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 - wtmatlock/plasmid-model-cli

Contribute to wtmatlock/plasmid-model-cli development by creating an account on GitHub.

github.com

Will Matlock@wtmatlock.bsky.social · 7mo ago

🚨 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...

Want to analyse bacterial genomes yourself? ONE-BAG 2026 at @i2sysbio.es takes you from raw reads to interpretable phylogenies, with hands-on training in QC, SNPs, assembly, annotation, pangenomes, outbreaks, AMR and typing. Learn more: onebag.uv.es

ONE-BAG 2026 | Bacterial Genomics for One Health

From raw reads to a tree you can defend. Four days in Valencia, free for EOHA full members and 300 euro for everyone else. Applications close 1 October 2026.

onebag.uv.es

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!

It’s out! 🥹🎉 We’re so incredibly happy and proud to see this work out in the world. And once again, a huge thank you to the great mastermind @jaescudero.bsky.social and all the co-authors; this wouldn’t have been possible without you! doi.org/10.1038/s415... @natmicrobiol.nature.com

High-throughput recovery of integron cassettes for gene discovery screens - Nature Microbiology

Integron insertion sites engineered into counterselection markers allow large-scale and high-throughput capture of integron-encoded genes from genetically tractable bacteria or DNA samples.

doi.org

Filipa Trigo da Roza@filipatr.bsky.social · 7mo ago

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...

🧵 How did chickens become the world's biggest source of Campylobacter? Changes in agriculture have transformed chickens into the world's largest reservoir of one of our most common bacterial pathogens. Here's the story... 👇 #MicroSky #OneHealth

🚨 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

Significant update to the AllTheBacteria paper, including discovering new antimicrobial peptides and testing in vitro and vivo. This has grown into a fantastic collaboration!

César de la Fuente@delafuentelab.bsky.social · 2mo ago

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...

Can bacterial genomics bring 70 years of epidemiological surveillance back to life? We're hiring a postdoc (2–3 years) to explore the historical evolution of Salmonella Typhi using a unique genomic dataset. More details: euraxess.ec.europa.eu/jobs/449895

New Perspective out co-led with Lisa Pagani! We look at how microbiome ecology and evolution shape AMR across scales, from within-host communities to hospitals and environments, and how mathematical models can help us understand them. @natmicrobiol.nature.com www.nature.com/articles/s41...

Modelling the role of the microbiome in antimicrobial resistance across scales - Nature Microbiology

The microbiome plays a significant yet underexplored role in antimicrobial resistance by influencing ecological and evolutionary processes. This Perspective proposes a framework to integrate microbiom...

nature.com

It's out! The LIN code approach for genomic taxonomy of microbial strains and its applications in genomic epidemiology journals.plos.org/plosbiology/...

Life Identification Numbers: A strain nomenclature approach to aid epidemiological surveillance of bacterial pathogens

Unified bacterial strain taxonomies are needed for coherent communication of findings in microbiological research. This Essay provides an overview of a novel bacterial strain taxonomy and describes ho...

journals.plos.org

New paper out! 🔈 Genomic Characterization of the RyC collection: 50 Multidrug Resistant Clinical Isolates of Escherichia coli and Klebsiella spp. 50 MDR gut isolates, 2 sequencing platforms, 4 “omes,” and 1 mission: provide a resource to decode AMR and MGE dynamics www.biorxiv.org/content/10.6...

New research article Emergence of carbapenemase-producing #Escherichia coli in acute care hospitals in 32 European countries (the CCRE survey) www.thelancet.com/journals/lan... #IDSky #ClinMicro #AMR #Ecoli #OpenAccess #OA

What if multireplicon plasmids are not an oddity, but an evolutionary strategy? We found that they are common, more mobile, broader-host-range, and enriched in AMR. Even more interesting: their assembly doesn’t look random. 👀 Paper preprint: www.biorxiv.org/content/10.6... Thread below!🧵👇

Happy to share our latest work on “In Host Mutational Adaptation of Mycobacterium Tuberculosis Complex Strains During Tuberculosis Infection” published in @jidjournal.bsky.social doi.org/10.1093/infd...

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...

Final version of our last paper is out! www.nature.com/articles/s41...

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.

nature.com

Excited to share our latest work! 📝 We measured the fitness effect of 136 AMR genes and found that many are neutral or even beneficial without selection. 🤯🧬 Oxygen availability can flip their fitness and our stochastic model indicates that oxygen fluctuations help maintain them. Learn more 👇🏼

bioRxiv Microbiology@biorxiv-microbiol.bsky.social · 7mo ago

Fitness effects of antimicrobial resistance genes in changing environments https://www.biorxiv.org/content/10.64898/2026.03.06.710025v1

Our faculty has a particularly interesting PhD position open on antimicrobial resistance, effects of antibiotics treatment on the microbiome and resistome, restoration of the equine microbiome using FMT. www.uu.nl/en/organisat... Please contact Mathijs Theelen, email address in the link below.

PhD candidate in Equine Intestinal Microbiome and Resistome

Join this PhD project to study how the equine gut microbiome and resistome can improve gastrointestinal health and combat antimicrobial resistance.

uu.nl

Last year, we proposed a model of plasmid evolution via fusion and fragmentation (via mge mediated recombination) generating mosaics, by studying historical isolates. Excited to see a MASSIVE paper from @jrpenades.bsky.social , @epcrocha.bsky.social expanding on this www.biorxiv.org/content/10.6...

A long time ago in a galaxy far away, there was a SARS-CoV-2 pandemic. Our paper, led by @martibartfast.bsky.social a) correcting errors in 4.5 million genomes & their phylogeny b) improving representation of the Global South in public data www.nature.com/articles/s41... (thread 1/n)

Addressing pandemic-wide systematic errors in the SARS-CoV-2 phylogeny - Nature Methods

This Resource paper presents a global SARS-CoV-2 phylogenetic tree of 4,471,579 high-quality genomes consistently constructed by Viridian, an efficient amplicon-aware assembler.

nature.com

Now published: our work using phylodynamics from surveillance data to quantify and experimentally validate the fitness impact of antibiotic resistance determinants & how this changes with patterns of antibiotic use: www.nature.com/articles/s41...

Quantifying the real-world impact of antibiotic use and genetic determinants of resistance on gonococcal dynamics

Nature Microbiology - Phylodynamic modelling shows how the changing antibiotic landscape and genetic determinants of resistance shape real-world gonococcal dynamics. Experiments validated that...

nature.com

Yonatan Grad@yhgrad.bsky.social · 2y ago

New preprint! How much does antibiotic use shape bacterial lineage dynamics, and how does that relate to the fitness costs/benefits of resistance determinants? All sorts of fun findings and a method that we hope will be broadly useful. See @dhelekal.bsky.social's thread and the preprint!

New paper out in @pnas.org, and it made the cover! 👁️ We represent plasmids as circles and mutations as dots, resembling an eye, because in this paper we literally 𝑤𝑎𝑡𝑐ℎ plasmids evolve. ‼️Check Paula’s 🧵 and the paper👇 𝗣𝗹𝗮𝘀𝗺𝗶𝗱 𝗺𝘂𝘁𝗮𝘁𝗶𝗼𝗻 𝗿𝗮𝘁𝗲𝘀 𝘀𝗰𝗮𝗹𝗲 𝘄𝗶𝘁𝗵 𝗰𝗼𝗽𝘆 𝗻𝘂𝗺𝗯𝗲𝗿 www.pnas.org/doi/10.1073/...

Paula Ramiro-Martínez@paularamiro.bsky.social · 8mo ago

New paper out in PNAS!!! 🎉 Do more plasmid copies mean faster evolution? 🧵 Dive into the story www.pnas.org/doi/10.1073/...

Bacteria chromosomes contain Genomic Islands that provide virulence, antibiotic resistance, MGE-defence,... They transfer between cells, but the mechanism of most remains elusive. Here we explore the conjugative capacity of these mysterious Genomic Islands. www.biorxiv.org/content/10.6...

Very happy to share our preprint on a mathematical model for Streptococcus pneumoniae population dynamics after vaccine introductions. It's a reusable model that describes vaccine replacement dynamics and can help to determine strategies for genomic surveillance: doi.org/10.64898/2025.12.18.695090

A reusable model of pangenome selection informs optimal surveillance strategies over vaccine introductions

The human pathogen Streptococcus pneumoniae is a major cause of disease, including pneumonia and meningitis. The introduction of Pneumococcal Conjugate Vaccines (PCVs) initially reduced the burden of ...

doi.org

What drives the K. pneumoniae species complex (KpSC) to thrive from hospitals to soils? In this study, we investigate how pangenome structure and functional diversity shape KpSC adaptability across phylogenetic and ecological contexts. (Thread) www.biorxiv.org/content/10.6...

A new tool we’ve developed to identify AMR-associated SNPs in short- and long-read metagenome data….allows a greater understanding of the total resistome of a sample

Aldert Zomer@aldertzomer.bsky.social · 10mo ago

MetaPointFinder: A new approach for detecting mutation-driven antimicrobial resistance directly from metagenomic reads. Fills a major gap in current resistome profiling by capturing chromosomal AMR mutations that metagenome tools miss. github.com/aldertzomer/...

Read 'Large-scale characterization of the nasal microbiome redefines Staphylococcus aureus colonization status' from @sangerinstitute.bsky.social, @cam.ac.uk, @imperialcollegeldn.bsky.social and their collaborators in @natcomms.nature.com here ⬇️ www.nature.com/articles/s41...

Large-scale characterisation of the nasal microbiome redefines Staphylococcus aureus colonisation status - Nature Communications

Here, using samples from ~1,100 individuals, the authors define the nasal microbiome linked to Staphylococcus aureus colonization, identifying seven communities- either S. aureus-dominated or dominate...

nature.com

🧬 A new “Life Identification Number (LIN)” system aims to modernize bacterial classification with a clearer, more stable hierarchy. A step forward for genomic taxonomy! 📖 shorturl.at/vkQuS ✍️ @sylvainbrisse.bsky.social & coll. @pasteur.fr @ox.ac.uk @monashuniversity.bsky.social @lshtm.bsky.social

London interdisciplinary #PhD position now open with myself, @sergemostowylab.bsky.social, & @gmknght.bsky.social on #phage -bacteria-host immune dynamics for WHO priority bacterial pathogens #Klebsiella, #Shigella, and #Staph. Combines cellular microbiology, genomics, & mathematical modelling.

🚨 Excited to share our new paper is out! 🎉 We show how interactions within gut microbiomes allow certain antibiotic-resistant E. coli strains to persist even without antibiotics, helping explain how resistance is maintained in the human gut. Now published in @natcomms.nature.com rdcu.be/eOf63

Multi-layered ecological interactions determine growth of clinical antibiotic-resistant strains within human microbiomes

Nature Communications - The role of ecological factors in modulating the spread of antibiotic-resistance bacteria in the gut remains unclear. Here, the authors use anaerobic microcosms to study the...

rdcu.be