March, 19-21: God is a comedian A stiff drink is recommended

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/...

Adapted from Axelsson et al. 2013 Fig 2c: Histogram showing the distribution of diploid amylase copy number in wolf (n=35, blue) and dog (n=136, red). Dogs carry more copies of the starch-digesting gene AMY2B than wolves. Additional copies make dogs better than wolves at digesting starchy foods like grains & vegetables.

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...

Uncomplicated Urinary Tract Infections: From an Invisible Impact to a Visible Change in Complex Care Uncomplicated UTIs may have high recurrence rates in subsets of patients, causing a substantial burden. Increasing antimicrobial resistance in uropathogens

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

Genomic Perplexity and the Evolution of Context-Dependent Function Abstract. The fundamental principle that selection acts on a gene’s function often assumes implicitly that this function is fixed and intrinsic. However, e

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/...

Integrating measles wastewater and clinical whole-genome sequencing enables high-resolution tracking of virus evolution and transmission Measles outbreaks have surged globally in recent years, but current surveillance systems have limited capacity to monitor measles virus (MeV) transmission and evolution at population scale. Although M...

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 - Critica... Background Enterococcal infections represent 10% of intensive care unit (ICU)-acquired infections and are associated with adverse outcomes, particularly in the case of E. faecium infections. Some stud...

'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...

Intracellular competition shapes plasmid population dynamics From populations of multicellular organisms to selfish genetic elements, conflicts between levels of biological organization are central to evolution. Plasmids are extrachromosomal, self-replicating g...

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/...

A table showing profit margins of major publishers. A snippet of text related to this table is below. 1. The four-fold drain 1.1 Money Currently, academic publishing is dominated by profit-oriented, multinational companies for whom scientific knowledge is a commodity to be sold back to the academic community who created it. The dominant four are Elsevier, Springer Nature, Wiley and Taylor & Francis, which collectively generated over US$7.1 billion in revenue from journal publishing in 2024 alone, and over US$12 billion in profits between 2019 and 2024 (Table 1A). Their profit margins have always been over 30% in the last five years, and for the largest publisher (Elsevier) always over 37%. Against many comparators, across many sectors, scientific publishing is one of the most consistently profitable industries (Table S1). These financial arrangements make a substantial difference to science budgets. In 2024, 46% of Elsevier revenues and 53% of Taylor & Francis revenues were generated in North America, meaning that North American researchers were charged over US$2.27 billion by just two for-profit publishers. The Canadian research councils and the US National Science Foundation were allocated US$9.3 billion in that year.

A figure detailing the drain on researcher time. 1. The four-fold drain 1.2 Time The number of papers published each year is growing faster than the scientific workforce, with the number of papers per researcher almost doubling between 1996 and 2022 (Figure 1A). This reflects the fact that publishers’ commercial desire to publish (sell) more material has aligned well with the competitive prestige culture in which publications help secure jobs, grants, promotions, and awards. To the extent that this growth is driven by a pressure for profit, rather than scholarly imperatives, it distorts the way researchers spend their time. The publishing system depends on unpaid reviewer labour, estimated to be over 130 million unpaid hours annually in 2020 alone (9). Researchers have complained about the demands of peer-review for decades, but the scale of the problem is now worse, with editors reporting widespread difficulties recruiting reviewers. The growth in publications involves not only the authors’ time, but that of academic editors and reviewers who are dealing with so many review demands. Even more seriously, the imperative to produce ever more articles reshapes the nature of scientific inquiry. Evidence across multiple fields shows that more papers result in ‘ossification’, not new ideas (10). It may seem paradoxical that more papers can slow progress until one considers how it affects researchers’ time. While rewards remain tied to volume, prestige, and impact of publications, researchers will be nudged away from riskier, local, interdisciplinary, and long-term work. The result is a treadmill of constant activity with limited progress whereas core scholarly practices – such as reading, reflecting and engaging with others’ contributions – is de-prioritized. What looks like productivity often masks intellectual exhaustion built on a demoralizing, narrowing scientific vision.

A table of profit margins across industries. The section of text related to this table is below: 1. The four-fold drain 1.1 Money Currently, academic publishing is dominated by profit-oriented, multinational companies for whom scientific knowledge is a commodity to be sold back to the academic community who created it. The dominant four are Elsevier, Springer Nature, Wiley and Taylor & Francis, which collectively generated over US$7.1 billion in revenue from journal publishing in 2024 alone, and over US$12 billion in profits between 2019 and 2024 (Table 1A). Their profit margins have always been over 30% in the last five years, and for the largest publisher (Elsevier) always over 37%. Against many comparators, across many sectors, scientific publishing is one of the most consistently profitable industries (Table S1). These financial arrangements make a substantial difference to science budgets. In 2024, 46% of Elsevier revenues and 53% of Taylor & Francis revenues were generated in North America, meaning that North American researchers were charged over US$2.27 billion by just two for-profit publishers. The Canadian research councils and the US National Science Foundation were allocated US$9.3 billion in that year.

The costs of inaction are plain: wasted public funds, lost researcher time, compromised scientific integrity and eroded public trust. Today, the system rewards commercial publishers first, and science second. Without bold action from the funders we risk continuing to pour resources into a system that prioritizes profit over the advancement of scientific knowledge.

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/...

A joke scientific paper with the title "Over 90% of children diagnosed with autism consumed breast milk and/or formula mileL a comprehensive cross-sectional analysis of the obvious"

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.

Napoleon's retreat from Moscow CREDIT Barbieri et al., Current Biology

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

Fluorescent acid-fast stains for diagnosing mycobacteria and beyond: back to the future? Acid-fast stains (AFS) remain indispensable in modern diagnostic microbiology; they are used for detecting mycobacteria (including Mycobacterium tuberculosis and Mycobacterium leprae), acid-fast paras...

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.

GTDB release 10: a complete and systematic taxonomy for 715 230 bacterial and 17 245 archaeal genomes Abstract. The Genome Taxonomy Database (GTDB; https://gtdb.ecogenomic.org) provides a phylogenetically consistent and rank normalized genome-based taxonomy

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-...

Non-conjugative plasmids limit their mobility to persist in nature Sabnis et al. explain why non-conjugative plasmids move at a low rate in nature. While increased mobility can easily evolve by incorporating phage DNA into plasmids, this is disadvantageous because it...

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...