Matthew J Shepherd

Massive congratulations to our own @magdalenakurteu.bsky.social for winning the poster prize at #MicroEvo25!! Her poster describes coalescence dynamics in hot spring microbial communities, and featured wonderful photos from Icelandic field work

Incredibly insightful talk this afternoon by @matthewjshepherd.bsky.social speaking about within-patient ciprofloxacin resistance in P. aeruginosa #MicroEvo25

New work from @colomer-winter.bsky.social shows that E. faecalis doesn’t wait for mutations at all - it immediately rewires its membrane lipids as a stress response to daptomycin. And surprisingly, the cell ends up looking a lot like a resistant strain before any genetic change happens.

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...

🚨#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...

Forecasting multi-trait resistance evolution under antibiotic stress Many bacteria rely on efflux pumps to survive antibiotic stress, and exposure to antibiotics often leads to mutations in pump genes or their regulators that increase pump expression. Predicting the sp...

We have a new preprint modeling the regulatory networks of efflux pumps to predict the evolution of multidrug resistance in P. aeruginosa. Also explore cross-resistance, collateral sensitivity & loss of resistance. With @suvamroy.bsky.social @elibbyscience.bsky.social www.biorxiv.org/content/10.1...

Sharp global rise in antibiotic-resistant infections in hospitals, WHO finds Experts describe findings as deeply concerning and predict 70% increase in related deaths by 2050 Hospitals across the world have recorded an alarming rise in common infections that are resistant to antibiotics, with doctors saying the number of deaths driven by drug resistance will increase sharply in the years ahead. One in six laboratory-confirmed bacterial infections were resistant to antibiotic treatments in 2023, with more than 40% of antibiotics losing potency against common blood, gut, urinary tract and sexually-transmitted infections between 2018 and 2023, records show. Continue reading...

Sharp global rise in antibiotic-resistant infections in hospitals, WHO finds

100k and rising!

This number will continue to grow.

Making hope normal again.
Join us.
join.greenparty.org.uk

On the biological meaning of the population pangenome The prokaryotic pangenome, the full complement of genes within a species, is strikingly large. To understand how ecological forces shape this diversity, it is useful to examine the variable gene pool within a single population, defined as cells of the same species coexisting in the same time and place. This single-population pangenome reflects the minimal flexible gene repertoire required in a specific environmental context. Recent long-read metagenomic studies of marine prokaryotes show that local population pangenomes remain large, often comprising thousands of genes. Specifically, cells belonging to the same species of the streamlined alfaproteobacterium Pelagibacter, coming from the same sampling site and even sample, contain more than a thousand genes. Many of these genes are related variants that collectively expand the population’s metabolic potential, akin to paralogs within a single large genome. We propose for them the name 'metaparalogs' together with the idea that these data reflect cooperative, population-level strategies, where the flexible genome operates as a public good (sensu Samuelson), enhancing both adaptability and ecological resilience. A role for extracellular vesicles in facilitating resource sharing is also suggested.

On the biological meaning of the population pangenome

The evolutionary foundations of transcriptional regulation in animals www.nature.com/articles/s41... (read free: rdcu.be/evDcA) 🧬🖥️🧪

The evolution of high-order genome architecture revealed from 1,000 species www.biorxiv.org/content/10.1... 🧬🖥️🧪 github.com/xjtu-omics/H...

Tissue destruction during food spoilage is associated with the formation of biofilms by Pseudomonas species https://www.biorxiv.org/content/10.1101/2025.07.11.664243v1

Patterns of compensatory mutations in rpoA/B/C genes of multidrug resistant M. tuberculosis in Uganda https://www.biorxiv.org/content/10.1101/2025.07.11.664293v1

1/27 We have a new paper out! Turns out that snowflake yeast have been hiding a secret from us - they've evolved a (very!) crude circulatory system. Not with blood vessels or a heart, but through spontaneous fluid flows powered by their metabolism. 🧪🔬

www.science.org/doi/full/10....

Higher-order epistasis drives evolutionary unpredictability toward novel antibiotic resistance https://www.biorxiv.org/content/10.1101/2025.07.08.663783v1

A few hours left for you to sneak in a cheeky last minute abstract! ECRs, you know what to do…
#mevosky

Fresh from peer review a new and improved version of @taoranfu.bsky.social’s paper out today in @asm.org mSystems
journals.asm.org/eprint/8NWNW...

Go Team! Deeply honoured that the MERMan lab reps won an @manchester.ac.uk‬ "FMBH heroes" award - thanks ‪@fbmh-uom.bsky.social‬ and @mermanchester.bsky.social for nominating us ❤️❤️❤️

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...

Curious about plasmid biology? Our latest paper is out now in Nature Communications! 🚨

doi.org/10.1038/s414...

We analyzed thousands of diverse bacterial plasmids to shed light for the first time on a key aspect of plasmid biology: plasmid copy number. 1/7 👇

Research Technician :Oxford Road

📣 Position available: Research tech in microbial experimental evolution! Working alongside postdoc Louise Flanagan (@flanagella.bsky.social) on understanding how Pseudomonas evolves resistance to antibiotics. 🦠🧫
Closing 9 July #Microsky
www.jobs.manchester.ac.uk/Job/JobDetai...

Mystique, a broad host range Acinetobacter phage, reveals the impact of culturing conditions on phage isolation and infectivity Author summary Bacterial infections caused by Acinetobacter baumannii are a major global health concern due to high antibiotic resistance, earning it a critical priority pathogen ranking by the WHO. P...

Mystique is here! When I started my position at @cmdi.bsky.social there were no readily available phage against my A. baumannii focal strain. The solution? Finding my own phage ofc. Mystique is a broad host range Acinetobacter phage, and I'm thrilled to see this work out today #PhageSky 🧪🦠

We're on a mission to #KeepAntibioticsWorking for generations to come, but we need your help

@profkevinfenton.bsky.social, @fphuk.bsky.social, tells us why this is such an important mission

📅 Join us on 7 April to learn exactly what steps you can take to help tackle this growing health challenge

Delighted to have won a poster prize at #microbio25 this week! Had a really great time at this conference, learned so much and met so many old (and some new!) faces. Thanks so much to the organisers for a great event and to the society for the travel grant too! 🚝🧪🦠

The MERMan contingent at #microbio25 headed home today after a great week in Liverpool for the @microbiologysociety.org annual conference - Thanks to the society and organisers for putting on a great event, and supporting us in presenting 6 talks and 5 posters packed full of microbial evolution!

@brockhurstlab.bsky.social giving a talk about eco-evolutionary mechanisms of AMR in the AMR session at #Microbio25

Microbiology Society Microbiology 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...

To all enjoying #MicroBio25 remember: all @microbiologysociety.org events rely on our journals - every paper pays 4x travel grants!

Make 2025 when you submit a paper to a MicroSoc journal www.microbiologyresearch.org

$0 OA for Publish+Read institutions www.microbiologyresearch.org/publish-and-...

Had a fab time presenting a flash talk at #microbio25 in the urogenital microbes session this afternoon. If you love a good biofilm or polymicrobial communities and want to find out more, I'd love to chat at my poster tomorrow - B086 👩🏼‍🏫 @microbiologysociety.org

Nice talk by @dralhubb.bsky.social at #microbio25. Urobiome as a possible reservoir of AMR for UTIs, including HGT and selection of spontaneous mutants!

Understanding and predicting microbial evolutionary dynamics - 2025 meeting

Thanks! Come to this awesome meeting in November if you can!? (Also in Liverpool!) - would be great to catch up!

microbiologysociety.org/event/societ...

@matthewjshepherd.bsky.social talking about clinical PA in chronic lung infection suggesting picking 10~20 colonies is pretty good for diagnosing pre-existing AMR #Mircobio25