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Reposted by Luis E. Valentin-Alvarado

Allison G @assemblerag.bsky.social · 8d

Most plasmids described in E. coli are small compared to the megaplasmids we identified here! Check out the preprint if you want to learn about these mysterious large elements and their potential functions 🧬. I’m very grateful to have had the opportunity to work on this in @banfieldlab.bsky.social

bioRxiv Microbiology @biorxiv-microbiol.bsky.social · 8d

Megaplasmids associate with Escherichia coli and other Enterobacteriaceae https://www.biorxiv.org/content/10.1101/2025.09.30.679422v1

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Reposted by Luis E. Valentin-Alvarado

Erin Doherty @erinedoherty.bsky.social · 7d

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...

A miniature CRISPR–Cas10 enzyme confers immunity by inhibitory signalling - Nature

Panoptes, an anti-phage defence system against virus-mediated immune suppression, is revealed.

www.nature.com

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Reposted by Luis E. Valentin-Alvarado

Doudna Lab @doudna-lab.bsky.social · 7d

New paper online at @nature.com from co-leads @erinedoherty.bsky.social + @benadler.bsky.social !

Erin Doherty @erinedoherty.bsky.social · 7d

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...

A miniature CRISPR–Cas10 enzyme confers immunity by inhibitory signalling - Nature

Panoptes, an anti-phage defence system against virus-mediated immune suppression, is revealed.

www.nature.com

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Reposted by Luis E. Valentin-Alvarado

Ben Morehouse @benmorehouse.bsky.social · 8d

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

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.

www.nature.com

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Reposted by Luis E. Valentin-Alvarado

Ben Adler @benadler.bsky.social · 8d

Today in @nature.com , we highlight how a cousin of CRISPR-Cas10, mCpol, establishes an evolutionary trap in anti-phage immune systems.

Check out @erinedoherty.bsky.social and my work from @doudna-lab.bsky.social lab here:
www.nature.com/articles/s41...

A miniature CRISPR–Cas10 enzyme confers immunity by inhibitory signalling - Nature

Panoptes, an anti-phage defence system against virus-mediated immune suppression, is revealed.

www.nature.com

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Reposted by Luis E. Valentin-Alvarado

Joe Bondy-Denomy @jbdsf.bsky.social · 14d

Our Department of Microbiology & Immunology at UCSF is running a faculty search this year for a new Assistant Professor! Please see the ad below for details. Searching for a great colleague, mentor, and scientist!
aprecruit.ucsf.edu/JPF05807

Microbiology and Immunology – Faculty Position (Ladder Rank) – Assistant Professor

University of California, San Francisco is hiring. Apply now!

aprecruit.ucsf.edu

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Reposted by Luis E. Valentin-Alvarado

Jeremy Wilkinson @jewilki.bsky.social · 14d

Join us tomorrow if you can. Link below to register.

PacBio @pacbio.bsky.social · 14d

⏰ Last call! The human #microbiome webinar is tomorrow.

See how #PacBio HiFi sequencing delivers clarity with full-length 16S rRNA and shotgun metagenomics, revealing strain-level insights, novel taxa, and functional pathways.

Register now: bit.ly/46wBttB

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Reposted by Luis E. Valentin-Alvarado

Ryan Wick @rrwick.bsky.social · 16d

New blog post!

metaMDBG (@gaetanbenoit.bsky.social) and Myloasm (@jimshaw.bsky.social) have had recent releases, so I updated the benchmarks from the Autocycler paper:
rrwick.github.io/2025/09/23/a...

Both tools improved considerably! Time to update your conda environments 😄

Benchmark update: metaMDBG and Myloasm

a blog for miscellaneous bioinformatics stuff

rrwick.github.io

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Reposted by Luis E. Valentin-Alvarado

Dan Sloan @sloanevolab.bsky.social · Sep 8

The Department of Biology at Colorado State University is hiring an Assistant Professor in the area of plant-microbe interactions! Please spread the word!

jobs.colostate.edu/postings/165...

Assistant Professor Plant-Microbe Interactions

We seek a creative, collaborative, and visionary plant biologist to establish an internationally recognized research program at the forefront of plant-microbe interactions aimed at understanding how t...

jobs.colostate.edu

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Reposted by Luis E. Valentin-Alvarado

Karolin Luger @nucleosomepolice.bsky.social · Sep 8

❤️❤️❤️ CSU. Fort Collins is a lovely place to live, and students / faculty are awesome. I should know, I taught there for 15 years! Apply!

Dan Sloan @sloanevolab.bsky.social · Sep 8

The Department of Biology at Colorado State University is hiring an Assistant Professor in the area of plant-microbe interactions! Please spread the word!

jobs.colostate.edu/postings/165...

Assistant Professor Plant-Microbe Interactions

We seek a creative, collaborative, and visionary plant biologist to establish an internationally recognized research program at the forefront of plant-microbe interactions aimed at understanding how t...

jobs.colostate.edu

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Reposted by Luis E. Valentin-Alvarado

Jennifer Biddle @jenbiddle.bsky.social · Sep 8

This is the dept where I got my PhD! Hiring for microbiology!

Seth Bordenstein @symbionticism.bsky.social · Sep 8

🎙️ Job Announcement: Penn State is seeking an ASSISTANT PROFESSOR in MICROBIOLOGY (any subdiscipline) in the Department of Biochemistry and Molecular Biology.

Learn more and Join the Microbiome Jubilee: psu.wd1.myworkdayjobs.com/en-US/PSU_Ac...

Assistant Professor in Microbiology

APPLICATION INSTRUCTIONS: CURRENT PENN STATE EMPLOYEE (faculty, staff, technical service, or student), please login to Workday to complete the internal application process. Please do not apply here, a...

psu.wd1.myworkdayjobs.com

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Reposted by Luis E. Valentin-Alvarado

Kranzusch Lab @kranzuschlab.bsky.social · Sep 5

How can we understand the earliest events in evolution of eukaryotic immunity? @yao-li.bsky.social reports incredible molecular fossils of complete bacterial-like operons in eukaryotes that illuminate how animal immunity was first acquired from anti-phage defense

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

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Reposted by Luis E. Valentin-Alvarado

Marie C. Schölmerich @mschoelmerich.bsky.social · Sep 3

🦠Exciting PhD opportunity @ ETH Zürich!
Our Environmental Microbiology group is looking for a motivated student to study microbial processes in peatland restoration — from fieldwork to metagenomics and lab experiments.

🗓 Start: Spring 2026
⏳ Deadline: 3 Oct 2025
👉 Apply: lnkd.in/eSPiy6vQ
Please 🔁

This link will take you to a page that’s not on LinkedIn

lnkd.in

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Reposted by Luis E. Valentin-Alvarado

Anne Daebeler @anne-daebeler.bsky.social · Sep 1

📢 🦠 A new methanotroph from Czech peat! Through an effort led by PhD student in my group Justus Nweze we isolated and describe a new CH4-muncher. Potential for a flexible (annaerobic) metabolisms and cool pH adaptations.

www.biorxiv.org/content/10.1...
#microbesky #microbiomesky

Genomic and physiological characterization of 'Candidatus Methylocystis sumavensis', a novel acid-tolerant methanotroph from peatland

Methanotrophic bacteria in peatlands mitigate emissions of methane (CH4), a potent greenhouse gas. Yet, the identity, physiology, and adaptive traits of methanotrophs inhabiting acidic peatlands are s...

www.biorxiv.org

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Reposted by Luis E. Valentin-Alvarado

Kranzusch Lab @kranzuschlab.bsky.social · Aug 22

The beautiful, ever-expanding universe of viral proteins targeting nucleotide immune signals!

Paper by @reneechang.bsky.social in @cp-molcell.bsky.social on a nucleotide sponge www.cell.com/molecular-ce...

and preprint by @doudna-lab.bsky.social on viral nucleases www.biorxiv.org/content/10.1...

A widespread family of viral sponge proteins reveals specific inhibition of nucleotide signals in anti-phage defense

Chang et al. discover anti-CBASS 4 (Acb4), a family of viral sponges that inhibits bacterial immunity by sequestering nucleotide immune signals. Acb4 homologs in phages that infect hosts across all ma...

www.cell.com

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Reposted by Luis E. Valentin-Alvarado

Doudna Lab @doudna-lab.bsky.social · Aug 22

New pre-print from Doudna lab members @erinedoherty.bsky.social & @jnoms.bsky.social ✨

Here we explore how recurrent adaptation of a single anti-defense protein fold enables evasion of distinct immune systems.

Erin Doherty @erinedoherty.bsky.social · Aug 22

Excited to share our new preprint co-led by @jnoms.bsky.social!

Here we reveal an exceptional diversity of viral 2H phosphodiesterases (PDEs) that enable immune evasion by selectively degrading oligonucleotide-based messengers. This 2H PDE fold has evolved striking substrate breath & specificity.

Divergent viral phosphodiesterases for immune signaling evasion

Cyclic dinucleotides (CDNs) and other short oligonucleotides play fundamental roles in immune system activation in organisms ranging from bacteria to humans. In response, viruses use phosphodiesterase...

www.biorxiv.org

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Reposted by Luis E. Valentin-Alvarado

Daan Speth @daanspeth.bsky.social · Aug 11

At the request of @bradleyph.bsky.social, we have now added the Bacterial and Archaeal trees (credit to @aroneys.bsky.social) used to infer the GlobDB taxonomy to the website globdb.org

Feel free to reach out if there's other resources you'd like to see added. No promises, but happy to chat 🖥️🧬🦠

home | GlobDB

globdb.org

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Reposted by Luis E. Valentin-Alvarado

James Lingford @jameslingford.bsky.social · Aug 11

Does sequence clustering confound AlphaFold2?
www.sciencedirect.com/science/arti... From @hkws.bsky.social

Does sequence clustering confound AlphaFold2?

Predicting multiple conformational states of proteins represents a significant open challenge in structural biology. Increasingly many methods have be…

www.sciencedirect.com

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Reposted by Luis E. Valentin-Alvarado

Joshua Hamm @joshnhamm.bsky.social · Aug 8

New preprint up now!

Interested in the evolution of halophily within DPANN archaea we decided to investigate the sister phylum to the Nanohaloarchaeota, GTDB phylum EX4484-52, for which we propose the name Caliditerrarchaeota
www.biorxiv.org/content/10.1...

Caliditerrarchaeota, a new sister to Nanohaloarchaeota, provides insights into the evolution of DPANN halophily

The Nanohaloarchaeota are a clade of halophilic symbionts with small cells and genomes. Originally placed within the Euryarchaeota, they are now widely thought to belong to the DPANN archaea. However,...

www.biorxiv.org

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Reposted by Luis E. Valentin-Alvarado

Owen Tuck @owentuck.bsky.social · Jul 29

Excited to finally share this work!
We noticed a pair of genes - a nuclease and a protease - shuffles between antiviral systems. We show how proteolysis activates the nuclease, triggering defense in known and unknown immune contexts.
tinyurl.com/2uwwy4ty

Recurrent acquisition of nuclease-protease pairs in antiviral immunity

Antiviral immune systems diversify by integrating new genes into existing pathways, creating new mechanisms of viral resistance. We identified genes encoding a predicted nuclease paired with a trypsin...

tinyurl.com

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Reposted by Luis E. Valentin-Alvarado

Doudna Lab @doudna-lab.bsky.social · Jul 29

‼️ New pre-print from co-leads @owentuck.bsky.social and Jason Hu! Check out this fascinating example of how coevolution enables defense system innovation.

Owen Tuck @owentuck.bsky.social · Jul 29

Excited to finally share this work!
We noticed a pair of genes - a nuclease and a protease - shuffles between antiviral systems. We show how proteolysis activates the nuclease, triggering defense in known and unknown immune contexts.
tinyurl.com/2uwwy4ty

Recurrent acquisition of nuclease-protease pairs in antiviral immunity

Antiviral immune systems diversify by integrating new genes into existing pathways, creating new mechanisms of viral resistance. We identified genes encoding a predicted nuclease paired with a trypsin...

tinyurl.com

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Reposted by Luis E. Valentin-Alvarado

Kevin Forsberg @kvnforsberg.bsky.social · Jul 29

Very proud to have our lab’s first work published in @cp-cellhostmicrobe.bsky.social!

In this work, we use functional metagenomics to find phage defenses from human and soil microbiomes!

Congrats to first author @luis840alberto.bsky.social !

www.cell.com/cell-host-mi...

(1/3)

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Reposted by Luis E. Valentin-Alvarado

Karolin Luger @nucleosomepolice.bsky.social · Jul 26

if i were a better person i would do a tweetorial on our recent paper - but, hey, read the paper. its right there, waiting for you. #Giantvirus #histones are cool! their #nucleosomes are cool. check it out.! thats the tweetorial.
rdcu.be/exXBX

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Reposted by Luis E. Valentin-Alvarado

Stephan Köstlbacher @stephkoe.bsky.social · Jul 20

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🧵 New preprint out!
WitChi: a fast, open-source Python tool to detect, quantify & prune compositional bias in MSAs.
Lightweight, tree-free, scalable to 5k+ taxa... so we applied it to the GTDB archaea MSA.
#ArchaeaSky #MEvoSky #MicroSky
🔗 doi.org/10.1101/2025...
💻 github.com/stephkoest/w...

WitChi: Efficient Detection and Pruning of Compositional Bias in Phylogenomic Alignments Using Empirical Chi-Squared Testing

Convergent evolution, where unrelated taxa independently evolve similar nucleotide or amino acid compositions, can introduce compositional bias into biological sequence data. Such biases distort phylo...

www.biorxiv.org

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Reposted by Luis E. Valentin-Alvarado

Thijs J. G. Ettema 🦠🔬🇳🇱🇸🇪🇪🇺 @ettema.bsky.social · Jul 20

Our latest work, driven by the fabulous @stephkoe.bsky.social! WitChi takes care of compositional bias in large phylogenomic datasets! WitChi is fast, efficient and free, try it out!

With @kassipan.bsky.social and @danieltamarit.bsky.social

Stephan Köstlbacher @stephkoe.bsky.social · Jul 20

1.
🧵 New preprint out!
WitChi: a fast, open-source Python tool to detect, quantify & prune compositional bias in MSAs.
Lightweight, tree-free, scalable to 5k+ taxa... so we applied it to the GTDB archaea MSA.
#ArchaeaSky #MEvoSky #MicroSky
🔗 doi.org/10.1101/2025...
💻 github.com/stephkoest/w...

WitChi: Efficient Detection and Pruning of Compositional Bias in Phylogenomic Alignments Using Empirical Chi-Squared Testing

Convergent evolution, where unrelated taxa independently evolve similar nucleotide or amino acid compositions, can introduce compositional bias into biological sequence data. Such biases distort phylo...

www.biorxiv.org

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