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Jeroen Meijer

@jeroenmeijer.bsky.social
916 followers 597 following 35 posts

postdoc at Viral Ecology and Omics group, @microverse.bsky.social @uni-jena.de. Phages, metagenomics, evolutionary modeling, microbial communities, kendo.

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Reposted by Jeroen Meijer
Jolien van Hooff @jvhooff.bsky.social · 06/10/2026
We're looking for a PhD candidate who's eager to study how the genomes of fascinating eukaryotic microbes evolve and organize - and we have a fully funded PhD position available!
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C. Brandon Ogbunu @cbo.bsky.social · 27/09/2026
In my latest for @undark.org, I compare AI adoption in science to the Ship of Theseus: "If you swap out every wooden plank on a ship over time, is it still the same vessel?" I argue that science derives authority from something more than data generation + publication. undark.org/2026/09/25/o...
undark.org
AI Presents Science with a ‘Ship of Theseus’ Problem
Opinion | AI can replace each part of the scientific process, leaving the enterprise recognizable but devoid of human judgment.
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Joshua Weitz @joshuasweitz.bsky.social · 28/09/2026
“I’ve heard from a bunch of people in our field who say, ‘Uh oh, are they training on my prompts?’” Dr. Shipman said. “We can’t not think about it.” ... '[A]fter Anthropic’s announcement last week, he is winding down his projects with Claude.' “I’m shutting down everything,” [Dr. Mestre] said.
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Bas E. Dutilh @bedutilh.bsky.social · 25/09/2026
Are you into sequence graphs and looking for a PhD position in viral ecology? Join the VEO Group in beautiful Jena, Germany! 👇👇 jobs.uni-jena.de/jobposting/a...
jobs.uni-jena.de
Doctoral Researcher in Bioinformatics: Quantifying quasispecies: Tool development and applications
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Follow the Money @ftm.nl · 24/09/2026
Ken je Hyves nog? Het sociale platform van de krabbels en dansende bananen maakt een comeback. Deze week kondigde De Telegraaf aan Hyves nieuw leven in te blazen. Volgens de hoofdredacteur draait het platform op Europese software. Maar dat klopt niet. www.ftm.nl/artikelen/hy...
ftm.nl
Hyves draait wél op Amerikaanse tech, in tegenstelling tot wat eigenaar De Telegraaf beweert
Deze week kondigde De Telegraaf aan Hyves nieuw leven in te blazen. Volgens de hoofdredacteur draait de socialenetwerksite ‘voor de veiligheid, voor de zekerheid’ op Europese software. Maar dat klopt ...
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Systems Ecology @systems-ecology.bsky.social · 21/09/2026
🌱 Systems Ecology is now live! A new independent, researcher-run, diamond OA journal for ecological research through systems science. Free to read. Free to publish. No APCs. We are now open for submissions: systems-ecology.org Please help spread the word!
systems-ecology.org
Systems Ecology
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Jeroen Meijer @jeroenmeijer.bsky.social · 18/09/2026
Any other bioinformaticians feel they’re the temporary, meat-flavored glue between experimental biologists and LLMs like Claude?
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Jeroen Meijer @jeroenmeijer.bsky.social · 17/09/2026
Wonderful tool that solves the problem that "Conventional research papers require readers to understand...the paper’s code, data and methods to their work"
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Reposted by Jeroen Meijer
Vaughn Cooper @vscooper.micropopbio.org · 16/09/2026
Authors!🚨 While you scramble for scarce $ 🤔 “Springer Nature reports revenue growth of 6.2%..and adjusted operating profit growth of 7.7%. They reported even more stunning submission growth of 30% and published article growth of 13%.” Publishing in society journals helps YOU not them👇🏻. Pass it on.
static.klipy.com
Man Lying on a Pile of Money
ALT: Man Lying on a Pile of Money
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Rafal Mostowy @rafalmostowy.bsky.social · 04/09/2026
🧬 Postdoc ad is now live: evolutionary genomics of Klebsiella pneumoniae phages. How do prophage depolymerases vs SGNH-esterases shape phage host range? Krakow, Poland. Deadline 21 Sept: mostowylab.com/job-postdoc-...
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Joshua Weitz @joshuasweitz.bsky.social · 01/09/2026
Delighted to share news that our preprint “Slower-than-exponential viral decay is prevalent and can reshape virus-microbe dynamics” is now online, led by Akash Arani (UMD-BEES PhD), Paul Fremont (UMD-Biology postdoc) and Emma Wachter (former UMD Honors Bio student) www.biorxiv.org/content/10.6...
Examples of viral decay curves spanning biphasic (red), exponential (blue-dashed) fit to data (black points). ~50% are better represented by biphasic rather than exponential.

https://www.biorxiv.org/content/10.64898/2026.08.27.747580v2.full.pdf
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Christian Kost @kostchristian.bsky.social · 24/08/2026
Very happy that our paper Obligate cross-feeding of metabolites is common in soil microbial communities just came out in Nature Microbiology. See here 👇 Paywalled version: www.nature.com/articles/s41... Free read-only version: rdcu.be/fBHAb
nature.com
Obligate cross-feeding of metabolites is common in soil microbial communities - Nature Microbiology
Cultivation-dependent techniques, computational analyses and genome-scale metabolic models show widespread amino acid auxotrophies, suggesting that soil microorganisms exist within integrated ecologic...
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Guy Shrubsole @guyshrubsole.bsky.social · 21/08/2026
Rewilded land remains green amid drought-stricken English countryside, images show. Excellent work by the National Trust at Holnicote. #MakeBritainWetAgain www.theguardian.com/environment/...
theguardian.com
Rewilded land remains green amid drought-stricken English countryside, images show
National Trust’s Holnicote estate says restored wetlands and rivers offer proof of resilience to drought, wildfires and flooding
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Bas E. Dutilh @bedutilh.bsky.social · 21/08/2026
Join us and become part of PhageOrder: study the evolution of phage genetic modules!
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Paul Rainey @paulbrainey.bsky.social · 21/08/2026
A third-year student draws poster PS3.20.305 -- far corner, farthest wall -- and commits to standing there two hours. Barely anyone makes it that far. Two floors up, a senior colleague is having the week of his life. Same conference. A new essay. academicrenewal.substack.com/p/why-we-sti...
academicrenewal.substack.com
Why we still fly
The scientific conference was invented to solve a transport problem we no longer have. What is it for now?
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Colin Carlson @colincarlson.bsky.social · 10/08/2026
I wrote about a reason not to use generative AI in your writing that I haven't seen anyone talking about. Once I realized this, banning GenAI in our lab's writing became a no-brainer. Feel free to share, I think this is probably useful especially for trainees: www.carlsonlab.bio/thoughts/the...
carlsonlab.bio
The only reason you’ll ever need not to write with AI — The Carlson Lab
Over the last year, our lab has been developing a policy on AI use. To do this, we did three main things: We read a lot of academic publications and tech news. We set up an #ai channel on our la...
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Sultan Nazir @sultannazir.bsky.social · 07/08/2026
🚨 New paper with @bramvandijk.bsky.social, out now in Genome Biology and Evolution! Why do accessory genes so often hitch a ride on temperate phages? We show that spatial structure alone can tip selection toward a prophage locus over a chromosomal one. doi.org/10.1093/gbe/... 🧵 Two mechanisms:
doi.org
Viral Lifecycle Dynamics and Spatial Structure Explain Why Accessory Genes Are Associated With Temperate Phages
Abstract. Genes encoding for virulence factors are frequently found on prophages, yet the evolutionary forces driving this association remain unclear. The
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Genome Biology and Evolution @genomebiolevol.bsky.social · 04/08/2026
Nazir & @bramvandijk.bsky.social demonstrate how phage lifecycle dynamics and spatial heterogeneity drive mobile genetic element–gene associations, providing new insights into the evolution of phage-encoded virulence. 🔗 doi.org/10.1093/gbe/evag181 #societyjournal #virus
doi.org
Viral Lifecycle Dynamics and Spatial Structure Explain Why Accessory Genes Are Associated With Temperate Phages
Abstract. Genes encoding for virulence factors are frequently found on prophages, yet the evolutionary forces driving this association remain unclear. The
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Reposted by Jeroen Meijer
Miaoxiao Wang (Roy) @miaoxiaor.bsky.social · 27/07/2026
Happy to share our latest review on @isme-microbes.bsky.social. We discussed how (intra- or interpopulation) cell-cell distances shape microbial interactions and enable community-level outcomes. Several hypotheses are proposed and we are testing them! doi.org/10.1093/isme...
doi.org
Influence of cell-cell distance on the ecology and evolution of microbial communities
Abstract. Microorganisms assemble into spatially structured communities in which neighboring cells are separated by highly heterogeneous cell-cell distance
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Nature Communications @natcomms.nature.com · 22/07/2026
🦠 #Bacteria organise themselves to hitchhike across large distances @susiegriggo.bsky.social @flinders.university.bsky.social #chemotaxis #metagenomics #EnvironmentalMicrobiology
dlvr.it
Bacteria organise themselves to hitchhike across large distances
Microbes rarely travel alone. In any given environment, millions of microbial species compete with each other for resources while locked in an endless state of warfare […]
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Rob Edwards @linsalrob.bsky.social · 22/07/2026
Starting with the DNA sequence of a #phage genome, #PholdAPhage will create a 3D reconstruction of the complete phage, almost like you did cryoEM on it! Check out Renee's awesome software github.com/reneegreen81... to assemble unknown phage particles one protein at a time
A computer generated 3D reconstruction of a phage, based solely on its genome sequence. For this image, we started with the genome, and used PholdAPhage to create the structures. Colours are based on pLDDT scores.
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Nature Communications @natcomms.nature.com · 19/07/2026
🦠 #Bacteria organise themselves to hitchhike across large distances @susiegriggo.bsky.social @flinders.university.bsky.social #chemotaxis #metagenomics #EnvironmentalMicrobiology
dlvr.it
Bacteria organise themselves to hitchhike across large distances
Microbes rarely travel alone. In any given environment, millions of microbial species compete with each other for resources while locked in an endless state of warfare […]
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Reposted by Jeroen Meijer
Joshua Weitz @joshuasweitz.bsky.social · 15/07/2026
Bacteriophage continue to have so much to teach us. It's in our interest to understand how they work and impact human & environmental health. New joint work led by @mariandm.bsky.social & @rantahan.bsky.social inferring single-cell latent period & burst size heterogeneity from population dynamics.
science.org
Inferring single-cell heterogeneity of bacteriophage lysis-associated life-history traits from population-scale dynamics
Theory-guided experiments reveal single-cell heterogeneity of lysis-associated bacteriophage traits from population scale data.
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Jeroen Meijer @jeroenmeijer.bsky.social · 15/07/2026
Thanks for having me! I really enjoyed the discussion as well.
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Dr. Kat Napaaqtuk❄️ @napaaqtuk.bsky.social · 15/07/2026
@jeroenmeijer.bsky.social is presenting today on this paper. They studied the eco-evo dynamics in 10 paired open and closed communities with a focus on viral communities. bsky.app/profile/paul...
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Dr. Kat Napaaqtuk❄️ @napaaqtuk.bsky.social · 15/07/2026
If you are interested in microbiomes, this is an excellent group of international researchers coming together to discuss current research.
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Cameron Thrash @jcamthrash.bsky.social · 10/07/2026
Bacterial community adaptation after brackish and freshwater coalescence academic.oup.com/ismecommun/a... #jcampubs
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Jeroen Meijer @jeroenmeijer.bsky.social · 11/07/2026
For some reason people had less difficulty finding my poster than usual
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Microbial Systems Ecology Lab @micsysecolab.bsky.social · 10/07/2026
Excited to share our new paper! Emanuele and @benjaminraach.bsky.social combine experiments and modelling to show that phage-mediated lysis can increase the growth rate of surviving bacteria by releasing resources back into the environment. 👇 www.cell.com/iscience/ful...
cell.com
Phage-mediated lysis increases growth rate of surviving bacterial cells
Microbiology
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Jeroen Meijer @jeroenmeijer.bsky.social · 09/07/2026
Enjoyed speaking about viruses driving state shifts in microbial communities at #VoM2026. All 120 seconds of it. Catch me this afternoon at poster 236 if you want to know more. #phagesky
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MEEhubs @meehubs.bsky.social · 07/07/2026
🚨The program for MEEHubs2026 is now online, as is more detailed information about the hubs! Check it out at meehubs.org and register‼️ Less than a month before the conference kicks off! 🦠
meehubs.org
Home
A hub-based conference on Microbial Ecology and Evolution
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Yuval Mulla @yuvalmulla.bsky.social · 06/07/2026
Interested in a PhD on bacteriophages? Check out www.academictransfer.com/nl/jobs/3623... #phagesky if you are interested and also happen to be at #VOM2026, send me a dm
academictransfer.com
How do phages kill dormant bacteria
Are you excited about exploring the biology behind phages infecting dormant bacteria? Join forces to uncover fundamental biology with great potential for clinical impact. We offer a fully funded PhD p...
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Johannes Cairns @jcairns.bsky.social · 06/07/2026
Final version is out! 🎉 Community state shifts driven by total carbon availability over resource complexity in a synthetic microbial community In ISME Communications with @teppo-h.bsky.social and coauthors. academic.oup.com/ismecommun/a...
academic.oup.com
Community state shifts driven by total carbon availability over resource complexity in a synthetic microbial community
Abstract. Even though complex microbial communities are ubiquitous and provide essential services for natural and human-associated ecosystems, our knowledg
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Jeroen Meijer @jeroenmeijer.bsky.social · 02/07/2026
Snel ruilen met Macron voor de mosasaurus, voordat het toch niét d’Artagnan blijkt te zijn? www.nrc.nl/nieuws/2026/...
nrc.nl
Nog onduidelijk of gevonden skelet in Maastricht van ‘vierde musketier’ d’Artagnan is: ‘veel informatie verloren gegaan’
Archeologie: Onderzoekers van de gemeente Maastricht zeiden donderdag nog zeker zes maanden nodig te hebben om te bepalen of de in maart onder een kerk gevonden botten toebehoren aan de beroemde graaf...
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Amelia Barber @ameliabarberphd.bsky.social · 30/06/2026
Exciting news! After a wonderful four years at @uni-jena.de, I'm excited to announce the next chapter as a group leader at @fzborstel.bsky.social and professor at @uni-kiel.de.
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Simon Roux @simrouxvirus.bsky.social · 29/06/2026
🚨New paper alert 🚨 Here we tried to leverage an (incredible) metagenome time-series to better understand MGE diversity and activity in soil across decade(s). @scbagby.bsky.social has an amazing thread about this work with all the details - bsky.app/profile/scba...
nature.com
Mobile genetic elements shape microbial diversity and functions in thawing permafrost soils - Nature Microbiology
An 8-year soil meta-omic time series shows how mobile genetic elements shape permafrost microbial diversity and impact a range of functions, including carbon and nutrient cycling.
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Sarah Bagby @scbagby.bsky.social · 29/06/2026
Out today in Nature Microbiology: a paper that started in 2021 with an email from @sullivan-lab.bsky.social. Subject line: "Crazy ideas". www.nature.com/articles/s41... 1/23
Screenshot of an email header with subject line "Crazy ideas"
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Paul Rainey @paulbrainey.bsky.social · 26/06/2026
I really value: the dynamics of community assembly on 2 contrasting C sources. Daily sampling of communities derived from compost & maintained over 8 wks. No difference in diversity maintained on simple or complex C. AmaZinG. 🙏 all enviromicro-journals.onlinelibrary.wiley.com/doi/10.1111/...
enviromicro-journals.onlinelibrary.wiley.com
Diverse Microbial Communities Assemble on Both Recalcitrant and Labile Carbon Sources
Taxonomically and functionally distinct communities assemble on cellulose and its monomer, glucose. Although single carbon sources were provided, high and comparable diversity was maintained in both ...
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Cameron Thrash @jcamthrash.bsky.social · 26/06/2026
Diverse Microbial Communities Assemble on Both Recalcitrant and Labile Carbon Sources enviromicro-journals.onlinelibrary.wiley.com/doi/10.1111/... #jcampubs
enviromicro-journals.onlinelibrary.wiley.com
Diverse Microbial Communities Assemble on Both Recalcitrant and Labile Carbon Sources
Taxonomically and functionally distinct communities assemble on cellulose and its monomer, glucose. Although single carbon sources were provided, high and comparable diversity was maintained in both ...
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Emmanuele Severi @emmseveri.bsky.social · 25/06/2026
#microsky #phagesky Years ago a stray temperate #phage lysogenised an E. coli mutant of mine unable to take in a Sia. The small portion of lysed cells was enough to predigest the Sia into catabolites the cells could take in and use for growth!!! And here I was 1/2 academic.oup.com/ismej/advanc...
academic.oup.com
Bacteriophage-mediated cell lysis externalizes a metabolically valuable nutrient to broadly modulate bacterial communities
Abstract. Cobamides, including vitamin B12, are essential cofactors exchanged between organisms across diverse ecosystems including oceans, soils, and the
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Faisal فيصل @faisalhamadah.bsky.social · 20/06/2026
It will never stop being funny to me that the street fighter subreddit has a much better, well reasoned ai policy vis a vis literally all universities.
Hi, thanks for posting! We do appreciate you thinking of us even though we have to moderate.

Our stance on all AI generated content (Images, Video, Voiceovers, and whatever else LLM based AI gets up to in the future):

At best, they are approximations of street fighter characters as the AI has no clue what it is trying to create. Because of this, there is no street fighter content so they are not allowed. (rule 1)

Also, they aren't allowed per our source rule. As AI sources cannot be tracked, we must assume that they use uncredited sources in the learning data. (rule 5)

Finally, AI images, video, text, and voiceovers are barely any different than posting a screenshot of a google search. The level of effort is so low that we consider it spam (rule 3).

Because of these reasons, AI art and other AI content is not allowed.

If you would like to contact the moderators about this removal, you can do so here.
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David Giron Villalobos @dagivi.bsky.social · 22/06/2026
1/4. Excited to share the first preprint from my PhD at @binfutrecht.bsky.social and @uti-revisited.bsky.social 🐥. In this work, we explored the urinary tract microbiome composition (urobiome) by combining data from multiple metagenomic sequencing studies 💛🦠. www.biorxiv.org/content/10.6...
biorxiv.org
Cross-study metagenomics analysis reveals distinct microbial signatures of urinary tract infections
Background Urinary tract infections (UTIs) represent a major public health concern, increasingly complicated by rising antibiotic resistance, diminishing treatment efficacy, and increasing prevalence ...
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Paul Rainey @paulbrainey.bsky.social · 19/06/2026
New on Academic Renewal: early-career voices. I’d like to include written interviews with ECRs on publication pressure, career strategy, mentoring, metrics, and the pursuit of knowledge. Named or anonymous contributions welcome. DM is interested academicrenewal.substack.com/p/early-care...
academicrenewal.substack.com
Early-career voices
Academic renewal cannot be a conversation among senior academics alone.
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Leonora Bittleston @leonorabit.bsky.social · 16/06/2026
Can we use ecological principles to increase coexistence in synthetic bacterial communities? Our new paper is now out in @isme-microbes.bsky.social: "Environmental complexity shapes maintenance of bacterial diversity through context-dependent interactions among niche axes" doi.org/10.1093/isme...
academic.oup.com
Environmental complexity shapes maintenance of bacterial diversity through context-dependent interactions among niche axes
Abstract. Microbial communities are often more species-rich than predicted from classical ecological models. The high levels of coexistence observed in nat
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Microbial Systems Ecology Lab @micsysecolab.bsky.social · 11/06/2026
Very excited to share our new preprint, led by Alyssa Henderson! We ask why auxotrophy is so widespread in bacteria, and find that phylogeny is the dominant predictor of autotrophy, as opposed to environmental context. Check it out! 👇
doi.org
Amino acid auxotrophy is a feature of a distinct bacterial lifestyle across environments
Amino acid auxotrophy, the loss of biosynthetic potential for an amino acid, is a highly prevalent feature of microbial life, yet the evolutionary processes driving its distribution in nature remain u...
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Paul Rainey @paulbrainey.bsky.social · 06/06/2026
I’ve started Academic Renewal, a Substack on research culture, scholarship and the pursuit of knowledge. The first post asks how private concerns about academic life might become an open conversation about incentives, assessment and responsibility. academicrenewal.substack.com/p/why-academ...
academicrenewal.substack.com
Why academic renewal?
From private concern to shared conversation
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Nobuto Takeuchi @nobuto.bsky.social · 05/06/2026
Belatedly sharing an opinion piece with Kuni Kaneko. We propose that 𝘁𝗵𝗲 𝗰𝗲𝗻𝘁𝗿𝗮𝗹 𝗱𝗼𝗴𝗺𝗮 is one instance of a more general pattern that has evolved repeatedly across levels of biological organisation. doi.org/10.1098/rstb...
doi.org
Generalizing the central dogma as a cross-hierarchical principle of biology
Abstract. The central dogma of molecular biology, as originally proposed by Crick, asserts that information passed into protein cannot flow back out. This
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Paul Rainey @paulbrainey.bsky.social · 01/06/2026
Pleased to see this beautiful paper out. Kudos to @jeroenmeijer.bsky.social who took @stevenquistad.bsky.social data and dug deep, revealing a new phage that erupts to astonishing abundance. As theory predicts, the life of SGEs is fuelled by encounters with new hosts www.science.org/doi/10.1126/...
science.org
Eco-evolutionary dynamics of massive, parallel bacteriophage outbreaks in compost communities
A single bacteriophage can dominate microbial communities yet only evolves when migration changes its ecological context.
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MPI for Evolutionary Biology @mpi-evolbio.bsky.social · 01/06/2026
New in Science Advances: A bacteriophage stayed genetically stable for months, then evolved rapidly in a new microbial community. www.evolbio.mpg.de/3884217/viru... @jeroenmeijer.bsky.social @paulbrainey.bsky.social @uni-jena.de @utrechtuniversity.bsky.social @bedutilh.bsky.social
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Jeroen Meijer @jeroenmeijer.bsky.social · 01/06/2026
Thrilled that our paper "Eco-evolutionary dynamics of massive, parallel bacteriophage outbreaks in compost communities" is out! 🎉🦠🧬 www.science.org/doi/10.1126/... w/ @paulbrainey.bsky.social, Petros Skiadas, Paulien Hogeweg, @bedutilh.bsky.social
science.org
Eco-evolutionary dynamics of massive, parallel bacteriophage outbreaks in compost communities
A single bacteriophage can dominate microbial communities yet only evolves when migration changes its ecological context.
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