Elisabetta Cacace
@elisca.bsky.social
Incoming SNSF Ambizione group leader at EPFL. Interested in bacteria-host interactions in health and disease. https://elisabettacacace.github.io/BHI-Lab/
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.
Nature Microbiology@natmicrobiol.nature.com · 3mo agoOut Now! In silico typing maps the natural diversity of Escherichia coli transporter-dependent capsules #MicroSky
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...
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...
doi.org
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/ 🧪
We are hiring for group leaders again — EBI is a great place to start your research group! embl.wd103.myworkdayjobs.com/EMBL/job/Hin...
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...
embl.wd103.myworkdayjobs.com
🚨 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
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...
rdcu.be
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...
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...
biorxiv.org
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...
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...
Job Details
my.corehr.com
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 💉🧬🦠🔬🧫
The Dunn School, Oxford@dunnschool.bsky.social · 11mo agoWe're hiring (again)! We are looking for an associate professor in cell and molecular biology, with a particular focus on immunology (defined broadly) If you have a great record and exciting plans, consider joining our thriving and welcoming department www.path.ox.ac.uk/vacancy/asso...
🎉 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
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 ...
doi.org
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... 🧪🧫🔬
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, ...
biorxiv.org
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
Metalog is a repository of manually annotated metadata (or contextual data) for metagenomic sequencing data from across the globe.
metalog.embl.de
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
Eric Topol@erictopol.bsky.social · last yr.Summary Table of the massive defunding of biomedical research in the United States www.nytimes.com/interactive/...
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...
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.
nature.com
Chris Mancuso@mancusosci.bsky.social · 2y agoWhy don’t people who live together have the same strains of microbes? Tami Lieberman (@contaminatedsci.bsky.social) and I put forward one underexplored reason in our new preprint: Intraspecies warfare restricts strain coexistence in human skin microbiomes
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 🧵.
bioRxiv Microbiology@biorxiv-microbiol.bsky.social · last yr.A census of hidden and discoverable microbial diversity beyond genome-centric approaches https://www.biorxiv.org/content/10.1101/2025.06.26.661807v1
Looking forward to #EESMicrobiology and excited to present our latest work on E. coli capsules on Friday! www.embl.org/about/info/c...
New approaches and concepts in microbiology
embl.org
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.
Michael Jendrusch@mjendrusch.bsky.social · last yr.Happy to announce the first paper from my PhD at Korbel group at @embl.org has finally been published: embopress.org/doi/full/10.1038… Collaborating with @typaslab.bsky.social, @hennig-lab.bsky.social and the EMBL PEPCF, we designed de novo inhibitors to a bacterial phage defense system 1/🧵
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
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/...
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 ...
biorxiv.org
Our paper has been selected among Editors' Highlights for Microbiology! @natcomms.nature.com www.nature.com/collections/... 🧪🔬🧫
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 ...
nature.com
Elisabetta Cacace@elisca.bsky.social · last yr.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...
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...
Thomas Clavel@tclavel.bsky.social · last yr.Here we share thoughts on next-gen cultivation: rdcu.be/ejPSb. Hope it helps 😄 Was fun to write with great colleagues @lisamaierlab.bsky.social @jselkrig.bsky.social @baerboletta.bsky.social @typaslab.bsky.social @mmmicrobiomelab.bsky.social @leibniz-dsmz.bsky.social @westermannlab.bsky.social
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
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...
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.
path.ox.ac.uk
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
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,...
rdcu.be
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...
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
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 🧪🧫🔬
Postdoctoral researcher –Understanding bacterial metabolism in the urinary tract
jobs.ethz.ch
"The world has been through anti-science cycles before" not microbiology related, but a 🧵 worth reading
a grassland chase 🌾🌾🌾🌾@chasesolidago.bsky.social · 2y agoThe world has been through anti-science cycles before, to disastrous results On a detour on my lit review, a mosey through the history of our familiar friend, the standard onion (Allium cepa) brought me right to one of botany's greatest cautionary tales of what happens when ideology overrides data
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...
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” 🧪
