João Botelho
@joaoftsbotelho.bsky.social
CEEC Researcher at UCP 🇵🇹
https://sciproj.ptcris.pt/en/12767EEC
Before: Maria Zambrano fellow @cbgpmadrid.bsky.social 🇪🇸 and postdoc at Max Planck Institute 🇩🇪
MGEs, AMR, defense systems
https://scholar.google.com/citations?user=_Sz69QgAAAAJ&hl=en
https://sciproj.ptcris.pt/en/12767EEC
Before: Maria Zambrano fellow @cbgpmadrid.bsky.social 🇪🇸 and postdoc at Max Planck Institute 🇩🇪
MGEs, AMR, defense systems
https://scholar.google.com/citations?user=_Sz69QgAAAAJ&hl=en
Reposted by João Botelho
🚨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 João Botelho
We're thrilled to announce SeqHub, an AI-enabled platform for biological sequence analysis. SeqHub brings together sequence search, genome annotation, and data sharing in one place.
October 28, 2025 at 1:47 PM
We're thrilled to announce SeqHub, an AI-enabled platform for biological sequence analysis. SeqHub brings together sequence search, genome annotation, and data sharing in one place.
Reposted by João Botelho
📣 PhD opportunity led by @madhvimenon.bsky.social with @kathelse.bsky.social , @tracyh9494.bsky.social , and me open now:
"Sex Differences in Immune Responses to Infection: The Role of the Microbiota in Shaping Lymphocyte Dynamics"
apps due 15 November 2025 📣
www.findaphd.com/phds/project...
"Sex Differences in Immune Responses to Infection: The Role of the Microbiota in Shaping Lymphocyte Dynamics"
apps due 15 November 2025 📣
www.findaphd.com/phds/project...
(Bicentenary) Sex Differences in Immune Responses to Infection: The Role of the Microbiota in Shaping Lymphocyte Dynamics at The University of Manchester on FindAPhD.com
PhD Project - (Bicentenary) Sex Differences in Immune Responses to Infection: The Role of the Microbiota in Shaping Lymphocyte Dynamics at The University of Manchester, listed on FindAPhD.com
www.findaphd.com
October 27, 2025 at 3:24 PM
📣 PhD opportunity led by @madhvimenon.bsky.social with @kathelse.bsky.social , @tracyh9494.bsky.social , and me open now:
"Sex Differences in Immune Responses to Infection: The Role of the Microbiota in Shaping Lymphocyte Dynamics"
apps due 15 November 2025 📣
www.findaphd.com/phds/project...
"Sex Differences in Immune Responses to Infection: The Role of the Microbiota in Shaping Lymphocyte Dynamics"
apps due 15 November 2025 📣
www.findaphd.com/phds/project...
Reposted by João Botelho
Is a healthy microbiome one that is rich in phages? 🦠 Excited to share our paper out in Lancet Microbe with @bkoskella.bsky.social & @dholtappels.bsky.social where we test whether virome diversity can be used a broad signature of microbiome health 📈
New research article
Evaluation of bacteriophages as a signature of #microbiome health: a systematic review and meta-analysis
www.thelancet.com/journals/lan...
#IDSky #ClinMicro #ViroSky #Phage #OpenAccess #OA
Evaluation of bacteriophages as a signature of #microbiome health: a systematic review and meta-analysis
www.thelancet.com/journals/lan...
#IDSky #ClinMicro #ViroSky #Phage #OpenAccess #OA
October 10, 2025 at 1:12 PM
Is a healthy microbiome one that is rich in phages? 🦠 Excited to share our paper out in Lancet Microbe with @bkoskella.bsky.social & @dholtappels.bsky.social where we test whether virome diversity can be used a broad signature of microbiome health 📈
Reposted by João Botelho
Imagine we could travel back in time ⏪⌛️to explore the world of bacterial pathogens before humans discovered and industrialised antibiotics
We just did that to study the history of #AMR spread @science.org
doi.org/10.1126/scie...
If you like time travel & biology, this 🧵is for you👇
We just did that to study the history of #AMR spread @science.org
doi.org/10.1126/scie...
If you like time travel & biology, this 🧵is for you👇
Pre- and postantibiotic epoch: The historical spread of antimicrobial resistance
Plasmids are now the primary vectors of antimicrobial resistance, but our understanding of how human industrialisation of antibiotics influenced their evolution is limited by a paucity of data predati...
doi.org
October 6, 2025 at 10:42 AM
Imagine we could travel back in time ⏪⌛️to explore the world of bacterial pathogens before humans discovered and industrialised antibiotics
We just did that to study the history of #AMR spread @science.org
doi.org/10.1126/scie...
If you like time travel & biology, this 🧵is for you👇
We just did that to study the history of #AMR spread @science.org
doi.org/10.1126/scie...
If you like time travel & biology, this 🧵is for you👇
Reposted by João Botelho
OK, here it is. Come work with me at the University of Liverpool making ALL THE AI models from ALL THE prokaryote pangenome data. Heck, we will make models from ALL the pangenomes, even eukaryotes!!! (link below👇) 1/4
September 25, 2025 at 9:49 AM
OK, here it is. Come work with me at the University of Liverpool making ALL THE AI models from ALL THE prokaryote pangenome data. Heck, we will make models from ALL the pangenomes, even eukaryotes!!! (link below👇) 1/4
Incredibly proud to be named one of the World’s Top 2% Scientists for 2025 by Stanford/Elsevier, alongside my brilliant colleagues from CBQF at UCP!
cbqf.esb.ucp.pt/news/eight-c...
cbqf.esb.ucp.pt/news/eight-c...
CBQF | Centre for Biotechnology and Fine Chemistry
Eight researchers from the Centre for Biotechnology and Fine Chemistry (CBQF) at the Faculty of Biotechnology of Universidade Católica Portuguesa are listed among the world’s most cited scientists in ...
cbqf.esb.ucp.pt
October 1, 2025 at 8:10 PM
Incredibly proud to be named one of the World’s Top 2% Scientists for 2025 by Stanford/Elsevier, alongside my brilliant colleagues from CBQF at UCP!
cbqf.esb.ucp.pt/news/eight-c...
cbqf.esb.ucp.pt/news/eight-c...
Exclusion systems preserve host cell homeostasis and fitness, ensuring successful dissemination of conjugative plasmids and associated resistance genes url: academic.oup.com/nar/article/...
Exclusion systems preserve host cell homeostasis and fitness, ensuring successful dissemination of conjugative plasmids and associated resistance genes
Abstract. Plasmid conjugation is a major driver of antibiotic resistance dissemination in bacteria. In addition to genes required for transfer and maintena
academic.oup.com
September 19, 2025 at 9:30 AM
Exclusion systems preserve host cell homeostasis and fitness, ensuring successful dissemination of conjugative plasmids and associated resistance genes url: academic.oup.com/nar/article/...
Reposted by João Botelho
Feels surreal to say but: I'm hiring! If you are or know anyone interested in looking at the evolution of phage resistance using A. baumannii and natural transformation, then this might be for you
www.jobbnorge.no/en/available...
www.jobbnorge.no/en/available...
Research position in Microbial Pharmacology and Population Biology (282139) | UiT The Arctic University of Norway
Job title: Research position in Microbial Pharmacology and Population Biology (282139), Employer: UiT The Arctic University of Norway, Deadline: Wednesday, August 27, 2025
www.jobbnorge.no
August 8, 2025 at 7:52 AM
Feels surreal to say but: I'm hiring! If you are or know anyone interested in looking at the evolution of phage resistance using A. baumannii and natural transformation, then this might be for you
www.jobbnorge.no/en/available...
www.jobbnorge.no/en/available...
Reposted by João Botelho
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.
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
July 28, 2025 at 7:43 PM
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 João Botelho
The preprint of my first article is available on bioRxiv! We use a transposon ecology framework to analyze the distribution of insertion sequences within prokaryotic genomes. We characterize their ecological niche and show evidence of niche construction 🧪🧬💻
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Unwelcome guests: characterizing the ecological niche of insertion sequences within prokaryotic genomes
Insertion sequences (ISs) are widespread prokaryotic transposable elements, often regarded as genomic parasites that primarily cause deleterious mutations. However, they can also promote adaptive chan...
www.biorxiv.org
July 28, 2025 at 2:19 PM
The preprint of my first article is available on bioRxiv! We use a transposon ecology framework to analyze the distribution of insertion sequences within prokaryotic genomes. We characterize their ecological niche and show evidence of niche construction 🧪🧬💻
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Reposted by João Botelho
Fold first, ask later: structure-informed function annotation of Pseudomonas phage proteins
Structural predictions to improve #phage genome annotation!
@hannelorelongin.bsky.social @gbouras13.bsky.social y.social @susiegriggo.bsky.social @veravannoort.bsky.social
www.biorxiv.org/content/10.1...
Structural predictions to improve #phage genome annotation!
@hannelorelongin.bsky.social @gbouras13.bsky.social y.social @susiegriggo.bsky.social @veravannoort.bsky.social
www.biorxiv.org/content/10.1...
Fold first, ask later: structure-informed function annotation of Pseudomonas phage proteins
Phages, the viruses of bacteria, harbor an incredibly diverse repertoire of proteins capable of manipulating their bacterial hosts, inspiring many medical and biotechnological applications. However, t...
www.biorxiv.org
July 22, 2025 at 12:27 AM
Fold first, ask later: structure-informed function annotation of Pseudomonas phage proteins
Structural predictions to improve #phage genome annotation!
@hannelorelongin.bsky.social @gbouras13.bsky.social y.social @susiegriggo.bsky.social @veravannoort.bsky.social
www.biorxiv.org/content/10.1...
Structural predictions to improve #phage genome annotation!
@hannelorelongin.bsky.social @gbouras13.bsky.social y.social @susiegriggo.bsky.social @veravannoort.bsky.social
www.biorxiv.org/content/10.1...
Reposted by João Botelho
🦠🧍♀️From bacterial to human immunity.
We report in @science.org the discovery of a human homolog of SIR2 antiphage proteins that participates in the TLR pathway of animal innate immunity.
Co-led wt @enzopoirier.bsky.social by D. Bonhomme and @hugovaysset.bsky.social
www.science.org/doi/10.1126/...
We report in @science.org the discovery of a human homolog of SIR2 antiphage proteins that participates in the TLR pathway of animal innate immunity.
Co-led wt @enzopoirier.bsky.social by D. Bonhomme and @hugovaysset.bsky.social
www.science.org/doi/10.1126/...
www.science.org
July 24, 2025 at 6:23 PM
🦠🧍♀️From bacterial to human immunity.
We report in @science.org the discovery of a human homolog of SIR2 antiphage proteins that participates in the TLR pathway of animal innate immunity.
Co-led wt @enzopoirier.bsky.social by D. Bonhomme and @hugovaysset.bsky.social
www.science.org/doi/10.1126/...
We report in @science.org the discovery of a human homolog of SIR2 antiphage proteins that participates in the TLR pathway of animal innate immunity.
Co-led wt @enzopoirier.bsky.social by D. Bonhomme and @hugovaysset.bsky.social
www.science.org/doi/10.1126/...
Reposted by João Botelho
Here's our new broad review on the extended mobility of plasmids, about all mechanisms driving and limiting their transfer. From conjugation to conduction, phage-plasmids to hitchers, molecular to evolutionary dynamics, ecology to biotech. The state of affairs. 1/9 academic.oup.com/nar/article/...
July 23, 2025 at 7:35 AM
Here's our new broad review on the extended mobility of plasmids, about all mechanisms driving and limiting their transfer. From conjugation to conduction, phage-plasmids to hitchers, molecular to evolutionary dynamics, ecology to biotech. The state of affairs. 1/9 academic.oup.com/nar/article/...
Reposted by João Botelho
And the story is published now!🍾
www.nature.com/articles/s41...
Open access link: rdcu.be/exnOc
Many years in the making, great collaboration with @archaellum.bsky.social & @tunglejic.bsky.social
Thanks @ukri.org BBSRC & @leverhulme.ac.uk for funding, reviewers & editor!! 🙏
#microsky #archaeasky
www.nature.com/articles/s41...
Open access link: rdcu.be/exnOc
Many years in the making, great collaboration with @archaellum.bsky.social & @tunglejic.bsky.social
Thanks @ukri.org BBSRC & @leverhulme.ac.uk for funding, reviewers & editor!! 🙏
#microsky #archaeasky
July 22, 2025 at 9:06 PM
And the story is published now!🍾
www.nature.com/articles/s41...
Open access link: rdcu.be/exnOc
Many years in the making, great collaboration with @archaellum.bsky.social & @tunglejic.bsky.social
Thanks @ukri.org BBSRC & @leverhulme.ac.uk for funding, reviewers & editor!! 🙏
#microsky #archaeasky
www.nature.com/articles/s41...
Open access link: rdcu.be/exnOc
Many years in the making, great collaboration with @archaellum.bsky.social & @tunglejic.bsky.social
Thanks @ukri.org BBSRC & @leverhulme.ac.uk for funding, reviewers & editor!! 🙏
#microsky #archaeasky
Reposted by João Botelho
🚨🚨New paper out in @natcomms.nature.com!!
Come for the first large-scale analysis of plasmid copy number across species,
stay for one of the most intriguing results of my lab: universal scaling laws in plasmid biology! 📈🧬
👉 www.nature.com/articles/s41...
Come for the first large-scale analysis of plasmid copy number across species,
stay for one of the most intriguing results of my lab: universal scaling laws in plasmid biology! 📈🧬
👉 www.nature.com/articles/s41...
Universal rules govern plasmid copy number - Nature Communications
Plasmids exhibit a broad range of sizes and copies per cell, and these two parameters appear to be negatively correlated. Here, Ramiro-Martínez et al. analyse the copy number of thousands of diverse b...
www.nature.com
July 2, 2025 at 11:08 AM
🚨🚨New paper out in @natcomms.nature.com!!
Come for the first large-scale analysis of plasmid copy number across species,
stay for one of the most intriguing results of my lab: universal scaling laws in plasmid biology! 📈🧬
👉 www.nature.com/articles/s41...
Come for the first large-scale analysis of plasmid copy number across species,
stay for one of the most intriguing results of my lab: universal scaling laws in plasmid biology! 📈🧬
👉 www.nature.com/articles/s41...
Reposted by João Botelho
🚨 Reminder! You have just over two weeks to submit an abstract, if you want to present at the @microbiologysociety.org meeting "Understanding and predicting microbial evolutionary dynamics" in Liverpool in November! #microsky 🦠🧫🔬
‼️Update! Abstract submission is now open for the 2025 Liverpool UK @microbiologysociety.org meeting on "Understanding and predicting microbial evolutionary dynamics”! Deadline July 7th #microsky 🧪🧫🦠 microbiologysociety.org/event/societ...
June 20, 2025 at 2:35 PM
🚨 Reminder! You have just over two weeks to submit an abstract, if you want to present at the @microbiologysociety.org meeting "Understanding and predicting microbial evolutionary dynamics" in Liverpool in November! #microsky 🦠🧫🔬
Reposted by João Botelho
Thank you to everyone who attended the 3rd UK MGE workshop. What an incredible few days of science and community building! Next stop: York 2026, hosted by @pcmfogg.bsky.social. See you all next year! #UKMGE
June 19, 2025 at 11:04 AM
Thank you to everyone who attended the 3rd UK MGE workshop. What an incredible few days of science and community building! Next stop: York 2026, hosted by @pcmfogg.bsky.social. See you all next year! #UKMGE
Reposted by João Botelho
Defence Systems are so hot right now 🔥 🔥 🔥 so check out our latest preprint to see how DSes contribute to niche adaptation, interact with each other, and drive accessory genome interactions in Pseudomonas aeruginosa 1/n
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Defence systems drive accessory genome interactions in Pseudomonas aeruginosa
As well as undergoing mutational selection, bacterial genomes are shaped by a complex evolutionary interplay among diverse accessory genome elements (AGEs). In this study we define AGEs as encompassin...
www.biorxiv.org
May 23, 2025 at 6:33 PM
Defence Systems are so hot right now 🔥 🔥 🔥 so check out our latest preprint to see how DSes contribute to niche adaptation, interact with each other, and drive accessory genome interactions in Pseudomonas aeruginosa 1/n
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Reposted by João Botelho
We still have space for additional attendees, and we encourage you to share this invitation within your networks so others can benefit from the fantastic panel we have assembled for this edition. Better program than your favourite paid conference - just saying 😉
The program for the 3rd MGE Workshop is now live! Check out this year's speakers using the link below.
The deadline for registration closes on Friday 30th May ⏰
We look forward to seeing you all in Southampton in a few weeks time!
#MGE #MGEWorkshop #Southampton
www.ukmgeworkshop.org
The deadline for registration closes on Friday 30th May ⏰
We look forward to seeing you all in Southampton in a few weeks time!
#MGE #MGEWorkshop #Southampton
www.ukmgeworkshop.org
www.ukmgeworkshop.org
May 25, 2025 at 3:25 PM
We still have space for additional attendees, and we encourage you to share this invitation within your networks so others can benefit from the fantastic panel we have assembled for this edition. Better program than your favourite paid conference - just saying 😉
Reposted by João Botelho
The program for the 3rd MGE Workshop is now live! Check out this year's speakers using the link below.
The deadline for registration closes on Friday 30th May ⏰
We look forward to seeing you all in Southampton in a few weeks time!
#MGE #MGEWorkshop #Southampton
www.ukmgeworkshop.org
The deadline for registration closes on Friday 30th May ⏰
We look forward to seeing you all in Southampton in a few weeks time!
#MGE #MGEWorkshop #Southampton
www.ukmgeworkshop.org
www.ukmgeworkshop.org
May 25, 2025 at 2:03 PM
The program for the 3rd MGE Workshop is now live! Check out this year's speakers using the link below.
The deadline for registration closes on Friday 30th May ⏰
We look forward to seeing you all in Southampton in a few weeks time!
#MGE #MGEWorkshop #Southampton
www.ukmgeworkshop.org
The deadline for registration closes on Friday 30th May ⏰
We look forward to seeing you all in Southampton in a few weeks time!
#MGE #MGEWorkshop #Southampton
www.ukmgeworkshop.org
Reposted by João Botelho
One week to register your talk! We have 20 confirmed speakers but still have room for a few more. Why attend? Excellent panel of colleagues participating, talent recruiting event (see website) at no cost! Sharing appreciated
Registration for the 3rd MGE Workshop is live! 🧬
Join us on Mon 16th and Tue 17th June, to learn about the latest MGE research.
Deadline to register for a talk - Fri 16th May
General registration deadline - Fri 30th May
We look forward to seeing you all there!
www.ukmgeworkshop.org
Join us on Mon 16th and Tue 17th June, to learn about the latest MGE research.
Deadline to register for a talk - Fri 16th May
General registration deadline - Fri 30th May
We look forward to seeing you all there!
www.ukmgeworkshop.org
MGE Workshop
www.ukmgeworkshop.org
May 11, 2025 at 7:41 PM
One week to register your talk! We have 20 confirmed speakers but still have room for a few more. Why attend? Excellent panel of colleagues participating, talent recruiting event (see website) at no cost! Sharing appreciated
Reposted by João Botelho
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/...
Reposted by João Botelho
Come join us in Southampton! You need to register to participate (free registration!). To give everyone an opportunity to showcase their science, we extended the deadline for title submission to May 16. Share widely!
We are pleased to announce that registration for 3rd MGE Workshop is now live!
If you are interested in giving a talk please register online through our website by Friday 16th May.
We look forward to seeing you all in Southampton in June!
www.ukmgeworkshop.org
If you are interested in giving a talk please register online through our website by Friday 16th May.
We look forward to seeing you all in Southampton in June!
www.ukmgeworkshop.org
MGE Workshop
www.ukmgeworkshop.org
May 1, 2025 at 11:57 AM
Come join us in Southampton! You need to register to participate (free registration!). To give everyone an opportunity to showcase their science, we extended the deadline for title submission to May 16. Share widely!
Reposted by João Botelho
Join the Blokesch lab (@EPFL) as a postdoc in Molecular Microbiology 🤩
Study Vibrio cholerae defense systems (phage/plasmid) in a dynamic, collaborative environment in Lausanne close to Lake Geneva in 🇨🇭!
Please visit my lab's webpage for details about the position and how to formally apply.
Study Vibrio cholerae defense systems (phage/plasmid) in a dynamic, collaborative environment in Lausanne close to Lake Geneva in 🇨🇭!
Please visit my lab's webpage for details about the position and how to formally apply.
April 25, 2025 at 4:15 PM
Join the Blokesch lab (@EPFL) as a postdoc in Molecular Microbiology 🤩
Study Vibrio cholerae defense systems (phage/plasmid) in a dynamic, collaborative environment in Lausanne close to Lake Geneva in 🇨🇭!
Please visit my lab's webpage for details about the position and how to formally apply.
Study Vibrio cholerae defense systems (phage/plasmid) in a dynamic, collaborative environment in Lausanne close to Lake Geneva in 🇨🇭!
Please visit my lab's webpage for details about the position and how to formally apply.