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

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.

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 - 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 …

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/

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...

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

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

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.

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

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...

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...

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...

Archaeal symbioses all the way down
by Mike Dyall-Smith

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

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/...

Thanks Rodrigo❤ (c(ˆ⌣ˆc)

Thanks Basile🥰

10: Similar phenomenon (9) is also happening in nanohaloarchaea; 11: the archaeal host carries a CRISPR array with spacers targeting both viruses and virus satellites.

8: Spindle-shaped HVs infect a haloarchaeal host without interference of virus satellites (SRCEs); 9: Spindle-shaped HVs and SRCEs co-infect a haloarchaeal host. SRCEs replicate and consume the virion components of HVs, which lead
to a decrease in HV production;

4: Similar CRISPR-Cas immunity processes (1, 2, 3) are happening in nanohaloarchaea; 5: A gene transfer from an icosahedral HV to an icosahedral NHV; 6: A gene transfer from a head-tailed NHV to a head-tailed
HV; 7: A gene transfer from a nanohaloarchaeal host to a head-tailed virus;

1: Viruses infect a haloarchaeal host; 2: A spacer is acquired from viral DNA by the haloarchaeal CRISPR-Cas system; 3: CRISPR spacers are transcribed, matured, and matched with target viral DNA with the help of Cas proteins, leading to the cleavage of the invading viral DNA;

The complexity of interactions between haloarchaea, nanohaloarchaea, their respective viruses and virus satellites. Haloarchaeal virus (HV); nanohalo archaeal virus (NHV)

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...

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...

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.

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

🚨 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

Thank you❤️❤️

(1/2) Preprint alert! In collaboration with @yifanzhou.bsky.social and @mkrupovic.bsky.social we describe host-parasite layers in hypersaline systems of the Danakil Depression. Haloarchaea host nanohaloarchea and both are infected by viruses (12 new families found).

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

5/n In addition to HVs and NHVs, we describe plasmid-derived virus satellites (named SRCEs) that appear to have originated convergently to parasitize spindle-shaped viruses of both haloarchaea and nanohaloarchaea, uncovering an additional layer of parasitism!!!

4/n No evidence of host switching between HVs and NHVs was obtained, but multiple horizontal transfers of genes implicated in virion structure and morphogenesis between HVs and NHVs were detected.

3/n The complete virus genome can be classified into 16 families (12 newly described). Deep divergence between HVs and NHVs strongly suggests that HVs and NHVs from all four groups have diverged early, likely concomitantly with the radiation of archaeal lineages.