Megan Phillips

Transition of Staphylococcus aureus tetracycline resistance plasmid pT181 from independent multicopy replicon to predominantly integrated chromosomal element over 65 years https://www.biorxiv.org/content/10.1101/2025.09.14.675889v1

Heads up: ignore samtools dot org, similarly minimap2 dot com and likely others. It's owned by a known phishing site and while the binaries they offer look valid currently (but note they may be serving us different binaries to others), that could change.

Ie: it's not us (Samtools team)! Be warned

Delighted to see the first version of our new ELife paper. A collaboration with Levi Morran, we show how an intact antibiotic resistance gene (mecA) changes the course of S. aureus evolution on a new host. Kudos to Michelle Su and Kim Hoang for making this happen.

elifesciences.org/reviewed-pre...

It was a great pleasure to contribute to this work by Jemma Fendley, @mmolari.bsky.social, and Boris Shraiman on pan-genomes, linkage, and recombination in phage genomes.

We analyzed data collected by the fantastic SEA-PHAGES program in phagesdb.org.

[1/6]

www.biorxiv.org/content/10.1...

ecoevojobs.net 2025-26

The 2025-26 Eco-Evo job list is out. Good luck to those applying!

docs.google.com/spreadsheets...

Population structure in a fungal human pathogen is potentially linked to pathogenicity Nature Communications - Genetic diversity between clinical and environmental fungal isolates of Aspergillus flavus is poorly studied. Here, the authors analysed genomic data from a global set of...

Thrilled to share that the final chapter of my PhD with @rokaslab.bsky.social is now out in @natcomms.nature.com 🎉
Read it to find out how population structure impacts pathogenicity in Aspergillus flavus, a fungus that infects humans 🧪
rdcu.be/eAToj

Slide designs that present themselves: The assertion–evidence template Your slides are not your talk.

A simple design framework that will massively improve your slides and your public speaking
clauswilke.substack.com/p/slides-tha...

These are the most challenging times for early-career scientists and engineers.

My team is doing its bit to help by maintaining and even expanding our database of funding opportunities for early-career researchers.

We found 437 of them.

Download it freely here: research.jhu.edu/rdt/funding-...

graphical abstract of the article the extended mobility of plasmids

Here's our new broad review on the extended mobility of plasmids, about all mechanisms driving and limiting their transfer. From conjugation to conduction, phage-plasmids to hitchers, molecular to evolutionary dynamics, ecology to biotech. The state of affairs. 1/9 academic.oup.com/nar/article/...

Looking forward to seeing everyone, new and old, at the Microbial Population Biology GRS + GRC in just a couple days!

go.bsky.app/GGxRjzC

Title slide for June 24, 2025 talk "The little plasmid that could: evolution of a small antimicrobial resistance element," in the Bioinformatics & Molecular Evolution Session. Orange slide background with white circular outline around talk information. Presenting/1st author is Megan Phillips (at Emory University), other authors are Robert Petit, Daniel Weissman, & Timothy Read.

I’m excited to present my work on mobile genetic element evolution at #Evol2025 on Tuesday, June 24! Come by the Bioinformatics & Molecular Evolution session at 9:45am for my talk, “The little plasmid that could: evolution of a small antimicrobial resistance element” (room Athena F)

Our very first Wild Yeast Sampling day!!

From garden to genome - this summer our group is going to learn how to find and sequence wild yeast

Awesome collab with @morgancarterphd.bsky.social

My hope is that we can bring this to the classroom very soon!

Do people in the same household share strains when they have the same species?

How many cells transmit when a strain is shared?
Can strain composition be dynamic when species composition is stable?

We answer these and related questions for the facial skin microbiome in our latest paper.

🧵[1/10]

It's NOT safe for non-citizens to cross the US border at this time.
- Academic conferences in the US must recognize the right of authors abroad who'd prefer not to travel.
- Those outside the US must recognize the right of non-citizen authors in the US who'd prefer not to travel.
NO QUESTIONS ASKED.

Geographic divergence of methicillin-resistant Staphylococcus aureus ST5-SCCmecI in the aftermath of a major earthquake and tsunami: impact of a plasmid harboring heavy metal resistance genes | mBio Methicillin-resistant Staphylococcus aureus (MRSA) is a major cause of life-threatening infections worldwide and a growing public health concern. The rise of antibiotic-resistant bacteria, such as MRSA, is often linked to genetic adaptations that enhance ...

Proud to be part of this group! journals.asm.org/doi/10.1128/...

LoVis4u: a locus visualization tool for comparative genomics and coverage profiles Abstract. Comparative genomic analysis often involves visualization of alignments of genomic loci. While several software tools are available for this task

Excited to share that our paper on locus visualisation tool LoVis4u is out! Entirely driven by fantastic PhD student Artyom Egorov @egorov.bsky.social academic.oup.com/nargab/artic...

2025 Study section tracking

Wondering if your study section cancelled? I update this sheet daily. As of today, 56/124 study sections that should have met since Jan 2, 2025 have "not met as scheduled." docs.google.com/spreadsheets...

Do you work in ecology/evolution? Did you do a study that is too small to publish as a full manuscript? Negative results? Part of a larger effort? Consider publishing in microPublication Biology: EEB!

www.micropublication.org/journals/bio...

Short papers, one figure. And we peer review! Please RT

Many purported pseudogenes in bacterial genomes are bona fide genes - BMC Genomics Background Microbial genomes are largely comprised of protein coding sequences, yet some genomes contain many pseudogenes caused by frameshifts or internal stop codons. These pseudogenes are believed ...

This is very intriguing -

Many purported pseudogenes in bacterial genomes are bona fide genes

bmcgenomics.biomedcentral.com/articles/10....

Mandatory reading and surprising results from Michael Hall and colleagues - much better bacterial SNP/indel calling results from latest nanopore (beating illumina), and deep learning methods really doing well. Extremely thorough work
www.biorxiv.org/content/10.1...

Please share: Our 2024-25 RaMP postbac scholars program is now open for applications. If you (or anyone you know) recently graduated and are interested in microbiome research but didn’t have the opportunity to engage in meaningful research during your degree, check us out!!

A poster for a workshop called “Communication, Narratives, and Antimicrobial Resistance”. 9am to 6pm 16th May 2024. Merton College, University of Oxford.

Very excited to announce our transdisciplinary AMR workshop 🎉

Join us to hear perspectives and discussion from patient activists, journalists, philosophers, microbiologists, historians, clinicians, policy makers, and artists. More info: www.torch.ox.ac.uk/event/commun...

Plasmid-encoded insertion sequences promote rapid adaptation in clinical enterobacteria bioRxiv - the preprint server for biology, operated by Cold Spring Harbor Laboratory, a research and educational institution

New preprint in collaboration with @asantoslopez.bsky.social lab and led by Jorge Sastre. Combining experimental evolution and analyses of longitudinal samples from hospitalised patients, we unveiled a new mechanism of plasmid-mediated evolution beyond HGT 1/8
www.biorxiv.org/content/10.1...

How to validate a Bayesian evolutionary model https://www.biorxiv.org/content/10.1101/2024.02.11.579856v1 Biology has become a highly mathematical discipline in which probabilistic models play a central rol

How to validate a Bayesian evolutionary model https://www.biorxiv.org/content/10.1101/2024.02.11.579856v1

my hopes for gen z taking over the academic process is that it will be matched for harshness, but at least more efficient

Atlanta @meehubs.bsky.social participants, join us at 2:15pm in the main room for the ggtricks() workshop! Hone your ggplot and data manipulation R skills by exploring a dataset of Pokémon stats 📊
github.com/veganm/MEEHu...

A new study from our group and Tim Read at Emory, focused on understanding the role of genomic diversity of Pseudomonas aeruginosa on antibiotic resistance diversity in cystic fibrosis patients. journals.asm.org/doi/10.1128/...

Mutators can drive the evolution of multi-resistance to antibiotics Author summary The global rise in antimicrobial resistance means we urgently need new approaches that halt its spread. Combination therapy, using multiple antibiotics as one treatment, proposes to do ...

📣 Paper: We show that mutators can drive the evolution of multi-resistance to antibiotics, in cases where purely wild type populations can't

This came out earlier this year while the other place was imploding

But it's a story I'm proud of for many reasons...

1/n

journals.plos.org/plosgenetics...

#R Package Update:

There are ~2x as many colorblind-friendly color palettes🎨 in ggpubfigs, which can help make your #figures📊 accessible to as many people as possible

Link to GitHub: github.com/JLSteenwyk/g...
Link to Publication: journals.asm.org/doi/10.1128/...