We’re so excited to share our new paper, where we tackle the wealth of structural and functional diversity of anti-phage sensors across bacteria (1/6)

Nature@nature.com · last wk.

Nature research paper: Diverse bacterial pattern recognition receptors sense the core phage proteome go.nature.com/45fpXCZ

🎉final print version in PLOS Genetics @sullivan-lab.bsky.social @biosci.lbl.gov journals.plos.org/plosgenetics...

Cross-family and phage-specific gene requirements for Klebsiella infection revealed by scalable RB-TnSeq genetic screens

Author summary Bacteriophages, or phages, are viruses that infect bacteria and play central roles in shaping microbial communities across ecosystems. Despite their ecological importance, the bacterial...

journals.plos.org

Vivek Mutalik@vivekmutalik.bsky.social · 5mo ago

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

Bacteriocins in archaea and archaeocins in bacteria. @romainstrock.bsky.social surveys the the exchange of molecular weaponry between archaea and bacteria. www.biorxiv.org/content/10.6...

Bacteriocins in archaea and archaeocins in bacteria

Archaea and bacteria routinely live side by side in microbial communities and must interact at least on occasion. Whether such cross-Domain interactions are dominated by mutual disregard, co-operation...

biorxiv.org

Phage hijacks host phosphorothioate DNA modification machinery to circumvent bacterial Ssp defences | Nature Microbiology

Phage hijacks host phosphorothioate DNA modification machinery to circumvent bacterial Ssp defences - Nature Microbiology

The phage-encoded protein PptA enables its DNA to masquerade as the host and evade cleavage, providing a potential foundation for engineering therapeutic phages that could bypass this widespread defence system.

nature.com

Discovery of a Turing reaction-diffusion system in Archaea! www.biorxiv.org/content/10.6...

A self-organized geometry sensing oscillator spatially regulates cell division in archaea

Cell division must be tightly regulate in time and space. Many bacteria and eukaryotes employ geometry sensing systems to regulate cell division spatiotemporally. However, how archaea ensure they divi...

biorxiv.org

Clever little buggers, geminiviruses...😎

GeminiTeamLab@geminiteamlab.bsky.social · 2w ago

How does a geminivirus replicate its genome using a pick&mix strategy with host proteins? 🦠🦠🌱🧬 Our new preprint identifies plant proteins repurposed by geminiviruses to carry out rolling-circle replication. Congrats @chaonan123.bsky.social , who spearheaded this work! www.biorxiv.org/content/10.6...

Surface architecture of the bacterial envelope determines phage adsorption route in pathogenic Escherichia coli O157:H7 www.biorxiv.org/content/10.6...

Surface architecture of the bacterial envelope determines phage adsorption route in pathogenic Escherichia coli O157:H7

The outermost surface layers of Gram-negative bacteria determine phage access to terminal receptors, yet their genetic basis has been mapped almost exclusively in laboratory strains that lack them. He...

biorxiv.org

Come work on exciting AI for biology projects in Paris!! 🇫🇷 Details and application below, deadline sept 1st!

Antigen Evolution & Design Lab@antigenevo.bsky.social · 2w ago

🚨 JOB ALERT🚨 We are very excited to be hiring the lab's ✨very first postdoc✨! Work on new AI technologies for decoding antigen protein evolution in a fresh research environment, at the heart of Paris 🇫🇷 Details & link to apply: research.pasteur.fr/en/job/postd... Deadline: Sep 1st

Check out this fun collaboration on phages and Polyamines with the Marshall Lab! #microsky #phagesky 🧪🧫🧬🔬

Chris Marshall@sirmicrobe.bsky.social · 3w ago

This is our 2nd recently posted paper where we wanted to build off the fantastic 2023 PNAS paper by @prsecor.bsky.social group (www.pnas.org/doi/10.1073/...) 1/3

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

Our paper out in Science today: The Metis defense system senses molecular byproducts released when a phage degrades the bacterial genome, and then prevents replication of the phage in the infected cell Congratulations @ostermanilya.bsky.social and co-authors!

Bacteria sense virus-induced genome degradation via methylated mononucleotides

Phages often degrade the genome of their bacterial host to individual nucleotides. Here we describe Metis, a bacterial defense system that directly senses phage-mediated host genome degradation. Metis...

science.org

Osterman Ilya@ostermanilya.bsky.social · 4w ago

Excited to share that our Metis story is now published in Science! 🎉 Bacteria can sense phage-induced degradation of their genome and activate immunity. Many thanks to everyone who contributed to this work. 📄 www.science.org/doi/10.1126/... More details in my earlier thread 🧵⬇️

#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

Lab account is official! go follow @antigenevo.bsky.social 👇👇👇 research.pasteur.fr/en/team/anti...

Antigen Evolution & Design - Research

Most pathogens have proteins on their surface which are recognised by our immune system and prime it to make antibodies that protect us from future infection. Vaccines contain these proteins to activa...

research.pasteur.fr

Antigen Evolution & Design Lab@antigenevo.bsky.social · 4w ago

Inaugural post! We are a brand new lab @pasteur.fr studying how pathogen antigens evolve and how we can exploit these proteins' evolution to make better vaccines! Read a few words from the currently sole member of the lab @spyroslytras.bsky.social below! 😁 www.pasteur.fr/en/research-...

🚨 Registration for VEGA26 is 👏 officially open 👏 🚨 The 5th edition of our Viral EcoGenomics and Applications symposium will be held November 18-19, 2026, on the UC Berkeley campus 🧬 🦠 🔬 🧫 Event website ➡️ jgi.doe.gov/work-with-us... Registration link ➡️ cvent.me/e0RnA0

Excited to share our new preprint led by Fred and me in collaboration with the archaeal community! We found that the molecular foundation of histone-based chromatin has pre-eukaryotic roots in Asgard archaea. (1/4) #ArchaeaSky www.biorxiv.org/content/10.6...

Emergence of histone-based chromatin complexity in Asgard archaea

The emergence of the eukaryotes coincided with the diversification of histone proteins and their post-translational modifications by enzymes that constitute the core of eukaryotic chromatin. Yet the e...

biorxiv.org

🚨New paper alert 🚨 Here we tried to leverage an (incredible) metagenome time-series to better understand MGE diversity and activity in soil across decade(s). @scbagby.bsky.social has an amazing thread about this work with all the details - bsky.app/profile/scba...

Mobile genetic elements shape microbial diversity and functions in thawing permafrost soils - Nature Microbiology

An 8-year soil meta-omic time series shows how mobile genetic elements shape permafrost microbial diversity and impact a range of functions, including carbon and nutrient cycling.

nature.com

Sarah Bagby@scbagby.bsky.social · last mo.

Out today in Nature Microbiology: a paper that started in 2021 with an email from @sullivan-lab.bsky.social. Subject line: "Crazy ideas". www.nature.com/articles/s41... 1/23

Microbes that have the greatest genomic potential for secondary metabolism tend to be multicellular. Here, we show that signatures of ancestral BGC expansions within 3 bacterial phyla and 2 fungal lineages coincide with origins of complex multicellularity [1/12] 🧵 www.nature.com/articles/s41...

Complex multicellularity is linked with expanded specialized metabolite production in microorganisms - Nature Microbiology

The evolutionary emergence of complex multicellularity in bacteria and fungi, such as the ability for mycelial growth, is strongly associated with increased genomic carriage of biosynthetic machinery ...

nature.com

#gbdraw v0.12.1 is now live with a massive update! Powerful new features are now available in your local environment: ​You can now generate circular comparisons (homology rings) and interactive SVG files directly on your machine 🧬 #bioinformatics #genomics

Review summarises how viruses dominate genetic diversity on Earth and evolve through multiple origins, gene sharing, and host–virus arms races, reshaping the global virosphere and replicator space 🧬🌍🦠 #Virology #Evolution #Metagenomics 📄 doi.org/10.5802/crbi... 👤 EVBC member: Mart Krupovic

Our paper on the evolution of cellular miniaturization is now out in PNAS! www.pnas.org/doi/10.1073/... A short recap 🧵

Marco Fumasoni@marcofumasoni.bsky.social · 8mo ago

🗞️ New preprint from the lab, led by our postdoc Ana Garoña (not on here) in collab with @andreagiometto.bsky.social: “Experimental evolution of cellular miniaturization reveals a mechanism for cell size evolution”, aka: “honey, we shrank the yeasts!” 🎥 www.biorxiv.org/content/10.6...

Excited to share our new preprint! 🧬❄️ by brilliant @mdreimann.bsky.social and great collaborators! Using cryo-ET&EM, we reveal archaeal chromatin in a near-native state: variable-beads-on-a-string fibers shaped by growth phase and histone composition #ArchaeaSky www.biorxiv.org/content/10.6...

Our paper on the YprA family of helicases and their roles in bacterial defence is now out! We describe ARMADA, a defence system synergise with Druantia and show that both systems spread horizontally on a novel type of mobile genetic element that we call SPIDERs www.sciencedirect.com/science/arti...

YprA-family helicases provide the missing link between diverse prokaryotic immune systems

Bacteria and archaea possess an enormous variety of antiviral immune systems that often share homologous proteins and domains. YprA-family helicases a…

sciencedirect.com

The peer-reviewed version: www.science.org/doi/10.1126/...

Enteric viral infections promote systemic accelerated aging in Drosophila

Enteric viruses act as age-distorters, with infection severity tied to aging hallmarks and consequences.

science.org

Rubén González@rubengonzalez.bsky.social · 9mo ago

Version 2 is out! More comprehensive text plus new tissue- and pathway-specific analysis revealing how different viruses trigger systemic aging through diverse mechanisms. www.biorxiv.org/content/10.1...

Archaea are the hornets of the microbial world. Discuss. www.biorxiv.org/content/10.6... TLDR: Archaeon kills bacterium with secreted phospholipase. Pretty nifty way to kill bacteria for a microbe with a very different lipid make-up, I reckon. No need to worry about accidentally killing yourself.

Our paper "Gene ancestries reveal diverse microbial associations during eukaryogenesis.” is finally out in Nature. Eukaryogenesis was likely a gradual process shaped by multiple microbial partners and virus-mediated gene transfer, rather than a single binary symbiosis. doi.org/10.1038/s415...

I'm happy to share the first pre-print of out Lab! 🎉 Introducing ArchaeaHQ www.biorxiv.org/content/10.6... We curated 21,644 genomes across all 4 archaeal kingdoms to bridge the gap in public datasets for computational biology What is inside ArchaeaHQ... (1/2)

Our paper is out in Nature Microbiology: functional analysis of 80 phage sponges, revealing new sponges that inhibit bac immunity by binding the immune signals cCMP, cUMP and N7-cADPR Thanks to all coauthors and our collaborators at the Kranzusch Lab. Congrats Romi! www.nature.com/articles/s41...

Functional diversity of phage sponge proteins that sequester host immune signals - Nature Microbiology

A functional screen reveals phage sponge proteins that bind Pycsar, Thoeris and CBASS signalling molecules to inhibit bacterial immunity.

nature.com

Romi Hadary@romihadary.bsky.social · 2mo ago

Excited to see our work out in @natmicrobiol.nature.com! We uncovered broad functional diversity within phage sponge families🧽. Huge thanks to all coauthors and brilliant collaborators @kranzuschlab.bsky.social @reneechang.bsky.social ! www.nature.com/articles/s41...

Chromatin organization in Asgard archaea: histones, SMC complexes, and the archaeal roots of eukaryotic chromatin: Trends in Genetics www.cell.com/trends/genet... New review by @jvhooff.bsky.social & @damelab.bsky.social

Chromatin organization in Asgard archaea: histones, SMC complexes, and the archaeal roots of eukaryotic chromatin

The genomes of organisms across the tree of life are structurally and functionally organized into chromatin. In eukaryotes, within an organelle called the nucleus, chromatin is shaped by histones and ...

cell.com

Check out our new review with @mfarjo.bsky.social on what we know about the functional and evolutionary consequences of virus-virus interactions within viral populations, out now in @annualreviews.bsky.social: www.annualreviews.org/content/jour... Hope you like it!

Heterogeneity and Collective Interactions Within Viral Populations

The existence of viruses as obligate intracellular parasites with high mutation rates sets them apart from other forms of life in fundamental ways. Frequent errors in replication and assembly processe...

annualreviews.org

Excited to share our latest research on leveraging machine learning with helical fusions for the design of novel protein cages! Preprint: “Design and structure of protein cages based on helical fusion and machine learning” Link: www.biorxiv.org/content/10.6...