Reposted by Raphael Laurenceau
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...
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...
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
doi.org
February 9, 2026 at 8:31 PM
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...
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...
Reposted by Raphael Laurenceau
Cytosine methylation contributes to the fitness of Caulobacter cells naturally expressing a Vsr-like protein: iScience www.cell.com/iscience/ful... 🦠
Cytosine methylation contributes to the fitness of Caulobacter cells naturally expressing a Vsr-like protein
Properties of biomolecules; Epigenetics; Microbial genomics; Transcriptomics
www.cell.com
February 7, 2026 at 8:15 AM
Cytosine methylation contributes to the fitness of Caulobacter cells naturally expressing a Vsr-like protein: iScience www.cell.com/iscience/ful... 🦠
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
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
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
February 5, 2026 at 9:54 AM
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
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
Reposted by Raphael Laurenceau
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...).
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...
www.nature.com
February 3, 2026 at 10:52 AM
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...).
I had never heard of this ABS... Some E. coli can apparently ferment sugars into alcohol within the gut 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 ...
www.nature.com
February 3, 2026 at 1:25 PM
I had never heard of this ABS... Some E. coli can apparently ferment sugars into alcohol within the gut www.nature.com/articles/s41...
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...
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...
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.
www.nature.com
January 30, 2026 at 1:44 PM
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...
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...
Wow.. 😔 www.nature.com/immersive/d4...
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.
www.nature.com
January 21, 2026 at 7:54 AM
Wow.. 😔 www.nature.com/immersive/d4...
Reposted by Raphael Laurenceau
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...
doi.org
January 13, 2026 at 1:40 PM
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...
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...
www.nature.com/articles/s41...
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...
www.nature.com
January 8, 2026 at 7:43 AM
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...
www.nature.com/articles/s41...
Reposted by Raphael Laurenceau
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
Novel genes arise from genomic deletions across the bacterial tree of life https://www.biorxiv.org/content/10.64898/2026.01.05.697752v1
January 6, 2026 at 4:12 PM
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
Reposted by Raphael Laurenceau
🚨 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!
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!
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...
www.cell.com
January 5, 2026 at 8:29 AM
🚨 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!
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!
Reposted by Raphael Laurenceau
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...
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...
December 13, 2025 at 8:09 AM
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...
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...
Reposted by Raphael Laurenceau
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/...
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
academic.oup.com
December 12, 2025 at 8:57 AM
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/...
Reposted by Raphael Laurenceau
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
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
December 10, 2025 at 6:06 PM
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
A membrane-sheathed flagellum! I had never heard of that www.nature.com/articles/s41...
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...
www.nature.com
December 3, 2025 at 8:03 AM
A membrane-sheathed flagellum! I had never heard of that www.nature.com/articles/s41...
Reposted by Raphael Laurenceau
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.
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.
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'
www.cnrs.fr
December 1, 2025 at 9:44 PM
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.
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.
Reposted by Raphael Laurenceau
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.
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.
www.quantamagazine.org
November 30, 2025 at 9:04 PM
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.
Reposted by Raphael Laurenceau
🧬🛡️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...
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...
November 27, 2025 at 9:35 AM
🧬🛡️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...
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...
Reposted by Raphael Laurenceau
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
🔗 doi.org/10.1093/molbev/msaf259
#evobio #molbio
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
doi.org
November 26, 2025 at 5:42 PM
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
🔗 doi.org/10.1093/molbev/msaf259
#evobio #molbio
Reposted by Raphael Laurenceau
Winter Is Coming: And the Earth’s oldest organisms are prepping. 🥶
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.
www.quantamagazine.org
November 23, 2025 at 4:46 PM
Winter Is Coming: And the Earth’s oldest organisms are prepping. 🥶
Reposted by Raphael Laurenceau
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
A bacteriophage genus infects carbapenem resistant Acinetobacter baumannii via a non-capsular receptor and provides protection in vivo
Microbiology; Virology
www.cell.com
November 22, 2025 at 1:11 PM
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
www.sciencedirect.com/science/arti...
A clever metabolic engineering framework in P. putida
A clever metabolic engineering framework in P. putida
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
November 23, 2025 at 9:44 AM
www.sciencedirect.com/science/arti...
A clever metabolic engineering framework in P. putida
A clever metabolic engineering framework in P. putida
www.nature.com/articles/s41... Nice phage host-range work with useful application
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
November 21, 2025 at 8:06 AM
www.nature.com/articles/s41... Nice phage host-range work with useful application