Between this and my other recent preprint on plasmid host-lineage preferences, I think we should be more cautious about how we model plasmid sequence data. Mobility does not imply promiscuity, and apparent evolutionary signals may disappear once plasmid and host ancestry are accounted for. (1/2)

Will Matlock@wtmatlock.bsky.social · 2w ago

🚨 New preprint with @annadewar.bsky.social 🚨 Do plasmids “ameliorate” towards their hosts? Maybe… We show that the classic plasmid-host GC correlation is confounded by population structure, and argue that plasmid mobility shapes the opportunity for host-associated compositional evolution.

🚨 New preprint with @annadewar.bsky.social 🚨 Do plasmids “ameliorate” towards their hosts? Maybe… We show that the classic plasmid-host GC correlation is confounded by population structure, and argue that plasmid mobility shapes the opportunity for host-associated compositional evolution.

Mobility shapes plasmid GC content evolution

Plasmids are frequently AT-rich relative to their bacterial hosts. Despite this tendency towards lower GC content, plasmid and host chromosome GC content are positively correlated across diverse collections of plasmid-host pairs. However, the evolutionary processes underlying this pattern remain unclear. The classic model of amelioration predicts that horizontally acquired DNA gradually converges on host nucleotide composition. However, because plasmids can repeatedly transfer between bacterial hosts, the opportunity for such host-associated evolution may depend on their transmission dynamics. Using 50,936 plasmid-host pairs from a public sequence database, we found that the apparent global correlation between plasmid and host chromosome GC content was largely driven by differences between bacterial species rather than within species. We therefore accounted for plasmid and host population structure when testing how plasmid mobility shaped host-associated compositional evolution. We compared two contrasting regimes: a population of 3,682 Enterobacterales plasmids distributed across diverse host backgrounds, and six long-term host-associated plasmids from a Rhizobium leguminosarum lineage with INSeq-determined gene essentiality data. In the Enterobacterales population, GC content variation was overwhelmingly explained by plasmid lineage rather than host phylogeny, and conjugative plasmids showed greater similarity to their host chromosomes than mobilisable or non-mobilisable plasmids. In the Rhizobium leguminosarum plasmids, synonymous-site composition was more similar to the host chromosome among genes required across multiple host life stages. Together, these results support a model in which plasmid mobility influences the opportunity for host-associated evolutionary processes to alter nucleotide composition. ### Competing Interest Statement The authors have declared no competing interest. Wellcome Trust, 319534/Z/24/Z St. John's College, University of Oxford, UK

doi.org

Biology has plenty of data—the challenge is making it usable. AllTheBacteria transforms 2.44 million public bacterial and archaeal genomes into an open, uniformly processed, searchable, AI-ready resource. www.biorxiv.org/content/10.1...

AllTheBacteria: a community resource empowers biology and discovers novel peptide antibiotics

Public microbial genomes encode an immense record of biological diversity, evolution and molecular function, but much of this information remains difficult to reuse because raw sequencing data are not...

biorxiv.org

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/...

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...

journals.plos.org

Excited to share this new paper from the lab: academic.oup.com/ismej/articl...! See thread below

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

academic.oup.com

My first foray into linear plasmids in a new-to-me bug (VRE) - they are pretty neat! 🧵1/n

medRxivpreprint@medrxivpreprint.bsky.social · 3mo ago

Linear plasmid prevalence and linezolid resistance gene carriage in vancomycin-resistant Enterococcus in Canada from 2009-2024 https://www.medrxiv.org/content/10.64898/2026.05.08.26352429v1

Happy to share that our latest research on the eco-evolutionary dynamics of MDR plasmids and PDPs is now out (open access vAuthor) in The ISME Journal doi.org/10.1093/isme... Here, we explored how plasmid-dependent phages (PDPs) act as a selective pressure against the spread of multidrug resistance

Eco-evolutionary responses to plasmid-dependent phage constrain the spread of multidrug resistance plasmids

Abstract. Phage therapy offers a promising alternative to antibiotics for treating multidrug-resistant infections. Plasmid-dependent phages (PDPs) are part

doi.org

How social is social resistance? Check out our new mini-review, co-authored by Rosie Randall. Her first paper! 👏🏽 portlandpress.com/essaysbioche... Thanks to @friendlymicrobe.bsky.social and @rachelmwheatley.bsky.social for the invitation. @biology.ox.ac.uk @ilesla.bsky.social

New preprint alert!!! 🚀🤓 We are very happy to finally share this with the world — the result of seven years of work and a new tool to study integrons and discover new functions encoded in these bacterial platforms. If you want to know more, here is a thread 🧵 www.biorxiv.org/content/10.6...

Horizontal gene transfer is often depicted as a process distributing pre-existing functions to novel genetic backgrounds. Yet HGT can also increase the rate of functional innovation after transfer. Here's a brief review on the topic: ecoevorxiv.org/repository/v... #evosky #microsky

Cancer therapies exploit DNA repair defects to kill tumours. We asked whether the same logic could constrain antibiotic resistance evolution... www.biorxiv.org/content/10.6...

Conjugation structures plasmid populations through host-lineage restriction https://www.biorxiv.org/content/10.64898/2026.02.19.706745v1

🚨 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...

If you're interested, click on www.ox.ac.uk/admissions/g... - Life and Medical Sciences, Clinical Medicine 04!

UNIQplus projects | University of Oxford

Projects available for entry in 2026As part of your UNIQplus Research Internship, you will be working on a project under the supervision of academic staff from our community of world-leading

ox.ac.uk

Modernising Medical Microbiology@modmedmicro.bsky.social · 6mo ago

MMM has an exciting UNIQ+ project running this summer -apply now! Bacteria, microplastics & resistance — what’s the connection? #Microplastics are everywhere, even in hospitals. But what happens when bacteria stick to them? Come and find out! @afswinkels.bsky.social @nstoesser.bsky.social

Neisseria gonorrhoeae carries an unusually large number of restriction–modification systems (up to 16!), many of which are phase-variable. How does this affect plasmid transmission in gonococci? doi.org/10.64898/202...

🔊 Job Opportunity: Postdoctoral Research Fellow in Bacterial Evolution. Looking to recruit a postdoc to join a UKRI FLF-funded project on antibiotic resistance evolution in the microbiome 🦠 3 years funding, deadline 26th Jan, please share! hrwebapp.qub.ac.uk/tlive_webrec...

Excited to share some new work on plasmid host specificity and co-occurrence!

ESCMID_ESGMAP@esgmap.bsky.social · 8mo ago

🧬Are we getting closer to understanding plasmid evolution? Join this exciting talk, as the @escmid.bsky.social ESGMAP web symposium series continues. 💥 Dr. William Matlock presents "Models of plasmid evolution" 📅 Dec 3, 12:00-13:00 CET 🔗 Registration required (link in comments) #ESGMAP #Plasmid

Delighted to have played a small part in this great study from colleagues in CaPES: doi.org/10.1038/s414...

Plasmid dynamics driving carbapenemase gene dissemination in healthcare environments: a nationwide analysis of closed Enterobacterales genomes - Nature Communications

Plasmid-mediated transmission plays a significant role in the spread of carbapenem-resistant Enterobacterales. Here, analyzing 1,115 carbapenemase-producing plasmids from Singapore, the authors sugges...

doi.org

There's a PhD position now available with me in Bath, on the evolution of symbiosis. www.findaphd.com/phds/project.... The supervisory team also includes @anja1.bsky.social @phil-donoghue.bsky.social and others. NB, this is open both to UK-based students *and* to international students :)

The genomic basis of symbiotic integration at University of Bath on FindAPhD.com

PhD Project - The genomic basis of symbiotic integration at University of Bath, listed on FindAPhD.com

findaphd.com

We have a fully funded PhD studentship available @modmedmicro.bsky.social in Oxford to work on a really cool project looking at population heterogeneity in bloodstream infections www.ndm.ox.ac.uk/study/dphil-... Please spread the word/get in touch if you'd like to chat.

Please feel free to message me with any questions! ☺️

Craig MacLean@craigmaclean.bsky.social · 10mo ago

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...

🔊 Fully-funded 4yr PhD studentship with the NWB DTP, working on novel regulators of bacterial nitrogen metabolism 🦠 Primary supervisor: @ariannebabina.bsky.social (University of Glasgow) Co-supervisors: myself (Queen’s Belfast)+ Dónal Wall (Glasgow) 🌟 please share 🌟 www.gla.ac.uk/postgraduate...

Come and work with Nicole Stoesser and I in Oxford with the fantastic team @modmedmicro.bsky.social - great opportunity for a postdoc in microbial genomics to do some creative research with great datasets as part of our HPRU. my.corehr.com/pls/uoxrecru...

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!

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.

nature.com

Will Matlock@wtmatlock.bsky.social · 2y ago

🚨 New preprint! 🚨 We reveal that blaTEM-1 expression varies across the E. coli phylogeny, driving differences in co-amoxiclav resistance: www.biorxiv.org/content/10.1...

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

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....

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...

biorxiv.org

Plasmids link antibiotic resistance genes and phage defense systems in E. coli https://www.biorxiv.org/content/10.1101/2025.07.25.666796v1

New Comment—Reinforcing social safety for transgender and non-binary communities amidst global legislative threats tinyurl.com/v3jvjzs5

Reinforcing social safety for transgender and non-binary communities amidst global legislative threats

In 2017, we called for multisector public health initiatives to address discrimination and violence against transgender and non-binary communities, offering tangible recommendations for protecting the...

tinyurl.com

Delighted to see this paper from danderson123.bsky.social 's PhD out. We have been building tools for AMR gene detection for over a decade now, but multicopy genes remain challenging. Dan shows that with a gene-space de Bruijn graph and long reads, you can do well www.biorxiv.org/content/10.1...

That was fun: 2 days of bacterial genome evolution in beautiful Bath Ta @edfeil.bsky.social @eseb.bsky.social Great to see @craigmaclean.bsky.social @wtmatlock.bsky.social @jpjhall.bsky.social @taylorlabgroup.bsky.social @zaminiqbal.bsky.social @epcrocha.bsky.social @jomcinerney.bsky.social &co