Reposted by Jeroen MeijerJolien van Hooff @jvhooff.bsky.social · 06/10/2026We'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! 01315
Reposted by Jeroen MeijerC. Brandon Ogbunu @cbo.bsky.social · 27/09/2026In 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.orgAI Presents Science with a ‘Ship of Theseus’ ProblemOpinion | AI can replace each part of the scientific process, leaving the enterprise recognizable but devoid of human judgment. 58547
Reposted by Jeroen MeijerJoshua 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. 57530
Reposted by Jeroen MeijerBas E. Dutilh @bedutilh.bsky.social · 25/09/2026Are 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.deDoctoral Researcher in Bioinformatics: Quantifying quasispecies: Tool development and applications 044
Reposted by Jeroen MeijerFollow the Money @ftm.nl · 24/09/2026Ken 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.nlHyves draait wél op Amerikaanse tech, in tegenstelling tot wat eigenaar De Telegraaf beweertDeze 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 ... 37284166
Reposted by Jeroen MeijerSystems 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 16958
Jeroen Meijer @jeroenmeijer.bsky.social · 18/09/2026Any other bioinformaticians feel they’re the temporary, meat-flavored glue between experimental biologists and LLMs like Claude? 030
Jeroen Meijer @jeroenmeijer.bsky.social · 17/09/2026Wonderful tool that solves the problem that "Conventional research papers require readers to understand...the paper’s code, data and methods to their work" 020
Reposted by Jeroen MeijerVaughn Cooper @vscooper.micropopbio.org · 16/09/2026Authors!🚨 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.comMan Lying on a Pile of MoneyALT: Man Lying on a Pile of Money 410371
Reposted by Jeroen MeijerRafal 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-... 22629
Reposted by Jeroen MeijerJoshua Weitz @joshuasweitz.bsky.social · 01/09/2026Delighted 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... 32210
Reposted by Jeroen MeijerChristian Kost @kostchristian.bsky.social · 24/08/2026Very 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/fBHAbnature.comObligate cross-feeding of metabolites is common in soil microbial communities - Nature MicrobiologyCultivation-dependent techniques, computational analyses and genome-scale metabolic models show widespread amino acid auxotrophies, suggesting that soil microorganisms exist within integrated ecologic... 814256
Reposted by Jeroen MeijerGuy Shrubsole @guyshrubsole.bsky.social · 21/08/2026Rewilded land remains green amid drought-stricken English countryside, images show. Excellent work by the National Trust at Holnicote. #MakeBritainWetAgain www.theguardian.com/environment/...theguardian.comRewilded land remains green amid drought-stricken English countryside, images showNational Trust’s Holnicote estate says restored wetlands and rivers offer proof of resilience to drought, wildfires and flooding 12522172
Reposted by Jeroen MeijerBas E. Dutilh @bedutilh.bsky.social · 21/08/2026Join us and become part of PhageOrder: study the evolution of phage genetic modules! 034
Reposted by Jeroen MeijerPaul Rainey @paulbrainey.bsky.social · 21/08/2026A 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.comWhy we still flyThe scientific conference was invented to solve a transport problem we no longer have. What is it for now? 12711
Reposted by Jeroen MeijerColin Carlson @colincarlson.bsky.social · 10/08/2026I 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.bioThe only reason you’ll ever need not to write with AI — The Carlson LabOver 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... 351564633
Reposted by Jeroen MeijerSultan 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.orgViral Lifecycle Dynamics and Spatial Structure Explain Why Accessory Genes Are Associated With Temperate PhagesAbstract. Genes encoding for virulence factors are frequently found on prophages, yet the evolutionary forces driving this association remain unclear. The 1249
Reposted by Jeroen MeijerGenome Biology and Evolution @genomebiolevol.bsky.social · 04/08/2026Nazir & @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 #virusdoi.orgViral Lifecycle Dynamics and Spatial Structure Explain Why Accessory Genes Are Associated With Temperate PhagesAbstract. Genes encoding for virulence factors are frequently found on prophages, yet the evolutionary forces driving this association remain unclear. The 054
Reposted by Jeroen MeijerMiaoxiao Wang (Roy) @miaoxiaor.bsky.social · 27/07/2026Happy 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.orgInfluence of cell-cell distance on the ecology and evolution of microbial communitiesAbstract. Microorganisms assemble into spatially structured communities in which neighboring cells are separated by highly heterogeneous cell-cell distance 074
Reposted by Jeroen MeijerNature Communications @natcomms.nature.com · 22/07/2026🦠 #Bacteria organise themselves to hitchhike across large distances @susiegriggo.bsky.social @flinders.university.bsky.social #chemotaxis #metagenomics #EnvironmentalMicrobiologydlvr.itBacteria organise themselves to hitchhike across large distancesMicrobes 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 […] 094
Reposted by Jeroen MeijerRob Edwards @linsalrob.bsky.social · 22/07/2026Starting 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 39347
Reposted by Jeroen MeijerNature Communications @natcomms.nature.com · 19/07/2026🦠 #Bacteria organise themselves to hitchhike across large distances @susiegriggo.bsky.social @flinders.university.bsky.social #chemotaxis #metagenomics #EnvironmentalMicrobiologydlvr.itBacteria organise themselves to hitchhike across large distancesMicrobes 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 […] 084
Reposted by Jeroen MeijerJoshua Weitz @joshuasweitz.bsky.social · 15/07/2026Bacteriophage 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.orgInferring single-cell heterogeneity of bacteriophage lysis-associated life-history traits from population-scale dynamicsTheory-guided experiments reveal single-cell heterogeneity of lysis-associated bacteriophage traits from population scale data. 26229
Jeroen Meijer @jeroenmeijer.bsky.social · 15/07/2026Thanks for having me! I really enjoyed the discussion as well. 031
Reposted by Jeroen MeijerDr. 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... 172
Reposted by Jeroen MeijerDr. Kat Napaaqtuk❄️ @napaaqtuk.bsky.social · 15/07/2026If you are interested in microbiomes, this is an excellent group of international researchers coming together to discuss current research. 1177
Reposted by Jeroen MeijerCameron Thrash @jcamthrash.bsky.social · 10/07/2026Bacterial community adaptation after brackish and freshwater coalescence academic.oup.com/ismecommun/a... #jcampubs 032
Jeroen Meijer @jeroenmeijer.bsky.social · 11/07/2026For some reason people had less difficulty finding my poster than usual 0111
Reposted by Jeroen MeijerMicrobial Systems Ecology Lab @micsysecolab.bsky.social · 10/07/2026Excited 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.comPhage-mediated lysis increases growth rate of surviving bacterial cellsMicrobiology 193
Jeroen Meijer @jeroenmeijer.bsky.social · 09/07/2026Enjoyed 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 291
Reposted by Jeroen MeijerMEEhubs @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.orgHomeA hub-based conference on Microbial Ecology and Evolution 11713
Reposted by Jeroen MeijerYuval Mulla @yuvalmulla.bsky.social · 06/07/2026Interested 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 dmacademictransfer.comHow do phages kill dormant bacteriaAre 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... 01215
Reposted by Jeroen MeijerJohannes Cairns @jcairns.bsky.social · 06/07/2026Final 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.comCommunity state shifts driven by total carbon availability over resource complexity in a synthetic microbial communityAbstract. Even though complex microbial communities are ubiquitous and provide essential services for natural and human-associated ecosystems, our knowledg 075
Jeroen Meijer @jeroenmeijer.bsky.social · 02/07/2026Snel ruilen met Macron voor de mosasaurus, voordat het toch niét d’Artagnan blijkt te zijn? www.nrc.nl/nieuws/2026/...nrc.nlNog 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... 010
Reposted by Jeroen MeijerAmelia Barber @ameliabarberphd.bsky.social · 30/06/2026Exciting 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. 104711
Reposted by Jeroen MeijerSimon 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.comMobile genetic elements shape microbial diversity and functions in thawing permafrost soils - Nature MicrobiologyAn 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. 13113
Reposted by Jeroen MeijerSarah Bagby @scbagby.bsky.social · 29/06/2026Out 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 37533
Reposted by Jeroen MeijerPaul Rainey @paulbrainey.bsky.social · 26/06/2026I 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.comDiverse Microbial Communities Assemble on Both Recalcitrant and Labile Carbon SourcesTaxonomically 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 ... 0168
Reposted by Jeroen MeijerCameron Thrash @jcamthrash.bsky.social · 26/06/2026Diverse Microbial Communities Assemble on Both Recalcitrant and Labile Carbon Sources enviromicro-journals.onlinelibrary.wiley.com/doi/10.1111/... #jcampubsenviromicro-journals.onlinelibrary.wiley.comDiverse Microbial Communities Assemble on Both Recalcitrant and Labile Carbon SourcesTaxonomically 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 ... 062
Reposted by Jeroen MeijerEmmanuele 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.comBacteriophage-mediated cell lysis externalizes a metabolically valuable nutrient to broadly modulate bacterial communitiesAbstract. Cobamides, including vitamin B12, are essential cofactors exchanged between organisms across diverse ecosystems including oceans, soils, and the 1135
Reposted by Jeroen MeijerFaisal فيصل @faisalhamadah.bsky.social · 20/06/2026It 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. 45170406107
Reposted by Jeroen MeijerDavid Giron Villalobos @dagivi.bsky.social · 22/06/20261/4. 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.orgCross-study metagenomics analysis reveals distinct microbial signatures of urinary tract infectionsBackground Urinary tract infections (UTIs) represent a major public health concern, increasingly complicated by rising antibiotic resistance, diminishing treatment efficacy, and increasing prevalence ... 32010
Reposted by Jeroen MeijerPaul Rainey @paulbrainey.bsky.social · 19/06/2026New 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.comEarly-career voicesAcademic renewal cannot be a conversation among senior academics alone. 021
Reposted by Jeroen MeijerLeonora Bittleston @leonorabit.bsky.social · 16/06/2026Can 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.comEnvironmental complexity shapes maintenance of bacterial diversity through context-dependent interactions among niche axesAbstract. Microbial communities are often more species-rich than predicted from classical ecological models. The high levels of coexistence observed in nat 13214
Reposted by Jeroen MeijerMicrobial Systems Ecology Lab @micsysecolab.bsky.social · 11/06/2026Very 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.orgAmino acid auxotrophy is a feature of a distinct bacterial lifestyle across environmentsAmino 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... 0158
Reposted by Jeroen MeijerPaul Rainey @paulbrainey.bsky.social · 06/06/2026I’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.comWhy academic renewal?From private concern to shared conversation 0127
Reposted by Jeroen MeijerNobuto Takeuchi @nobuto.bsky.social · 05/06/2026Belatedly 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.orgGeneralizing the central dogma as a cross-hierarchical principle of biologyAbstract. The central dogma of molecular biology, as originally proposed by Crick, asserts that information passed into protein cannot flow back out. This 012
Reposted by Jeroen MeijerPaul Rainey @paulbrainey.bsky.social · 01/06/2026Pleased 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.orgEco-evolutionary dynamics of massive, parallel bacteriophage outbreaks in compost communitiesA single bacteriophage can dominate microbial communities yet only evolves when migration changes its ecological context. 0137
Reposted by Jeroen MeijerMPI for Evolutionary Biology @mpi-evolbio.bsky.social · 01/06/2026New 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 1187
Jeroen Meijer @jeroenmeijer.bsky.social · 01/06/2026Thrilled 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.socialscience.orgEco-evolutionary dynamics of massive, parallel bacteriophage outbreaks in compost communitiesA single bacteriophage can dominate microbial communities yet only evolves when migration changes its ecological context. 24419