Pepe Flores

Co-occurrence is associated with horizontal gene transfer across marine bacteria independent of phylogeny Abstract. Understanding the drivers and consequences of horizontal gene transfer (HGT) is a key goal of microbial evolution research. Although co-occurring

Now out & nicely formatted in @isme-microbes.bsky.social

A big analysis of ocean genomes & metagenomes co-led by former postdocs, now PIs, @gmdouglas.bsky.social & @cyanophage.bsky.social along with co-PIs @lbobay.bsky.social & Samuel Chaffron.

A few highlights... 🧵 (1/n)

doi.org/10.1093/isme...

The paradox of immune systems conservation between prokaryotes and eukaryotes - Nature Reviews Microbiology The widespread prokaryotic immune systems, in particular restriction–modification, CRISPR–Cas and defensive toxin–antitoxin systems, are absent in eukaryotes, whereas relatively rare ones, such as Arg...

The immune systems paradox

Some widespread prokaryotic immune systems are absent in eukaryotes, whereas relatively rare ones became central to eukaryotic innate immunity

@audeber.bsky.social & E. Koonin hypothesize the answer is #HGT

shareable link: rdcu.be/e2EmD

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

What causes tipping points in complex microbial ecosystems? Check this @pnas.org paper by @thilogross.bsky.social showing that cross-feeding networks create strong interdependencies & small structural changes can trigger abrupt collapses. @akhilesh-nandan.bsky.social www.pnas.org/doi/epdf/10....

LLMs are good at idea quality, but weak on idea variance. GPT-4's brainstorm pools are less diverse than humans, unless you prompt for diversity explicitly. CoT prompting gets closest to “team human.” papers.ssrn.com/sol3/papers....

Priority effects inhibit the repeated evolution of phototrophy - npj Complexity npj Complexity - Priority effects inhibit the repeated evolution of phototrophy

New paper out! Here's a puzzle: phototrophy, the ability to use light for energy, is one of life's great innovations. It evolved early and transformed the biosphere. But it evolved 2x. Why not just once, why not more? Our work suggests the answer is priority effects.

www.nature.com/articles/s44...

A pore-forming antiphage defence is activated by oligomeric phage proteins - Nature Bacteria use diverse defence systems against phages, including a 164-residue prophage-encoded protein, Rip1, which senses conserved phage assembly rings to form membrane pores that block virion matura...

A pore-forming antiphage defence is activated by oligomeric phage proteins www.nature.com/articles/s41...

from 2019. A novel uncultured marine cyanophage lineage with lysogenic potential linked to a putative marine Synechococcus ‘relic’ prophage enviromicro-journals.onlinelibrary.wiley.com/doi/10.1111/...

Mapping of the viral shunt across widespread coccolithophore blooms using metabolic biomarkers | PNAS The viral shunt is a fundamental ecosystem process which diverts the flux of organic carbon fixed through photosynthesis during algal bloom events ...

🌊Paper announcement! 📣
Viral infections rewire the metabolic makeup of their host and thereby create distinct chemical signatures. Can we use metabolic biomarkers to diagnose infections of algal blooms in the ocean?
Well, take a look at our new article led by Conny Kuhlisch in @pnas.org
>>

Blog post on this one coming soon. I fired up the Codex app to modify a 15-year old #Rstats package I wrote to switch from base R to ggplot2. Nailed it. Updated functions, documentation, vignettes, README, DESCRIPTION, etc. devtools::check() passed. One shot.

We need to move beyond the accept/reject binary in peer review - LSE Impact Binary reject/accept peer review has become conflated with validation. The authors outline three myths sustaining this confusion and how we might escape it.

💥New | We need to move beyond the accept/reject binary in peer review

✍️ @georgealfredcurrie.bsky.social & Damian Pattinson

#PeerReview #AcademicSky #AcademicPublishing

Paralleled Dynamics of Arabidopsis Root Exudation and SynCom Assembly in a Controlled Environment

from @kschlaeppi.bsky.social

www.biorxiv.org/content/10.6...

Viral NblA proteins negatively affect oceanic cyanobacterial photosynthesis - Nature Viral NblA accelerates the cyanophage infection cycle, directs degradation of the host phycobilisome and other proteins, and reduces host photosynthetic light-harvesting efficiency.

This is such a cool paper as it experimentally addresses the role of the auxiliary metabolic gene nblA in cyanophages showing a large benefit of NblA to the cyanophage and a negative effect on the host photosynthetic apparatus and host photosynthesis

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

It's been 25 years since the publishing of the human genome project.

I'd like to commission a review article for CSH Protocols on how the sequencing methods have evolved and where we might be headed. If you're interested, let me know!

A new paper from the lab on virus-like particles called eCISs www.nature.com/articles/s41...

How bacteria evolved thousands of precision nanoinjectors?

Some bacteria don’t secrete toxins — they inject them using phage-derived machines called extracellular contractile injection systems (eCISs).

Curious, what's the best-practice tool at this point for taxonomically classifying long reads from metagenomes from less well-characterised environments?

My impression is that Kraken will give lots of false positives and mis-classify taxa not in its database.

Please share around for visibility.

When writing proposals/applications, don't worry about the page limit (p) unless your first draft p x 2+1 pages. Anything less than that can likely be fixed with formatting and dropping words and clauses that are no longer needed on second read.

The disputed identity of Pseudomonas putida KT2440: when taxonomists rename your favorite microbe journals.asm.org/doi/full/10.... #jcampubs

New Article: "Unravelling the predominant genetic paths for asexual reproduction in Kalanchoe" rdcu.be/e1pxI

With News & Views: "Genomic cradle for thousands" rdcu.be/e1pxK

How ‘mother of thousands’ plants sprout new plantlets from their leaves.

Multiple protein structure alignment at scale with FoldMason Protein structure is conserved beyond sequence, making multiple structural alignment (MSTA) essential for analyzing distantly related proteins. Computational prediction methods have vastly extended ou...

FoldMason is out now in @science.org. It generates accurate multiple structure alignments for thousands of protein structures in seconds. Great work by Cameron L. M. Gilchrist and @milot.bsky.social.
📄 www.science.org/doi/10.1126/...
🌐 search.foldseek.com/foldmason
💾 github.com/steineggerla...

@bejalab.bsky.social

Novel artificial selection method improves function of simulated microbial communities Author summary Artificial selection has been extremely powerful in improving properties of complex biological or biochemical entities. The most familiar examples come from the breeding of animals and ...

Thrilled to see this paper finally out! journals.plos.org/ploscompbiol... It was a difficult story to communicate and took us a while to get right. Big congratulations to @wbjorn.bsky.social, Pablo Guridi and Flora Arias-Sanchez!! And thank you the reviewers who helped improve it. Keep reading...

Illuminating how the bird inner retina works without oxygen solves a 350-year-old structural mystery Neurons in the bird eye’s inner retina lack a blood supply. Finding how these neurons function without oxygen reveals a role for an enigmatic eye structure.

Illuminating how the bird inner retina works without oxygen solves a 350-year-old structural mystery www.nature.com/articles/d41...

Peer Bork - personal thoughts | Ewan Birney Personal thoughts on the passing of Peer Bork

I have been one of the many people across the world impacted by the sudden death of Peer Bork - a friend, colleague and remarkable scientist. I now have enough time this weekend to write some personal thoughts about Peer. www.linkedin.com/posts/ewan-b...

Using micropatterning & thousands of hours on the microscope
@manuelthery.bsky.social and the #CytoMorphoLab reimagined the Musée D’Orsay. Accompanied by an orchestra and poet, their images transported us into the cellular universe. I remembered why I am a cell biologist. All of this is in us. Wow!

📣 Please spread: we’re hiring a Lab Manager! It is a critical position in our new lab. As our lab moves to Barcelona and joins the @crg.eu, we’re looking for a Lab Manager to help build the lab and set the lab atmosphere.
🔗 Apply here 👉 recruitment.crg.eu/content/jobs...

speaking of ... here is a great ring of phytoplankton off the coase of #NewZealand as seen by NASA's OCI instrument and its respective retrieval of chlorophyll concentration.

Phold's manuscript is now available @narjournal.bsky.social thanks to @susiegriggo.bsky.social @npbhavya.bsky.social @vijinim.bsky.social @linsalrob.bsky.social @martinsteinegger.bsky.social @milot.bsky.social @eunbelivable.bsky.social & others not on bsky #phagesky academic.oup.com/nar/article/...

No bull: This Austrian cow has learned to use tools First evidence for tool use in cattle includes a skill previously seen only in humans and chimpanzees

About a decade ago, a baker in a small mountainous village in southern Austria noticed his cow doing something unusual... My latest for @science.org about the first documented case of tool use in cattle!

I've spent the few days writing a 'mega multicellularity' lecture, integrating philosophy, paleontology, comparative cell bio, experimental evolution and theory into a (hopefully) comprehensive picture.

It's 105 slides long and could easily be 200.

It's kinda making me want to write a book.

In remembrance of Peer Bork  | EMBL EMBL and its community are deeply saddened by the death of Peer Bork, the organisation’s Interim Director General.

This is very sad news

'It is with great sadness that EMBL announces that Interim Director General Professor Peer Bork passed away from natural causes on 16 January 2026.'

www.embl.org/news/embl-an...