April Hayes

Cover of Microbiology Outlooks featuring an article by Dr Damien Meyer on integrating game dynamics with within-host evolution genomics.

Is virulence a fixed trait? This first commentary in Microbiology Outlooks considers why it may be better understood as a context-dependent evolutionary strategy. Discover the Open Access article: https://doi.org/10.1099/mout.0.00001

🚨 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...

(President's Doctoral Scholar Award) A mechanistic understanding of microbe-immune cross talk in the face of pollutant challenge at The University of Manchester on FindAPhD.com PhD Project - (President's Doctoral Scholar Award) A mechanistic understanding of microbe-immune cross talk in the face of pollutant challenge at The University of Manchester, listed on FindAPhD.c...

📣 2026 PhD studentship 📣
Via @manchester.ac.uk 's President's Doctoral Scholar Awards, we are encouraging applications for a PhD on the effect of pollutant exposure on microbe-immune cross talk. This project will incorporate microbiology, immunology, & bioinformatics. Deadline: 16 March 2026!

He may have only barely known about bacteria, and not at all about viruses, but Darwin was right about hating an ill-defined species concept

The Resistance-Nodulation-Division efflux pump EefABC is highly conserved within lineages of E. coli commonly associated with infection Resistance-nodulation-division (RND) efflux pumps confer multidrug resistance in Gram-negative bacteria and are critical for many physiological functions including virulence and biofilm formation. The...

The coolest finding of my PhD is finally out! E. coli has a 7th RND pump that is present in phylogroups B2/D/E/F but absent in A/B1/C. As a result EefABC has been absent in all K-12 RND studies! Co-authored by the very talented Dr. Lizzy Darby. @jessicamablair.bsky.social
doi.org/10.1099/mgen...

Genome-wide association analyses highlight the role of the intestinal molecular environment in human gut microbiota variation - Nature Genetics Population-based studies from Sweden with replication in Norway identify associations between host genetic variants and gut microbial composition and implicate short-chain fatty acid chemosensors as m...

Delighted to have contributed to this impressive work led by @tovefall.bsky.social & many others👏 (w/ @gazollavolpiano.bsky.social from our side). This novel microbiome GWAS (n=~16k+12k valid) expands knowledge on genetic factors associated w/ gut microbiota variation.
www.nature.com/articles/s41...

Co-occurrence is associated with horizontal gene transfer across marine bacteria independent of phylogeny Abstract. Understanding the drivers and consequences of horizontal gene transfer (HGT) is a key goal of microbial evolution research. Although co-occurring

Now out & nicely formatted in @isme-microbes.bsky.social

A big analysis of ocean genomes & metagenomes co-led by former postdocs, now PIs, @gmdouglas.bsky.social & @cyanophage.bsky.social along with co-PIs @lbobay.bsky.social & Samuel Chaffron.

A few highlights... 🧵 (1/n)

doi.org/10.1093/isme...

I am pleased to share that our paper is now published in Cell!
www.cell.com/cell/fulltex...
I am deeply grateful to all co-authors for making this possible.

This work was made possible through the guidance of Dr. Peer Bork. I share this in grateful memory and with deep respect for his mentorship.

(CODE M) Losing your head: how do bacterial viruses evolve into anti-competitor weapons? at The University of Manchester on FindAPhD.com PhD Project - (CODE M) Losing your head: how do bacterial viruses evolve into anti-competitor weapons? at The University of Manchester, listed on FindAPhD.com

🚨 PhD Studentship available! 🚨

We're hiring a UK student to start in Oct '26 via the BBSRC CODEM scheme. Full studentship plus £10k top-up PA. Study the mysterious ZOMBIE PHAGES 🧟 🦠 with our fabulous @mermanchester.bsky.social and @uommib.bsky.social communities!

www.findaphd.com/phds/project...

At long last, my final PhD chapter is out: we developed a novel evolutionary simulator of bacterial pangenomes, Pansim, fitting it to data from >600K genomes using a likelihood-free framework, PopPUNK-mod, to explore neutral and adaptive pangenome dynamics www.biorxiv.org/content/10.6...

Historical contingency limits adaptive diversification in a spatially structured environment Abstract. Understanding how genotype-by-environment (G × E) interactions influence evolutionary trajectories and contribute to historical contingency is ke

Historical contingency limits adaptive diversification in a spatially structured environment

@evolletters.bsky.social from @megbehri.bsky.social

academic.oup.com/evlett/artic...

New round of PhD studentships in microbial engineering, including one with me on engineering non-canonical DNA mismatch repair into E. coli 🦠🧬
www.findaphd.com/phds/project...

PhD projects in microbial engineering now up, including one with @whelanfj.bsky.social @willpjsmith.bsky.social and me! 🦠

www.findaphd.com/phds/project...

Novel artificial selection method improves function of simulated microbial communities Author summary Artificial selection has been extremely powerful in improving properties of complex biological or biochemical entities. The most familiar examples come from the breeding of animals and ...

Thrilled to see this paper finally out! journals.plos.org/ploscompbiol... It was a difficult story to communicate and took us a while to get right. Big congratulations to @wbjorn.bsky.social, Pablo Guridi and Flora Arias-Sanchez!! And thank you the reviewers who helped improve it. Keep reading...

🚨 Fully‑funded PhD for Home Students🚨

We'll explore non-antibiotic alternatives in relatistic environments, uncovering how they work, if they affect antibiotic activity and whether they influcence AMR acquistion. Come join a wonderful supervisory team!

#MicroSky #UTISky #AMar

tinyurl.com/38u552bu

How to lead a journal club you won’t be embarrassed by later One of the jobs facing an early-career scientist, and a developing writer, is to learn what their field’s literature looks like. One of the best tools to that end is the journal club. If you’ve nev…

It's easier to tear down than build up, and in science we have a bad case of that. So: how to lead a journal club that actually finds value in what you read. scientistseessquirre... 🧪

"84.9% of colleagues on FTCs reported that their contracts had negative impacts upon their wellbeing"

^ As long as fixed-term contracts (FTC's) are the norm for early-career scholars + many others, then our workplaces are structurally screwing us.

There's still a few days left to apply for our AI-Intervene PhD project mapping the drivers of avian influenza using viral genomics, bird migration data and AI-powered phylodynamics.

Come join us! Details below.

#FindaPhD #LondonPhD #genomics

Biased sampling driven by bacterial population structure confounds machine learning prediction of antimicrobial resistance Machine learning methods have emerged as promising tools to predict antimicrobial resistance (AMR) and uncover resistance determinants from genomic data. This study shows that sampling biases driven b...

Our preprint on predicting drug resistance in bacteria is now out in @plosbiology.org. We show ignoring phylogenetic structure in genome collections leads to overly optimistic evaluations of machine learning methods for AMR prediction. Work from @yanyingyu.bsky.social with @nwheeler443.bsky.social.

🦠🧫 a collaboration with the Institute for Tropical Medicine in Tübingen and CERMEL in Gabon @cmfi.bsky.social

Asexuality is a global identity.

That’s a major finding in a study I recently published with @francescorampazzo.com in Demographic Research.

Analyzing dating app data spanning 162 countries from over 900,000 users, we found that asexuality showed up in every age group and in every region.

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/...

We're excited to release metaTraits.embl.de! 🦠 Interactively explore 140+ 𝗺𝗶𝗰𝗿𝗼𝗯𝗶𝗮𝗹 𝗽𝗵𝗲𝗻𝗼𝘁𝘆𝗽𝗶𝗰 𝘁𝗿𝗮𝗶𝘁𝘀, harmonized & integrated from culture-derived collections 🔬 & genome-based predictions 🧬 for >2M MAGs & genomes.

Publication at NAR: doi.org/10.1093/nar/... @narjournal.bsky.social #microsky 🧵 1/8

It’s not only medications—environmental chemicals can also inadvertently harm our gut microbes. Excited to have contributed a bit to this important study!

Microplastics pose a human health risk in more ways than one New study shows that microplastics in the natural environment are colonized by pathogenic and antimicrobial resistant bacteria. The study team calls for urgent action for waste management and strongly

🚨‼️ New paper alert!

‘Sewers to Seas: exploring pathogens and antimicrobial resistance on microplastics from hospital wastewater to marine environments’

FULL ARTICLE: www.sciencedirect.com/science/arti...

➡️ Check out @pml.ac.uk’s coverage: pml.ac.uk/news/micropl...

Great to see our @exeter.ac.uk and @pml.ac.uk research highlighted in @uk.theconversation.com 🤟🙏

➡️ theconversation.com/plastic-bio-...

Are you looking for a wild PhD opportunity? 🦠🧵

There are several opportunities to join the Wild Microbiome Lab in 2026! Scroll for more information, or visit the link below for full project descriptions and application information👇

xavharrison.github.io

NERC RED-ALERT CDT: Green Rivers: harnessing freshwater algae for bioremediation and critical metal recovery. at University of Exeter on FindAPhD.com PhD Project - NERC RED-ALERT CDT: Green Rivers: harnessing freshwater algae for bioremediation and critical metal recovery. at University of Exeter, listed on FindAPhD.com

Exciting PhD position on algal-driven metal remediation with Dr Michiel Vos and collaborators at the University of Exeter. This project combines plant and microbial ecology, and geochemistry to develop innovative biological solutions for metal pollution

www.findaphd.com/phds/project...

Geographics and bacterial networks differently shape the acquired and latent global sewage resistomes - Nature Communications Antimicrobial resistance genes that have been mobilized between bacterial species represent a subset of the naturally occurring resistome. Here, the authors compare the abundance, diversity and geogra...

📢 New paper in @natcomms.nature.com

Geographics and bacterial networks differently shape the acquired and latent global sewage resistomes
doi.org/10.1038/s414...

Thrilled to share this massive global effort led by H.M. Martiny, @patrickmunk.bsky.social, F. Aarestrup & the Global Sewage Consortium

A lot has happened since our first announcement of #ExE2026, an evolutionary ecology conference hosted by @uniexecec.bsky.social in #Cornwall from June 29 to July 3 2026.

Have a look at our new website to see our confirmed plenary speakers, the mid-conference excursions, and more.

👉 evoxeco.uk 👈