Institut Pasteur researchers describe LIN codes in PLOS Biology: a standardized numerical system for identifying bacterial strains from genome data, now used in BIGSdb-Pasteur and Pathogenwatch for outbreak surveillance. @sylvainbrisse.bsky.social ↘️ doi.org/10.1371/journal.pbio.3003781

Life Identification Numbers: A strain nomenclature approach to aid epidemiological surveillance of bacterial pathogens

Unified bacterial strain taxonomies are needed for coherent communication of findings in microbiological research. This Essay provides an overview of a novel bacterial strain taxonomy and describes ho...

doi.org

Some bacteria use the CRISPR/Cas systems as transcriptional repressors of other anti-phage systems, such that when CRISPR interfered with, gene expression of repressed anti-phage systems goes up www.nature.com/articles/s41...

CRISPR–Cas regulates expression of embedded anti-phage defence systems - Nature

CRISPR–Cas systems transcriptionally tune diverse innate defences using CRISPR RNA-like guides to balance antiviral protection with fitness, and hyperactivate these defences when compromised, establis...

nature.com

1/4 Every good defence needs a backup! 🛡️⚔ Out now in @natrevmicro.nature.com our Comment on "𝗶𝗺𝗺𝘂𝗻𝗲 𝘀𝗮𝗳𝗲𝗴𝘂𝗮𝗿𝗱𝗶𝗻𝗴"! 🎉 🔗 www.nature.com/articles/s41...

Immune safeguarding as a conserved principle of antiviral defence - Nature Reviews Microbiology

All organisms defend against viral infections through active immunity mechanisms that clear the virus or population-level mechanisms that cause regulated cell death. Recent research increasingly shows...

nature.com

Starting with the DNA sequence of a #phage genome, #PholdAPhage will create a 3D reconstruction of the complete phage, almost like you did cryoEM on it! Check out Renee's awesome software github.com/reneegreen81... to assemble unknown phage particles one protein at a time

Out @cp-cellhostmicrobe.bsky.social, natural products meet bacterial immunity! We used genomics to identify lanthivirins: a family of >2,000 lanthipeptide BGCs that protect Actinobacteria against phages. Led by @hshomar.bsky.social & @mariegllm.bsky.social www.sciencedirect.com/science/arti...

A family of lanthipeptides with anti-phage function

Bacteria produce natural products to adapt to their environments, with phage interactions as major ecological and evolutionary drivers. While some nat…

sciencedirect.com

Significant update to the AllTheBacteria paper, including discovering new antimicrobial peptides and testing in vitro and vivo. This has grown into a fantastic collaboration!

César de la Fuente@delafuentelab.bsky.social · 2w ago

Biology has plenty of data—the challenge is making it usable. AllTheBacteria transforms 2.44 million public bacterial and archaeal genomes into an open, uniformly processed, searchable, AI-ready resource. www.biorxiv.org/content/10.1...

1/10 🚨Preprint! One RING to rule them all (phages)👑💍⚔️ Bacteria build giant DNA-scaffolded RNase rings (larger than the ribosome!) to shut down viral infection🧬🧵👇 biorxiv.org/content/10.6...

Bacteriophage continue to have so much to teach us. It's in our interest to understand how they work and impact human & environmental health. New joint work led by @mariandm.bsky.social & @rantahan.bsky.social inferring single-cell latent period & burst size heterogeneity from population dynamics.

Inferring single-cell heterogeneity of bacteriophage lysis-associated life-history traits from population-scale dynamics

Theory-guided experiments reveal single-cell heterogeneity of lysis-associated bacteriophage traits from population scale data.

science.org

Job Opportunity: #CNRS Chemistry - #InstitutPasteur Mid-Career Group Leader (Chemistry for Health) is open in Paris, France. This is a fantastic opportunity for a standout chemist to establish themselves in a world-class environment. research.pasteur.fr/en/call/mid-...

Mid-career Group Leader position in Chemistry for Health at Institut Pasteur, Paris - Research

Institut Pasteur and the CNRS are launching a joint call for a mid-career group leader position in Medicinal Chemistry and Chemistry for Health. We are looking for an experienced researcher (typically...

research.pasteur.fr

Characterizing the ecological niche of insertion sequences within prokaryotic genomes academic.oup.com/ismej/advanc... #jcampubs

Characterizing the ecological niche of insertion sequences within prokaryotic genomes

Abstract. Insertion sequences (ISs) are widespread prokaryotic transposable elements, often regarded as genomic parasites that primarily cause deleterious

academic.oup.com

Fate of Horizontally Acquired Genes: Rapid Initial Turnover Followed by Long-Term Persistence | Molecular Biology and Evolution | Oxford Academic

The Fate of Horizontally Acquired Genes: Rapid Initial Turnover Followed by Long-Term Persistence

Abstract. A major driver of bacterial evolution is horizontal gene transfer (HGT), the acquisition of genes from other strains or species. Transfers betwee

dx.doi.org

We are looking for a motivated PhD student in phage genomics! Please find the details attached. Application deadline 24/07. Don't hesitate to spread the word!

Les nouvelles règles d'éligibilité de l'AAPG 2027 de @agencerecherche.bsky.social sont une catastrophe. Comment se fait-il qu'il n'y ait pas plus de réactions dans la communauté ? Sommes-nous à ce point résignés, ou individualistes ? #ESR

#microsky New preprint from the lab! Widespread immune systems protect bacteria against conjugative plasmids www.biorxiv.org/content/10.6... Kudos to the extremely talented lead author Ludovic Poiré! Key contributions by @francoisrousset.bsky.social and also help from C. Lesterlin/TacC lab. 🧵⬇️

Widespread immune systems protect bacteria against conjugative plasmids

Conjugative plasmids are a class of mobile genetic elements capable of efficient transfer between bacterial cells. Although they can introduce beneficial traits such as antibiotic resistance to recipi...

biorxiv.org

Discovery of bacterial immunity against plasmid conjugation. Massive effort, impressive work

Xavier Charpentier@labxc.bsky.social · 4w ago

#microsky New preprint from the lab! Widespread immune systems protect bacteria against conjugative plasmids www.biorxiv.org/content/10.6... Kudos to the extremely talented lead author Ludovic Poiré! Key contributions by @francoisrousset.bsky.social and also help from C. Lesterlin/TacC lab. 🧵⬇️

Glad to see it finally out in #mSystems @asm.org! 🥳 See the thread below to read what it is about! journals.asm.org/doi/10.1128/...

Global distribution of isoprenoid quinones across Bacteria | mSystems

Isoprenoid quinones are small electron-carrying molecules found in the membranes of organisms that produce energy through photosynthesis or respiration and participate in other important cellular processes. Recent advances in the characterization of their biosynthesis pathways enable their automated annotation from genome analyses. In this article, we performed the genomic analysis of over 26,000 cultured and uncultured bacteria, which was complemented by literature data compiled on over 6,000 cultured bacteria. This enabled us to provide an unprecedented overview of quinone distribution across the bacterial diversity. Creating such a comprehensive data set revealed new information about quinone distribution and evolutionary paths and will facilitate future exploration of various aspects of quinone biology, including their role in the evolution and diversification of bacterial metabolism.

journals.asm.org

Sophie Abby@soabby.bsky.social · 11mo ago

Really glad to announce a new preprint from our lab: Global distribution of quinones in Bacteria! We here combine comparative genomics and text mining to leverage information on quinones distribution from thousands of articles describing new species and from dozens of thousands of genomes! 1/5

Check out our latest T7SS toxin story. These reverse toxins aren’t as rare as we thought!

bioRxiv Microbiology@biorxiv-microbiol.bsky.social · last mo.

A novel reverse lipase toxin substrate of the Staphylococcus aureus type VII secretion system https://www.biorxiv.org/content/10.64898/2026.06.22.733114v1

Le @cnrsbiologie.bsky.social #CNRS #ESR recherche son futur Directeur/sa future Directrice Poste à pourvoir janvier 2027 Candidature avant 1er septembre 2026 carrieres.cnrs.fr/recrutement-...

1/ Deep-time phylogenetics is hard: overly simplistic substitution models can mislead tree estimation at the billion year timescale. Our new preprint introduces GTRspmix, a protein modeling framework designed to more realistically model site-to-site heterogeneity in amino acid replacement. 🧵

New preprint up: the power of protein language models - using a single gene (adenylate kinase) to predict the temperature optima of bacteria and bacterial communities from genomes or metagenomes www.biorxiv.org/content/10.6...

Predicting optimal growth temperatures of bacteria using learned structural information from a single protein

Temperature is a fundamental determinant of bacterial physiology and ecology. Optimal growth temperature (OGT) is highly variable across species, contributing to differences in where and when species ...

biorxiv.org

How useful are phages in explaining cholera disease severity? Accordingly to our latest little paper, possibly quite useful — up there with patient age and hospital location, and possibly more important than antibiotic exposures!

The Journal of Infectious Diseases@jidjournal.bsky.social · 2mo ago

Ranked placement of phage predation as a determinant of dehydration severity among cholera patients in Bangladesh ✅ Just Accepted 🔗 https://bit.ly/3Q2eDGi

Phage therapy via receptor-constrained evolutionary traps: Trends in Microbiology www.cell.com/trends/micro... #phage #phagesky

Phage therapy via receptor-constrained evolutionary traps

Phage therapy often fails when bacteria evolve resistance. We argue that phage selection should begin with receptors whose modification imposes predictable costs, turning resistance into reduced virul...

cell.com

I’ve officially resigned as Associate Editor for Frontiers in Systems Neuroscience. It used to be a reputable journal, but became a case study in how forced automation destroys academic integrity. 👇

Phage receptor-binding proteins are known for their LEGO-like modularity, but we still do not fully understand their evolutionary potential and how it shapes phage host range. Our new preprint examines this systematically in Klebsiella phages. 🔗 www.biorxiv.org/content/10.6... Thread 🧵

sPYce is now published in Nature Ecology and Evolution! sPYce is a method to integrate single-cell regulatory data across species, without requiring whole-genome alignments between species. More below ⬇️ www.nature.com/articles/s41...

Our piece about academic renewal is now out in the Times Higher Education. It deals with a familiar topic on which there have been multiple high-level declarations. We need to move beyond the symbolic. Early career researchers, pls read + ask questions! www.timeshighereducation.com/depth/academ...

Academic renewal needs pressure from below and responsibility from above

High-level declarations pledging not to misuse metrics in research assessment are important, but they are far from enough. Senior academics, in particular, must use their influence to ensure instituti...

timeshighereducation.com

👉 Only 2 weeks to go for registrations to the famous ICARe course on #antimicrobials and #resistance in #Annecy, France: www.icarecourse.org Great course, great venue, great networking opportunity with @gdwantibiotics.bsky.social and other huge legends in the field

📢 We are recruiting! I’m looking for a Research Associate in Structural Biology to join my lab at Imperial College London to study horizontal gene transfer using cryo-EM, biochemistry and microbiology. Please share with interested candidates! Apply: shorturl.at/gmJGS

Description

Please note that job descriptions are not exhaustive, and you may be asked to take on additional duties that align with the key responsibilities ment...

imperial.ac.uk

🌎 🧬 🖥️ logan-search.org the tool to query all SRA sequences (Dec 2023 snapshot) — just got major updates. Here's what's new. 🧵 1/12

One week left to apply. Help us find new antimicrobials and understand the inner workings of bacteria – as a technical assistant in the Machine Biophotonics and Nanoscale Bacteriology labs at the Rudolf-Virchow-Zentrum, University of Würzburg – See details below (in German). Please spread the word.