#MENI2026 was brilliant. Excellent talks, posters, and discussions. Thanks @siderophile.bsky.social @paulinedscanlan.bsky.social for the invite and for organising such a great event!
Pauline Scanlan
@paulinedscanlan.bsky.social
School of Microbiology and APC Microbiome Ireland, University College Cork 🇮🇪 Microbial Ecology | Microbial Evolution | Gut Microbiome
And that’s a wrap on #MENI2026! What a great day of microbial evolution research, and a pleasure to host at Trinity with @paulinedscanlan.bsky.social
Looking forward to a full day of microbial evolution today! I’ll be talking this morning about evolution of AMR from my work with @alanmcn1.bsky.social
Much has been written about The Selfish Gene, and few books have been both as influential and as persistently contested. To commemorate its 50th anniversary, here are some brief thoughts in the latest issue of @science.org. www.science.org/doi/10.1126/...
A provocative view of evolution turns 50
The Selfish Gene continues to challenge readers half a century later
science.org
Nine (not so simple) steps: a practical guide to using machine learning in microbial ecology Step 1: Determine whether machine learning is necessary or even worth doing journals.asm.org/doi/10.1128/...
Nine (not so simple) steps: a practical guide to using machine learning in microbial ecology | mBio
Microbial ecologists are increasingly turning to machine learning (ML) models to better identify and predict meaningful biological patterns and relationships in molecular microbial community data (inc...
journals.asm.org
See several blog posts by @paulbrainey.bsky.social 🤔 e.g. The demand behind predatory publishing academicrenewal.substack.com/p/the-demand... 👇🧵 [1/5]
The demand behind predatory publishing
How predatory publishing led to academic renewal
academicrenewal.substack.com
Very happy that this piece of research finally sees the daylight! Super nice collaboration between Nanjing, York and Helsinki. Fun fact: we started this work over 10 years ago when I was working as a fellow at Imperial College. Sometimes good things come to those who wait.
Nature Microbiology@natmicrobiol.nature.com · 2mo agoOut Now! Bacteria–phage coevolution drives variation in bacterial wilt disease incidence via resistance–virulence trade-offs #MicroSky
Do you study human microbiomes? Have you used the word "commensal"? Then this paper was written with you in mind! It was an absolute pleasure to write this with the incomparable @ginalewin.bsky.social journals.asm.org/doi/10.1128/...
mGem: Tapping into the language of symbiosis to advance human microbiome research | mBio
An overarching goal in microbiome research is to understand how the complex communities in our bodies contribute to health and disease, and ultimately, we aim to leverage and control these communities...
journals.asm.org
This is very cool: a simple statistical test of dysbiosis, or really any microbiome composition data relative to a reference. Outperforms Bray-Curtis and every other metric, while simultaneously being very simple to compute. Probably would work on RNAseq data too.
bioRxiv Microbiology@biorxiv-microbiol.bsky.social · 3mo agoRatio Percentile Deviation (RPD): A nonparametric, compositionally robust method for measuring the divergence of a microbial sample from a reference dataset https://www.biorxiv.org/content/10.64898/2026.05.27.728224v1
Wrote a short piece on Transposable Elements as catalysts of evolutionary innovation for a forthcoming special issue of @naturerevgenet.bsky.social on, duh, Evolutionary Innovation! www.nature.com/articles/s41...
Transposable elements as catalysts of evolutionary innovation - Nature Reviews Genetics
In this Comment, Cedric Feschotte highlights evidence from diverse lineages showing that transposable elements are key drivers of evolutionary innovation, repeatedly introducing regulatory and coding ...
nature.com
Great piece and cover @science.org about how our field is uncovering the evolutionary and mechanistic connections between bacterial and eukaryotic immunity ! www.science.org/content/article/ancient-wars-between-microbes-gave-us-key-immune-defenses
Being a PI is an intricate juggling act that requires tough decisions – intellectual, financial, strategic. Yet we are expected to navigate these dangerous waters with very little support. The solo PI model is deeply problematic. My latest blog post #AcademicSky occamstypewriter.org/mindthegap/2...
In which no scientist is an island – but that’s what we signed up for | Mind the Gap
occamstypewriter.org
With Eugene Koonin, we wrote a rather comprehensive review on the origin, evolution and organization of the #virosphere. We describe all 10 viral realms and the logic behind them, and so much more. Check it out! comptes-rendus.academie-sciences.fr/biologies/ar...
Pollution levels in Paris after 10 years of advancing sustainable transport.
Heterogeneity in microbial antibiotic responses: genetic basis and within-host evolution @cp-trendsgenetics.bsky.social review by Qingyun Liu and Liang-Dong Lyu (吕亮东) www.cell.com/trends/genet...
Heterogeneity in microbial antibiotic responses: genetic basis and within-host evolution
Antibiotic response phenotypes have traditionally been classified as either sensitive or resistant. However, accumulating evidence indicates that bacterial responses to antibiotics are far more hetero...
cell.com
Many thanks to the @microbiologysociety.org for inviting me to give a talk on #Blastocystis during the #microbio26 in Belfast! It was such a great opportunity to share the work of our @blastocystiscost.bsky.social as well! @costprogramme.bsky.social
🆒 new pub! Rapid evolution of Klebsiella pneumoniae biofilms in vitro -> adaptations selected during infection by @gretazabo.bsky.social & Linus Sandegren *hypermucoidy evolves via 📈c-di-GMP, overlaps w/ mutations in UTI and wound isolates. *pleasure to advise this! www.nature.com/articles/s41...
Rapid evolution of Klebsiella pneumoniae biofilms in vitro delineates adaptive changes selected during infection - Nature Communications
Biofilm formation on implanted medical devices facilitates infection by the pathogen Klebsiella pneumoniae. Here, Zaborskytė et al. use experimental evolution to show that the bacteria rapidly evolve ...
nature.com
How should new #Blastocystis subtypes be named? A new @cp-trendsparasitol.bsky.social forum paper argues for minimum standards, incl. near full-length SSU rRNA data & replication, to keep subtype naming stable across studies. With @paulinedscanlan.bsky.social #Parasitology 📰 buff.ly/PVvtrxO
This is absolutely fantastic. ht: @maddenifico.bsky.social
Our work on 'hidden diversity' in unbinned contigs is now published in @natmicrobiol.nature.com : www.nature.com/articles/s41... See the linked threads for more details!
Unbinned contigs expand known diversity in the global microbiome - Nature Microbiology
Re-analysis of over 92,000 metagenomes reveals hundreds of thousands of previously undescribed Bacterial and Archaeal clades hidden in plain sight.
nature.com
Sebastian Schmidt@tsbschm.bsky.social · 9mo agoWe've updated our recent @biorxivpreprint.bsky.social on 'Hidden but discoverable diversity in the global microbiome', led by @vishnuprasoodanan.bsky.social & @omaistrenko.bsky.social www.biorxiv.org/content/10.1...
It's me in the Financial Times, detailing the deep and pernicious influence of one-size-fits-all management consultancy in our universities... Take a look! 👇 www.ft.com/content/5032...
Management consultants are ruining UK universities
Relentless off-the-peg commercial rewiring has undermined British higher education
ft.com
Thanks to @siderophile.bsky.social for an excellent seminar today @uccmicrobiology.bsky.social showcasing how multiple stressors effect the ecology and evolution of soil microbes thanks to @microscrum.bsky.social for organising!
MEEHubs2026 registration and abstract submission is now online! 🚨🦠✨ Join us Aug 3 - 5, 2026 at one of the 7 hubs or online. We are incredibly excited about our lineup of speakers, and hope that you submit an abstract to contribute too! More information and registration links at: meehubs.org
Home
meehubs.org
New paper 🔔 Collaboration @sullivan-lab.bsky.social Marissa Gittrich led the work Klebsiella phage biology has focused almost entirely on capsulated strains, but capsule loss is the #1 resistance mechanism under phage predation. We used a naturally acapsular host to reveal the receptor landscape
With @saramitri.bsky.social, @sonjalehtinen.bsky.social and L. Lehmann we’ve launched the UNIL Center for Theory in Ecology and Evolution @unil.bsky.social🇨🇭 To kick things off, we’re offering short visiting fellowships for theorists in ecology & evolution. Apply & pls RP 😀 tinyurl.com/2wem36zz
Unil center for theory in ecology and evolution (UCTEE) - FBM Unil
Page Unil Center for Theory in Ecology and Evolution of site Faculty of Biology and Medicine hosted by the University of Lausanne
unil.ch
I’ve spent a lot of time over the past two years thinking about genome evolution and how recent research revealing complex gene-gene interactions has complicated traditional ‘gene-centric’ genomic approaches to evolution. So here is a review that consolidates these thoughts! rdcu.be/e6pHY
Epistasis and co-adaptation in bacterial genome evolution
Nature Reviews Genetics - Bacterial genome evolution is shaped by epistasis, which can constrain or promote specific evolutionary paths. The authors review how integrating the effects of epistatic...
rdcu.be
📢 Hiring a Postdoc in Computational Phage Biology (Kraków, Poland) We study the evolution & structural modularity of prophage-encoded glycan-degrading enzymes in Klebsiella pneumoniae — combining genomics and AlphaFold-based analyses. Details in attached PDF 👇
Postdoc Ad
Postdoctoral Position in Computational Phage Biology Microbial Genomics Group, Malopolska Centre of Biotechnology (MCB), Jagiellonian University, Kraków PL Summary We are seeking a postdoctoral rese...
docs.google.com
Courtesy of @martibartfast.bsky.social , we have a new release of AllTheBacteria which adds another 322,920 assemblies, covering all ENA (illumina, isolate) prokaryotes to May 2025. allthebacteria.readthedocs.io/en/latest/ov...
Overview — AllTheBacteria documentation
allthebacteria.readthedocs.io
here is a comprehensive history of the use of agar in microbiology by corrado nai 👇 🙏 thx for pointing this out @microbingle.bsky.social earlier, corrado told the story of fanny angelina hesse in STC. #MicroSky
Have you ever heard of Fanny Angelina Hesse?
by Corrado Nai — A graphic novel about this forgotten woman in science is on its way – but it's unlikely to make an impact without the strong support from the microbiology community. If you have n…
smallthingsconsidered.blog
microbingle.bsky.social@microbingle.bsky.social · 6mo agoThe origins of agar www.asimov.press/p/agar
Our latest is out today in @plosbiology.org: "Metabolic modeling reveals determinants of prebiotic and probiotic treatment efficacy across multiple human intervention trials" @isbscience.org @uwbioe.bsky.social @uwgenome.bsky.social doi.org/10.1371/jour...
Metabolic modeling reveals determinants of prebiotic and probiotic treatment efficacy across multiple human intervention trials
Prebiotic and probiotic interventions can induce therapeutically relevant shifts in the human microbiome, but their effects are variable across individuals. This study shows that metabolic models can ...
doi.org