Audun Sivertsen
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adnsvrtsn.bsky.social
Audun Sivertsen
@adnsvrtsn.bsky.social
110 followers 240 following 8 posts
MD PhD, clinical microbiologist @ Haukeland Uni. Hospital, Bergen, Norway. Research side-hustle, interested in epidemiology, comparative genomics, AMR, HGT, sequencing of isolates and clinical samples in diagnostic endeavors.
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Reposted by Audun Sivertsen
hansonmark.bsky.social
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 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.
November 11, 2025 at 11:52 AM
Reposted by Audun Sivertsen
watershedlab.bsky.social
Who did this?!
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"
November 1, 2025 at 8:38 PM
Reposted by Audun Sivertsen
benlangmead.bsky.social
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.
Index zone by BenLangmead
benlangmead.github.io
October 30, 2025 at 6:11 PM
Reposted by Audun Sivertsen
cellpress.bsky.social
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
Napoleon's retreat from Moscow CREDIT Barbieri et al., Current Biology
October 24, 2025 at 3:00 PM
Reposted by Audun Sivertsen
gpollara.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...
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...
www.thelancet.com
October 25, 2025 at 6:40 PM
Reposted by Audun Sivertsen
rickbitloo.bsky.social
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...
October 23, 2025 at 8:16 PM
Reposted by Audun Sivertsen
curiouscoding.nl
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.
rickbitloo.bsky.social Rick Beeloo @rickbitloo.bsky.social · 23d
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...
October 23, 2025 at 9:28 PM
Reposted by Audun Sivertsen
ace-gtdb.bsky.social
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-...
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
academic.oup.com
October 22, 2025 at 2:20 PM
Reposted by Audun Sivertsen
sanmillan.bsky.social
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...
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...
www.cell.com
October 22, 2025 at 1:12 PM
Reposted by Audun Sivertsen
absteward.bsky.social
🆕🔥🔥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...
October 19, 2025 at 4:34 AM
Reposted by Audun Sivertsen
gpollara.bsky.social
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
A randomized phase 1 study investigating gut microbiome changes with moxifloxacin vs. oral vancomycin: Implications for Clostridioides difficile risk
AbstractBackground. The epidemic, hypervirulent Clostridioides difficile ribotype (RT) 027 strain is associated with bacterial virulence traits, including
academic.oup.com
October 19, 2025 at 2:18 PM
Reposted by Audun Sivertsen
wvschaik.bsky.social
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....
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...
aricjournal.biomedcentral.com
October 18, 2025 at 7:54 PM
Reposted by Audun Sivertsen
diplomatofnight.com
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
Aftonbladet
October 15, 2025 at 4:45 PM
Reposted by Audun Sivertsen
olainnset.bsky.social
www.ft.com/content/6cc8...
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
October 7, 2025 at 6:30 PM
Reposted by Audun Sivertsen
erc.europa.eu
#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
September 20, 2025 at 7:01 AM
Reposted by Audun Sivertsen
antimicrobial.bsky.social
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...
www.unn.no
September 16, 2025 at 5:34 PM
Reposted by Audun Sivertsen
annizlab.bsky.social
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
Alignment algorithms represent a balance between speed and accuracy. We evaluated this balance across aligners, with accuracy measured by suboptimal alignments. We found that the relationship between alignment time (with 30 threads) and suboptimal alignment rates exhibits diminishing returns, where X-Mapper stands out as an outlier, offering the highest accuracy with competitive speed.
September 15, 2025 at 2:32 AM
Reposted by Audun Sivertsen
annizlab.bsky.social
Beautiful work 🎉 that resolved a long standing question: tumor microbiome, do they exist?🦠🧪 #microbesky
gibbological.bsky.social Sean Gibbons 🦠💩 @gibbological.bsky.social · Sep 12
The landscape of microbial associations in human cancer www.science.org/doi/10.1126/...

TLDR -- most cancers do not have microbiomes...but a few do have consistent microbe associations (i.e., colorectal and oral cancers). Make sense!
The landscape of microbial associations in human cancer
Differences between cancer types, infectious disease, and potential prognostic markers are uncovered by studying microbes within cancer DNA.
www.science.org
September 13, 2025 at 4:19 PM
Reposted by Audun Sivertsen
wvschaik.bsky.social
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)
August 20, 2025 at 10:29 AM
Reposted by Audun Sivertsen
jimshaw.bsky.social
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.
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
github.com
August 13, 2025 at 2:19 PM
Reposted by Audun Sivertsen
erictopol.bsky.social
A natural experiment provides evidence for promoting moderate-vigorous physical activity: the importance of walkable cities
www.nature.com/articles/s41...
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...
www.nature.com
August 13, 2025 at 5:28 PM
Reposted by Audun Sivertsen
bedec.bsky.social
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
Genome assemblies for a respiratory metagenomics positive control | ARTIC network - pathogen genomics from sample to response
artic.network
August 12, 2025 at 8:14 AM
Reposted by Audun Sivertsen
diegoforni.bsky.social
I had a great time working with @adnsvrtsn.bsky.social on this one!
journals.asm.org/doi/10.1128/...
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 ...
journals.asm.org
July 31, 2025 at 4:04 PM
Reposted by Audun Sivertsen
k4tj4.bsky.social
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...
Brain Surfaces of 70 primate species
July 27, 2025 at 5:26 PM
Reposted by Audun Sivertsen
epcrocha.bsky.social
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/...
graphical abstract of the article the extended mobility of plasmids
July 23, 2025 at 7:35 AM