Valuable summary of a couple days of our war no01.substack.com/p/march-19-2...

New preprint alert!!! 🚀🤓 We are very happy to finally share this with the world — the result of seven years of work and a new tool to study integrons and discover new functions encoded in these bacterial platforms. If you want to know more, here is a thread 🧵 www.biorxiv.org/content/10.6...

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/...

Dogs evolved to eat your leftovers! Comparing dog & wolf genomes revealed dogs have up to 30 EXTRA copies of the amylase gene (AMY2B) that helps digest starch. This is a key genomic signature of living alongside humans & table scraps for thousands of years 🐕 www.nature.com/articles/nat... #2026MMM

A single course of antibiotics can have lasting effects on your gut microbiome, with changes that last well beyond 4 years. Three types of antibiotics stood out for their long term disruptive impact (3 at left, Figure) nature.com/articles/s41...

Positive selection targeted primate genes that encode transposable element repressors academic.oup.com/gbe/article/...

New post, on whether I could get Claude Code to complete a data task that had taken me AGES a decade ago… kucharski.substack.com/p/how-much-t...

Good overview of an increasingly rapid-evolving field, including newly updated guidelines, non-antibiotic treatments and focus on quality of life. #UTISky academic.oup.com/cid/advance-...

This is amazing. www.getyourfuckingmoneyback.com

New paper out in MBE! 🧵 "Genomic Perplexity and the Evolution of Context-Dependent Function" The big idea: genes don't have fixed functions. Function emerges from context - genomic, cellular, environmental. And we can quantify this. academic.oup.com/mbe/article/...

New preprint from our Gates-funded Modjadji initiative showing that whole-genome surveillance of measles virus from wastewater greatly expands our ability for monitoring and control. Here, with our colleagues in South Africa - U.S., unfortunately, likely up next. www.medrxiv.org/content/10.6...

New Preprint 📢 from our team 🔎 Critical assessment of #intratumor and #low #biomass #microbiome using #longread sequencing Some studies suggest bacteria 🦠 live inside tumors and influence cancer treatment. But there’s also been a major #debate: in these very​ low-microbe tissue samples, how much 1/

Second paper from MRes (!!) student Caitlin Duggan; #AMR mechanisms and the challenges of actually measuring and defining what is "resistant", deep dive into #cefiderocol susceptibility testing & resistance mutations #MicroSky #IDSky 💻🧬 #MicrobiomeSky www.biorxiv.org/content/10.6...

Congrats to @carolinamicro.bsky.social for leading this study! We looked at genome rearrangements over short evolutionary timescales. Among other things, we found that genomes are highly syntenic within most species. However, several bacteria experienced sudden and massive genome rearrangements.

We just released #anvio v9, "eunice" 🎉 This version represents over 2,000 changes in the codebase since v8, increasing the total number of programs in the anvi'o ecosystem to 176. Read the release notes: github.com/merenlab/anv... Visit our up-to-date web page: anvio.org

Enterococcus fans: Check out our latest on E. faecalis EET, advancing our understanding of both the fundamental physiology of this bug and new mechanisms of its virulence. This is the product of a thrilling collaboration with friends in Singapore @gthibault.bsky.social led by @aarontan.bsky.social.

With this regime anything is possible…

Multiple large natural experiments have documented Shingles vaccine is linked with ~20-25% reduced risk of dementia and Alzheimer's disease. A new report today adds to that and extends the to slowing the progression of dementia @cellcellpress.bsky.social www.cell.com/cell/fulltex...

'Daptomycin is associated with higher treatment failure rates than alternatives for Enterococcus faecium bloodstream infections in critically ill patients: a multicentric retrospective cohort' link.springer.com/article/10.1...

Hot off the press! Our latest paper led by @fernpizza.bsky.social, understanding how plasmids evolve inside cells. These small, self-replicating DNA circles live inside bacteria and carry antibiotic resistance genes, but also compete with one another to replicate. 1/ www.science.org/doi/10.1126/...

We wrote the Strain on scientific publishing to highlight the problems of time & trust. With a fantastic group of co-authors, we present The Drain of Scientific Publishing: a 🧵 1/n Drain: arxiv.org/abs/2511.04820 Strain: direct.mit.edu/qss/article/... Oligopoly: direct.mit.edu/qss/article/...

Who did this?!

October 2025 batch of Kraken 2 indexes, including core_nt and many others, available: benlangmead.github.io/aws-indexes/k2 Coming soon to K2: a feature for querying many K2 indexes as though they're a single index. Highly useful if the index you want to query is too big to build and/or fit in RAM.

DNA from Napoleon’s 1812 army identifies the pathogens likely responsible for the army’s demise during their Russian retreat. www.cell.com/current-biol... Nicolás Rascovan & colleagues @currentbiology.bsky.social

Ok, I've learned something new - acid fast stains bind nucleic acids and not mycolic acid on mycobacterial cell wall. The lipid-rich cell wall simply prevents acid-alcohol decolourisation, hence acid -fast. #TBSky #IDSky @lancetmicrobe.bsky.social www.thelancet.com/journals/lan...

Around 10% of your Nanopore reads (SQK-RBK114) are incorrectly trimmed. Here is why, and how our new tool Barbell solves it: www.biorxiv.org/content/10.1... Want to get started? github.com/rickbeeloo/b...

Really exciting that the preprint on Barbell, a new demultiplexer, is finally out! It's the first tool that builds on Sassy, the approximate-DNA-searching tool that @rickbitloo.bsky.social and myself developed earlier this year, specifically with this application in mind.

Our @narjournal.bsky.social manuscript is out! It explores the growth of the GTDB (gtdb.ecogenomic.org) since its inception, as well as updates to the website, methodology, policies, and major taxonomic and nomenclatural changes over the past three years. academic.oup.com/nar/advance-...

New paper with my (amazing) friend and mentor @jrpenades.bsky.social Really looking forward to see what plasmid aficionados think of this one!! With @asantoslopez.bsky.social @wfigueroac3.bsky.social Akshay Sabins and others www.cell.com/cell-reports...

🆕🔥🔥CloCeBa RCT Cloxacillin versus cefazolin for MSSA Bacteraemia Cefazolin has a non-inferior efficacy regarding mortality, microbiological or clinical endpoints and was associated with a lower rate of serious adverse events #IDSky www.thelancet.com/journals/lan...

At first seems like comparing apples and oranges: moxifloxacin vs vancomycin?! Results a bit surprising ("narrow spectrum" vancomycin change microbiome more), but this is just helicopter view. More broadly, 👏 to these experimental medicine approaches for discovery science #IDSky #ClinMicro #AMR

Remarkable increase in vancomycin resistance among clinical Enterococcus faecium isolates in Italy (from 11.5% in 2015 to 32.4% in 2023). aricjournal.biomedcentral.com/articles/10....

#EuropeanResearchersNight is starting early in some countries! Today, from 11:00 to 16:00, Randi Bertelsen's team will be at the Research Square at Festplassen in Bergen. Her stand is called ''Puss, puss for friske lunger'' 🦷 🫁 🪥 🔬 🦠 More info: bit.ly/46uUi0v

Annual Norwegian NORM/NORM-VET report released. Norway’s strict antibiotic policies pay off. Record-low use in humans & animals, and some of Europe’s lowest #AMR rates. But ESBL & VRE are on the rise, so vigilance is vital. www.unn.no/4a675d/sitea...

X-Mapper 🦠🧬🧪 - a sequence aligner developed for microbes, now on Bioconda! 🚀 • 11–24× fewer suboptimal alignments (same for human genome) • 3–579× lower inconsistency • improves on ~30% of reads aligned to non-target species github.com/mathjeff/map... bioconda.github.io/recipes/x-ma... #microsky

Beautiful work 🎉 that resolved a long standing question: tumor microbiome, do they exist?🦠🧪 #microbesky

When using ARG databases, it is much better to have a low number of false positives, then to identify every gene under the Sun as a potential ARG. My preferred options are ResFinder and CARD (with the latter having some entries that are probably better considered housekeeping genes)

skani v0.3.0 is released. github.com/bluenote-157... - 30-40% potential reduction in memory with approximately the same runtime. - Breaking changes to indexing and searching databases Calculate ANI for contigs, genomes -- even search > 140k genomes. Pre-indexed GTDB-R226 available for download.

A natural experiment provides evidence for promoting moderate-vigorous physical activity: the importance of walkable cities www.nature.com/articles/s41...

Interested in respiratory metagenomics? We assembled nearly all of the virus genomes in a respiratory verification panel manufactured by ZeptoMetrix. Blog: artic.network/2025-07-26_p... Assemblies: github.com/bede/zmrp @scalene.bsky.social @pathogenomenick.bsky.social @articnetwork.bsky.social

I had a great time working with @adnsvrtsn.bsky.social on this one! journals.asm.org/doi/10.1128/...

1 To predict the behaviour of a primate, would you rather base your guess on a closely related species or one with a similar brain shape? We looked at brains & behaviours of 70 species, you’ll be surprised! 🧵Thread on our new preprint with @r3rt0.bsky.social , doi.org/10.1101/2025...

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/...

Interesting overview of the limitations of AlphaFold. As with all AI tools, try not to get hit by the hype-train. open.substack.com/pub/clauswil... (h/t @steveroyle.bsky.social)

Interesting, important paper on contamination in gut virome studies. I am not too keen on the term negativeome though www.nature.com/articles/s41...

🚨🚨New paper out in @natcomms.nature.com!! Come for the first large-scale analysis of plasmid copy number across species, stay for one of the most intriguing results of my lab: universal scaling laws in plasmid biology! 📈🧬 👉 www.nature.com/articles/s41...

Deacon: fast sequence filtering and contaminant depletion https://www.biorxiv.org/content/10.1101/2025.06.09.658732v1

The First Law of GPTs - "The more complex the topic, the more wrong it'll be".