Will Matlock

Will Matlock

@wtmatlock.bsky.social

Wellcome Early-Career Award Fellow @milnerevolution.bsky.social working on plasmid evolution and ecology (he/him) 🏳️‍⚧️🇵🇸 Formerly @biology.ox.ac.uk and @modmedmicro.bsky.social

636 followers498 following48 posts

Will Matlock
@wtmatlock.bsky.social

Want to explore host-plasmid and plasmid-plasmid distributions in your dataset? Or any tree with a set of binary traits? I’ve made a CLI for our model here: github.com/wtmatlock/pl...

github.comGitHub - wtmatlock/plasmid-model-cliContribute to wtmatlock/plasmid-model-cli development by creating an account on GitHub.
Will Matlock@wtmatlock.bsky.social

🚨 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...

Will Matlock reposted

Thomas Ipoutcha
@tomipou.bsky.social

Finally out! 🎉 After 3 years of postdoc in London, here is my main work, now published in Nature Comm. (and as co-corresponding author!) Using a combination of bioinformatic and experimental approaches, we propose a model of plasmid evolution in Staphylococcus. www.nature.com/articles/s41... ⬇️ 1/4

nature.comMobile genetic elements drive a plasmid fusion and deletion lifecycle shaping evolution and antimicrobial resistance - Nature CommunicationsPlasmids drive bacterial adaptation, but how their diversity arises has remained unclear. Here, they show that in Staphylococcus aureus, mobile genetic elements repeatedly fuse and delete plasmids, re...

Will Matlock reposted

David Sünderhauf
@davvi36.bsky.social

Please share! We are looking for a PhD student excited about gene transfer, and tackling Antimicrobial Resistance in Klebsiella pneumoniae. 🧬 More details & applications on funder website by 21st Oct 👇🏻 gw4biomed.ac.uk/developing-c...

gw4biomed.ac.ukDeveloping CRISPR-Cas antimicrobials to tackle antibiotic resistance spread in Klebsiella pneumoniae - GW4 BioMed MRC DTPProject Code IIAR27Ex van Houte Project Type Wet lab Research Theme Infection, Immunity, and Antimicrobial Resistance Project Summary Download Summary Antimicrobial resistance (AMR) poses a major thre...
Will Matlock
@wtmatlock.bsky.social

Does an AMR gene on a plasmid diversify differently to an AMR gene on a chromosome? We are looking for a PhD student to work on this question in Bath!

gw4biomed.ac.ukTurning up the volume: plasmid copy number and gene duplications as drivers of antimicrobial resistance evolution - GW4 BioMed MRC DTPProject Code IIAR27Ba Matlock Project Type Wet lab Research Theme Infection, Immunity, and Antimicrobial Resistance Project Summary Download Summary Plasmids are important drivers of antimicrobial res...
Will Matlock
@wtmatlock.bsky.social

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

🚨 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.

doi.orgMobility shapes plasmid GC content evolutionPlasmids 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
Will Matlock
@wtmatlock.bsky.social

What is the sampling unit? Plasmids? Plasmid lineages? Plasmid-host pairs? Plasmid genes? What generates non-independence? Shared ancestry? Transmission networks? Sampling strategy? These are difficult questions and the field lacks a clear framework. (2/2)

Will Matlock
@wtmatlock.bsky.social

🚨 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.

doi.orgMobility shapes plasmid GC content evolutionPlasmids 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

Will Matlock reposted

César de la Fuente
@delafuentelab.bsky.social

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...

biorxiv.orgAllTheBacteria: a community resource empowers biology and discovers novel peptide antibioticsPublic 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...

Will Matlock reposted

Craig MacLean
@craigmaclean.bsky.social

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.orgResistance potentiators: Evolutionary catalysts of antibiotic resistanceHow 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...

Will Matlock reposted

Nicole Lerminiaux
@nic-ler.bsky.social

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

medRxivpreprint@medrxivpreprint.bsky.social

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

Will Matlock reposted

Daniel Cazares
@danielcazares.bsky.social

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

doi.orgEco-evolutionary responses to plasmid-dependent phage constrain the spread of multidrug resistance plasmidsAbstract. Phage therapy offers a promising alternative to antibiotics for treating multidrug-resistant infections. Plasmid-dependent phages (PDPs) are part

Will Matlock reposted

Ashleigh Griffin
@asgriffin.bsky.social

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

portlandpress.comHow social is social resistance?Abstract. β-lactamases are central to bacterial resistance against β-lactam antibiotics and are often treated as a textbook example of cooperative resistance. The cooperative aspect of their action ar...

Will Matlock reposted

nstoesser.bsky.social
@nstoesser.bsky.social

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

ox.ac.ukUNIQplus projects | University of OxfordProjects 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
Modernising Medical Microbiology@modmedmicro.bsky.social

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

Will Matlock
@wtmatlock.bsky.social

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

ESCMID_ESGMAP@esgmap.bsky.social

🧬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

Will Matlock
@wtmatlock.bsky.social

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

doi.orgPlasmid dynamics driving carbapenemase gene dissemination in healthcare environments: a nationwide analysis of closed Enterobacterales genomes - Nature CommunicationsPlasmid-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...

Will Matlock reposted

Tom Williams
@tweethinking.bsky.social

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 :)

findaphd.comThe genomic basis of symbiotic integration at University of Bath on FindAPhD.comPhD Project - The genomic basis of symbiotic integration at University of Bath, listed on FindAPhD.com
Will Matlock
@wtmatlock.bsky.social

Please feel free to message me with any questions! ☺️

Craig MacLean@craigmaclean.bsky.social

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.comJob Details
Will Matlock
@wtmatlock.bsky.social

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.comEscherichia coli phylogeny drives co-amoxiclav resistance through variable expression of TEM-1 beta-lactamase - Nature CommunicationsThis 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.
Will Matlock@wtmatlock.bsky.social

🚨 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...

biorxiv.orgE. coli phylogeny drives co-amoxiclav resistance through variable expression of blaTEM-1bioRxiv - the preprint server for biology, operated by Cold Spring Harbor Laboratory, a research and educational institution

Will Matlock reposted

Craig MacLean
@craigmaclean.bsky.social

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.orgPlasmids link antibiotic resistance genes and phage defense systems in E. coliPhage 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...

Will Matlock reposted

The Lancet
@thelancet.com

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

tinyurl.comReinforcing social safety for transgender and non-binary communities amidst global legislative threatsIn 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...

Will Matlock reposted

Jamie Hall
@jpjhall.bsky.social

🆕New in @plosbiology.bsky.social: we show compensatory mutations make plasmids play Rock-Paper-Scissors and turn conjugation into a weapon🛡️💫✂️🦠 w/Rosanna Wright, Jamie Wood, @mbottery.bsky.social, @kmudz.bsky.social, @scottishwormboy.bsky.social, Ellie Harrison & @brockhurstlab.bsky.social #MicroSky

journals.plos.orgA chromosomal mutation is superior to a plasmid-encoded mutation for plasmid fitness cost compensationPlasmids spread important traits in microbiomes but impose fitness costs on their hosts. This study of the ecological consequences of plasmid-bacterial compensatory evolution reveals benefits to bacte...

Will Matlock reposted

Zamin Iqbal
@zaminiqbal.bsky.social

Latest data from AllTheBacteria described in our updated preprint. All illumina WGS bacterial+archaeal sequence data to Aug 2024 consistently assembled, QC, and now AMR profiling. That's 2.4 million genomes. Gene annotations almost done , coming next. Please use! www.biorxiv.org/content/10.1...

biorxiv.orgAllTheBacteria - all bacterial genomes assembled, available and searchableThe bacterial sequence data publicly available at the global DNA archives is a vast source of information on the evolution of bacteria and their mobile elements. However, most of it is either unassemb...

Will Matlock reposted

Eduardo Rocha
@epcrocha.bsky.social

Our paper on identifying novel origins of transfer by conjugation is out! One can now expand the known oriTs from 1% to 80% in species like Acinetobacter baumannii. This contributes to unravel hitcher plasmid mobility beyond model elements. #microsky www.nature.com/articles/s41...

nature.comExpanding the diversity of origin of transfer-containing sequences in mobilizable plasmids - Nature MicrobiologyCharacterization of known plasmid oriT features facilitates identification of 21 oriT-containing sequence families which, alongside candidate sequence validation, expands our understanding of plasmid ...

Will Matlock reposted

Michael Brockhurst
@brockhurstlab.bsky.social

Use it or lose it: Unless we publish papers in our society owned and published journals they will cease to be, along with all the conferences and meetings the proceeds support. Microbiology Society publishes many excellent journals, all edited by experts. #microsky www.microbiologyresearch.org

microbiologyresearch.orgMicrobiology SocietyMicrobiology Society journals contain high-quality research papers and topical review articles. We are a not-for-profit publisher and we support and invest in the microbiology community, to the benefi...
Will Matlock
@wtmatlock.bsky.social

Now updated to include the NCBI accessions for the short- and long-reads and hybrid assemblies… please use them!

Will Matlock@wtmatlock.bsky.social

🚨 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...

biorxiv.orgE. coli phylogeny drives co-amoxiclav resistance through variable expression of blaTEM-1bioRxiv - the preprint server for biology, operated by Cold Spring Harbor Laboratory, a research and educational institution

Will Matlock reposted

Zamin Iqbal
@zaminiqbal.bsky.social

Now out in MGen! Daria Frolova's paper on measuring plasmid relatedness using rearrangement distances www.microbiologyresearch.org/content/jour... #microsky

Zamin Iqbal@zaminiqbal.bsky.social

First paper from my student Daria Frolova's PhD now on biorxiv: www.biorxiv.org/content/10.1... The key question: plasmids change structurally ~as fast as they mutate, so how can we decide whether 2 plasmids are "the same plasmid" for epi purposes? 1/n

biorxiv.orgbiorxiv.org
Will Matlock
@wtmatlock.bsky.social

Exciting work from Sam and colleagues!

Onisillos@onisillos.bsky.social

New research article in The Lancet Microbe Exploring uncatalogued genetic variation in antimicrobial resistance gene families in Escherichia coli: an observational analysis www.thelancet.com/journals/lan... #AMR #IDSky #MicroSky #OpenAccess #OA

thelancet.comExploring uncatalogued genetic variation in antimicrobial resistance gene families in Escherichia coli: an observational analysisWe highlight substantial uncatalogued genetic variation with respect to known ARGs, although a relatively small proportion of these alleles are repeatedly observed in a large international dataset sug...