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Elisabetta Cacace

@elisca.bsky.social
383 followers 478 following 17 posts

Incoming SNSF Ambizione group leader at EPFL. Interested in bacteria-host interactions in health and disease. elisabettacacace.github.io/BHI-Lab

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Reposted by Elisabetta Cacace
Typas Lab @typaslab.bsky.social · 20/08/2026
Excited to share our paper with @savitski-lab.bsky.social, led by @tarabartolec.bsky.social, Karin Mitosch & Clément Potel, out now in @nature.com. We show that T7 phage broadly disables bacterial defenses using a unique ‘loose cannon’ protein kinase. www.nature.com/articles/s41...
nature.com
Pervasive phosphorylation by phage T7 kinase disarms bacterial defences - Nature
The T7 bacteriophage deactivates bacterial defence systems through T7K phosphorylation of nearly all host and phage proteins during infection.
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Elisabetta Cacace @elisca.bsky.social · 24/04/2026
Check out our work on E. coli capsules! Including a 3x extended catalog of capsule loci from >37K genomes, a scalable tool to type them in silico (kTYPr) and new associations with ecology and disease! A joint effort from @microbiomeresearch.bsky.social @mucosalimmunology.bsky.social at @ethz.ch.
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Microbiome Research Lab, ETH Zürich @microbiomeresearch.bsky.social · 25/02/2026
We are thrilled to announce the newest study from our lab (and great collaborators) is out now in @nature.com We show that #coral #microbes are untapped "biosynthetic reservoirs", full of unique natural products. doi.org/10.1038/s415...
doi.org
Coral microbiomes as reservoirs of unknown genomic and biosynthetic diversity - Nature
Reconstructing microbial genomes from 820 reef-building corals collected at 99 reefs across 32 islands throughout the Pacific Ocean highlights the importance of conserving coral reefs as vital reservo...
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Elisabetta Cacace @elisca.bsky.social · 06/02/2026
Excited to announce my upcoming @snsf.ch Ambizione research group at EPFL on bacteria-host interactions, combining systems approaches and microphysiological models. 🚨 We have an open PhD position! More info on projects and how to apply here: elisabettacacace.github.io/BHI-Lab/ 🧪
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John Lees @johnlees.bacpop.org · 30/01/2026
We are hiring for group leaders again — EBI is a great place to start your research group! embl.wd103.myworkdayjobs.com/EMBL/job/Hin...
embl.wd103.myworkdayjobs.com
Research Group Leader
Do you want to lead groundbreaking research in computational biology? Join us at EMBL-EBI! EMBL's European Bioinformatics Institute (EMBL-EBI) is seeking talented and highly-motivated scientists to jo...
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Reposted by Elisabetta Cacace
Ricardo León-Sampedro @rleonsampedro.bsky.social · 07/11/2025
🚨 Excited to share our new paper is out! 🎉 We show how interactions within gut microbiomes allow certain antibiotic-resistant E. coli strains to persist even without antibiotics, helping explain how resistance is maintained in the human gut. Now published in @natcomms.nature.com rdcu.be/eOf63
rdcu.be
Multi-layered ecological interactions determine growth of clinical antibiotic-resistant strains within human microbiomes
Nature Communications - The role of ecological factors in modulating the spread of antibiotic-resistance bacteria in the gut remains unclear. Here, the authors use anaerobic microcosms to study the...
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Taylor priest @taylorpriest.bsky.social · 14/08/2025
The JEDI marker - a new approach for measuring #biodiversity that captures all domains of life and is applicable across biological and ecological scales. It's time to change the way we perceive biodiversity - www.biorxiv.org/content/10.1...
biorxiv.org
The JEDI marker as a universal measure of planetary biodiversity
Despite its critical importance in the formation and maintenance of ecosystems and homeostasis on Earth, biodiversity remains a complex and non-unified concept. Consequently, standards for measuring b...
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Typas Lab @typaslab.bsky.social · 13/10/2025
Excited to share our preprint led by Carlos Voogdt et al We developed new genetic tools & genome-wide libraries for species of the Bacteroidales order; constructed saturated barcoded transposon libraries in key representatives of three genera. www.biorxiv.org/content/10.1...
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Craig MacLean @craigmaclean.bsky.social · 25/09/2025
New ERC funded computational postdoc position in my lab! We are looking for someone who will study the genomics of bacterial evolution using samples from experimental evolution and clinical trials. Lots of opportunities for interesting and fun collaboration! my.corehr.com/pls/uoxrecru...
my.corehr.com
Job Details
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Emma Slack @mucosalimmunology.bsky.social · 10/09/2025
Come and be my colleague at the Dunn School! It‘s a brilliant place to work and exciting to be building up our immunology team. Do apply. Do pass on the news 💉🧬🦠🔬🧫
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Reposted by Elisabetta Cacace
Ina Huppertz @inahuppertz.bsky.social · 24/08/2025
🎉 We’re excited to share our very first preprint!! 🎉 "Metabolic Crossroads: AMDHD2 Couples the Hexosamine Biosynthetic Pathway to Acetyl-CoA Homeostasis in Pluripotent Stem Cells" 👉 doi.org/10.1101/2025... #FirstPreprint #StemCells #Metabolism #Epigenetics #AcetylCoA #HBP #Pluripotency #NewScience
doi.org
Metabolic Crossroads: AMDHD2 Couples the Hexosamine Biosynthetic Pathway to Acetyl-CoA Homeostasis in Pluripotent Stem Cells
Pluripotent stem cells (SCs) rely on metabolic rewiring to regulate self-renewal and differentiation. The hexosamine biosynthetic pathway (HBP) integrates multiple metabolic inputs to produce uridine ...
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Elisabetta Cacace @elisca.bsky.social · 15/08/2025
How diverse are E. coli capsules? How are they linked to ecology and disease? Find out with > 25,000 genomes and MAGs including undersampled environments and hosts from all over the world. Great genomics - glycobiology synergy in Sunagawa and Slack groups at ETH! www.biorxiv.org/content/10.1... 🧪🧫🔬
biorxiv.org
The natural diversity of E. coli transporter-dependent capsules
Serotyping of bacteria using genomic information ( in silico serotyping) has increasingly replaced serology. However, the E. coli capsule serotyping system has been largely abandoned since the 1990s, ...
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Reposted by Elisabetta Cacace
Michael Kuhn @biocs.bsky.social · 15/08/2025
We're very happy to release our new database Metalog metalog.embl.de ! It offers manually curated and harmonised contextual data for 110k metagenomics samples across the globe, incl. precomputed taxonomic profiles, for interactive browsing and for download 🧵 1/7 #microsky
metalog.embl.de
Metalog
Metalog is a repository of manually annotated metadata (or contextual data) for metagenomic sequencing data from across the globe.
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Quinn Sievers @quinnsievers.bsky.social · 06/07/2025
As a first-year oncology fellow at Memorial Sloan Kettering in New York City I had the privilege of rotating through all of the clinics. Lung, beast, ovarian, leukemia, lymphoma. 1/7
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Tami Lieberman @contaminatedsci.bsky.social · 30/06/2025
Our paper demonstrating that within-species warfare interactions are ecologically important on human skin is now published in Nature Micro! www.nature.com/articles/s41...
nature.com
Intraspecies warfare restricts strain coexistence in human skin microbiomes - Nature Microbiology
About 15,000 pairwise interactions within S. epidermidis from 18 people in 6 families reveal the antagonism and molecular trade-offs that shape the skin microbiota.
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Sebastian Schmidt @tsbschm.bsky.social · 27/06/2025
The team's first preprint is out! Led by ‪ ‪@vishnuprasoodanan.bsky.social‬‬ & @omaistrenko.bsky.social , we asked a question (almost) as old as microbiology: how many prokaryotic species exist on Earth? More specifically, how much diversity is "hiding" in existing metagenomic data? A 🧵.
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Elisabetta Cacace @elisca.bsky.social · 24/06/2025
Looking forward to #EESMicrobiology and excited to present our latest work on E. coli capsules on Friday! www.embl.org/about/info/c...
embl.org
New approaches and concepts in microbiology
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Elisabetta Cacace @elisca.bsky.social · 21/06/2025
Check out this framework for de novo protein design by @mjendrusch.bsky.social and Kashif Sadiq! Happy we could contribute with our favourite phage defence system.
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Gregor Rot 🌈 @grexor.bsky.social · 10/05/2025
Habemus pubScan! 🎉 Introducing pubScan, a new way to explore your PubMed publications through the lens of co-authorship. 🔍 Check it out at: pubscan.expressrna.org ❤️ Love it? Show your support by liking, sharing, and spreading the word. #pubscan
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Marjon de Vos @lizscurious.bsky.social · 08/05/2025
When things add up: environmental structure and microbial interactions drive antibiotic-resistance plasmid evolution. New paper from the lab, and the third chapter of Lars Zandbergen’s thesis! www.biorxiv.org/cgi/content/...
biorxiv.org
When things add up: environmental structure and microbial interactions drive antibiotic-resistance plasmid evolution
Antimicrobial resistance is recognized as a major global health threat. Pathogens can rapidly evolve resistance which diminishes the impact of antimicrobial treatments. The presence of other microbes ...
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Elisabetta Cacace @elisca.bsky.social · 05/05/2025
Our paper has been selected among Editors' Highlights for Microbiology! @natcomms.nature.com www.nature.com/collections/... 🧪🔬🧫
nature.com
Microbiology and infectious diseases
This page highlights recent articles on all aspects of bacteriology, mycology, parasitology and virology, covering the biology of pathogens, host-pathogen ...
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Reposted by Elisabetta Cacace
Lisa Maier Lab | Tübingen @lisamaierlab.bsky.social · 30/04/2025
Here are our ideas on developing tools and technologies for anaerobic bacteria! We hope you enjoy the read as much as we enjoyed brainstorming on the topic...
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Elisabetta Cacace @elisca.bsky.social · 24/04/2025
Do we really know the antibiotics that we already have? Check out our story on 60y old drug nitroxoline and its new tricks! @goetheuni.bsky.social @embl.org www.nature.com/articles/s41... + great piece from the synchrotron @esrf.fr where we chased nx effects on metals www.esrf.fr/home/news/ge...
nature.com
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The Dunn School, Oxford @dunnschool.bsky.social · 04/04/2025
New study by @mucosalimmunology.bsky.social (Dunn School and @ethzurich.bsky.social) with Médéric Diard (@biozentrum.unibas.ch) reveals how combining vaccines with friendly bacteria can boost vaccination efficacy and potentially reduce reliance on antibiotics www.path.ox.ac.uk/news-article...
path.ox.ac.uk
Boosting vaccines with harmless bacteria to fight intestinal pathogens - Dunn School
Published in Science, a ground-breaking study by the Slack group reveals how combining vaccines with friendly bacteria can boost vaccination efficacy and potentially reduce reliance on antibiotics.
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Annika Hausmann @hausmannannika.bsky.social · 23/03/2025
I am very excited to share our latest publication on the effect of systemic #endotoxin on intestinal #microbiota spearheaded by the brilliant Sanne Kroon at the Hardt lab @eth-dbiol.bsky.social @ethzurich.bsky.social @naturecomms.bsky.social 👉🏼 rdcu.be/eelLn
rdcu.be
Sublethal systemic LPS in mice enables gut-luminal pathogens to bloom through oxygen species-mediated microbiota inhibition
Nature Communications - Acute systemic immune activation may affect gut-luminal colonisation dynamics. Here, the authors show that LPS exposure in mice elevates gut-luminal oxygen species levels,...
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Shraddha Shitut @shetoot.bsky.social · 04/03/2025
Excited to share our paper published in @currentbiology.bsky.social that explores the consequences of having multiple genomes in a bacterial model system and it’s benefits in a multidrug environment ! www.cell.com/current-biol...
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Brochado Lab @brochadolab.bsky.social · 20/02/2025
Brochado and Maier labs in Germany are looking for a PhD student to study horizontal gene transfer in bacteria. ENDAMR Marie Curie doctoral network (endamr.eu) - an amazing opportunity to work with top scientists in the field all around Europe! www.cmfi.uni-tuebingen.de/mariecuriephd
endamr.eu
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Emma Slack @mucosalimmunology.bsky.social · 26/01/2025
Interested in microbial #metabolism, #mucosalbiology and #UTI? Then check out the open postdoctoral position in the Mucosal Immunology Group at ETH Zurich! NB: All applications must go via the ETH job portal: www.jobs.ethz.ch/job/view/JOP... Closing date: 24th Feburary 🧪🧫🔬
jobs.ethz.ch
Postdoctoral researcher –Understanding bacterial metabolism in the urinary tract
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STCmicrobeblog @stcmicrobeblog.bsky.social · 24/01/2025
"The world has been through anti-science cycles before" not microbiology related, but a 🧵 worth reading
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Typas Lab @typaslab.bsky.social · 16/12/2024
You want to learn about microbiology from a fantastic lineup of speakers on a beautiful Greek island? PhD students apply now for the @EMBO | @FEBSnews Lecture Course The New Microbiology! Registration: 1 Apr 2025 Course: 03 – 11 Sep 2025 | Spetses, Greece meetings.embo.org/event/25-new...
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Kai Kupferschmidt @kakape.bsky.social · 10/01/2025
More than 60 German-speaking universities and research institutes have just jointly announced they will cease activities on X because “the current orientation of the platform is not compatible with their core values” incl. scientific integrity, transparency and democratic discourse” 🧪
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Aude Bernheim @audeber.bsky.social · 09/01/2025
What is the diversity of antiphage systems out there ? We used protein and genomic language models (and defense score!) to start bringing some answers: >45 000 protein families. Leb by E. Mordret. www.biorxiv.org/content/10.1... Interactive UMAP to have fun mdmparis.github.io/antiphage-la...
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Typas Lab @typaslab.bsky.social · 23/12/2024
Excited to share our preprint with @savitski_lab led by @tarabartolec.bsky.social, @KMitosch & Clément Potel! We uncovered a mechanism by which the T7 phage broadly counteracts DNA-targeting bacterial defenses by deploying a loose cannon kinase in its genome @embl.org www.biorxiv.org/content/10.1...
biorxiv.org
Pervasive phosphorylation by phage T7 kinase disarms bacterial defenses
Bacteria and bacteriophages are in a constant arms race to develop bacterial defense and phage counter-defense systems. Currently known phage counter-defense systems are specific to (the activity of) ...
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Reposted by Elisabetta Cacace
Noah Whiteman @nkwhiteman.bsky.social · 20/12/2024
Delighted that @tarnopol.bsky.social’s paper (dissertation ch.) is online @currentbiology.bsky.social! “Experimental horizontal transfer of phage-derived genes to Drosophila confers innate immunity to parasitoids.” Phage toxin genes became a feature of insect immune systems millions of years ago…👇🏼
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Michael Fischbach @mfgrp.bsky.social · 11/12/2024
Today we report that an engineered skin bacterium, swabbed gently on the head of a mouse, can unleash a potent antibody response against a pathogen. Could lead to topical vaccines that are applied in a cream. @djenetbousbaine.bsky.social led the charge... @natureportfolio.bsky.social 1/55
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Elisabetta Cacace @elisca.bsky.social · 02/12/2024
Interested in antibiotic cross-resistance/sensitivity? Tired of experimental evolution? Then check our new story led by brilliant @nazgulsakenova.bsky.social, now out on Nature Microbiology @naturemicrobiol.bsky.social !
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Gabriele Corso @gcorso.bsky.social · 17/11/2024
Thrilled to announce Boltz-1, the first open-source and commercially available model to achieve AlphaFold3-level accuracy on biomolecular structure prediction! An exciting collaboration with Jeremy, Saro, and an amazing team at MIT and Genesis Therapeutics. A thread!
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STCmicrobeblog @stcmicrobeblog.bsky.social · 03/10/2024
Thoughts on O-Antigen Variation by Roberto — The O-side chains of lipopolysaccharides (LPS), the outer most feature of most Gram-negative's outer membrane, are highly variable in terms of their chain length and chemical composition. In my last post... Read more > tinyurl.com/54fzpdd9 #MicroSky
Schematic of LPS. Source: https://www.bmglabtech.com/en/blog/what-are-endotoxins/#pid=3
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Elisabetta Cacace @elisca.bsky.social · 20/04/2024
Trying to fit “high-throughput bacterial viability assay” in the acronym TETRIS
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Wolfgang Huber @wkhuber.bsky.social · 24/03/2024
Honed by many rounds of collaborative paper writing with PhD students and postdocs, my list of 24 scientific writing tips: www.huber.embl.de/group/posts/... Subjective and personal, but hopefully useful for somebody.
huber.embl.de
Huber Group @ EMBL - Scientific writing tips
An eclectic and subjective list
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Marjon de Vos @lizscurious.bsky.social · 01/02/2024
New collaborative work from our lab on the transmission of AMR in a community context. www.biorxiv.org/content/10.1... We find that Gram positive bacteria, particularly enterocci, increase the conjugation efficiency of uropathogenic E.coli.
biorxiv.org
Community context influences the conjugation efficiency of E. coli
bioRxiv - the preprint server for biology, operated by Cold Spring Harbor Laboratory, a research and educational institution
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Tami Lieberman @contaminatedsci.bsky.social · 21/12/2023
Please add microbiome-related conferences for 2024 in this thread. Thanks.
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Emma Slack @mucosalimmunology.bsky.social · 07/12/2023
I’ll be in Stockholm (Karolinska) for a seminar and for talking all things mucosal-immunology-related next week! news.ki.se/calendar/int... Zoom options also available I think. I’m looking forward to some exciting exchanges!
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Bram van Dijk 🏳️‍🌈 @bramvandijk.bsky.social · 19/11/2023
🦠 Do microbiomes have their own microbiomes? 🦠 Well... kind of. Much smaller than bacteria, there is a whole zoo of Darwinian entities that depend on microbial hosts. We could call these collectives "nanobiomes", and there's much to explore! 🧵 A thread (originally on Twitter, now on Bsky) ⬇️
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Chenxin Li, PhD @chenxinli2.bsky.social · 08/11/2023
Not enough people know about bioicons.com Open source vector graphics. Free alternatives to BioRender.
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Marco Galardini @mgalactus.bsky.social · 09/11/2023
We have published a manuscript describing a software tool to reduce ambiguity and improve interpretability in microbial GWAS, called panfeed. Here's a quick explainer: www.microbial-pangenomes-lab.org/2023/11/09/M... And here's the link to the paper: www.microbiologyresearch.org/content/jour...
microbiologyresearch.org
Reduced ambiguity and improved interpretability of bacterial genome-wide associations using gene-clu...
The wide adoption of bacterial genome sequencing and encoding both core and accessory genome variation using k-mers has allowed bacterial genome-wide association studies (GWAS) to identify genetic var...
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