Jan Claesen
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claesengroup.bsky.social
Jan Claesen
@claesengroup.bsky.social
4.2K followers 1.6K following 210 posts
Associate Professor at Lerner Research Institute, Cleveland Clinic.
Lover of bacteria in isolation and in communities.
Dissecting the human microbiome on a molecular level.
🇧🇪🇺🇸 Father of two. Views are my own.
https://claesengroup.org/
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claesengroup.bsky.social
Jan Claesen @claesengroup.bsky.social · Oct 19
Hi everyone, I tried assembling a Microbiome & friends starter pack.
🦠🧫🔬

Still learning to use bluesky and might have missed you, let me know if you would like to be included.

go.bsky.app/Fq36egy
Reposted by Jan Claesen
suez.bsky.social
It's increasingly clear that commensal viruses play important roles in human health, but how do you study them?

Our review "Tools and approaches to study the human gut virome: from the bench to bioinformatics" is out today in mSystems! journals.asm.org/doi/10.1128/...

@haleybiont.bsky.social
A figure from the paper that provides an overview of available culture-dependent and culture-independent approaches for characterizing the human gut virome. Both culture-dependent and culture-independent approaches should be used to study the gut virome. At the bench, many protocols have been adapted to enrich viruses in a sample and isolate them using a sensitive host. Once a virus is isolated, various assays can be used to characterize how the virus interacts with its bacterial host. On the command line, viral genomes can be predicted and viral taxonomy can be identified within a sample. Once procured, multiple tools can be used to annotate viral genomes for predicted gene content and viral lifestyle and predict bacterial host taxonomy.
February 4, 2026 at 4:05 PM
Reposted by Jan Claesen
blekhman.bsky.social
Our new paper, where we use metabolic modeling to show Fusobacterium grows faster in colorectal tumor vs normal tissue microenvironments, and use computational + experimental approach to find specific metabolic pathways driving host-microbiome interactions in cancer

www.biorxiv.org/content/10.6...
February 4, 2026 at 2:17 PM
Reposted by Jan Claesen
maxkozlov.bsky.social
🚨 New from me: Grant review at more than half of NIH's institutes could be frozen by the end of the year.

That's because crucial NIH grant-review panels are slated to be empty at those institutes by Jan 2027.

A wonky bureaucratic problem with big implications.

A short 🧵
Exclusive: key NIH review panels due to lose all members by the end of 2026
Thirteen of the agency’s advisory councils, which must review grant applications before funding is awarded, are on track to have no voting members.
www.nature.com
January 22, 2026 at 7:46 PM
Reposted by Jan Claesen
arcadiascience.com
A free, open-access library of high-quality organism illustrations for science communication
A free, open-access library of high-quality organism illustrations for science communication
We create vector graphics of model organisms and emerging biological research organisms to enhance our publications. We’re sharing these editable graphics under a CC0 license for other scientists to...
doi.org
December 29, 2025 at 6:03 PM
Reposted by Jan Claesen
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
claesengroup.bsky.social
Ruin a book with a car:

Ford of the rings
moartoast.bsky.social Jo @moartoast.bsky.social · Sep 25
Ruin a book with a car:

The Old Man and the C-Class
September 25, 2025 at 11:43 AM
Reposted by Jan Claesen
glennyrodge.bsky.social
Music FACT: Placebo were originally a Cure tribute band
September 19, 2025 at 8:15 AM
claesengroup.bsky.social
She's a real hero!
💪👇
tsnofficial.bsky.social TSN @tsnofficial.bsky.social · Sep 8
Gabrielle Wall sets the Guinness World Record for fastest 100M on LEGO at 24.75 seconds! 😂🤕

(🎥: Guinness World Records)
September 8, 2025 at 6:20 PM
Reposted by Jan Claesen
rebecca-keogh.bsky.social
✨ Exciting News ✨I am thrilled to share that I have accepted a position as an Assistant Professor in the Department of Infectious Diseases and Microbiology (IDM), at the University of Pittsburgh School of Public Health!
September 3, 2025 at 3:48 PM
claesengroup.bsky.social
Slightly diminish a band:
The green mild bell peppers
mbrobergmoffitt.bsky.social Matthew Broberg-Moffitt (any/all) @mbrobergmoffitt.bsky.social · Aug 13
Slightly diminish a band: Bronze Maiden
mbrobergmoffitt.bsky.social Matthew Broberg-Moffitt (any/all) @mbrobergmoffitt.bsky.social · Aug 13
Slightly diminish a band: Twenty Pilots
August 13, 2025 at 3:54 AM
Reposted by Jan Claesen
nadineziemert.bsky.social
Conferencing with my favorite natural product chemist this week at the #ASP2025 in Grands Rapids, Michigan. Great science, inspiring talks, and reconnecting with friends and colleagues! @claesengroup.bsky.social @eustaquiolab.bsky.social @balunaslab.bsky.social #SecMet #NaturalProducts
August 7, 2025 at 12:49 PM
claesengroup.bsky.social
Potato, potahto, tomato, tomahto
Let's call the whole thing off 🎶🎶

www.theguardian.com/science/2025...
‘This wasn’t obvious’: the potato evolved from a tomato ancestor, researchers find
Hybridisation event took place about 9 million years ago, helping to ‘spark the emergence of a new organ’
www.theguardian.com
August 4, 2025 at 2:25 PM
Reposted by Jan Claesen
nadineziemert.bsky.social
Check out the Ziemert Lab’s new YouTube channel
m.youtube.com/@ZiemertLab
We’ve uploaded short tutorial videos on how to use our tools for genome mining and natural product discovery.
Thanks Semih, @martinaadamek.bsky.social @turgutmesut.bsky.social ! #GenomeMining #SecMet #naturalproducts
ZiemertLab
The Ziemert lab is interested in the evolution and distribution of bacterial secondary metabolites. These bioactive compounds are especially important in human medicine as the chemical scaffolds are t...
m.youtube.com
July 8, 2025 at 8:09 PM
Reposted by Jan Claesen
ravenscimaven.bsky.social
NASA is more than rockets and moonwalks. NASA is behind much of our everyday technology. From space discovery, to Air Jordans, to CAT scans, NASA has played a role. We get it all on less than a penny of every federal dollar. Now their science may be gutted by 50%.
#NASADidThat
July 10, 2025 at 10:39 PM
Reposted by Jan Claesen
science.org
🎉 Congratulations to Djenet Bousbaine, winner of the 2025 NOSTER & Science Microbiome Prize for her work to illuminate how the immune system responds to the beneficial skin microbiome.

Learn more: scim.ag/4lVwpFx
Photo of Djenet Bousbaine
July 4, 2025 at 2:07 PM
Reposted by Jan Claesen
abaumler.bsky.social
The new open access policy of NIH will take effect next week (July 1st). All NIH funded research 🔬🧪🧬accepted after July 1st must be open access upon publication. Worried about fees? 💸 Check out how IAI stacks up against other journals—you might be surprised. #OpenAccess #SciComm #Microbiology
June 26, 2025 at 9:47 PM
claesengroup.bsky.social
When all this pollution is causing you headaches...

💪🦠
June 24, 2025 at 11:26 AM
Reposted by Jan Claesen
greenwoodbritt.bsky.social
Well this is f’in sad #ASMicrobe
An empty booth at ASM that should have housed the NSF
June 21, 2025 at 8:40 PM
Reposted by Jan Claesen
pamferretti.bsky.social
Interested in microbiome GWAS and heritability studies? Check out our new Review in Nature Reviews Genetics! We explore key findings, challenges, and future directions of the field.
rdcu.be/epoRR

@blekhman.bsky.social @sambhawa.bsky.social and Dr. Kelsey Johnson.
Genomics of host–microbiome interactions in humans
Nature Reviews Genetics - In this Review, Ferretti et al. discuss advances in our understanding of interactions between the human genome and the microbiome, including the effects of the microbiome...
rdcu.be
June 4, 2025 at 4:52 PM
Reposted by Jan Claesen
cibiocm.bsky.social
🥁NEW publication from our lab:
the largest meta-analysis of gut microbiome associations with CRC!

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

🧵⬇️

1/6
Pooled analysis of 3,741 stool metagenomes from 18 cohorts for cross-stage and strain-level reproducible microbial biomarkers of colorectal cancer - Nature Medicine
An analysis of 18 metagenomic datasets of individuals with colorectal cancer, adenomas and healthy controls yields improved cancer prediction accuracy based solely on gut metagenomics, as well as the ...
www.nature.com
June 3, 2025 at 10:43 AM
Reposted by Jan Claesen
microbeminded.bsky.social
Opening for a #postdoc in the lab available immediately. Please spread the word.

DETAILS HERE: jobrxiv.org/job/baylor-c...

cc: #academicJobs #postdocJobs #microbiome #Celegans #organoids #IBD #PathSky #Medsky #AcademicSky 🧪 🧬 🦠
Postdoctoral Associate in IBD genetics in C. elegans and organoids
Post a job in 3min, or find thousands of job offers like this one at jobRxiv!
jobrxiv.org
May 31, 2025 at 4:28 PM
Reposted by Jan Claesen
cyrilpedia.bsky.social
'If successful, it would be the first new class of antibiotic capable of killing acinetobacter or any other “Gram-negative” bacteria to be developed for more than 50 years. This type of bug has a structure that makes it more difficult to treat.'
www.ft.com/content/1f94...
Roche extends trials of promising antibiotic against resistant superbug
If successful, it would be the first new class of drug against certain bacteria strains for more than 50 years
www.ft.com
May 26, 2025 at 9:45 AM
claesengroup.bsky.social
I'm delighted to share the preprint on Layan's investigation into the effect of nisin Z on intestinal tumor formation! 🎉 🎉🎉
May 20, 2025 at 12:31 PM
claesengroup.bsky.social
🚨🚨🚨
Excited to share Sara's work on the importance of gut microbial metabolism of dietary polyphenols in preventing obesity and prediabetes associated disorders!
🚨🚨🚨

Check out her preprint here:

(1/5)
May 19, 2025 at 8:58 AM
Reposted by Jan Claesen
pauldcotter.bsky.social
PLEASE SHARE We’re hiring a contract #bioinformatician (research officer) to analyse #microbiome data from an ongoing, exciting project focusing on preterm birth prevention with oral probiotics

topjobs-teagasc.thehirelab.com/LiveJobs/Job...
May 12, 2025 at 10:12 AM