations by Asgard archaea shaped the DNA replication machinery of the early eukaryotic ancestor”. www.nature.com/articles/s41... #microsky #archaeasky

Serial innovations by Asgard archaea shaped the DNA replication machinery of the early eukaryotic ancestor - Nature Ecology & Evolution

Phylogenetic and biochemical analyses show a diversity of components of the DNA replication machinery in different Asgard archaea that contributed to the eukaryotic DNA replication machinery.

nature.com

Viruses and virus satellites of haloarchaea and their nanosized DPANN symbionts reveal intricate nested interactions Out now in Nature Microbiology, by Yifan Zhou, Mart Krupovic & colleagues. @mkrupovic.bsky.social @yifanzhou.bsky.social @deemteam.bsky.social www.nature.com/articles/s41...

Viruses and virus satellites of haloarchaea and their nanosized DPANN symbionts reveal intricate nested interactions - Nature Microbiology

An exploration of the viromes of haloarchaea and their ultra-small DPANN symbionts reveals plasmid-derived satellites of viruses from both archaeal groups, highlighting the complexity of nested symbio...

nature.com

Archaeal symbioses all the way down by Mike Dyall-Smith www.nature.com/articles/s41...

Archaeal symbioses all the way down - Nature Microbiology

Ethiopian salt lakes feature unique microbial communities with nesting layers of symbioses, where haloarchaea and their ultra-small archaeal symbionts are prey to viruses, which are in turn hijacked b...

nature.com

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/...

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...

biorxiv.org

Our work on viruses and virus satellites of haloarchaea and their DPANN symbionts is out today in Nature Microbiology! @mkrupovic.bsky.social @deemteam.bsky.social @anagtz.bsky.social www.nature.com/articles/s41...

Viruses and virus satellites of haloarchaea and their nanosized DPANN symbionts reveal intricate nested interactions - Nature Microbiology

An exploration of the viromes of haloarchaea and their ultra-small DPANN symbionts reveals plasmid-derived satellites of viruses from both archaeal groups, highlighting the complexity of nested symbio...

nature.com

www.science.org/doi/full/10....

The Viral AlphaFold Database of monomers and homodimers reveals conserved protein folds in viruses of bacteria, archaea, and eukaryotes

VAD is a Viral AlphaFold Database of protein monomers and homodimers from viruses infecting hosts across the tree of life.

science.org

🚨 New Web Resource Alert! 🚨 We're delighted to share Viro3D a database of >85000 viral protein structure predictions from >4400 human & animal viruses. 🔗 viro3d.cvr.gla.ac.uk 📄 www.embopress.org/doi/full/10.... @molsystbiol.org @cvrinfo.bsky.social @uofgmvls.bsky.social #Virology #AlphaFold 🧪 🦠

Computational function prediction of bacteria and phage proteins journals.asm.org/doi/abs/10.1... #jcampubs