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Reposted by Romain Strock

Michael Brockhurst @brockhurstlab.bsky.social · 4d

New preprint!

Ever wondered why only a fraction of genomes encode CRISPR immunity? 🧬 🦠

Turns out CRISPR is rarely beneficial against virulent phages, being most beneficial against those for which resistance mutations are rare!

An epic effort by Rosanna Wright

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

Resistance mutation supply modulates the benefit of CRISPR immunity against virulent phages

Only a fraction of bacterial genomes encode CRISPR-Cas systems but the selective causes of this variation are unexplained. How naturally virulent bacteriophages (phages) select for CRISPR immunity has...

www.biorxiv.org

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Reposted by Romain Strock

Nature Microbiology @natmicrobiol.nature.com · 17d

#NewResearch

Structure of a functional archaellum in bacteria of the Chloroflexota phylum

#MicroSky

@archaellum.bsky.social @sshamphavi.bsky.social @loumollat.bsky.social ‬ @mariejoest.bsky.social @sgribaldo.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.

www.nature.com

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Reposted by Romain Strock

Sofya Garushyants @garushyants.bsky.social · 24d

hey bluesky 👋 visa hurdles mean I’m looking for opportunities outside the US. I’m a computational biologist (bacterial + phage genomics, postdoc in Koonin’s group @ NIH). I am interested in teaming up on funding apps. reach out if this resonates!

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Reposted by Romain Strock

Zamin Iqbal @zaminiqbal.bsky.social · 29d

Sometimes you meet absolutely incredible bioinfo-magicians.
It was a huge privilege when @shenwei356.bsky.social
joined our group for a year on an @embl.org sabbatical.
While here, he developed a new way of aligning to
millions of bacteria, called LexicMap 1/n
www.nature.com/articles/s41...

Efficient sequence alignment against millions of prokaryotic genomes with LexicMap - Nature Biotechnology

LexicMap uses a fixed set of probes to efficiently query gene sequences for fast and low-memory alignment.

www.nature.com

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Reposted by Romain Strock

Tobias Warnecke @tobiaswarnecke.bsky.social · Sep 8

Please re-post:

Interested in chromatin and its evolution? Good news! There's still time to join us in beautiful Catalonia (9-12 Dec) to discuss eukaryotic, bacterial, archaeal, and viral chromatin and how it all hangs together meetings.embo.org/event/24-evo...

Abstract deadline: 30 September

EvoChromo: Evolutionary approaches to research in chromatin

Chromatin is the complex of DNA, RNA and protein that is found making up the chromosomes in eukaryotic cells. Chromatin is essential for proper genome function and is involved in chromosome segregati…

meetings.embo.org

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Reposted by Romain Strock

Sorek Lab @soreklab.bsky.social · Sep 2

Preprint: De-novo design of proteins that inhibit bacterial defenses

Our approach allows silencing defense systems of choice. We show how this approach enables programming of “untransformable” bacteria, and how it can enhance phage therapy applications

Congrats Jeremy Garb!
tinyurl.com/Syttt
🧵

Synthetically designed anti-defense proteins overcome barriers to bacterial transformation and phage infection

Bacterial defense systems present considerable barriers to both phage infection and plasmid transformation. These systems target mobile genetic elements, limiting the efficacy of bacteriophage-based t...

www.biorxiv.org

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Reposted by Romain Strock

Tobias Warnecke @tobiaswarnecke.bsky.social · Sep 1

Please re-post: If you know (or are!) somebody who might fancy doing a PhD (Oct 2026 start) in my group @oxfordbiochemistry.bsky.social, working on chromatin evolution in prokaryotes (or other things we're interested in), please have a look at www.bioch.ox.ac.uk/supervisors-...

Supervisors and Projects

www.bioch.ox.ac.uk

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Reposted by Romain Strock

Jerónimo Rodríguez-Beltrán @jerorb.bsky.social · Jul 22

Do plasmids evolve faster 🐇, slower 🐢, or just like chromosomes 🧬?

In our new paper, we tackled this question using theory, simulations, bioinformatics, and experiments!

👇 Check out all the details in Paula’s thread!

Hint: 🐇 (most of the time)

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Reposted by Romain Strock

Mark O. Martin @markowenmartin.bsky.social · Aug 30

I was #TWiMAdjacent about the much missed Elio Schaechter. I tried to discuss an article later, but I was stressed for time. The first part about Elio is so worth your time, as is the paper I discussed, about how archaea make enzymes that break down the bacterial cell wall!

asm.org/podcasts/twi...

Missing the Company of Elio

Paying tribute to Elio Schaechter, former TWiM host, blogger, and microbiologist extraordinaire, and review of the finding that Archaea produce peptidoglycan hydrolases that kill bacteria - a form of ...

asm.org

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Reposted by Romain Strock

Kate Baker @ksbakes.bsky.social · Aug 27

Awesome to see the transparent, systematic, and evidence-based approach behind the WHO Bacterial Priority Pathogens List 2024 out in the Lancet Infectious Diseases www.thelancet.com/journals/lan...

The WHO Bacterial Priority Pathogens List 2024: a prioritisation study to guide research, development, and public health strategies against antimicrobial resistance

The 2024 WHO BPPL is a key tool for prioritising research and development investments and informing global public health policies to combat AMR. Gram-negative bacteria and rifampicin-resistant M tuber...

www.thelancet.com

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Reposted by Romain Strock

Thalia, PhD @thalia.bsky.social · Aug 25

I cannot fully put into words what publishing this Review has meant to me, so I leave you with how we closed the paper.

"The humble bacterium is still a relevant tool for the study of the underlying mechanisms that are conserved throughout life."

🧪🧫🧬📚
doi.org/10.1093/gene...

The nature of mutation: a legacy of bacterial genetics

Abstract. A central question in the fields of genetics and evolution was the nature and origin of spontaneous mutation. Bacterial genetic experiments throu

doi.org

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Reposted by Romain Strock

Ákos T Kovács @evolvedbiofilm.bsky.social · Aug 19

When we started sampling soil to isolate Bacilli and other bacterial species within @cemist.bsky.social, I did not expect that so many direct and indirect publications and numerous chapters in 6 PhD theses in my group will originate from those efforts

🧵 [1/n]

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Reposted by Romain Strock

Zamin Iqbal @zaminiqbal.bsky.social · Aug 17

"We show that unrelated proteins have a universal tendency towards convergent evolution of secondary and tertiary motifs, causing an excess of high-scoring FP alignment... previous methods routinely overestimate significance by up to six orders of magnitude."
www.biorxiv.org/content/10.1...

Protein structure alignment significance is often exaggerated

Machine learning has generated millions of high-quality predicted protein structures, creating a need for computationally efficient structure search algorithms and robust estimates of statistical sign...

www.biorxiv.org

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Reposted by Romain Strock

Sarah Gurev @sarahgurev.bsky.social · Aug 17

🚨New paper 🚨

Can protein language models help us fight viral outbreaks? Not yet. Here’s why 🧵👇
1/12

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Reposted by Romain Strock

Nejc Haberman @nejchaberman.bsky.social · Aug 15

📣 ABSTRACT DEADLINE EXTENDED UNTIL 18TH AUGUST!

Register here: register.oxfordabstracts.com/event/75604?...
Abstract submission: app.oxfordabstracts.com/stages/79029...

londonomics.bsky.social @londonomics.bsky.social · Jul 29

Are you an Early Career Researcher in bioinformatics? Then this symposium is for you 💡

Join us for a day of talks, networking and career discussions. Present your work to get fresh new ideas and the chance to win prizes 💸

Featuring @avsecz.bsky.social of Google DeepMind as our keynote speaker⚡️

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Romain Strock @romainstrock.bsky.social · Aug 15

Not something we tested explicitly but the catalytic domains involved have not been shown to cleave pseudomurein. Also, very few pseudomurein producers encode PGHs, ruling out auto-lysis as the main function.

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Reposted by Romain Strock

PLOS Biology @plosbiology.org · Aug 15

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

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

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Romain Strock @romainstrock.bsky.social · Aug 15

PGHs are unlikely to be the sole kind of weapons deployed by archaea to kill bacteria. We close by discussing a road map to uncover more of the archaeal arsenal deployed against bacteria. Have a read for more details! 6/6

Romain Strock @romainstrock.bsky.social · Aug 15

We experimentally show that two PGHs encoded by salt-loving archaeon Halogranum salarium B-1 do kill one of the predicted targets, salt-tolerant bacterium Halalkalibacterium halodurans. 5/6

Plate with bacterium Halalkalibacterium halodurans growing on top. Four inhibition zones are visible, caused by peptidoglycan hydrolase proteins secreted by archaeon Halogranum salarium B-1.

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Romain Strock @romainstrock.bsky.social · Aug 15

We developed a structural homology-based pipeline to infer the putative bacterial targets of these proteins and found that most seem to target monoderm bacteria living in the same environment as the producer. 4/6

Pipeline to predict the putative bacterial targets of archaeal epptidoglycan hydrolases.

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Romain Strock @romainstrock.bsky.social · Aug 15

Here, we show that about 5% of archaea encode peptidoglycan hydrolases (PGHs) in their genomes, though most archaea do not use peptidoglycan. They are enriched on plasmids and display a high level of structural conservation with their bacterial counterpart, hinting at their use as weapons. 3/6

Heatmap of the presence of peptidoglycan hydrolases in archaea.

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Romain Strock @romainstrock.bsky.social · Aug 15

Archaea and bacteria live in the same environments across the biosphere, yet only a handful of studies describe antagonistic interactions between the two domains of life (Atanasova et al., 2013 is particularly relevant). 2/6

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Romain Strock @romainstrock.bsky.social · Aug 15

This first-author publication is my… first! Archaea kill bacteria by targeting their Achilles’ heel: peptidoglycan. Big shoutout to @ahocher.bsky.social‬, @valeriesoo.bsky.social‬, Pauline Misson, @tobiaswarnecke.bsky.social‬ and MRC LMS Proteomics. A thread 🔽
journals.plos.org/plosbiology/...

Archaea produce peptidoglycan hydrolases that kill bacteria

Archaea regularly interact with bacteria but reports of archaea killing bacteria are very rare. This study shows that many archaea encode peptidoglycan hydrolases, which specifically target bacterial ...

journals.plos.org

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Reposted by Romain Strock

Antoine Hocher @ahocher.bsky.social · Aug 15

@romainstrock.bsky.social work is out!
Why should you care? Because it helps shift our view of archaea — from rare extremophiles to not-so-passive bystanders. Some archaea can also fend off bacteria.
Glad to be part of this cool project from @tobiaswarnecke.bsky.social. Opens lots of Questions.

Tobias Warnecke @tobiaswarnecke.bsky.social · Aug 14

Archaea are often surrounded by bacteria. But is there ever active conflict between the two? Can archaea kill bacteria? If so, how do they do it?

Work by @romainstrock.bsky.social shows that some archaea can kill bacteria by secreting peptidoglycan hydrolases. journals.plos.org/plosbiology/...

Archaea produce peptidoglycan hydrolases that kill bacteria

Archaea regularly interact with bacteria but reports of archaea killing bacteria are very rare. This study shows that many archaea encode peptidoglycan hydrolases, which specifically target bacterial ...

journals.plos.org

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Reposted by Romain Strock

Valerie Soo @valeriesoo.bsky.social · Aug 15

Very happy to see this work published + getting the recognition it deserves! Archaea are very cool + understudied organisms and we are only scratching the surface! Since the preprint last year, we (@romainstrock.bsky.social) have included more evidence of bacteria getting killed by archaeal arsenal.

Tobias Warnecke @tobiaswarnecke.bsky.social · Aug 14

Archaea are often surrounded by bacteria. But is there ever active conflict between the two? Can archaea kill bacteria? If so, how do they do it?

Work by @romainstrock.bsky.social shows that some archaea can kill bacteria by secreting peptidoglycan hydrolases. journals.plos.org/plosbiology/...

Archaea produce peptidoglycan hydrolases that kill bacteria

Archaea regularly interact with bacteria but reports of archaea killing bacteria are very rare. This study shows that many archaea encode peptidoglycan hydrolases, which specifically target bacterial ...

journals.plos.org

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