Matthew J Shepherd

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

An image of University of Manchester scientists with details of their poster numbers and titles on display at the Microbiology annual conference.

In addition to @brockhurstlab.bsky.social @matthewjshepherd.bsky.social 's upcoming talks in the AMR session today, we have many @mermanchester.bsky.social posters on display! Come learn from our talented scientists about evolution, AMR, and microbiomes #microbio25

Looking forward to speaking in the AMR mechanisms and regulation session at #Microbio25 today. I'll be speaking right after @brockhurstlab.bsky.social who will discuss our within-patient resistance evolution project, and I'll outline some measures we can take against resistance evolution in-host

Absolute treat to see @relenski.bsky.social tell the story of 37 years of science and evolution at #microbio25, a proper 'conference bucket list' moment for me, reading the LTEE story as an undergrad definitely motivated me to get into experimental evolution!

Great talk on the rising issue of biocide tolerance by Vicky Bennet in the AMR mechanisms and regulation session - multiple mutations from evolution experiments of Proteus mirabilis match those seen in clinical isolates!

Great talk by @mermanchester.bsky.social member @whelanfj.bsky.social at Microbiology Society annual conference - insights on 600 cumulative years of P. aeruginosa within-patient evolution by the prairie epidemic strain! 🤯

Etats-Unis : un chercheur français refoulé pour avoir exprimé « une opinion personnelle sur la politique menée par l’administration Trump » Le ministre de la recherche a dit sa « préoccupation », mercredi, après cette décision des autorités américaines. Le chercheur du CNRS aurait subi un contrôle aléatoire à son arrivée, avant que son or...

French researcher, going to a conference in Houston, was forbidden entry to US; his work and personal electronics were both confiscated.

Why? Because a “random search” of his cell phone revealed a negative personal opinion on Trump and the Trump administration. www.lemonde.fr/internationa...

Screenshot of text from a Nature Ecology & Evolution Editorial entitled "Deep cuts"

In our latest Editorial we discuss the continuing damage being done to US science, and its impact on researchers and the environment 👇

Deep cuts: www.nature.com/articles/s41...

They are talking about going back to *already awarded grants* and canceling them, or slashing the budget of them, for doing the *legally mandated* broader impacts.