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Craig MacLean

@craigmaclean.bsky.social
1.9K followers 197 following 232 posts

Scientist working on antibiotic resistance, evolution, and mobile genetic elements. Prof at U.Oxford and Fellow of All Souls College

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Craig MacLean @craigmaclean.bsky.social · 30/09/2026
Postdoc position available in my group to work on ERC funded project on evolutionary biology of antibiotic resistance. Looking for someone with expertise in bacterial genetics, AMR, and evolutionary biology. www.jobs.ac.uk/job/DSZ416/p...
jobs.ac.uk
Postdoctoral Research Associate at University of Oxford
Explore an exciting academic career as a Postdoctoral Research Associate. Don't miss out on other academic jobs. Click to apply and explore more opportunities.
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Craig MacLean @craigmaclean.bsky.social · 06/07/2026
New Essay: 'Resistance potentiators: Evolutionary catalysts of antibiotic resistance' To understand the evolutionary drivers of #AMR we need to move beyond resistance genes to thinking about the ability of genomes to generate AMR variants. #microsky journals.plos.org/plosbiology/...
journals.plos.org
Resistance potentiators: Evolutionary catalysts of antibiotic resistance
How do bacteria evolve resistance to antibiotics? Drawing on evidence from experimental evolution, pathogen genomics, and molecular microbiology, this Essay argues that the evolution of antibiotic res...
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Craig MacLean @craigmaclean.bsky.social · 27/06/2026
New #microsky#AMR Perspective paper with @penamiller.bsky.social rdcu.be/fqBJo ANTIBIOTIC RESISTANCE (IE MIC) AND TOLERANCE ARE NOT BACTERIAL TRAITS! Please read on if you want an explanation for this provocative claim.
rdcu.be
Beyond resistance and tolerance: rethinking evolutionary responses to antibiotics from the perspective of individual bacterial cells
Nature Communications - Beyond resistance and tolerance: rethinking evolutionary responses to antibiotics from the perspective of individual bacterial cells
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Kayla King, Ph.D. @kayla-king.bsky.social · 24/06/2026
Evolutionary rescue in a phage community! New paper from former PhD student, Sam Greenrod, with brilliant colleague @craigmaclean.bsky.social : academic.oup.com/ismej/advanc...
academic.oup.com
Rapid adaptation accelerates competitive suppression in a parasite community
Abstract. Environmental stress leads to changes in community composition by altering competitive hierarchies and pushing taxa towards extinction. Parasites
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Craig MacLean @craigmaclean.bsky.social · 03/06/2026
Excited to share this new paper from the lab: academic.oup.com/ismej/articl...! See thread below
academic.oup.com
Eco-evolutionary responses to plasmid-dependent phage constrain the spread of multidrug-resistance plasmids
Abstract. Phage therapy offers an alternative to antibiotics for treating multidrug-resistant infections. Plasmid-dependent phages (PDPs) are promising the
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Britt Koskella @bkoskella.bsky.social · 19/05/2026
Please share widely! Abstract submissions open for the 2026 Jacques Monod conference: Ecology and evolution of host-parasite interactions in a changing world! Held in beautiful Roscoff France from November 2- 6, 2026. Abstracts submission deadline : June 6 cjm.sb-roscoff.fr/en/conferenc...
cjm.sb-roscoff.fr
Ecology and evolution of host-parasite interactions in a changing world | CNRS - Conférences Jacques Monod (CJM)
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Craig MacLean @craigmaclean.bsky.social · 07/04/2026
I have been reading through papers on evolution and microbes from the 1940s to 1960s. I have found some amazing work, but I am sure that there is much more that I haven’t found. Can you send me links to classic evolution+microbiology papers from pre Levin era?
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Tatiana Dimitriu @tatianadimitriu.bsky.social · 02/04/2026
And the preprint is out! www.biorxiv.org/content/10.6... We compared plasmid conjugation in liquid and on solid across 13 AMR plasmids with different types of conjugative pili.
biorxiv.org
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Alvaro San Millan @sanmillan.bsky.social · 13/03/2026
Final version of our last paper is out! www.nature.com/articles/s41...
nature.com
Plasmids promote antimicrobial resistance through insertion sequence-mediated gene inactivation - Nature Microbiology
Inactivation of chromosomal genes through plasmid-encoded IS elements is an extended mechanism of antimicrobial resistance evolution in bacteria.
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Michael Brockhurst @brockhurstlab.bsky.social · 20/02/2026
How does treatment induced antibiotic resistance happen in real-world infections? We analysed 25k Pseudomonas isolates from 180 patients in a clinical trial to find out! TLDR: The ecological and evolutionary paths are surprisingly diverse & complex even in patients receiving identical treatment…
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Richard Lenski @relenski.bsky.social · 24/02/2026
Happy 38th birthday to the #LTEE! #BOTD in 1988. Keep on evolving! #science #evolution #microbiology
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Craig MacLean @craigmaclean.bsky.social · 23/02/2026
New #AMR pre-print Combining antibiotics with genotoxins can efficiently suppress bacterial in high throughput experimental models. www.biorxiv.org/content/10.6... Fun collaboration with Nassos Typas lab led by @mulkern.bsky.social
biorxiv.org
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Vaughn Cooper @vscooper.micropopbio.org · 16/02/2026
🧵 New preprint! Our 4-lab team evolved Streptococcus pneumoniae in antibiotic-treated mice of varying immune states and discovered something surprising: bacteria rarely evolved resistance. Instead, they found a different way to survive — by rewiring RNA turnover. 🔗 www.biorxiv.org/content/10.6...
biorxiv.org
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Michael Brockhurst @brockhurstlab.bsky.social · 06/10/2025
New preprint! Ever wondered why only a fraction of genomes encode CRISPR immunity? 🧬 🦠 Turns out CRISPR is rarely beneficial against virulent phages, being most beneficial against those for which resistance mutations are rare! An epic effort by Rosanna Wright www.biorxiv.org/content/10.1...
biorxiv.org
Resistance mutation supply modulates the benefit of CRISPR immunity against virulent phages
Only a fraction of bacterial genomes encode CRISPR-Cas systems but the selective causes of this variation are unexplained. How naturally virulent bacteriophages (phages) select for CRISPR immunity has...
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Craig MacLean @craigmaclean.bsky.social · 20/02/2026
New pre-print with @wtmatlock.bsky.social!!! www.biorxiv.org/content/10.6... What shapes the distribution of plasmids across bacteria? Our paper shows that conjugative plasmids actually have a very narrow distribution compared to mobilizable plasmids. Conjugative systems restrict plasmid transfer!
biorxiv.org
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Will Matlock @wtmatlock.bsky.social · 20/02/2026
🚨 New preprint 🚨 How promiscuous really are conjugative plasmids, and what does that mean for plasmid co-occurrence? A pleasure to collaborate with @craigmaclean.bsky.social on the first paper of my fellowship! www.biorxiv.org/content/10.6...
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Ville Friman @frimanscience.bsky.social · 29/12/2025
A four-year postdoc focusing on "plant growth-promoting bacteriophages" available in my group. Skills in metaviromics and metagenomics essential. Application deadline: 2.2.2026. For more info, see the link.
jobs.helsinki.fi
Postdoctoral Researcher in discovering the benefits of plant growth-promoting bacteriophages
Postdoctoral Researcher in discovering the benefits of plant growth-promoting bacteriophages
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Didier Mazel @amazeld.bsky.social · 12/12/2025
We've come full circle! I began my postdoctoral career by identifying the peptidyl deformylase gene. Today, we show that half of bacterial species harbor multiple PDF genes (up to 7, for always a single Met-tRNA transformylase), and while the role of these PDFs ... academic.oup.com/mbe/article/...
academic.oup.com
Unraveling the Prevalence and Multifaceted Roles of Accessory Peptide Deformylases in Bacterial Adaptation and Resistance
Abstract. Peptide deformylases (PDFs) are enzymes that are essential for bacterial viability and attractive targets for antibiotic development. Yet, despit
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Craig MacLean @craigmaclean.bsky.social · 12/12/2025
Good news for Canada and Canadian science. It is the right time to aggressively target top international and expatriate scientific talent. Although I am a blue skies scientist, I think that it is right to focus on research with societal and economic impact ... www.canada.ca/en/innovatio...
canada.ca
Government of Canada launches new initiative to recruit world-leading researchers - Canada.ca
Canada will invest $1.7 billion to attract top global talent
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Craig MacLean @craigmaclean.bsky.social · 11/12/2025
Just wrote my last grant review of 2025. UKRI: if you ask me to review another grant next week I will give it a 0 out of principle!
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Craig MacLean @craigmaclean.bsky.social · 28/11/2025
Back in Oxford, but still buzzing with excitement from #MicroEvo25 ! Great science, friendly and relaxed atmosphere, and a brilliant opportunity to catch up with friends and colleagues. Liverpool is a good place for scientific meetings.
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Craig MacLean @craigmaclean.bsky.social · 25/11/2025
Just finished reading this amazing history of biology by #massivelegendofscience Francois Jacob. Some of the evolutionary biology and microbiology is outdated, but the perspective is compelling and the breadth of scientific scholarship is amazing.
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Michael Baym @baym.lol · 20/11/2025
Hot off the press! Our latest paper led by @fernpizza.bsky.social, understanding how plasmids evolve inside cells. These small, self-replicating DNA circles live inside bacteria and carry antibiotic resistance genes, but also compete with one another to replicate. 1/ www.science.org/doi/10.1126/...
science.org
Intracellular competition shapes plasmid population dynamics
From populations of multicellular organisms to selfish genetic elements, conflicts between levels of biological organization are central to evolution. Plasmids are extrachromosomal, self-replicating g...
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Jamie Hall @jpjhall.bsky.social · 18/11/2025
🚨#PhD studentship opportunity! Plasmids provide bacteria with antimicrobial resistance, but do they have more fundamental effects on behaviour? 🧫🦠💫🧟‍♂️ Apply for a 4y funded MRC DiMeN position with me and Jamie Wheeler @livuni-ives.bsky.social www.findaphd.com/phds/project...
findaphd.com
MRC DiMeN Doctoral Training Partnership: Resistant zombies: how drug-resistance plasmids manipulate the behaviour of the opportunistic pathogen Pseudomonas aeruginosa at University of Liverpool on Fin...
PhD Project - MRC DiMeN Doctoral Training Partnership: Resistant zombies: how drug-resistance plasmids manipulate the behaviour of the opportunistic pathogen Pseudomonas aeruginosa at University of Li...
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Craig MacLean @craigmaclean.bsky.social · 06/11/2025
New paper: www.sciencedirect.com/science/arti... Klebs can evolve resistance to Colistin through mgrB mutation or by acquiring the mcr-1 gene. Both routes have similar fitness costs against a bacterial competitor, but mgrB mutations are associated with enhanced virulence.
sciencedirect.com
mgrB inactivation confers enhanced pathogenicity and immune evasion over mcr-1 expression in colistin-resistant Klebsiella pneumoniae
Colistin is one of the last treatment options against human infections caused by multi-drug resistant Klebsiella pneumoniae. Colistin resistant K. pne…
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Craig MacLean @craigmaclean.bsky.social · 29/10/2025
I can't wait for the day that I see a paper entitled "One health papers on AMR are a major source of AMR"
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Anna Dewar @annadewar.bsky.social · 08/01/2025
Our review is out in Nature Reviews Genetics! rdcu.be/d5AY2 We show how phylogeny-based methods can resolve the problem of non-independence in genomic datasets. These methods must be considered an essential part of the comparative genomics toolkit. @lauriebelch.bsky.social @stuwest.bsky.social
rdcu.be
A phylogenetic approach to comparative genomics
Nature Reviews Genetics - Controlling for phylogeny is essential in comparative genomics studies, because species, genomes and genes are not independent data points within statistical tests. The...
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Craig MacLean @craigmaclean.bsky.social · 27/10/2025
New pre-print: Plasmid dependent phage effectively eliminate AMR bacteria and block plasmid transmission in the chicken gut microbiome Fun collaboration with Tao He lab (JAAS) and @brockhurstlab.bsky.social lab (Manchester) #phagesky#microsky www.biorxiv.org/content/10.1...
biorxiv.org
Plasmid dependent phage eliminate pathogenic bacteria and antibiotic resistance plasmids from the chicken gut microbiome
Conjugative plasmids are a key reservoir of antimicrobial resistance (AMR) in commensal and pathogenic bacteria within the gut microbiome. Plasmid-dependent phage (PDPs) are a promising therapeutic op...
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Cell Press @cellpress.bsky.social · 24/10/2025
DNA from Napoleon’s 1812 army identifies the pathogens likely responsible for the army’s demise during their Russian retreat. www.cell.com/current-biol... Nicolás Rascovan & colleagues @currentbiology.bsky.social
Napoleon's retreat from Moscow CREDIT Barbieri et al., Current Biology
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Michael Brockhurst @brockhurstlab.bsky.social · 09/10/2025
Three Bicentenary research fellowships on offer at @officialuom.bsky.social @fbmh-uom.bsky.social for exceptional ECRs with <3y postdoc experience 3yrs salary + £30k pa research expenses Do you have a great idea & want to join @mermanchester.bsky.social? www.bmh.manchester.ac.uk/research/sup...
bmh.manchester.ac.uk
Bicentenary Early Career Research Fellowships | Biology, Medicine and Health | University of Manchester
Find out about and apply for a Bicentenary Early Career Research Fellowship.
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Craig MacLean @craigmaclean.bsky.social · 09/10/2025
New pre-print www.biorxiv.org/content/10.1... Plasmid-dependent phage (PDPs) are ubiquitous, but the selective pressures that they impose on plasmids are not well understood. Project led by Daniel Cazares in collaboration with @brockhurstlab.bsky.social! #phagesky#microsky
biorxiv.org
Trade-offs between phage resistance and conjugative ability shape the ecological and evolutionary response of a multidrug resistance plasmid to plasmid-dependent phage
Phage therapy is a promising alternative to antibiotics to treat multidrug resistant infections. Plasmid dependent phages (PDPs) are particularly attractive as therapeutics because they can both kill ...
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Emmanuele Severi @emmseveri.bsky.social · 09/10/2025
hosting.northumbria.ac.uk/nu-omics/vom... #phagesky #phage #microsky Come and join us for Viruses of Microbes UK 2026 at @northumbriauni.bsky.social ! Fantastic chance for ECRs to showcase their work 🙂
hosting.northumbria.ac.uk
VOM-UK Conferences - NU-OMICS
Viruses of Microbes UK (VoM-UK) Conference The Virus of Microbes UK (VoM-UK) Conference is hosted by Microbiome Excellence Peak of Excellence at Northumbria University. This two-day conference takes place annually at the end of January/beginning of February and is a chance for researchers to gather and share their knowledge. The VoM-UK conference is designed to […]
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Craig MacLean @craigmaclean.bsky.social · 02/10/2025
Interesting job opportunity: duunitori.fi/tyopaikat/ty...
duunitori.fi
Professor or Associate professor (Tenure Track/Full) in Microbial Genetics of Health - Turun yliopisto - Työpaikat - Duunitori
Avoin työpaikka: Professor or Associate professor (Tenure Track/Full) in Microbial Genetics of Health - Turun yliopisto, Turku. Duunitorilla lisäksi yli 30 000 muuta avointa työpaikkaa. Lue lisää nyt!
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Will Matlock @wtmatlock.bsky.social · 30/09/2025
Now published in @natcomms.nature.com 🎉 www.nature.com/articles/s41... With Gillian Rodger, @nstoesser.bsky.social, @samlipworth.bsky.social, @stat-sarah.bsky.social, and many others!
nature.com
Escherichia coli phylogeny drives co-amoxiclav resistance through variable expression of TEM-1 beta-lactamase - Nature Communications
This study found E. coli phylogenetic background shapes TEM-1 beta-lactamase expression and co-amoxiclav resistance. Phylogeny alone shifted isolates from susceptible to resistant, stressing a need for lineage-sensitive genotype-phenotype prediction.
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Craig MacLean @craigmaclean.bsky.social · 30/09/2025
New pre-print Competition between phage constrains adaptation to thermal fluctuating temperatures. More work led by Sam Greenrod in collaboration with @kayla-king.bsky.social lab. #Phagesky#Microsky www.biorxiv.org/content/10.1...
biorxiv.org
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Tami Lieberman @contaminatedsci.bsky.social · 29/09/2025
Precisely calling mutations across hundreds of bacterial isolates has been hard, requiring manual filtering and expertise. Until now, using AccuSNV. Herui Liao trained an ML model based on our previous meticulously called SNVs. www.biorxiv.org/content/10.1...
biorxiv.org
High-accuracy SNV calling for bacterial isolates using deep learning with AccuSNV
Accurate detection of mutations within bacterial species is critical for fundamental studies of microbial evolution, reconstructing transmission events, and identifying antimicrobial resistance mutati...
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Craig MacLean @craigmaclean.bsky.social · 29/09/2025
New pre-print: Eco-evolutionary responses of phage to different thermal regimes. Great work led by Sam Greenrod and fun collaboration with Kayla King's lab. 1/2 www.biorxiv.org/content/10.1...
biorxiv.org
Evolutionary rescue accelerates competitive exclusion in a parasite community
Environmental stress drives biodiversity loss by altering competitive hierarchies and pushing taxa towards extinction. Parasites and their communities are particularly vulnerable to stress due to envi...
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Zamin Iqbal @zaminiqbal.bsky.social · 25/09/2025
Delighted to see our paper studying the evolution of plasmids over the last 100 years, now out! Years of work by Adrian Cazares, also Nick Thomson @sangerinstitute.bsky.social - this version much improved over the preprint. Final version should be open access, apols. Thread 1/n
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Michael Brockhurst @brockhurstlab.bsky.social · 25/09/2025
Recent paper from the lab studying predictors of phage cocktail efficacy against complex clinical Pseudomonas populations royalsocietypublishing.org/doi/epdf/10.... Led by Rosanna Wright with extraordinary MSc (PhD) student Maisie Czernuska
royalsocietypublishing.org
Bacteria–phage infection network structure and genomic defence system content predict efficacy of a phage therapy cocktail against Pseudomonas aeruginosa from chronic lung infections
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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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Jörg Vogel @jorg-vogel-lab.bsky.social · 10/09/2025
Looking for a new approach to studying or eliminating phages? Check out our study introducing anti-phage ASOs (antisense oligos) out in @Nature today. nature.com/articles/s4158…
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José R Penadés @jrpenades.bsky.social · 09/09/2025
Our second paper with @tcostalab.bsky.social and GoogleDeepMind reports our experience with Google’s co-scientist: remarkably, the AI independently recapitulated our experimental discovery on cf-PICIs, showcasing AI’s potential to accelerate biology. www.cell.com/cell/fulltex...
cell.com
AI mirrors experimental science to uncover a mechanism of gene transfer crucial to bacterial evolution
By solving a previously unsolved biological question, the AI co-scientist predicted a complex mechanism of gene transfer and generated hypotheses that opened new research directions, illustrating AI's...
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José R Penadés @jrpenades.bsky.social · 09/09/2025
Thrilled to share our two latest papers with the @tcostalab.bsky.social lab! In the first, we uncover a new mechanism of satellite transfer: cf-PICIs hijack tails from diverse phages to spread across species. @imperialcollegeldn.bsky.social www.cell.com/cell/fulltex...
cell.com
Chimeric infective particles expand species boundaries in phage-inducible chromosomal island mobilization
Capsid-forming PICIs (cf-PICIs) produce their own capsids and exploit phage tails from unrelated species to transfer their DNA across bacterial hosts. This tail piracy enables broad dissemination and ...
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Craig MacLean @craigmaclean.bsky.social · 13/08/2025
This looks like a must read …
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Michael Brockhurst @brockhurstlab.bsky.social · 13/08/2025
We are also hiring a 4-year postdoc to study the dynamics and evolution of mobile genetic elements in the C-fixing Icelandic host-spring microbiomes Join our exciting multidisciplinary team funded by @ukri.org BBSRC sLoLa www.jobs.manchester.ac.uk/Job/JobDetai...
jobs.manchester.ac.uk
Research Associate in Microbial Evolution:Oxford Road
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Craig MacLean @craigmaclean.bsky.social · 29/07/2025
New pre-print from my lab! Plasmids link antibiotic resistance and phage defense. E.coli plasmids are hotspots for both antibiotic resistance and phage defense. Phage therapy has the potential to accidentally select for antibiotic resistance!!! #microsky#AMR#phage www.biorxiv.org/content/10.1....
biorxiv.org
Plasmids link antibiotic resistance genes and phage defense systems in E. coli
Phage therapy has been proposed as an alternative to antibiotics to treat resistant infections. However, we have a limited understanding of how antibiotic resistance genes (ARGs) associate with bacter...
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Jerónimo Rodríguez-Beltrán @jerorb.bsky.social · 02/07/2025
🚨🚨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...
nature.com
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...
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Craig MacLean @craigmaclean.bsky.social · 16/07/2025
New paper with @rwheatley8.bsky.social and Cedric Lood Actual title: Chromosomal capture of beneficial genes drives plasmids towards ecological redundancy. Sensationalist title: Plasmids carry useless genes academic.oup.com/ismej/articl...
academic.oup.com
Chromosomal capture of beneficial genes drives plasmids toward ecological redundancy
Abstract. Plasmids are a ubiquitous feature of bacterial genomes, but the forces driving genes and phenotypes to become associated with plasmids are poorly
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Jerónimo Rodríguez-Beltrán @jerorb.bsky.social · 03/07/2025
It was an honor and a joy to receive the National Research Prize for Young (!) Researchers. The highlight? My grandma greeting the King of Spain. What a day! www.youtube.com/watch?v=oSQP...
Felipe VI, king of Spain, greeting my grandmaFelipe VI and JeroA selfie of some of the Prize Recipients
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Jesse Shapiro @bjesseshapiro.bsky.social · 01/07/2025
One of my favourite serendipitous results from the lab came about because we were long-read sequencing bacterial: Vibrio cholerae, which is "supposed to" have TWO circular chromosomes (3 + 1 million base pairs) often has just ONE fused chromosome (4 Mbp). www.nature.com/articles/s41... (1/n)
nature.com
Prevalent chromosome fusion in Vibrio cholerae O1 - Nature Communications
The pathogenic bacterium Vibrio cholerae typically has two circular chromosomes. Here, Cuénod et al. analyse 467 clinical isolates and identify several independent chromosome fusion events that are li...
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