The Ancient Weapons Active in Your Immune System Today | Quanta Magazine Dozens of new discoveries reveal that defenses evolved by bacteria and viruses billions of years ago still define our own innate immune system.

Bacteria serve as a “maker space” for accelerated evolutionary experimentation that can spread across life forms. Even today, eukaryotes beg, borrow, and steal from bacteria’s innovations.

An enhanced domestication method for uncultured bacteria Abstract. When environmental bacteria transition to laboratory conditions, a process termed domestication, the shift from the native habitat to a culture m

Most bacteria remain uncultured with vast microbial ‘dark matter’ awaiting discovery.. to address this am excited to share EDEN - an enhanced domestication method to grow uncultured bacteria & new diversity. Using EDEN we isolate a new species active against MDR pathogens..

doi.org/10.1093/isme...

Structural basis for DNA processing and membrane translocation by ComEC in natural transformation Natural transformation is one of the major pathways of horizontal gene transfer in bacteria, enabling the acquisition of extracellular DNA and its integration into the host genome. ComEC is a membrane...

ComEC structure is out!! 😍
Congratulations to the authors! That’s not an easy one. We have been trying for years to get that structure…
We failed and gave up.

We then used DGRec across very different systems: phage λ host-range engineering, dCas9 evolution, nanobody affinity maturation, and established a first proof-of-concept for DGR in yeast. Plasmids available at Addgene, hope you will have fun with it 😉. Don't hesitate to reach out!

An exciting part was to understand how the DGR RT really mutates. We show mutagenesis is strongly shaped by immediate sequence context, naturally geared for exploring aa space while minimizing stop codons. This predictability allows us to tune the mut rate at the aa level inside the target window 🎯

Diversity-generating retroelements for programmable targeted hypermutagenesis - Nature Biotechnology Diversity-generating retroelements are engineered for directed evolution in E.coli.

🔈Paper out! We turned the most fascinating phage host-switch mechanism, diversity-generating retroelements, into a programmable mutagenesis tool, DGRec. You can perform targeted hypermutation of any 50-200bp sequence directly in vivo in E. coli www.nature.com/articles/s41...

Comparative characterization of Cas12f orthologs reveals mechanistic features underlying enhanced genome editing efficiency - Nature Structural & Molecular Biology Guan, Ocampo and colleagues report the discovery and mechanistic dissection of Al3Cas12f, a metagenome-derived miniature nuclease that retains notable genome-editing capacity. They engineer an RKK var...

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

Phage receptor prediction from genome sequencing alone. Bacterial receptor (blue) interacting with phage proteins (purple) is shown here

📣Huge preprint 🔔
Today we share something our group has been working toward for a long time, led by @lucasmoriniere.bsky.social We asked can we predict which receptor a phage targets from its genome sequence alone? For most phages, we couldn’t. So Lucas set out to do something I had only dreamed of.

Cool tool to capture genes using a hunter gatherer 🦠
Large-scale recovery of integron cassettes for gene discovery screens www.biorxiv.org/content/10.6...
by @jaescudero.bsky.social @afpcarvalho.bsky.social @filipatr.bsky.social

Congratulations @wshuai.bsky.social and co-authors!

We’re excited to introduce MODIFI, our new scalable method for detecting DNA modifications in PacBio metagenomic data and estimating ECE-host linkage.
Check out the preprint: www.biorxiv.org/content/10.6...

Rapid resistance evolution against phage cocktails Abstract. When bacteria are treated with multiple antibiotics simultaneously, resistance is highly unlikely to evolve. In contrast, resistance against mult

Rapid resistance evolution against phage cocktails

#ISMEJournal by Baltus van der Steen, Matti Gralka, and @yuvalmulla.bsky.social

academic.oup.com/ismej/advanc...

An overview of bacterial multicellular formations: biofilms, filaments, free-floating aggregates, motile collectives and fruiting bodies. For each form, we mention an analogous eukaryotic multicellular form (respectively animal epitelia, filaments in fungi, Volvox, Dictyostelium/social animals, Dictyostelium and other slime moulds)

How common is multicellularity in bacteria? And archaea?
And how does it evolve?

We wrote a short review "On the architecture and evolution of prokaryotic multicellularity".

Preprint link: bit.ly/4ta06Gq

Sharing and comments are much appreciated.
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QR code to access 'Structural diversification of phage tail fibres enables recognition of diverse type IV pili'

New paper showing how tailed #phages recognize diverse #Pseudomonas #T4P! Outstanding work by PhD candidate Ikram Qaderi, building on work started a decade ago during my sabbatical in the McArthur lab and in collaboration with the Guarné lab, now at #McGill. @mcmasteriidr.bsky.social

Serotype swapping in Klebsiella spp. by plug-and-play Understanding how complex, multi-gene systems evolve and function across genetic backgrounds is a central question in molecular evolution. While such systems often impose costs through epistatic inter...

How complex functions, with important physiological and evolutionary impacts get repeatedly and efficiently transferred across genomes?
That’s what we explored using one of the fastest-evolving loci in Bacteria: the capsule locus.
The paper: www.biorxiv.org/content/10.1...
Thread👇

Bacteriophage data on capsular Klebsiella bacteria barcoded library

New paper 🔔

Collaboration
@sullivan-lab.bsky.social
Marissa Gittrich led the work

Klebsiella phage biology has focused almost entirely on capsulated strains, but capsule loss is the #1 resistance mechanism under phage predation. We used a naturally acapsular host to reveal the receptor landscape

➡️ preprint from the lab! Bacteria have loads of antiviral defences in their mobile genetic elements (MGEs). So when MGEs move between bacteria, the defences move with them, generating a fast turnover of defences in bacteria. But what about the antiviral defence turnover in the MGEs themselves? 🤔

🧵👇

aeon.co/essays/what-...

Biologists marvel at new AI drug discovery tool – but details are hidden Isomorphic Lab’s proprietary drug-discovery model is a major advance, but scientists developing open-source tools are left guessing how to achieve similar results.

DeepMind has been playing fair up until Alphafold 3. I guess we can't blame them for keeping this new version for themselves www.nature.com/articles/d41...

Plus de 13 000 millionnaires ne paient aucun impôt sur le revenu, selon une note inédite de Bercy En 2024, des milliers de contribuables disposant d’un gros patrimoine immobilier ont coupé à l’impôt sur le revenu. Un document de Bercy confirme les déclarations de l’ancien ministre Eric Lombard. De...

www.lemonde.fr/politique/ar...

Fluorescence micrograph. Emma Miller and Alex Merz, unpublished.

🧵 After years out of the field, I and my lab are again working on bacterial type IV pili. We have just posted our first preprints, and I'm excited to share what we have discovered.

This shows Neisseria gonorrheae bacteria infecting a human epithelical cell. Here, you can see the pili in red.

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The fitness landscapes of binders targeting protein surfaces that are evolutionarily predisposed to engage in PPIs is much narrower and deeper than those that target surfaces with no known interacting proteins. This might be b/c random binding events is bad, and selected against

A short research stay in 2019 (back in the pre-COVID era) at José R. Penadés lab turned into the third chapter of my PhD and today it finally sees the light.

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...

Cytosine methylation contributes to the fitness of Caulobacter cells naturally expressing a Vsr-like protein Properties of biomolecules; Epigenetics; Microbial genomics; Transcriptomics

Cytosine methylation contributes to the fitness of Caulobacter cells naturally expressing a Vsr-like protein: iScience www.cell.com/iscience/ful... 🦠

Open-source AI tool beats giant LLMs in literature reviews — and gets citations right Researchers can deploy the cheap and transparent model on their own computer system.

www.nature.com/articles/d41...
I tried, and I'm impressed. Just input a general claim, it will return an expanded version backed by multiple experimental studies.
link to the Asta tool here openscilm.allen.ai

Evolution and diversity of oxidoreductases involved in redox balance and energy conservation - Nature Ecology & Evolution HORBEC are protein complexes involved in the regulation of redox balance and energy conservation. The authors develop a bioinformatic tool for HORBEC annotation in bacterial and archaeal genomes and r...

Passioned by #bioenergetics? Do not miss our new article on the evolutionary history of oxidoreductases with G. Borrel and @sgribaldo.bsky.social @archaeal.bsky.social @valdeanda.bsky.social @pasteur.fr @cnrs.fr @cnrsbiologie.bsky.social @natecoevo.nature.com (www.nature.com/articles/s41...).

Microbial ethanol production in patients with auto-brewery syndrome - Nature Microbiology In 22 patients with auto-brewery syndrome, we found enrichment of gut bacterial genes in metabolic pathways associated with ethanol production. Treatment with faecal microbiota transplantation in one ...

I had never heard of this ABS... Some E. coli can apparently ferment sugars into alcohol within the gut www.nature.com/articles/s41...

Elon Musk launches his version of Wikipedia | CNN Business Elon Musk launched Grokipedia – his version of Wikipedia – on Monday, as the richest man in the world further seeks to create an alternative information and media ecosystem molded to his views.

The fact that Musk is deliberately trying to replace it confirms its unique role in resisting the wave of AI disinformation
edition.cnn.com/2025/10/28/t...

Wikipedia is needed now more than ever, 25 years on The online encyclopedia is an antidote to an increasingly poisoned information ecosystem. Researchers should help to nourish it.

I couldn’t agree more! Help support Wikipedia.
It has been a pillar of high-quality knowledge sharing since the early web, and it’s more relevant than ever in the fuzzy age of AI
www.nature.com/articles/d41...