Aspect Ratio as Driver of Bacterial Competition! Our latest work uncovers this simple and powerful determinant of bacterial competition. We demonstrate that longer bacteria consistently dominate colony fronts—even when outnumbered. The mechanism? Collective alignment. www.nature.com/articles/s41...

When we say "no, everything hasn't been digitized," I need you to understand that we really mean is that virtually nothing has been digitized. This is because the realm of primary sources that historians use is incomprehensibly large.

Now published in @natcomms.nature.com 🎉 www.nature.com/articles/s41... With Gillian Rodger, @nstoesser.bsky.social, @samlipworth.bsky.social, @stat-sarah.bsky.social, and many others!

If you want an example of gold standard genomics across every aspect of a paper, read this. It levelled me up. Covers #Acinetobacter baumannii. Recontextualises the global pop + reveals genuine insights. Includes development of software which types genomes too. www.nature.com/articles/s41...

I wish people uploaded reads instead of assemblies onto NCBI/ENA, if they're only gonna do one? Better yet, do both. More can be done with reads, and they can be reassembled when newer assemblers are written. I feel like this should be mandatory. No assembly upload without reads, IMO

Academics are making the decision to shove unpublished original research that isn’t even theirs into the plagiarism machine. I can’t.

This approach to clustering, sensitivity exploration, and data visualisation is implemented in a R Shiny app 💻 📊📈 developed by @erkison.bsky.social klebsiella.shinyapps.io/transmission...

#AMR #Klebsiella cause >100,000 neonatal deaths globally each year. Our new preprint shows more than half of #Klebsiella pneumoniae neonatal sepsis cases in African and South Asian are nosocomial, acquired through transmission in neonatal units. #WAAW doi.org/10.1101/2025...

(1/7) Really pleased to have this published in @natcomms.nature.com We looked at all public genomes encoding blaIMP (carbapenem #AMR ) 🦠🧫🧬💊. We show 5 IMP variants achieved global endemicity while 2 are regionally endemic. www.nature.com/articles/s41... #MicroSky #microbiology #IDSky #EpiSky 🧪

Why so many co-circulating #Klebsiella pneumoniae clones? By studying >7000 isolates, @bananabenana.bsky.social @kelwyres.bsky.social &co identify structured, clone-specific #metabolic specialisation across the population that enables reciprocal cross-feeding @plosbiology.org 🧪 plos.io/4qdC2B2

Absolutely stoked to have this published in @plosbiology.org We looked at the metabolism of #Klebsiella pneumoniae 🦠🧫. We not only demonstrated lineage-specific #metabolism, but that lineages can cross-feed and support each other. journals.plos.org/plosbiology/... #MicroSky #microbiology 🧬 🧪 💊

So all those tet(A)'s you are seeing in public data is possibly encoding #tigecycline #AMR, yet only n=74 papers? It didn't used to be though: Tigecycline originally "showed good activity against strains expressing...tet(A) efflux resistance determinants" journals.asm.org/doi/10.1128/...

❤️ eggNOG

Is the human microbiome a source for hospital-associated infections (HAI) and are any genetic changes associated with HAI? In our new preprint, we longitudinally reconstruct the evolutionary processes within the human microbiome leading up to HAI: doi.org/10.1101/2025...

Arrows are tricky. For us, as the designer of the visual, it will be super clear what it means. But for someone looking at our visual for the first time, it can be highly ambiguous. Depending on the reader, the same arrow can mean sequence, zoom, range, label, movement,... 1/2

Wanted to highlight a cool recent paper I read. If you work on #Pseudomonas 🦠🧫🧬 you should check this out. 39(!) P. aeruginosa strains tested via C. elegans slow-kill assays, followed by GWAS to identify novel accessory genome virulence factors #MicroSky #Microbiology doi.org/10.3389/fmic...

#NewResearch A widespread hydrogenase supports fermentative growth of gut bacteria in healthy people @greening.bsky.social #microsky www.nature.com/articles/s41...

London interdisciplinary #PhD position now open with myself, @sergemostowylab.bsky.social, & @gmknght.bsky.social on #phage -bacteria-host immune dynamics for WHO priority bacterial pathogens #Klebsiella, #Shigella, and #Staph. Combines cellular microbiology, genomics, & mathematical modelling.

As part of leaving Windows 10 behind and refusing to upgrade to W11 spyware (Windows Recall, ads etc), I've moved everything over to Pop_OS!. Moving OS has been challenging, even as someone familiar with Linux. `echo 'echo This is the right move (and distro) and it will get easier' >> ~/.profile`

We strive to credit labs collecting specimens and generating sequence data prominently. But credit for data contributions is not zero sum – surfacing of data in popular tools generates visibility and does not infringe on future publications by the data generators. 2/5

New paper: www.sciencedirect.com/science/arti... Klebs can evolve resistance to Colistin through mgrB mutation or by acquiring the mcr-1 gene. Both routes have similar fitness costs against a bacterial competitor, but mgrB mutations are associated with enhanced virulence.

For the sake of the entire #biology 🧪🧬🦠🧫🔬💊and #medsky science 🩺community, I think @enasequence.bsky.social and the #bioinformatics community needs to prioritise development of new tools and functionality in-line with #NCBI and #Genbank, before it potentially goes down sometime in the near future.

- "This library appears to be damaged" - "ImAgE mAdE WiTh BioReNDeR" What is the obsession universities have with paying companies instead of supporting free, often better, open source? Paid software is scientifically undemocratic and goes against #OpenScience. #SciSky 🧪

#WHO report shows rising #antibiotic resistance in common bacteria @katholt.bsky.social & @josebengoechea.bsky.social explain resistance worryingly high in #Klebsiella & E.coli as 1 in 6 lab-confirmed #bacterial infections in 2023 shown resistant to antibiotics. www.lshtm.ac.uk/newsevents/n...

Very excited to share the latest work from our lab, which was published today in Nature! nature.com/articles/s41... PhD graduate and now post-doc Sofia Dahlman, along with co-senior author Sam Forster from The Hudson and other researchers from our lab and others.

Research also shows that spreading smaller amounts of funding out over more researchers generally delivers better scientific outcomes per dollar spent than focusing bigger grants on fewer researchers. journals.plos.org/plosone/arti...

Unbelievable, Bakta reached its 1,000th citation! A huge shout out and thank you to all Bakta users, bug reporters, those sharing ideas and suggesting features... ...just the entire incredibly supporting binfie community! Without you, Bakta wouldn't be the same. Thank you!

reject chromatic aberration, embrace chromosomal aberration

Our new #klebsiella O type nomenclature, codesigned with Chris Whitfield, is now live in @pathogenwatch.bsky.social! Need a quick explainer on the new names? Check out my blog post: tinyurl.com/y8yb3rbb (+link to full review article) #MicroSky @klebnet.bsky.social @tomstantonmicro.bsky.social

Happy to share that the paper describing Autocycler is now 100% up: doi.org/10.1093/bioi... (1/3)

And as for writing, don't get me started. Most often, the process of writing is not a laborious business of transcription, but a process of thinking itself. I'm not about to outsource my thinking to a machine.

Staggering analysis here linking ciprofloxacin resistance to specific mutations in #Klebsiella. In short, using ONLY genotype, one can reasonably predict phenotypic CIP MICs! See Fig 3 (below). Loving the splitting of MIC and disk diffusion data as well. #AMR #MicroSky #IDSky

Celia also wrote about how we fitted 4.5 billion years in one image, at scale. chezvoila.com/blog/saguenay/

journals.plos.org/plosgenetics... #MicroSky

In another preprint from the @brianhie.bsky.social Lab and @synbiogaolab.bsky.social, they introduce Germinal, a generative AI system for de novo antibody design. Germinal produces functional nanobodies in just dozens of tests, making custom antibody design more accessible than ever before.

Terrific @scientificdiscovery.dev post on randomized controlled trials in @ourworldindata.org. Including this important chart on the impact of pre-registration. Magically, when people had to pre-register outcomes, many of the benefits disappeared. ourworldindata.org/randomized-c...

Automated, almost-error-free consensus #assemblies with Autocycler Impressive benchmarks in Fig 2B (below): ≤10 median errors PER genome Once again, incredible, landmark work from @rrwick.bsky.social doi.org/10.1093/bioi... Tool here: github.com/rrwick/Autoc... #bioinformatics #genomics

MMseqs2-GPU sets new standards in single query search speed, allows near instant search of big databases, scales to multiple GPUs and is fast beyond VRAM. It enables ColabFold MSA generation in seconds and sub-second Foldseek search against AFDB50. 1/n 📄 www.nature.com/articles/s41... 💿 mmseqs.com

Spacedust: a tool for de novo identification of conserved gene clusters from metagenomic data. @ruoshiz.bsky.social @milot.bsky.social www.nature.com/articles/s41...

Thrilled to share this preprint on Klebsiella pneumoniae plasmids in a One Health setting 🦠 Fantastic work by @twinkler.bsky.social! 🎉 @irenlohr.bsky.social @margaretlam.bsky.social

🎉 Delighted to share the first pre-print from my lab where we demonstrate that intergenic DNA repeats mediate phase variation of the mucoid phenotype in hypervirulent Klebsiella pneumoniae: www.biorxiv.org/content/10.1... #klebclub

"Paying the filter tax" - Honours student Josh on how volume is lost during syringe filtration.

For anyone who has used pling for comparing plasmids using rearrangement distances ("how many structural events apart are these plasmids"), here's how to tweak parameters, and integrate it with typing info, and the host phylogeny www.biorxiv.org/content/10.1... github.com/iqbal-lab-or...

A deadly tropical disease known as sleeping sickness has been eliminated from Kenya in a significant public health triumph. Uganda, Rwanda, Benin, Ghana, Cote d’Ivoire, Guinea, Equatorial Guinea, Chad, & Togo have also eliminated sleeping sickness. www.goodnewsnetwork.org/who-declares...

New blog post! I added a new feature to @gbouras13.bsky.social's Pypolca: homopolymer-only polishing. Potentially useful for cross-sample polishing - early test on Cryptosporidium looks promising. Check it out here: rrwick.github.io/2025/09/04/h...

The people have spoken: Best Lightning Talk goes to @bananabenana.bsky.social and Best Medium Talk goes to @munazzahmaqbool.bsky.social. Congratulations winner and winner, it was a pleasure listening to your talks! #MicroSeq2025

🌏Jocelyn Hume shows us how #sequencing was able to characterise the evolutionary trajectory and driving forces behind IMP-4 transmission. Delve into one of the largest global and regional #epidemiology studies of blaIMP-4 in #bacterial isolates! #MicroSeq2025 #plasmid

"For pathogen surveillance, we identify the trapped mosquitos morphologically, painstakingly individually" - Peter Mee #MicroSeq2025

github.com/matevz-kovac... Incredible work. Someone made a word square with 10 words. Had to be done algorithmically and involved citations to species names.

Will they ever fix these issues? We pay to publish Pay to read Write for free Edit for free Proofread for free And they won’t even give us a single login across journals 🤪