Emmanuele Severi

#phage #phagesky #microsky Run, run as fast as you can. You can’t catch me, I’m the gingerbread man www.science.org/doi/10.1126/...

science.orgscience.org

biorxiv.orgSequential assembly in vivo of the bacteriophage P22 genome translocation channelBacteriophage P22 ejects four internal proteins into infected cells to assemble a channel for genome translocation across the cell envelope. However, how these proteins cooperate to build the trans-en...

10 Sept

#phagesky #microsky #phage www.biorxiv.org/content/10.6...

nature.comPervasive phosphorylation by phage T7 kinase disarms bacterial defences - NatureThe T7 bacteriophage deactivates bacterial defence systems through T7K phosphorylation of nearly all host and phage proteins during infection.

20 Aug

#microsky #phagesky T7’s phospho-bombing of host proteins overcomes (-whelms) E. coli #phage defence mechanisms www.nature.com/articles/s41...

Emmanuele Severi reposted

Jasper Gomez

@jasgomez.bsky.social

15 Aug

My PhD work with my awesome mentor Chris Waters and collaborator Jeff Barrick looking at how phages encode contingency loci to overcome phage defense systems and potentially other stresses via phase variation is out! www.nature.com/articles/s41...

nature.comPhage-encoded contingency loci enable bet-hedging against host defence mechanisms - Nature MicrobiologyDiverse E. coli phage genomes have hypermutable DNA regions that promote reversible frameshift mutations through DNA polymerase slippage, generating population heterogeneity that enables host exploita...

14 Aug

#microsky #phagesky #phage Phase variation FTW www.nature.com/articles/s41...

journals.plos.orgIntact architectures of myophage phi92 in extended and contracted statesAuthor summary With the increasing severity of the problem of drug-resistant bacteria, phage therapy is regaining renewed attention as an effective alternative strategy. Myophage phi92 exhibits broad-...

9 Aug

#microsky #phagesky #phage journals.plos.org/plospathogen...

nature.comAntiviral defence is a conserved function of diverse bacterial DNA glycosylases - Nature MicrobiologyDNA glycosylases, typically used for DNA repair, can also protect bacteria against phages that would otherwise evade host immunity by incorporating modified bases into their genomes.

7 Aug

#microsky #phagesky #phage defence www.nature.com/articles/s41...

science.orgGenerative design of bacteriophages with genome language modelsMany important biological functions arise not from single genes but from complex interactions encoded by entire genomes. We report the first generative design of complete bacteriophage genomes using g...

7 Aug

#microsky #phagesky #phage www.science.org/doi/10.1126/...

Emmanuele Severi reposted

Ákos T Kovács

@evolvedbiofilm.bsky.social

29 July

A novel stress response pathway mediates biofilm architecture in Pseudomonas aeruginosa PLOS Pathogens by Ainelen Piazza et al from Jakob Malone @johninnescentre.bsky.social with @friendlymicrobe.bsky.social journals.plos.org/plospathogen...

journals.plos.orgA novel stress response pathway mediates biofilm architecture in Pseudomonas aeruginosaAuthor summary Biofilm formation by the opportunistic pathogen Pseudomonas aeruginosa represents a major clinical challenge, with biofilms typically associated with chronic infection, increased antibi...

@micklefield-lab.bsky.social

29 July

#glycotime #glycotimesky Finally, the structure of the #sialic acid-binding SBP from the Streptococcal ABC transporter is determined! And binding alpha-NeuAc no less - interesting! Only one SBP left to solve now… www.nature.com/articles/s42...

nature.comnature.com

Emmanuele Severi reposted

Micklefield Lab

28 July

Hello Bluesky! 👋 We're a research group at Imperial College working at the interface of chemistry, biology & biotechnology. 🔬 #BiosyntheticPathways, #NaturalProducts & #Antibiotics 🧬 #EnzymeStructure, #EnzymeMechanism & #EnzymeEngineering ⚗️ #Biocatalysis & #SustainableSynthesis. News to follow

nature.comUnique adaptations in sulfatases underpin colonic mucin degradation by Akkermansia muciniphila - Nature MicrobiologyStructural and biochemical follow-up of a serendipitous discovery reveals that Akkermansia muciniphila carbohydrate sulfatases are uniquely adapted to digest colonic mucins in collaboration with other...

27 July

#glycotime #glycotimesky From Alan Cartmell and collaborators: sulfatases from Akk muciniphila involved in mucin degradation www.nature.com/articles/s41...

journals.asm.orgLeucine auxotrophic marker for genetic manipulation of Mycobacterium abscessus | Applied and Environmental MicrobiologyThe development of a leucine auxotroph-based genetic system for Mycobacterium abscessus addresses critical challenges in mycobacterial genetics. By avoiding established antibiotic resistance markers, ...

24 July

#microsky Leu auxotrophy as genetic marker for Mycobacterium abscessus #synbio journals.asm.org/doi/10.1128/...

Emmanuele Severi reposted

ISVM

@isvm-society.bsky.social

22 July

Looking for a 𝐩𝐨𝐬𝐭𝐝𝐨𝐜 in phage research? A 𝟐𝟒-𝐦𝐨𝐧𝐭𝐡 position is available at 𝐂𝐘 𝐂𝐞𝐫𝐠𝐲 𝐏𝐚𝐫𝐢𝐬 𝐔𝐧𝐢𝐯𝐞𝐫𝐬𝐢𝐭é starting 𝐉𝐚𝐧𝐮𝐚𝐫𝐲 𝟐𝟎𝟐𝟕 to develop genetically engineered therapeutic phages against 𝘚. 𝘢𝘶𝘳𝘦𝘶𝘴 biofilms. 📄Details in the attached announcement—please share! #PhageResearch #Postdoc #ISVM

cell.comA family of lanthipeptides with anti-phage functionShomar, Guillaume, et al. report the genomics-driven discovery of a family of more than 2,000 lanthipeptide biosynthetic gene clusters with anti-phage potential. They experimentally demonstrate anti-p...

20 July

#microsky #phagesky Lanthipeptides involved in #phage defence! What a blast!! www.cell.com/cell-host-mi...

journals.asm.orgFrom hijackers to architects: the role of prophages in bacterial genome evolution | Journal of BacteriologyBacteriophages (phages) are one of the most important drivers of bacterial evolution, regulating physiology, genetic diversity, population dynamics, and coevolution through complex host-phage interact...

17 July

#microsky #phagesky #phage The secret life of prophages journals.asm.org/doi/10.1128/...

cell.comA receptor-centered approach identifies Lom as a LamB-bound superinfection exclusion factor in bacteriophage λGe et al. develop a receptor-centered strategy to identify phage proteins that target host receptors during infection and discover the λ outer-membrane protein Lom. Lom binds and occludes LamB, blocki...

17 July

#phagesky #microsky #phage www.cell.com/cell-reports...

febs.onlinelibrary.wiley.comFEBS PressBiophysical characterisation shows that NanX, a membrane transport protein from the major facilitator superfamily (MFS), forms both monomers and dimers after purification. AlphaFold modelling and sub...

14 July

New #glycotime #glycotimesky paper reporting the super-fun isolation of “rule-breaking” #sialic acid transporter mutants! The phenotype is a real tease, much to ponder about. Worth a read: febs.onlinelibrary.wiley.com/doi/10.1002/...

Emmanuele Severi reposted

Nature Biotechnology

@natbiotech.nature.com

9 July

High-quality phage assembly from metagenomes with PALACE www.nature.com/articles/s41...

nature.comHigh-quality phage assembly from metagenomes with PALACE - Nature BiotechnologyPALACE combines homology features and deep learning to improve phage assembly from metagenomics.

Emmanuele Severi reposted

Biochemical Society

@biochemsoc.bsky.social

9 July

Registration is now open for Synthetic Biology UK 2026. Join the UK synthetic and engineering biology community on 2–3 November in Hampshire to explore the future of biological design and innovation. https://ow.ly/x7KT50ZlVF9 🧪

Emmanuele Severi reposted

Alex Crits-Christoph

@acritschristoph.bsky.social

8 July

What are your favorite papers that linked patients, traced outbreaks, or distinguished epidemiological hypotheses on the careful basis of just a few SNVs? Like ~ <20? Bacterial best, viruses OK too

Emmanuele Severi reposted

Sebastian S. Cocioba

@atinygreencell.bsky.social

8 July

@breakliquid.bsky.social and I are delighted to say our OpenEVO preprint is finally live! An open source hand-made turbidostat that's modular, affordable, and made to be customized. Designed with love for the research community. Enjoy!!!💚 www.biorxiv.org/content/10.6...

biorxiv.orgOpenEvo: An Open-Source Platform for Automated Evolution and AnalysisHere we introduce OpenEvo, a fully open-source, low-cost turbidostat platform for automated continuous culture and directed evolution experiments. Existing tools are expensive, complex, or lack open-s...

Emmanuele Severi reposted

Mart Krupovic

@mkrupovic.bsky.social

11 May

With Eugene Koonin, we wrote a rather comprehensive review on the origin, evolution and organization of the #virosphere. We describe all 10 viral realms and the logic behind them, and so much more. Check it out! comptes-rendus.academie-sciences.fr/biologies/ar...

Emmanuele Severi reposted

Xavier Charpentier

@labxc.bsky.social

7 July

#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. 🧵⬇️

biorxiv.orgWidespread immune systems protect bacteria against conjugative plasmidsConjugative 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...

Emmanuele Severi reposted

Microbiology Society

@microbiologysociety.org

2 July

Are you a UK-based researcher working in microbiology or environmental biotechnology? Researchers at the University of Edinburgh are seeking your views on the natural environment, microbes and microbiomes. Complete their survey by 17 July: https://microb.io/4y7OWoX

biorxiv.orgTargeted DNA nicking enables efficient, single-step and counterselection-free editing of bacteriophage genomesGenetic manipulation of bacteriophages is essential for interrogating phage biology and advancing antimicrobial therapies. However, current genome editing approaches can be inefficient, require multip...

27 June

#microsky #phagesky #phage 440K tail-fibre mutants… 440K… Mind-boggling doesn’t even start describing this

Vivek Mutalik@vivekmutalik.bsky.social

New preprint!! 🎉 A cool collaborative work with @copabio.bsky.social and Chase Beisel teams on the phage editing technology. @sarshad.bsky.social led the work from our side to validate & characterize the lib. #phage #phagesky www.biorxiv.org/content/10.6... Work supported by: phagefoundry.org

Emmanuele Severi reposted

Vivek Mutalik

@vivekmutalik.bsky.social

27 June

nature.comEND nucleases are antiphage defence systems targeting multiple phages with modified genomes - Nature MicrobiologyThe END nuclease targets eight phage families with at least ten different known DNA modifications, but not unmodified DNA. Its specificity is dictated by the C-terminal iEndoIII domain. To combat END,...

27 June

#microsky #phagesky #phage www.nature.com/articles/s41...

Emmanuele Severi reposted

Microbiology Society

@microbiologysociety.org

26 June

Access Microbiology is recruiting Editor Mentees across all fields of microbiology! Applications close 31 July 2026. For more information and details on how to apply, visit our website: https://microb.io/Vacancies #AcMi

Emmanuele Severi reposted

Jose Bengoechea

@josebengoechea.bsky.social

26 June

Recruiting a postdoc to join my lab at @lshtm.bsky.social to work in an MRC porgramme grant funded project to dissect the gut colonziation by Klebsiella. In vivo and in vitro models, and new approaches to identify Klebsiella factors involved. jobs.lshtm.ac.uk/vacancy.aspx...

jobs.lshtm.ac.ukJob Opportunity at LSHTM: Research FellowThe London School of Hygiene & Tropical Medicine (LSHTM) is one of the world’s leading public health universities. Our mission is to improve health and health equity in the UK and worldwide; working i...

Emmanuele Severi reposted

Oded Rechavi

@odedrechavi.bsky.social

23 June

Time from submission to acceptance: 3 UK Prime Ministers.

Emmanuele Severi reposted

ISVM

@isvm-society.bsky.social

📢 Join us at the ISVM General Meeting during #VoM2026 in Prague! 📅 6 July 2026 🕠 17:30–18:30 📍 Prague, Czech Republic We'll discuss: 🔹 ISVM development 🔹 Activities for members 🔹 Future directions and member engagement Programme: www.vom2026.org/program #ISVM #Virology #Microbiology #Phages

academic.oup.comBacteriophage-mediated cell lysis externalizes a metabolically valuable nutrient to broadly modulate bacterial communitiesAbstract. Cobamides, including vitamin B12, are essential cofactors exchanged between organisms across diverse ecosystems including oceans, soils, and the

25 June

#microsky #phagesky Years ago a stray temperate #phage lysogenised an E. coli mutant of mine unable to take in a Sia. The small portion of lysed cells was enough to predigest the Sia into catabolites the cells could take in and use for growth!!! And here I was 1/2 academic.oup.com/ismej/advanc...

25 June

2/2 thinking I’d discovered a cryptic Sia utilisation locus lololol

nature.comA Type VII-secreted toxin enables inter-mycobacterial competition - Nature CommunicationsMycobacteria have not yet been reported to engage in interbacterial competition via secretion of proteinaceous toxins. Here, Benedict et al. show that some mycobacteria can use their type-VII secretio...

25 June

Chuffed I was included for my mini contribution ❤️. Authentic tour de force and beautiful discovery by the REAL authors of the story! 🎉🎉👏👏👏

Patrick Moynihan@pmoyniha.bsky.social

New paper in collaboration with @proftracypalmer.bsky.social, @lislowe.bsky.social and many more. We show that mycobacteria produce Type VII secreted anti-bacterial protein toxins. Excited to explore this new area of mycobacterial biology. www.nature.com/articles/s41...

Emmanuele Severi reposted

Patrick Moynihan

@pmoyniha.bsky.social

@proftracypalmer.bsky.social

Emmanuele Severi reposted

Tracy Palmer

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

bioRxiv Microbiology@biorxiv-microbiol.bsky.social

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

Emmanuele Severi reposted

Nature Microbiology

@natmicrobiol.nature.com

go.nature.comPhages tame plant pathogensNature Microbiology, Published online: 23 June 2026; doi:10.1038/s41564-026-02395-3Predicting infection heterogeneity requires looking beyond the host. Phage–bacteria coevolution in tomato fields maintains diverse bacterial strategies and explains uneven disease occurrence across plant populations.

Out Now! Phages tame plant pathogens #MicroSky

nature.comStructure and substrate recognition by the bacterial twin-arginine translocation (Tat) core complex - Nature MicrobiologyCryo-EM structural, biochemical and functional analyses of the bacterial twin-arginine translocation system for protein transport across membranes reveal mechanisms of substrate binding.

22 June

#microsky More Tat!!! www.nature.com/articles/s41...

cell.comStructure of E. Coli twin-arginine translocase (Tat) complex with bound cargoThe structure of the Tat protein complex bound to a substrate reveals how folded proteins are recognized and offers insight into subsequent substrate transport across the membrane.

22 June

#microsky Gosh, Tat!! www.cell.com/molecular-ce...

Emmanuele Severi reposted

Matt Hutchings

@matthutchings.bsky.social

21 June

Structures of DnaA domain I reveal a dimer conserved across Actinomycetes academic.oup.com/nar/article/...

academic.oup.comStructures of DnaA domain I reveal a dimer conserved across ActinomycetesAbstract. DNA replication is a fundamental process in biology, and initiation marks a key regulatory step. In bacteria, DNA replication is initiated by the

nature.comUncovering bacterial pseudaminylation with pan-specific antibody tools - Nature Chemical BiologyPseudaminic acids (Pse) are a family of carbohydrates found within bacterial lipopolysaccharides, capsular polysaccharides and glycoproteins. Now, monoclonal antibodies have been developed that recogn...

20 June

#microsky #glycotime #glycotimesky and kinda #sialicacid New tools to study protein pseudaminylation www.nature.com/articles/s41...

Emmanuele Severi reposted

Ákos T Kovács

@evolvedbiofilm.bsky.social

17 June

Bacterial–fungal interactions: connections and consequences Essays Biochem by Rebecca A. Hall and @katherine-baxter.bsky.social portlandpress.com/essaysbioche...

nature.comStructure of a contractile injection system in Salmonella enterica subsp. salamae - Nature CommunicationsContractile injection systems (CISs) are nanomachines that inject proteins into target cells. Here, the authors resolve the atomic structure of a CIS in the opportunistic human pathogen Salmonella ent...

17 June

#microsky and kinda #phagesky www.nature.com/articles/s41...

Emmanuele Severi reposted

BejaLabTechnion

@bejalab.bsky.social

17 June

Viral theft of light: A cyanophage protein dismantles cyanobacterial photosynthesis to accelerate infection www.cell.com/cell-host-mi...

cell.comViral theft of light: A cyanophage protein dismantles cyanobacterial photosynthesis to accelerate infectionAuxiliary metabolic genes, acquired by cyanobacterial viruses (cyanophages) from their hosts, are thought to manipulate host metabolism during infection. A recent study by Nadel et al. performed in vi...

Emmanuele Severi reposted

Ákos T Kovács

@evolvedbiofilm.bsky.social

George O'Toole (he/him/his)

Biosynthetic gene clusters in Pseudomonas viridiflava have a fitness cost during Arabidopsis thaliana infection #mSystems by Alejandra Duque-Jaramillo et al from Talia Karasov, Detlef Weigel @plantevolution.bsky.social journals.asm.org/doi/10.1128/...

orcid.orgORCID

Emmanuele Severi reposted

@geiselbiofilm.bsky.social

@stcmicrobeblog.bsky.social

Check out out the 15 papers that are part of our collction called "The Pseudomonads: Versatile Organisms" - lots to learn about this interesting bug! journals.asm.org/topic/sss-ta... @asm.org #JBacteriol

Emmanuele Severi reposted

STCmicrobeblog

#MicroSky

George O'Toole (he/him/his)@geiselbiofilm.bsky.social

biorxiv.orgStructural modularity of receptor-binding proteins underlies host-range strategy diversification in Klebsiella pneumoniae phagesBacteriophage receptor-binding proteins (RBPs) determine bacterial host recognition and are central to phage host-range evolution, yet the structural principles governing how RBPs diversify and expand...

#microsky #phagesky AF3 models of Klebsiella #phage RBPs. This was done for coliphages and (to a lesser extent) phages against A. baumannii. Field heating up! www.biorxiv.org/content/10.6...