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@xavierdidelot.bsky.social et al. present the R package DiagnoDating for diagnosing issues in a reconstructed dated phylogeny, including outlier detection, posterior predictive checking, and residual analysis. 🔗 doi.org/10.1093/molbev/msag093 #evobio #molbio #compbio #phylogeny

DiagnoDating: diagnostics for dated phylogenies in microbial population genetics

Abstract. Microbial population genetic studies often involve the use of a dated phylogeny to show how the genomes are related over a relevant timescale. Ma

doi.org

Am stoked and thrilled that our latest paper is now out. A longitudinal study of invasive E. coli from children in the Netherlands over 50 years www.sciencedirect.com/science/arti...

Lineage dynamics of invasive Escherichia coli isolates in the Netherlands from 1975 to 2021: a retrospective longitudinal genomic analysis

Escherichia coli is a common cause of invasive infections such as bloodstream and cerebrospinal fluid infections in neonates. Strains positive for the…

sciencedirect.com

You can now view a tree of 2,399,238 bacterial genomes we made from AllTheBacteria (on the great Taxonium): taxonium.org/atb That's a big tree! (unless you're used to SC2 trees)

🚨Submissions open for the Cambridge Journal of Science and Policy (CJSP)! 🚨 CJSP invites submissions for Volume 7, Issue 1 under the theme "Infectious disease policy: research, surveillance, and resilience". Manuscripts for the themed issue must be received by 6th March 2026.

Great to share the latest work from our group and collaborators. First CARRIAGE study paper led by @drdaggarwal.bsky.social and the heroic efforts of Katie Bellis and Beth Blane in the lab plus all the team at @cambridge-ceu.bsky.social Huge thanks goes to the 22,000 participants of the study

Wellcome Sanger Institute@sangerinstitute.bsky.social · 8mo ago

People who persistently carry the bacterium Staphylococcus aureus have a much less diverse community of bacteria in their nose, while certain species may help keep it out. 🦠 These findings offer insight into who may be at higher risk of infection. 👇 www.sanger.ac.uk/news_item/la...

Happy to share our new AMR resource which has phenotypic AMR (usually MIC data) collected from publications and databases. This is paired with assemblies and annotations We're excited for users who might train new models, find phenotype/genotype mismatches, or any other use

EMBL-EBI@ebi.embl.org · 9mo ago

Antimicrobial resistance (AMR) is a growing health threat, making infections harder to treat and complicating routine medical care. EMBL-EBI’s new AMR portal brings together laboratory resistance data and bacterial genomes in one open platform. #WAAW2025 #ActOnAMR www.ebi.ac.uk/about/news/t... 🧬💻

On this day in 1955, Her Majesty Queen Elizabeth II and His Royal Highness The Duke of Edinburgh opened the Department of Veterinary Medicine building in Cambridge. Read more here: www.vet.cam.ac.uk/news/celebrating-70-years-cambridge-vet-school-building #CambridgeVet70 #VetMed #BeACambridgeVet

🐾 Exciting news The QVSH General Practice is open to pet owners across Cambs. We’re proud to be a not-for-profit practice and hospital. Register your pet - it's easy and you’ll be part of a community that helps shape the future of veterinary medicine. 👉 www.hospital.vet.cam.ac.uk/general-prac...

The next online version of our "Working with Bacterial Genomes" course is now open for registration. We aim to provide you with comprehensive training in analysing bacterial genomes covering everything from QC to clustering plasmids. Sign up here: www.training.cam.ac.uk/bioinformati...

I'm really excited to share the postdoc I completed before joining PHG. It combines two great passions - bacteria and horses!! Read more here: www.linkedin.com/posts/hayley... or go straight to the paper here: www.microbiologyresearch.org/content/jour...

Progressive evolution of Streptococcus equi from Streptococcus equi subsp.… | Hayley Wilson

I'm really excited to share this work with the world! As we know, academic research work will follow you even after you've left. So this is my post-doc project…

linkedin.com

Another week and more pipeline updates, this time my two assembly pipelines: Illumina: github.com/avantonder/a... ONT: github.com/avantonder/a... Have a try and let me know what you think

GitHub - avantonder/assembleBAC

Contribute to avantonder/assembleBAC development by creating an account on GitHub.

github.com

I've spent some time updating my two Nextflow-based bacterial QC pipelines (bacQC and bacQC-ONT). It'd be great to get some feedback. github.com/avantonder/b... github.com/avantonder/b...

GitHub - avantonder/bacQC-ONT: QC pipeline for ONT data

QC pipeline for ONT data. Contribute to avantonder/bacQC-ONT development by creating an account on GitHub.

github.com

Happy to share the findings of our latest work on mutational adaptation of Staphylococcus aureus during colonisation now published on @NatureComms rdcu.be/d55l3

The mutational landscape of Staphylococcus aureus during colonisation

Nature Communications - The authors applied a genomic and evolutionary approach to study Staphylococcus aureus in host adaptation during colonisation revealing signals of adaption in metabolic...

rdcu.be

📢 Apply now! We are recruiting an Associate Professor / Professor of Evolutionary Genomics to join our innovative research community! Find out more about the position and apply: https://buff.ly/4gIRTDf

Our paper investigating the mutational landscape during Staphylococcus aureus during colonisation is out now rdcu.be//d55l3 @fcic.bsky.social @sangerinstitute.bsky.social @ibv-csic.bsky.social University of Cambridge @julianparkhill.bsky.social

The mutational landscape of Staphylococcus aureus during colonisation

Nature Communications - The authors applied a genomic and evolutionary approach to study Staphylococcus aureus in host adaptation during colonisation revealing signals of adaption in metabolic...

rdcu.be

It’s official: The Microbiology Society is on Bluesky!

Great way to start the year! A paper in @nature.com by our amazing @noemie presenting a way to use sequences to identify pathogen lineages, quantify their fitness, and identify potentially important genes/snps . Works across bugs, even with minimally and biased set of sequences.

Noémie Lefrancq@noemielefrancq.bsky.social · 2y ago

Incredibly excited to share that our manuscript was just published in @nature.com ! What a way to start the new year! 🎉 https://buff.ly/4gyYCzx We present phylowave, a framework that enables to learn the fitness dynamics of pathogens from phylogenies. 🧵 A thread... 1/n #IDSky #IDModelling

Incredibly excited to share that our manuscript was just published in @nature.com ! What a way to start the new year! 🎉 https://buff.ly/4gyYCzx We present phylowave, a framework that enables to learn the fitness dynamics of pathogens from phylogenies. 🧵 A thread... 1/n #IDSky #IDModelling

Frustrating - I reviewed a paper that was highly problematic, mainly in scientific rigour undermining most of the conclusions, so I recommend Reject. However the editor decides to Revise presumably due to the more positive comments from reviewer 2... /1

Letter sent in to the Editor of the Guardian on brain microbiome nonsense.

* rolls up newspaper * No Guardian! Bad Guardian! An infection is not a microbiome! www.theguardian.com/lifeandstyle...

The brain microbiome: could understanding it help prevent dementia?

Long thought to be sterile, our brains are now believed to harbour all sorts of micro-organisms, from bacteria to fungi. How big a part do they play in Alzheimer’s and similar diseases?

theguardian.com

A big congratulations to Noémie Lefrancq on being awarded the Sir Kenneth Mather Memorial Prize🏅 for their exceptional PhD thesis on global dynamics of the bacterium behind whooping cough, using genomes from throughout Europe and the world! genetics.org.uk/medals-and-p...

Can colleagues amplify this appeal to journals and journal editors to open accounts on Bluesky, please? @MicrobioSoc @TrendsMicrobiol @CellCellPress @JBacteriology @jbiolchem @Nature @ScienceMagazine @PNASNews @MolMicroEditors @NAR_Open @NatureMicrobiol @NatureComms @ASMicrobiology 🙏 🦠🧪🧫🧬

We are looking for a Network Manager for TARGet (Transdisciplinary Antimicrobial Resistance Genomics network). Apply by scanning the QR code or via www.birmingham.ac.uk/jobs