Elisabetta Cacace
@elisca.bsky.social
MD, PhD. Postdoc in Slack and Sunagawa labs, ETH Institute of Microbiology. Typas lab alumna.
Bacteria as friends and foes.
Bacteria as friends and foes.
Pinned
Elisabetta Cacace
@elisca.bsky.social
· Aug 15
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, ...
www.biorxiv.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...
🧪🧫🔬
Great genomics - glycobiology synergy in Sunagawa and Slack groups at ETH!
www.biorxiv.org/content/10.1...
🧪🧫🔬
Reposted by Elisabetta Cacace
🚨 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
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
November 7, 2025 at 9:15 AM
🚨 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
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
Reposted by Elisabetta Cacace
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...
www.biorxiv.org
August 14, 2025 at 7:31 AM
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...
Reposted by Elisabetta Cacace
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...
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...
October 13, 2025 at 7:48 AM
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...
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...
Reposted by Elisabetta Cacace
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/pls/uoxrecru...
Job Details
my.corehr.com
September 25, 2025 at 2:31 PM
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/pls/uoxrecru...
Reposted by Elisabetta Cacace
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 💉🧬🦠🔬🧫
We'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 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...
September 10, 2025 at 8:11 PM
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 💉🧬🦠🔬🧫
Reposted by Elisabetta Cacace
🎉 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"
👉 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
August 24, 2025 at 11:29 AM
🎉 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"
👉 doi.org/10.1101/2025...
#FirstPreprint #StemCells #Metabolism #Epigenetics #AcetylCoA #HBP #Pluripotency #NewScience
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...
🧪🧫🔬
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, ...
www.biorxiv.org
August 15, 2025 at 1:55 PM
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...
🧪🧫🔬
Great genomics - glycobiology synergy in Sunagawa and Slack groups at ETH!
www.biorxiv.org/content/10.1...
🧪🧫🔬
Reposted by Elisabetta Cacace
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
#microsky
Metalog
Metalog is a repository of manually annotated metadata (or contextual data) for metagenomic sequencing data from across the globe.
metalog.embl.de
August 15, 2025 at 8:07 AM
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
#microsky
Reposted by Elisabetta Cacace
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
Summary Table of the massive defunding of biomedical research in the United States
www.nytimes.com/interactive/...
www.nytimes.com/interactive/...
July 6, 2025 at 4:33 PM
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
Reposted by Elisabetta Cacace
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...
June 30, 2025 at 12:26 PM
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...
Reposted by Elisabetta Cacace
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 🧵.
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 🧵.
A census of hidden and discoverable microbial diversity beyond genome-centric approaches https://www.biorxiv.org/content/10.1101/2025.06.26.661807v1
June 27, 2025 at 8:10 PM
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 🧵.
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 🧵.
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
www.embl.org
June 24, 2025 at 6:57 AM
Looking forward to #EESMicrobiology and excited to present our latest work on E. coli capsules on Friday! www.embl.org/about/info/c...
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.
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/🧵
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/🧵
June 21, 2025 at 5:29 PM
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.
Reposted by Elisabetta Cacace
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
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
May 10, 2025 at 7:22 AM
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
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
Reposted by Elisabetta Cacace
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/...
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 ...
www.biorxiv.org
May 8, 2025 at 9:36 AM
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/...
New paper from the lab, and the third chapter of Lars Zandbergen’s thesis!
www.biorxiv.org/cgi/content/...
Our paper has been selected among Editors' Highlights for Microbiology! @natcomms.nature.com www.nature.com/collections/... 🧪🔬🧫
May 5, 2025 at 9:44 AM
Our paper has been selected among Editors' Highlights for Microbiology! @natcomms.nature.com www.nature.com/collections/... 🧪🔬🧫
Reposted by Elisabetta Cacace
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...
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
Enabling next-generation anaerobic cultivation through biotechnology to advance functional microbiome research
Nature Biotechnology - Overcoming key hurdles for the development of next-generation anaerobic cultivation methods could have major impacts on microbial community research and applications.
rdcu.be
April 30, 2025 at 6:53 AM
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...
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...
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...
www.nature.com
April 24, 2025 at 7:16 AM
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...
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...
Reposted by Elisabetta Cacace
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...
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.
www.path.ox.ac.uk
April 4, 2025 at 10:30 AM
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...
www.path.ox.ac.uk/news-article...
Reposted by Elisabetta Cacace
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/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
March 23, 2025 at 9:15 AM
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/eelLn
Reposted by Elisabetta Cacace
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...
March 4, 2025 at 5:12 PM
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...
Reposted by Elisabetta Cacace
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
www.cmfi.uni-tuebingen.de/mariecuriephd
endamr.eu
February 20, 2025 at 9:15 AM
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
www.cmfi.uni-tuebingen.de/mariecuriephd
Reposted by Elisabetta Cacace
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
🧪🧫🔬
www.jobs.ethz.ch/job/view/JOP...
Closing date: 24th Feburary
🧪🧫🔬
Postdoctoral researcher –Understanding bacterial metabolism in the urinary tract
www.jobs.ethz.ch
January 26, 2025 at 1:25 PM
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
🧪🧫🔬
www.jobs.ethz.ch/job/view/JOP...
Closing date: 24th Feburary
🧪🧫🔬
Reposted by Elisabetta Cacace
"The world has been through anti-science cycles before"
not microbiology related, but a 🧵 worth reading
not microbiology related, but a 🧵 worth reading
The 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
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
January 24, 2025 at 10:09 AM
"The world has been through anti-science cycles before"
not microbiology related, but a 🧵 worth reading
not microbiology related, but a 🧵 worth reading
Reposted by Elisabetta Cacace
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...
Registration: 1 Apr 2025
Course: 03 – 11 Sep 2025 | Spetses, Greece
meetings.embo.org/event/25-new...
December 16, 2024 at 8:43 AM
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...
Registration: 1 Apr 2025
Course: 03 – 11 Sep 2025 | Spetses, Greece
meetings.embo.org/event/25-new...