Miguel Gómez-Raya

A miniature CRISPR–Cas10 enzyme confers immunity by inhibitory signalling - Nature Panoptes, an anti-phage defence system against virus-mediated immune suppression, is revealed.

Now online at @nature.com we show how the Panoptes defense system protects against viruses that attempt immune evasion - and expands our understanding of the role of oligonucleotides in immunity.

Check out this work co-led with @benadler.bsky.social here:

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

Our October issue is out now!

The images are negatively stained electron micrographs taken from archaella bundles isolated from the archaeon Sulfolobus acidocaldarius.

Check the issue out here:
www.nature.com/nmicrobiol/v...

The Panoptes system uses decoy cyclic nucleotides to defend against phage - Nature The Panoptes antiphage system defends bacteria by detecting phage-encoded counter-defences that sequester cyclic nucleotide signals, triggering membrane disruption and highlighting a broader strategy of sensing immune evasion through second-messenger surveillance.

Our story describing the Panoptes bacterial immune defense system is now finally peer-reviewed and published today! www.nature.com/articles/s41...

Who fixes carbon in the dark ocean? A new study led by Barbara Bayer (CeMESS, University of Vienna) discovered that ammonia-oxidizing microorganisms contribute much less to carbon fixation in the ocean than previously assumed. The study...

Who fixes carbon in the dark ocean? A new study in @nature.com, led by @barbarabayer.bsky.social @univie.ac.at shows that ammonia‐oxidizing microbes contribute much less to dark carbon fixation than previously thought – leaving room for unknown players.
Read more: 🔗 dome.univie.ac.at/news-events/...

Happy to share the Biodiversity Cell Atlas white paper, out today in @nature.com. We look at the possibilities, challenges, and potential impacts of molecularly mapping cells across the tree of life.
www.nature.com/articles/s41...

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...

Structure of a functional archaellum in Bacteria of the Chloroflexota phylum - Nature Microbiology Bona fide gene clusters for archaella are widespread across a bacterial phylum and encode functional motility machinery.

#NewResearch

Structure of a functional archaellum in Bacteria of the Chloroflexota phylum

@archaellum.bsky.social @sgribaldo.bsky.social & co

#microsky 🧪🦠

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

The largest study on late life virginity, based on >400k individuals, out now in @pnas.org

Open access link: pnas.org/doi/10.1073/...

Shoutout to shared first author @laurawesseldijk.bsky.social ❤️

Thread below 👇🏽

Long-term monitoring of a North American cheese cave reveals mechanisms and consequences of fungal adaptation Using a unique longitudinal sampling approach, Louw et al. demonstrate how a cheese-associated Penicillium population has adapted in an artisan cheese production facility in Vermont, USA. Adaptation i...

Such a delight to share our work on the evolution of a cheese rind fungus in @currentbiology.bsky.social.

This is the fantastic PhD work of @nicolasleonlouw.bsky.social and resulted from amazing collaborations, a wedding proposal(!), an undergrad course, & more!

🧵

www.cell.com/current-biol...

🦠➡️🧬 Community context matters!
In the second part of my PhD, we show how microbial complexity drives phage–bacteria ecology & evolution.
Check out the preprint 👇🏼

Looking for a new approach to studying or eliminating phages? Check out our study introducing anti-phage ASOs (antisense oligos) out in @Nature today. nature.com/articles/s4158…

Pasteur-Paris University International Doctoral Programme, The call for enrollment of students in October 2026 will be open from September 1st to October 20th, 2025

🎓 Applications for Institut Pasteur's PhD programs open Sept 1-Oct 20, 2025 for October 2026 entry.

Apply to up to 4 projects across 6 programs: PPU, PPU-IMAGINE @institutimagine.bsky.social, PPU-@ox.ac.uk, PPU-EID @upcite.bsky.social & more 🧬

Register now ✍️ www.pasteur.fr/en/education...

New research: With ancient origins & surprising flexibility, #BrownAlgae reveal a compelling story of sex chromosome evolution. This could rewrite how we view sex determination. Learn more: s.gwdg.de/YDoZ3L
Congrats to @agalip.bsky.social & Josue Barrera for their work in @natecoevo.nature.com

🚨 Imagine a bacterium that refuses to follow the textbook:
It grows as tangled filaments, divides unevenly, reshapes its own membranes… and even builds grappling hooks.
Meet Litorilinea aerophila — and here’s why it blew our minds.

Left: Results of spotting various supernatants onto lawns of Halalkalibacterium halodurans, Phycicoccus endophyticus, and Virgibacillus salexigens. a,b: top fraction (>3 kDa) of supernatant from Haloferax volcanii expressing an intact (a) or catalytic mutant (b) version of Woldo; c,d: bottom fraction (<3 kDa) of supernatant from H. volcanii expressing an intact (c) or catalytic mutant (d) version of Woldo; e: unfiltered supernatant from Halogranum salarium B-1; f,g: top fraction (>3 kDa) of supernatant from H. volcanii expressing (f) Danwoldo or (g) and empty plasmid control; h,i: bottom fraction (<3 kDa) of supernatant from H. volcanii expressing (h) Danwoldo or (i) and empty plasmid control. Top right: Structural overlay of zoocin A from Streptococcus zooepidemicus (UniProt ID: O54308) and Woldo, a candidate PGH from Halogranum salarium B-1 (UniProt ID: J2ZZK6), highlighting homologous M23 domains but divergent cell wall binding domains. TRD: target recognition domain. PG: peptidoglycan. Bottom right: Images of bacterial cells following exposure to H. volcanii supernatants expressing Woldo, Danwoldo or the control (as above). Bacteria are stained using LIVE/DEAD BacLight bacterial viability staining kit with ingress of red dye into bacterial cells indicative of cells with terminally compromised cell wall integrity.

Archaea-on-bacteria action! @romainstrock.bsky.social @tobiaswarnecke.bsky.social &co show that many #archaea encode #peptidoglycan hydrolases, which specifically target #bacterial cell walls, experimentally confirming the killing capacity of 2 of these enzymes @plosbiology.org 🧪 plos.io/4lrJBBa

Deep learning reveals antibiotics in the archaeal proteome - Nature Microbiology Use of artificial intelligence to mine proteomes of archaea led to the discovery of archaeasins, antimicrobials that kill drug-resistant bacteria in laboratory and animal models, offering a promising ...

(1/5)For over a century, the hunt for new antibiotics has focused almost exclusively on bacteria and fungi. Today, that paradigm shifts. By coupling state-of-the-art AI with the vast, largely uncharted diversity of Archaea, we open a new frontier for molecular discovery.

Manipulation of the nucleotide pool in human, bacterial and plant immunity - Nature Reviews Immunology Modification of the nucleotide pool is emerging as key to innate immunity in animals, plants and bacteria. This Review explains how immune pathways conserved from bacteria to humans manipulate the nuc...

NEW Review from @soreklab.bsky.social @dinahoch.bsky.social explains how immune pathways manipulate the availability of nucleotides, chemically modify nucleotides to generate immune signalling molecules, and produce altered nucleotides that poison viral replication
#immunosky #microsky #phagesky

‘Things keep evolving into anteaters.’ Odd animals arose at least 12 separate times Findings speak to the dramatic impact ants and termites can have on mammalian evolution

Crab-like creatures are famed for having evolved five times in evolutionary history. But anteaters have evolved at least 12 times--in half the evolutionary span. Cool story by @jakebuehler.bsky.social for @science.org

🦠🧍‍♀️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/...

My first first-authored paper is now out ahead of print in #mBio. It was a loooong way between journals, but here we are with a result that I believe will be highly relevant for anyone interested in microbiology and evolution! 🦠🧬
👇
journals.asm.org/doi/10.1128/...

And the story is published now!🍾
www.nature.com/articles/s41...

Open access link: rdcu.be/exnOc

Many years in the making, great collaboration with @archaellum.bsky.social & @tunglejic.bsky.social

Thanks @ukri.org BBSRC & @leverhulme.ac.uk for funding, reviewers & editor!! 🙏
#microsky #archaeasky

rdcu.be/evcPn

Transcription gets more noisy and co-expression more heterogeneous when S. islandicus cells age (in G2)
#aging #archaea #transcriptomes #networks
Thanks to Miguel Gomez Raya Vilanova :) and all great co-authors: Annette Baudisch, Claudio Franceschi, Yuping Dai, @jerometeu.bsky.social

#ArchaeaSky
#MicroSky

New groups of highly divergent proteins in families as old as cellular life with important biological functions in the ocean - Environmental Microbiome Background Metagenomics has considerably broadened our knowledge of microbial diversity, unravelling fascinating adaptations and characterising multiple novel major taxonomic groups, e.g. CPR bacteria...

📣 So excited to share the latest paper from my PhD with @aire-team.bsky.social, out now in Environmental Microbiome! 🥳

We mined a large ocean microbiome for remote homologues of core gene families in uncultured lineages.

Key points below ⤵️
environmentalmicrobiome.biomedcentral.com/articles/10....

Microbes can reduce their need for nickel Methanogenic archaea have a significant impact on the global climate due to their role in producing almost all methane from natural sources. This well-known process relies on enzymes containing metals such as iron (Fe) and nickel (Ni). However, a team of scientists from the Max Planck Institutes for Terrestrial Microbiology in Marburg and Biophysics in Frankfurt am Main discovered that these microbes can alter the pathway they use in conditions of low nickel bioavailability (as found in many natural habitats). Their study, published in Nature, significantly advances our understanding of microbial ecology and its potential impact on climate change.

#📢 Rethinking #methane metabolism: A team led by Seigo Shima has discovered that methanogenic #microbes🦠 🦠 can reduce their #nickel requirements when levels are low. This study sheds new light on the ecology of #methanogens and their impact on #climatechange. s.gwdg.de/qAOd9C

Thanks, Alex!!

Thanks to @danielabarilla.bsky.social and the other reviewers for their comments and suggestions, it is now a much more complete and exciting piece of research!

Elated to have our pre-print now published in @natcomms.nature.com #ArchaeaSky #Microbiology #MEvoSky
rdcu.be/euila
Our main results stay the same: S. islandicus follows a cell cycle akin to that of some eukaryotes, like the budding yeast, with cellular processes cycling similarly.
old🧵cited below👇

Enrichment cultivation and visualization of Ca. Methanonezhaarchaeum fastidiosum

Preprint🚨 #microsky 🦠 “Cultivation of Methanonezhaarchaeia, the third class of methanogens within the phylum Thermoproteota”, authored by @kohtzarchaeota.bsky.social & Sylvia Nupp, expands the diversity of methanogens! 90% enriched, methylotrophic culture from a hot spring. A 🧵 tinyurl.com/yw8ku2bj