Franklin Nobrega
@fnobrega.bsky.social
Phage Biology, Bacterial defense systems, CRISPR-Cas, Microbial communities, Mucus interactions
http://www.fnobregalab.org
http://www.klebphacol.org
http://www.phage-collection.org
http://www.fnobregalab.org
http://www.klebphacol.org
http://www.phage-collection.org
Pinned
Franklin Nobrega
@fnobrega.bsky.social
· Jul 28
Kiwa is a membrane-embedded defense supercomplex activated at phage attachment sites
Zhang, Todeschini, and Wu et al. show that the bacterial defense system Kiwa senses
phage attachment at the membrane and assembles a transmembrane complex that halts
infection by blocking phage DNA re...
www.cell.com
Thrilled to see our Kiwa story out today! A membrane-associated supercomplex that senses infection and blocks replication and transcription.
www.cell.com/cell/fulltex...
Huge congratulations to Yi and Zhiying for bringing it home, to Thomas for starting us off, and to all the collaborators.
www.cell.com/cell/fulltex...
Huge congratulations to Yi and Zhiying for bringing it home, to Thomas for starting us off, and to all the collaborators.
Reposted by Franklin Nobrega
🌍Open call: Junior Group Leader positions!
Join a world-class biomedical research institute at the heart of the Vienna BioCenter, where curiosity drives discovery.
Lead your own lab, pursue bold ideas, and shape the future of science at the IMP: www.imp.ac.at/career/open-...
Join a world-class biomedical research institute at the heart of the Vienna BioCenter, where curiosity drives discovery.
Lead your own lab, pursue bold ideas, and shape the future of science at the IMP: www.imp.ac.at/career/open-...
November 10, 2025 at 1:26 PM
🌍Open call: Junior Group Leader positions!
Join a world-class biomedical research institute at the heart of the Vienna BioCenter, where curiosity drives discovery.
Lead your own lab, pursue bold ideas, and shape the future of science at the IMP: www.imp.ac.at/career/open-...
Join a world-class biomedical research institute at the heart of the Vienna BioCenter, where curiosity drives discovery.
Lead your own lab, pursue bold ideas, and shape the future of science at the IMP: www.imp.ac.at/career/open-...
Reposted by Franklin Nobrega
Thinking about your first steps to independent research? We'd love to hear from you. More details below, or contact me directly for details - reposts appreciated!
www.nature.com/naturecareer...
www.nature.com/naturecareer...
Biomolecular Science Fellowship Day - St Andrews, Fife (GB) job with UNIVERSITY OF ST ANDREWS | 12848597
The School of Biology at the University of St Andrews is inviting applications from outstanding visionary Research Fellow and Future Leader candida...
www.nature.com
November 10, 2025 at 4:44 PM
Thinking about your first steps to independent research? We'd love to hear from you. More details below, or contact me directly for details - reposts appreciated!
www.nature.com/naturecareer...
www.nature.com/naturecareer...
Reposted by Franklin Nobrega
🔊 Applications for the tenure-track illuminate global challenge fellowships at Queen’s are now open!
Comes with 5 years protected research time, a PhD studentship, & 60k start-up. I had one of these before getting my FLF, happy to chat to anyone interested!
www.qub.ac.uk/Research/fel...
Comes with 5 years protected research time, a PhD studentship, & 60k start-up. I had one of these before getting my FLF, happy to chat to anyone interested!
www.qub.ac.uk/Research/fel...
Our Illuminate Global Challenges Fellowships | Research | Queen's University Belfast
www.qub.ac.uk
October 30, 2025 at 12:19 PM
🔊 Applications for the tenure-track illuminate global challenge fellowships at Queen’s are now open!
Comes with 5 years protected research time, a PhD studentship, & 60k start-up. I had one of these before getting my FLF, happy to chat to anyone interested!
www.qub.ac.uk/Research/fel...
Comes with 5 years protected research time, a PhD studentship, & 60k start-up. I had one of these before getting my FLF, happy to chat to anyone interested!
www.qub.ac.uk/Research/fel...
Reposted by Franklin Nobrega
An Asgard archaeon with internal membrane compartments
Brilliant study led by @fmacleod.bsky.social and Andriko von Kügelgen. Tight collaboration with @buzzbaum.bsky.social and lab. Congrats to all authors!
www.biorxiv.org/content/10.1...
Brilliant study led by @fmacleod.bsky.social and Andriko von Kügelgen. Tight collaboration with @buzzbaum.bsky.social and lab. Congrats to all authors!
www.biorxiv.org/content/10.1...
November 7, 2025 at 10:44 AM
An Asgard archaeon with internal membrane compartments
Brilliant study led by @fmacleod.bsky.social and Andriko von Kügelgen. Tight collaboration with @buzzbaum.bsky.social and lab. Congrats to all authors!
www.biorxiv.org/content/10.1...
Brilliant study led by @fmacleod.bsky.social and Andriko von Kügelgen. Tight collaboration with @buzzbaum.bsky.social and lab. Congrats to all authors!
www.biorxiv.org/content/10.1...
Reposted by Franklin Nobrega
Re-boosting! The Dept. of Microbiology 🧫 at the University of Tennessee is hiring two 9-month faculty! Come join a vibrant and growing department located in the foothills of the Smoky Mountains! #microsky
Come join us in Knoxville!
The Dept. of Microbiology 🧫🦠 at the University of Tennessee is hiring 2 Assistant Professors (tenure track, 9-month appt.).
Microbial Drivers of Chronic Disease: apply.interfolio.com/173153Quantitative Microbe-Plant-Environment Interactions: apply.interfolio.com/173345
The Dept. of Microbiology 🧫🦠 at the University of Tennessee is hiring 2 Assistant Professors (tenure track, 9-month appt.).
Microbial Drivers of Chronic Disease: apply.interfolio.com/173153Quantitative Microbe-Plant-Environment Interactions: apply.interfolio.com/173345
November 6, 2025 at 1:07 PM
Re-boosting! The Dept. of Microbiology 🧫 at the University of Tennessee is hiring two 9-month faculty! Come join a vibrant and growing department located in the foothills of the Smoky Mountains! #microsky
Reposted by Franklin Nobrega
🚨New preprint out!
We present a foundational genomic resource of human gut microbiome viruses. It delivers high-quality, deeply curated data spanning taxonomy, predicted hosts, structures, and functions, providing a reference for gut virome research. (1/8)
www.biorxiv.org/content/10.1...
We present a foundational genomic resource of human gut microbiome viruses. It delivers high-quality, deeply curated data spanning taxonomy, predicted hosts, structures, and functions, providing a reference for gut virome research. (1/8)
www.biorxiv.org/content/10.1...
November 6, 2025 at 5:26 PM
🚨New preprint out!
We present a foundational genomic resource of human gut microbiome viruses. It delivers high-quality, deeply curated data spanning taxonomy, predicted hosts, structures, and functions, providing a reference for gut virome research. (1/8)
www.biorxiv.org/content/10.1...
We present a foundational genomic resource of human gut microbiome viruses. It delivers high-quality, deeply curated data spanning taxonomy, predicted hosts, structures, and functions, providing a reference for gut virome research. (1/8)
www.biorxiv.org/content/10.1...
Reposted by Franklin Nobrega
After 5 years of waiting, the new #CRISPR classification by Makarova et al. is out @natmicrobiol.nature.com www.nature.com/articles/s41...
An updated evolutionary classification of CRISPR–Cas systems including rare variants - Nature Microbiology
An exploration of previously undescribed variants from the long tail of the CRISPR–Cas distribution.
www.nature.com
November 6, 2025 at 1:49 PM
After 5 years of waiting, the new #CRISPR classification by Makarova et al. is out @natmicrobiol.nature.com www.nature.com/articles/s41...
Reposted by Franklin Nobrega
Bacteria can sense when a virus starts shredding their genome — by detecting methylated mononucleotides.
Here’s the story of how we discovered the Metis defense system 👇
www.biorxiv.org/content/10.1...
Here’s the story of how we discovered the Metis defense system 👇
www.biorxiv.org/content/10.1...
November 6, 2025 at 5:00 AM
Bacteria can sense when a virus starts shredding their genome — by detecting methylated mononucleotides.
Here’s the story of how we discovered the Metis defense system 👇
www.biorxiv.org/content/10.1...
Here’s the story of how we discovered the Metis defense system 👇
www.biorxiv.org/content/10.1...
Reposted by Franklin Nobrega
If you're looking for a faculty position at the intersection of ecology and computing (both broadly defined), please apply to this joint search between the CEE Department and the College of Computing at MIT: cee.mit.edu/people/share...
Faculty Position in the Department of Civil and Environmental Engineering and the Schwarzman College of Computing - cee.mit.edu
The Department of Civil and Environmental Engineering (CEE), together with the Schwarzman College of Computing (SCC) at the Massachusetts Institute of Technology (MIT) in Cambridge MA, seeks candidate...
cee.mit.edu
November 5, 2025 at 7:27 PM
If you're looking for a faculty position at the intersection of ecology and computing (both broadly defined), please apply to this joint search between the CEE Department and the College of Computing at MIT: cee.mit.edu/people/share...
Reposted by Franklin Nobrega
Single-particle genomics uncovers abundant non-canonical marine viruses from nanolitre volumes
Very cool paper and method. I was looking forward to this coming out of preprint (short thread below on why)
www.nature.com/articles/s41...
Very cool paper and method. I was looking forward to this coming out of preprint (short thread below on why)
www.nature.com/articles/s41...
Single-particle genomics uncovers abundant non-canonical marine viruses from nanolitre volumes - Nature Microbiology
Environmental micro-compartment genomics provides efficient and high-throughput single-particle DNA sequencing that captures overlooked members of microbial communities.
www.nature.com
November 5, 2025 at 3:34 PM
Single-particle genomics uncovers abundant non-canonical marine viruses from nanolitre volumes
Very cool paper and method. I was looking forward to this coming out of preprint (short thread below on why)
www.nature.com/articles/s41...
Very cool paper and method. I was looking forward to this coming out of preprint (short thread below on why)
www.nature.com/articles/s41...
Reposted by Franklin Nobrega
There is now a complete tutorial in the GCUA distribution. If you are running bioinformatics practicals or workshops and you want a complete out-of-the-box simple tutorial, with theory and nice outputs, then think about including this in your curriculum: github.com/mol-evol/gcua #bioinformatics
GitHub - mol-evol/gcua: GCUA - General Codon Usage Analysis (v2)
GCUA - General Codon Usage Analysis (v2). Contribute to mol-evol/gcua development by creating an account on GitHub.
github.com
November 5, 2025 at 3:36 PM
There is now a complete tutorial in the GCUA distribution. If you are running bioinformatics practicals or workshops and you want a complete out-of-the-box simple tutorial, with theory and nice outputs, then think about including this in your curriculum: github.com/mol-evol/gcua #bioinformatics
Reposted by Franklin Nobrega
Exciting news! I have two positions open in my lab at the UoManchester: one PDRA and one Research Tech.
Join our team to study evolutionary mycology and help us understand antifungal resistance in fungal pathogens. A fantastic opportunity to join the brilliant Manchester Fungal Infection Group!
Join our team to study evolutionary mycology and help us understand antifungal resistance in fungal pathogens. A fantastic opportunity to join the brilliant Manchester Fungal Infection Group!
November 5, 2025 at 3:35 PM
Exciting news! I have two positions open in my lab at the UoManchester: one PDRA and one Research Tech.
Join our team to study evolutionary mycology and help us understand antifungal resistance in fungal pathogens. A fantastic opportunity to join the brilliant Manchester Fungal Infection Group!
Join our team to study evolutionary mycology and help us understand antifungal resistance in fungal pathogens. A fantastic opportunity to join the brilliant Manchester Fungal Infection Group!
Reposted by Franklin Nobrega
🚨 NEW: The majority holder of the world's genetic sequence data is a bad actor who can cut off access to critics and competing services. We've tolerated this for years, and now it threatens the pandemic treaty. Time for WHO to step in. With @ctrlalttim.com: www.thinkglobalhealth.org/article/to-f...
To Finish the Pandemic Agreement, WHO Needs a Trustworthy Viral Database | Think Global Health
Online platforms for sharing virus sequences are in disarray. The World Health Organization has a chance to build something new
www.thinkglobalhealth.org
November 5, 2025 at 3:31 PM
🚨 NEW: The majority holder of the world's genetic sequence data is a bad actor who can cut off access to critics and competing services. We've tolerated this for years, and now it threatens the pandemic treaty. Time for WHO to step in. With @ctrlalttim.com: www.thinkglobalhealth.org/article/to-f...
Reposted by Franklin Nobrega
The FPbase spectra viewer just had it's biggest software refactor in 6 years. It *should* be largely invisible to the end user (hopefully just faster and less buggy). Please let me know if you find any issues as you use it!
www.fpbase.org/spectra/
www.fpbase.org/spectra/
FPbase Fluorescence Spectra Viewer
An interactive fluorescence spectra viewer to evaluate the spectral properties of fluorescent proteins, organic dyes, filters, and detectors.
www.fpbase.org
November 4, 2025 at 3:03 PM
The FPbase spectra viewer just had it's biggest software refactor in 6 years. It *should* be largely invisible to the end user (hopefully just faster and less buggy). Please let me know if you find any issues as you use it!
www.fpbase.org/spectra/
www.fpbase.org/spectra/
Reposted by Franklin Nobrega
Hi everyone, a few years ago, we started a list of labs studying bacterial immunty for students, editors, conference organizers... (currently n=79).
Update time ! Send me a message to 1) add your lab or others 2) Correct info
docs.google.com/spreadsheets...
#Phagesky #Microsky
Update time ! Send me a message to 1) add your lab or others 2) Correct info
docs.google.com/spreadsheets...
#Phagesky #Microsky
Labs in bacterial immunity
docs.google.com
November 4, 2025 at 3:06 PM
Hi everyone, a few years ago, we started a list of labs studying bacterial immunty for students, editors, conference organizers... (currently n=79).
Update time ! Send me a message to 1) add your lab or others 2) Correct info
docs.google.com/spreadsheets...
#Phagesky #Microsky
Update time ! Send me a message to 1) add your lab or others 2) Correct info
docs.google.com/spreadsheets...
#Phagesky #Microsky
Reposted by Franklin Nobrega
Our department is hiring for 4 faculty positions! Come join a growing and dynamic group of scientists in a fun and engaging department!
Assistant Professor of Cell Biology: bit.ly/4okizhq
Assistant Professor of Microbiology:bit.ly/48ZVHz1
2 Lecturers of Microbiology: bit.ly/4qCwukr
Assistant Professor of Cell Biology: bit.ly/4okizhq
Assistant Professor of Microbiology:bit.ly/48ZVHz1
2 Lecturers of Microbiology: bit.ly/4qCwukr
November 3, 2025 at 7:31 PM
Our department is hiring for 4 faculty positions! Come join a growing and dynamic group of scientists in a fun and engaging department!
Assistant Professor of Cell Biology: bit.ly/4okizhq
Assistant Professor of Microbiology:bit.ly/48ZVHz1
2 Lecturers of Microbiology: bit.ly/4qCwukr
Assistant Professor of Cell Biology: bit.ly/4okizhq
Assistant Professor of Microbiology:bit.ly/48ZVHz1
2 Lecturers of Microbiology: bit.ly/4qCwukr
Reposted by Franklin Nobrega
Our new paper maps the tRNA modification landscape in Vibrio cholerae! 💫
We describe differences from E. coli and discuss links to decoding of stress-related codons 🦠
Huge thanks to amazing co-authors and collaborators!
@plos.org #rnasky #microsky #tRNAmodifications
We describe differences from E. coli and discuss links to decoding of stress-related codons 🦠
Huge thanks to amazing co-authors and collaborators!
@plos.org #rnasky #microsky #tRNAmodifications
The tRNA epitranscriptomic landscape and RNA modification enzymes in Vibrio cholerae
Author summary This study charts the first genome-wide map of transfer RNA (tRNA) modifications in the cholera pathogen, Vibrio cholerae, revealing how chemical marks on tRNAs shape translation and st...
journals.plos.org
November 3, 2025 at 11:58 PM
Our new paper maps the tRNA modification landscape in Vibrio cholerae! 💫
We describe differences from E. coli and discuss links to decoding of stress-related codons 🦠
Huge thanks to amazing co-authors and collaborators!
@plos.org #rnasky #microsky #tRNAmodifications
We describe differences from E. coli and discuss links to decoding of stress-related codons 🦠
Huge thanks to amazing co-authors and collaborators!
@plos.org #rnasky #microsky #tRNAmodifications
Reposted by Franklin Nobrega
Great to see this finally published!
Metalog: curated and harmonised contextual data for global metagenomics samples
now out in @narjournal.bsky.social
academic.oup.com/nar/advance-...
Metalog: curated and harmonised contextual data for global metagenomics samples
now out in @narjournal.bsky.social
academic.oup.com/nar/advance-...
Metalog: curated and harmonised contextual data for global metagenomics samples
Abstract. Metagenomic sequencing enables the in-depth study of microbes and their functions in humans, animals, and the environment. While sequencing data
academic.oup.com
October 31, 2025 at 3:16 PM
Great to see this finally published!
Metalog: curated and harmonised contextual data for global metagenomics samples
now out in @narjournal.bsky.social
academic.oup.com/nar/advance-...
Metalog: curated and harmonised contextual data for global metagenomics samples
now out in @narjournal.bsky.social
academic.oup.com/nar/advance-...
Reposted by Franklin Nobrega
We've just launched the first large, site-less (home, direct to participant) randomized trial for treatment of #LongCovid, testing tirzepatide (a GLP-1 drug) vs placebo. Please help spread the word
www.scripps.edu/news-and-eve...
www.scripps.edu/news-and-eve...
Scripps Research scientists launch new digital clinical trial to test repurposed drug for long COVID symptom relief
www.scripps.edu
October 31, 2025 at 5:07 PM
We've just launched the first large, site-less (home, direct to participant) randomized trial for treatment of #LongCovid, testing tirzepatide (a GLP-1 drug) vs placebo. Please help spread the word
www.scripps.edu/news-and-eve...
www.scripps.edu/news-and-eve...
Reposted by Franklin Nobrega
📣 Open position:
We are looking for a new #ScientificLead for the #SILVA database 🧬🖥️, who will be responsible for guiding the development of this important resource and for curating the #SILVA taxonomy🌳.
Read and share!
👉 www.dsmz.de/dsmz/career/...
🧪🦠🌱🦋💽
We are looking for a new #ScientificLead for the #SILVA database 🧬🖥️, who will be responsible for guiding the development of this important resource and for curating the #SILVA taxonomy🌳.
Read and share!
👉 www.dsmz.de/dsmz/career/...
🧪🦠🌱🦋💽
October 31, 2025 at 5:41 PM
📣 Open position:
We are looking for a new #ScientificLead for the #SILVA database 🧬🖥️, who will be responsible for guiding the development of this important resource and for curating the #SILVA taxonomy🌳.
Read and share!
👉 www.dsmz.de/dsmz/career/...
🧪🦠🌱🦋💽
We are looking for a new #ScientificLead for the #SILVA database 🧬🖥️, who will be responsible for guiding the development of this important resource and for curating the #SILVA taxonomy🌳.
Read and share!
👉 www.dsmz.de/dsmz/career/...
🧪🦠🌱🦋💽
Reposted by Franklin Nobrega
Excited to share: DNA glycosylases are diverse antiviral effectors. They recognize phage base modifications and initiate genome destruction. A structure‑guided approach made the scope of this discovery possible! 🧪 #phagesky doi.org/10.1101/2025... #phage #microbiology
Antiviral Defence is a Conserved Function of Diverse DNA Glycosylases
Bacteria are frequently attacked by viruses, known as phages, and rely on diverse defence systems like restriction endonucleases and CRISPR-Cas to survive. While phages can evade these defences by cov...
doi.org
October 30, 2025 at 12:16 PM
Excited to share: DNA glycosylases are diverse antiviral effectors. They recognize phage base modifications and initiate genome destruction. A structure‑guided approach made the scope of this discovery possible! 🧪 #phagesky doi.org/10.1101/2025... #phage #microbiology
Reposted by Franklin Nobrega
Please RT. Post-doc opportunity alert! 💥 closing 10th December.. Come join our team (www.thelowlab.org) at Imperial, London, working on the structure and mechanism of bacterial secretion systems.
For more details and to apply please see
www.imperial.ac.uk/jobs/search-...
For more details and to apply please see
www.imperial.ac.uk/jobs/search-...
October 29, 2025 at 5:11 PM
Please RT. Post-doc opportunity alert! 💥 closing 10th December.. Come join our team (www.thelowlab.org) at Imperial, London, working on the structure and mechanism of bacterial secretion systems.
For more details and to apply please see
www.imperial.ac.uk/jobs/search-...
For more details and to apply please see
www.imperial.ac.uk/jobs/search-...
Reposted by Franklin Nobrega
@prczhaoyansong.bsky.social’s deep dive into the dark matter of compost communities is now out 🎉 Genomic islands hijack jumbo phages—whose capsids enable transfer of large tracts of DNA—shedding new light on the scale & scope of phage-mediated gene flow 😎
www.pnas.org/doi/10.1073/...
www.pnas.org/doi/10.1073/...
Jumbo phage–mediated transduction of genomic islands | PNAS
Bacteria acquire new genes by horizontal gene transfer, typically mediated by mobile
genetic elements (MGEs). While plasmids, bacteriophages, and c...
www.pnas.org
October 28, 2025 at 6:36 PM
@prczhaoyansong.bsky.social’s deep dive into the dark matter of compost communities is now out 🎉 Genomic islands hijack jumbo phages—whose capsids enable transfer of large tracts of DNA—shedding new light on the scale & scope of phage-mediated gene flow 😎
www.pnas.org/doi/10.1073/...
www.pnas.org/doi/10.1073/...
Reposted by Franklin Nobrega
#microsky #mevosky @spp2389.bsky.social
A PhD position is available in my lab to work on:
Emergence and self-organisation of bacterial metabolism in consortia of cross-feeding bacteria.
Please RT
Deadline: 12.11.25
More infos 👇
shorturl.at/rAKAT
A PhD position is available in my lab to work on:
Emergence and self-organisation of bacterial metabolism in consortia of cross-feeding bacteria.
Please RT
Deadline: 12.11.25
More infos 👇
shorturl.at/rAKAT
October 28, 2025 at 8:43 AM
#microsky #mevosky @spp2389.bsky.social
A PhD position is available in my lab to work on:
Emergence and self-organisation of bacterial metabolism in consortia of cross-feeding bacteria.
Please RT
Deadline: 12.11.25
More infos 👇
shorturl.at/rAKAT
A PhD position is available in my lab to work on:
Emergence and self-organisation of bacterial metabolism in consortia of cross-feeding bacteria.
Please RT
Deadline: 12.11.25
More infos 👇
shorturl.at/rAKAT
Reposted by Franklin Nobrega
www.biorxiv.org/content/10.1...
#phagesky #phage #MGE a prophage-encoded endomuclease antagonises plasmid transmission
#phagesky #phage #MGE a prophage-encoded endomuclease antagonises plasmid transmission
A family of endonucleases that block nanotube-mediated plasmid dissemination
Small non-conjugative plasmids constitute a substantial portion of the bacterial mobile genome, driving the dissemination of beneficial genes, with their transfer primarily attributed to transformatio...
www.biorxiv.org
October 27, 2025 at 1:42 PM
www.biorxiv.org/content/10.1...
#phagesky #phage #MGE a prophage-encoded endomuclease antagonises plasmid transmission
#phagesky #phage #MGE a prophage-encoded endomuclease antagonises plasmid transmission