Jeroen Meijer
jeroenmeijer.bsky.social
Jeroen Meijer
@jeroenmeijer.bsky.social
postdoc at Viral Ecology and Omics group, @microverse.bsky.social @uni-jena.de. Phages, metagenomics, evolutionary modeling, microbial communities, kendo.
Reposted by Jeroen Meijer
🚨New preprint out!
We present a foundational genomic resource of human gut microbiome viruses. It delivers high-quality, deeply curated data spanning taxonomy, predicted hosts, structures, and functions, providing a reference for gut virome research. (1/8)
www.biorxiv.org/content/10.1...
November 6, 2025 at 5:26 PM
Reposted by Jeroen Meijer
Reposted by Jeroen Meijer
#microsky #mevosky @spp2389.bsky.social

A PhD position is available in my lab to work on:

Emergence and self-organisation of bacterial metabolism in consortia of cross-feeding bacteria.

Please RT

Deadline: 12.11.25

More infos 👇
shorturl.at/rAKAT
October 28, 2025 at 8:43 AM
Reposted by Jeroen Meijer
@prczhaoyansong.bsky.social’s deep dive into the dark matter of compost communities is now out 🎉 Genomic islands hijack jumbo phages—whose capsids enable transfer of large tracts of DNA—shedding new light on the scale & scope of phage-mediated gene flow 😎

www.pnas.org/doi/10.1073/...
Jumbo phage–mediated transduction of genomic islands | PNAS
Bacteria acquire new genes by horizontal gene transfer, typically mediated by mobile genetic elements (MGEs). While plasmids, bacteriophages, and c...
www.pnas.org
October 28, 2025 at 6:36 PM
Reposted by Jeroen Meijer
Happy to announce that our comparative metagenomic analysis of the gut microbiota of five honeybee species - spearheaded by @aiswarya.bsky.social - is finally published in a peer-reviewed journal! rdcu.be/eKMCs @fbm-unil.bsky.social @dmf-unil.bsky.social 🧵👇
Evolution of gut microbiota across honeybee species revealed by comparative metagenomics
Nature Communications - Here, the authors perform metagenomic analysis of honeybee gut microbes, uncovering many previously unidentified species and host specific differences in composition and...
rdcu.be
October 14, 2025 at 7:04 PM
Reposted by Jeroen Meijer
Very excited to share the latest work from our lab, which was published today in Nature!
nature.com/articles/s41...

PhD graduate and now post-doc Sofia Dahlman, along with co-senior author Sam Forster from The Hudson and other researchers from our lab and others.
Isolation, engineering and ecology of temperate phages from the human gut - Nature
Human host-associated cellular products may act as induction agents for bacteriophages.
nature.com
October 15, 2025 at 9:41 PM
Reposted by Jeroen Meijer
Phages evolve fast, or do they?
In oysters, some stay identical for years.
With >1,200 phages & 600 Vibrio genomes, we reveal long-term stability and new mobile elements.
Proud of this collaborative work across our teams (Roscoff-UdeM and @epcrocha.bsky.social www.biorxiv.org/cgi/content/...
Ecological constraints foster both extreme viral-host lineage stability and mobile element diversity in a marine community
Phages are typically viewed as very rapidly evolving biological entities. Little is known, however, about whether and how phages can establish long-term genetic stability. We addressed this eco-evolut...
www.biorxiv.org
October 12, 2025 at 9:16 PM
Reposted by Jeroen Meijer
Is a healthy microbiome one that is rich in phages? 🦠 Excited to share our paper out in Lancet Microbe with @bkoskella.bsky.social & @dholtappels.bsky.social where we test whether virome diversity can be used a broad signature of microbiome health 📈
New research article

Evaluation of bacteriophages as a signature of #microbiome health: a systematic review and meta-analysis

www.thelancet.com/journals/lan...

#IDSky #ClinMicro #ViroSky #Phage #OpenAccess #OA
October 10, 2025 at 1:12 PM
Reposted by Jeroen Meijer
Very nice documentary about the origins of complex life with my PhD advisor Berend Snel @binfutrecht.bsky.social!
October 9, 2025 at 8:46 AM
Reposted by Jeroen Meijer
Wetsvoorstel! Elke keer als een dichtgetikte boomer iets zegt dat dichtgetikte boomers al decennia roepen én daar aan toevoegt "dat je dit niet mag zeggen", krijgen ze daadwerkelijk een boete. Met je malle censuur-fetish.
October 2, 2025 at 7:31 AM
Reposted by Jeroen Meijer
Leuk interview met voormalig PhD student Lars Zandbergen over zijn promotie onderzoek in NRC.
www.nrc.nl/nieuws/2025/...
Is je blaas steriel? ‘Er leven wel honderd soorten bacteriën die elkaar beïnvloeden’
Jong geleerd: Ook in onze blaas leeft een complexe gemeenschap van microben. Hun onderlinge interacties hebben invloed op onze gezondheid, maar ook op antibioticaresistentie.
www.nrc.nl
September 26, 2025 at 10:38 AM
Reposted by Jeroen Meijer
How much of selection in human microbiomes is driven by phage?

Excited to share our latest, led by A. Delphine Tripp, showing a case where phage is just not that important:

Phage-mediated lysis does not determine Cutibacterium acnes colonization on human skin

www.biorxiv.org/content/10.1...

🧵
Phage-mediated lysis does not determine Cutibacterium acnes colonization on human skin
Despite Cutibacterium acnes being the most abundant and prevalent bacteria on human skin, only a single type of phage has been identified that infects this host. Here, we leverage this one-to-one syst...
www.biorxiv.org
September 22, 2025 at 5:57 PM
Reposted by Jeroen Meijer
Drop your backbone!

Close your eyes!

Focus on your science!

Don’t talk politics!!
September 23, 2025 at 11:20 AM
Reposted by Jeroen Meijer
jeetje de fascisten hebben gefascist hoe kan dat nou

(vanaf morgen in alle media:
-boze burgers
-zorgen serieus nemen
-links begrijpt hen niet
-links is eigenlijk erger
-je moet trans ideologie niet opdringen
-en de vluchtelingen dan
-ja die zijn ook erg
-misschien wel erger
-PVV 42 zetels?)
September 20, 2025 at 3:54 PM
Reposted by Jeroen Meijer
www.biorxiv.org/content/10.1...

#phagesky #phage
Anecdotally, a few years ago a very trigger-happy temperate had infected a strain of E. coli of mine and caused significant lysis. The release of enzymes in the medium degraded a sugar into a different form which could be used by the other cells.
Phage-mediated lysis increases growth rate of surviving bacterial cells
Bacterial phage infection and subsequent lysis are traditionally considered mechanisms of bacterial mortality and viral propagation; additionally, emerging evidence indicates that they may also contri...
www.biorxiv.org
September 19, 2025 at 7:57 AM
Reposted by Jeroen Meijer
💧🌊 What happens when freshwater bacteria meet their salty counterparts?
Our new preprint explores the ecological factors driving community coalescence 👉https://www.biorxiv.org/content/10.1101/2025.09.09.675091v1 @bedutilh.bsky.social @microverse.bsky.social
Bacterial community adaptation after freshwater and seawater coalescence
Microbial community coalescence, the merging of entire microbial communities, is common across ecosystems, particularly in estuaries where freshwater and seawater mix. The complexity of these habitats...
www.biorxiv.org
September 15, 2025 at 9:37 PM
Reposted by Jeroen Meijer
📢Join us for the next ECR #Viromics Webinar:
"Chronotyping the #Ocean Virome: Fine-Scale Temporal Clustering Reveals Viral Ecological and Evolutionary Patterns"
‍🎙️Luis Bolaños Avellaneda, Exeter, UK
🗓️10 Sep 2025, 4 PM CEST
📍Online, Zoom (register for login details)
🔗 evbc.uni-jena.de/events/ecr-v...
September 5, 2025 at 11:28 AM
Reposted by Jeroen Meijer
At last ! A tool specifically for phage-plasmid hunters. Check tyPPing by @karinailchenko.bsky.social and @eugenpfeifer.bsky.social
🚨 New preprint! 🧬

𝐏𝐡𝐚𝐠𝐞-𝐩𝐥𝐚𝐬𝐦𝐢𝐝𝐬 (𝐏-𝐏𝐬) are fascinating elements: both 𝐭𝐞𝐦𝐩𝐞𝐫𝐚𝐭𝐞 𝐩𝐡𝐚𝐠𝐞𝐬 and 𝐩𝐥𝐚𝐬𝐦𝐢𝐝𝐬 ➡️ tricky to detect.

We present 𝐭𝐲𝐏𝐏𝐢𝐧𝐠 — the first 𝐢𝐝𝐞𝐧𝐭𝐢𝐟𝐢𝐜𝐚𝐭𝐢𝐨𝐧 𝐚𝐧𝐝 𝐜𝐥𝐚𝐬𝐬𝐢𝐟𝐢𝐜𝐚𝐭𝐢𝐨𝐧 𝐭𝐨𝐨𝐥 🛠️designed specifically for P-Ps:
✅ Accurate
✅ Sensitive
✅ Easy to use

📖 www.biorxiv.org/content/10.1...
Efficient detection and typing of phage-plasmids
Phage-plasmids are temperate phages that replicate as plasmids during lysogeny. Despite their high diversity, they carry genes similar to phages and plasmids. This leads to gene exchanges, and to the ...
www.biorxiv.org
September 3, 2025 at 2:00 PM
Reposted by Jeroen Meijer
Really appreciated how @sethf.bsky.social described using AI in the evolution class that we co- teach: “ it’s like paying for a gym membership and then using a forklift to raise and lower your weights.”
August 28, 2025 at 2:43 AM
Reposted by Jeroen Meijer
Have you ever wondered what increasing environmental stress will do to microbial communities?

In our new preprint, @martinadalbello.bsky.social, Jeff Gore and I studied the impact of salinity on microbial community composition and function. 🧵 (1/5)
www.biorxiv.org/content/10.1...
Microbial communities demonstrate robustness in stressful environments due to predictable composition shifts
Environmental stress reduces species growth rates, but its impact on the function of microbial communities is less clear. Here, we experimentally demonstrate that increasing salinity stress shifts com...
www.biorxiv.org
August 25, 2025 at 2:33 PM
Reposted by Jeroen Meijer
Stoked to finally have a preprint out for Phold, our tool that uses protein structural information to enhance phage genome annotation #phagesky 1/n

www.biorxiv.org/content/10.1...
Protein Structure Informed Bacteriophage Genome Annotation with Phold
Bacteriophage (phage) genome annotation is essential for understanding their functional potential and suitability for use as therapeutic agents. Here we introduce Phold, an annotation framework utilis...
www.biorxiv.org
August 8, 2025 at 7:11 AM
Reposted by Jeroen Meijer
📝New preprint!

We investigated how spatial structure affects cooperation between phages, combining mathematical modelling and experiments.

A short thread 🧶
The ambivalent effect of spatial structure on the spread of cooperative anti-CRISPR phages https://www.biorxiv.org/content/10.1101/2025.08.06.668856v1
August 7, 2025 at 12:19 PM
Reposted by Jeroen Meijer
Protein Structure Informed Bacteriophage Genome Annotation with Phold https://www.biorxiv.org/content/10.1101/2025.08.05.668817v1
August 7, 2025 at 3:47 AM
Reposted by Jeroen Meijer
In the arms race between viruses and their hosts, viruses have found a dependable ally..
RFKJr’s gradual elimination of vaccines in USA is continuing and gathering pace as 22 federal contracts for mRNA-based vaccines being terminated including late stage research for bird flu vaccine #ImmunoSky 🧪🧵
RFK Jr’s health department to halt $500m in mRNA vaccine research
Agency to end 22 federal contracts, questioning safety of technology credited with helping end Covid pandemic
www.theguardian.com
August 6, 2025 at 9:10 AM
Reposted by Jeroen Meijer
Our new paper on experimental evolution in wild tree-holes -Eco-evolutionary robustness of wild bacterial communities to experimental perturbation

#ISMEJournal
@duhitasant.bsky.social Tom Smith Edgar Wong Juli Cohen
@kayla-king.bsky.social
Tom Bell

academic.oup.com/ismej/advanc...
Eco-evolutionary robustness of wild bacterial communities to experimental perturbation
Abstract. Most knowledge about bacterial evolution and ecological interactions comes from laboratory studies. One difference between the wild and most labo
academic.oup.com
August 1, 2025 at 8:44 AM