Raphael Laurenceau

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...

Effector–host interactome map links type III secretion systems in healthy gut microbiomes to immune modulation - Nature Microbiology Large-scale computational and in vitro analyses identify commensal type III secretion systems and substrates in the human gut microbiome that can interact with human proteins to modulate immune pathwa...

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

US science after a year of Trump: what has been lost and what remains A series of graphics reveals how the Trump administration has sought historic cuts to science and the research workforce.

Wow.. 😔 www.nature.com/immersive/d4...

Neisseria gonorrhoeae carries an unusually large number of restriction–modification systems (up to 16!), many of which are phase-variable. How does this affect plasmid transmission in gonococci? doi.org/10.64898/202...

aeon.co/videos/groun...

Introgression impacts the evolution of bacteria, but species borders are rarely fuzzy - Nature Communications It is commonly thought that bacterial species borders tend to be fuzzy, due to frequent exchange of DNA. Here, Diop et al. quantify the patterns of gene flow between core genomes across 50 major bacte...

A great paper. Perfect for non-experts like myself. So, can we definitively say that bacterial species follow the BSC model? Homologous recombination DOES "play a crucial role in maintaining species cohesiveness, much like sexual reproduction does in eukaryotes"
www.nature.com/articles/s41...

New preprint from my lab (with Arya Kaul, @fernpizza.bsky.social, and @brinda.eu), in which we explore new genes hitchhiking on the beneficial deletion that fused them together, and find them in the LTEE, M. Tb/bovis, and across the bacterial tree of life

Differential translocation of bacteriophages across the intestinal barrier in health and Crohn’s disease Intestinal barrier integrity is crucial for gut homeostasis. Douadi et al. show that bacteriophages can cross this barrier without causing damage and that translocation rates depend on the barrier sta...

🚨 New paper from our lab in Cell Reports @cp-cellreports.bsky.social, led by Clara Douadi!
We show that bacteriophages can cross the intestinal barrier, with increased translocation in Crohn's disease.
🔗 www.cell.com/cell-reports...
Many thanks to all the authors!

Happy to share that our work on HLp, a bacterial histone from Leptospira perolatii, is now published in Nature Communications 🎉

In this study, we show that HLp forms stable tetramers that wrap ~60 bp of DNA, revealing a distinct histone–DNA organization in bacteria.

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

Unraveling the Prevalence and Multifaceted Roles of Accessory Peptide Deformylases in Bacterial Adaptation and Resistance Abstract. Peptide deformylases (PDFs) are enzymes that are essential for bacterial viability and attractive targets for antibiotic development. Yet, despit

We've come full circle! I began my postdoctoral career by identifying the peptidyl deformylase gene. Today, we show that half of bacterial species harbor multiple PDF genes (up to 7, for always a single Met-tRNA transformylase), and while the role of these PDFs ... academic.oup.com/mbe/article/...

Selective elimination of donor bacteria enables global profiling of plasmid gene expression at early stages of conjugation Abstract. Conjugative plasmids are a major driving force for the dissemination of antimicrobial resistance. During conjugation, plasmid DNA is transferred

academic.oup.com/nar/article/... Collaboration with Y. Yamaichi. Killing donor bacteria in conjugation mixes using water enables transcriptomic profiling of early plasmid genes ! Superb tool for studying zygotic induction of these early genes, which include anti-SOS and anti-RM factors. #microsky

Structures of the sheathed flagellum reveal mechanisms of assembly and rotation in Vibrio cholerae - Nature Microbiology In situ cryo-electron microscopy structures show the spatial arrangement of flagellin proteins and provide insight into mechanisms of assembly and rotation of the sheathed flagellum in Vibrio cholerae...

A membrane-sheathed flagellum! I had never heard of that www.nature.com/articles/s41...

The CNRS is breaking free from the Web of Science From January 1st 2026, the CNRS will cut access to one of the largest commercial bibliometric databases, Clarivate Analytics'

Nice move @cnrs.fr
From 2026, no more Web of Science.
But is the community truly ready for qualitative evaluation? Hiring, promotions, grants… we’ve all been shaped by the metrics we grew up with. Changing the mindset is the real challenge and will take time.

A Cell So Minimal That It Challenges Definitions of Life | Quanta Magazine The newly described microbe represents a world of parasitic, intercellular biodiversity only beginning to be revealed by genome sequencing.

A newly discovered archaeal cell has a tiny genome and can’t metabolize biomolecules. It’s upending biologists’ definition of a living thing. “These types of organisms have been found before, but not as extreme as this,” said microbiologist Thijs Ettema.

🧬🛡️How are new immune mechanisms created?

We show how Lamassu antiphage system, originated from a DNA-repair complex and evolved into a compact and modular immune machine, wt Dinshaw Patel lab in @pnas.org.
👏 @matthieu-haudiquet.bsky.social, Arpita Chakravarti & all authors!

doi.org/10.1073/pnas...

Chromosomal Curing Drives an Arms Race Between Bacterial Transformation and Prophage Abstract. Transformation occurs when bacteria import exogenous DNA via the competence machinery and integrate it into their genome through homologous recom

Kwun et al. test whether transformation is an efficient mechanism for deleting prophage despite sensitivity to the ssDNA imported by competence machinery, identifying key interfaces in the evolutionary arms race between prophage and their hosts.

🔗 doi.org/10.1093/molbev/msaf259

#evobio #molbio

Even a Single Bacterial Cell Can Sense the Seasons Changing | Quanta Magazine Though they live only a few hours before dividing, bacteria can anticipate the approach of cold weather and prepare for it. The discovery suggests that seasonal tracking is fundamental to life.

Winter Is Coming: And the Earth’s oldest organisms are prepping. 🥶

A bacteriophage genus infects carbapenem resistant Acinetobacter baumannii via a non-capsular receptor and provides protection in vivo Microbiology; Virology

I started studying phages just over 4 years ago. The project that started it all is finally published. We isolated 6 closely related anti-Acinetobacter phages and showed that they are not capsule-specific and can reduce bacterial load in a rat model. More work still to come on this! #phagesky #IDsky

Predictive CRISPR-mediated gene downregulation for enhanced production of sustainable aviation fuel precursor in Pseudomonas putida CRISPR interference (CRISPRi) has emerged as a valuable tool for redirecting metabolic flux to enhance bioproduction. However, its application is ofte…

www.sciencedirect.com/science/arti...
A clever metabolic engineering framework in P. putida

Directed evolution of phages in biofilms enhances Pseudomonas aeruginosa control through improved lipopolysaccharide recognition - Nature Communications Phage therapy holds potential against Pseudomonas aeruginosa chronic lung infections in cystic fibrosis patients. Here, the authors demonstrate that biofilm heterogeneity limits phage effectiveness an...

www.nature.com/articles/s41... Nice phage host-range work with useful application

Introgression impacts the evolution of bacteria, but species borders are rarely fuzzy Nature Communications - It is commonly thought that bacterial species borders tend to be fuzzy, due to frequent exchange of DNA. Here, Diop et al. quantify the patterns of gene flow between core...

Our latest paper is out with @adiop.bsky.social and @gmdouglas.bsky.social. We analyzed the extent of homologous recombination between bacterial species (introgression) and how it affects species borders (it can vary a lot depending on the approach used to classify species!). rdcu.be/eQAMf

Heterogeneity in responses to ribosome-targeting antibiotics mediated by bacterial RNA repair - Nature Communications RNA repair helps bacteria survive antibiotic stress. Here, authors show that Rtc-driven repair causes cell-to-cell variation in resistance levels, revealing a potential form of heteroresistance, and i...

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

TraN variants mediate conjugation species specificity of IncA/C, IncH and Acinetobacter baumannii plasmids IncA/C and IncH plasmids commonly carry antimicrobial resistance genes, notably blaNDM-1. Although these plasmids disseminate among Gram-negative pathogens via conjugation, the mechanisms underlying m...

#microsky

TraN variants mediate conjugation species specificity of IncA/C, IncH and Acinetobacter baumannii plasmids

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

Ecology and health – phages interact with many bacteria in ecosystems Phages (bacteriophages), viruses that infect bacteria, are the most abundant genetic entities in our environment. A study published in Nature Microbiology challenges the common preconception that they...

🦠 Phages (bacteria-killing viruses) aren't as picky as we thought.
5-10% can infect multiple bacterial species, even genetically distant ones.
Potential implications for phage therapy against antibiotic-resistant infections 💊
@rkoszul.bsky.social study in Nature Microbiology
#Phages