Audun Sivertsen

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...

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

Temporal trend and individual and hospital characteristics associated to vancomycin-resistant Enterococcus faecium bloodstream infections: a retrospective analysis from the national surveillance syste... Background Several countries have reported an increase in vancomycin-resistant Enterococcus faecium (VREF), a pathogen classified by the WHO as a high-priority threat due to its role in healthcare-ass...

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....

Aftonbladet

Greta Thunberg: “Israeli soldiers hit, kicked, starved, and tortured me”

• They placed a flag next to me, and anytime the flag touched me, they kicked me
• Whenever I raised my head to look at Ben-Gvir, I was kicked
• She was filmed while stripped naked

Aftonbladet: tinyurl.com/a33vxatc

America is now one big bet on AI It’s seen as the magic fix for every threat to the US economy

www.ft.com/content/6cc8...

#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)

GitHub - bluenote-1577/skani: Fast, robust ANI and aligned fraction for (metagenomic) genomes and contigs. Fast, robust ANI and aligned fraction for (metagenomic) genomes and contigs. - bluenote-1577/skani

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.

Countrywide natural experiment links built environment to physical activity - Nature By analysing the smartphone data of 2,112,288 participants, in particular observing and comparing the activity of the same individual in two different environments, we find that increases in the walka...

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

Likewise! Optimal collaboration environment! A banger!

Reassessing taxonomy and virulence in the Fusobacterium nucleatum group—rebuttal of Fusobacterium animalis clades “Fna C1” and “Fna C2,” genome announcement for Fusobacterium watanabei, and descriptio... Considerable resources are being used to study associations between the human microbiota and malignancy. There is a particular interest in the connection between Fusobacterium animalis and colorectal ...

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

Brain Surfaces of 70 primate species

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...

graphical abstract of the article the extended mobility of plasmids

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/...

No, AlphaFold has not completely solved protein folding Biology is hard. Yes, even for AI.

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)

Negativeome characterization and decontamination in early-life virome studies - Nature Communications Contamination significantly impacts low-biomass studies. Here, the authors highlight its pervasive and study-specific effects, particularly on early-life virome samples, and offer practical strategies...

Interesting, important paper on contamination in gut virome studies.

I am not too keen on the term negativeome though

www.nature.com/articles/s41...

Universal rules govern plasmid copy number - Nature Communications Plasmids exhibit a broad range of sizes and copies per cell, and these two parameters appear to be negatively correlated. Here, Ramiro-Martínez et al. analyse the copy number of thousands of diverse b...

🚨🚨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