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
Reposted by Raphael Laurenceau
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
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...
rdcu.be
November 18, 2025 at 9:01 PM
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
Reposted by Raphael Laurenceau
#microsky
TraN variants mediate conjugation species specificity of IncA/C, IncH and Acinetobacter baumannii plasmids
www.biorxiv.org/content/10.1...
TraN variants mediate conjugation species specificity of IncA/C, IncH and Acinetobacter baumannii plasmids
www.biorxiv.org/content/10.1...
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...
www.biorxiv.org
November 16, 2025 at 9:59 AM
#microsky
TraN variants mediate conjugation species specificity of IncA/C, IncH and Acinetobacter baumannii plasmids
www.biorxiv.org/content/10.1...
TraN variants mediate conjugation species specificity of IncA/C, IncH and Acinetobacter baumannii plasmids
www.biorxiv.org/content/10.1...
Reposted by Raphael Laurenceau
🦠 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
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
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...
www.pasteur.fr
November 13, 2025 at 9:00 AM
🦠 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
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
Reposted by Raphael Laurenceau
Cool work from our neighbors at @cultivarium.bsky.social using components from the POSSUM Toolkit! What will they (or you!) find next?
Check out the toolkit here: www.addgene.org/kits/cultiva...
Check out the toolkit here: www.addgene.org/kits/cultiva...
November 12, 2025 at 8:03 PM
Cool work from our neighbors at @cultivarium.bsky.social using components from the POSSUM Toolkit! What will they (or you!) find next?
Check out the toolkit here: www.addgene.org/kits/cultiva...
Check out the toolkit here: www.addgene.org/kits/cultiva...
Reposted by Raphael Laurenceau
🚨New preprint out!
We present a foundational genomic resource of human gut microbiome viruses. It delivers high-quality, deeply curated data spanning taxonomy, predicted hosts, structures, and functions, providing a reference for gut virome research. (1/8)
www.biorxiv.org/content/10.1...
We present a foundational genomic resource of human gut microbiome viruses. It delivers high-quality, deeply curated data spanning taxonomy, predicted hosts, structures, and functions, providing a reference for gut virome research. (1/8)
www.biorxiv.org/content/10.1...
November 6, 2025 at 5:26 PM
🚨New preprint out!
We present a foundational genomic resource of human gut microbiome viruses. It delivers high-quality, deeply curated data spanning taxonomy, predicted hosts, structures, and functions, providing a reference for gut virome research. (1/8)
www.biorxiv.org/content/10.1...
We present a foundational genomic resource of human gut microbiome viruses. It delivers high-quality, deeply curated data spanning taxonomy, predicted hosts, structures, and functions, providing a reference for gut virome research. (1/8)
www.biorxiv.org/content/10.1...
The impressive molecular details of the retroelement Eco8 defense activation, a protein-RNA-DNA complex in which all three play a part
www.cell.com/molecular-ce...
www.cell.com/molecular-ce...
Phage SSB detection by retron Eco8 msDNA unleashes nuclease-mediated immunity
The cryo-EM structure of the retron Eco8 system reveals an autoinhibited 4:4:4 complex
of RT, msDNA, and OLD nuclease. Phage SSB binding to msdDNA unleashes non-specific
nuclease activity to restrict ...
www.cell.com
November 4, 2025 at 8:16 AM
The impressive molecular details of the retroelement Eco8 defense activation, a protein-RNA-DNA complex in which all three play a part
www.cell.com/molecular-ce...
www.cell.com/molecular-ce...
Reposted by Raphael Laurenceau
A brand-new Gordon Conference on Microbiomes!🦠 The opening session (Jan 2026) dives into microbiome editing - how fundamental research and new technologies can advance human health and environmental sustainability. Super looking forward!🧪 #microsky #microbiomesky #grc
www.grc.org/microbiome-e...
www.grc.org/microbiome-e...
2026 Microbiome Editing Conference GRC
The 2026 Gordon Research Conference on Microbiome Editing will be held in Pomona, California. Apply today to reserve your spot.
www.grc.org
October 31, 2025 at 9:42 AM
A brand-new Gordon Conference on Microbiomes!🦠 The opening session (Jan 2026) dives into microbiome editing - how fundamental research and new technologies can advance human health and environmental sustainability. Super looking forward!🧪 #microsky #microbiomesky #grc
www.grc.org/microbiome-e...
www.grc.org/microbiome-e...
Reposted by Raphael Laurenceau
@prczhaoyansong.bsky.social’s deep dive into the dark matter of compost communities is now out 🎉 Genomic islands hijack jumbo phages—whose capsids enable transfer of large tracts of DNA—shedding new light on the scale & scope of phage-mediated gene flow 😎
www.pnas.org/doi/10.1073/...
www.pnas.org/doi/10.1073/...
Jumbo phage–mediated transduction of genomic islands | PNAS
Bacteria acquire new genes by horizontal gene transfer, typically mediated by mobile
genetic elements (MGEs). While plasmids, bacteriophages, and c...
www.pnas.org
October 28, 2025 at 6:36 PM
@prczhaoyansong.bsky.social’s deep dive into the dark matter of compost communities is now out 🎉 Genomic islands hijack jumbo phages—whose capsids enable transfer of large tracts of DNA—shedding new light on the scale & scope of phage-mediated gene flow 😎
www.pnas.org/doi/10.1073/...
www.pnas.org/doi/10.1073/...
Reposted by Raphael Laurenceau
Our work on viruses and virus satellites of haloarchaea and their DPANN symbionts is out today in Nature Microbiology!
@mkrupovic.bsky.social @deemteam.bsky.social @anagtz.bsky.social
www.nature.com/articles/s41...
@mkrupovic.bsky.social @deemteam.bsky.social @anagtz.bsky.social
www.nature.com/articles/s41...
Viruses and virus satellites of haloarchaea and their nanosized DPANN symbionts reveal intricate nested interactions - Nature Microbiology
An exploration of the viromes of haloarchaea and their ultra-small DPANN symbionts reveals plasmid-derived satellites of viruses from both archaeal groups, highlighting the complexity of nested symbio...
www.nature.com
October 17, 2025 at 9:54 AM
Our work on viruses and virus satellites of haloarchaea and their DPANN symbionts is out today in Nature Microbiology!
@mkrupovic.bsky.social @deemteam.bsky.social @anagtz.bsky.social
www.nature.com/articles/s41...
@mkrupovic.bsky.social @deemteam.bsky.social @anagtz.bsky.social
www.nature.com/articles/s41...