Bram van Dijk 🏳️🌈
@bramvandijk.bsky.social
Assistant professor at Utrecht University (Theoretical Biology). Simulating microbes, mobile elements, horizontal gene transfer, and whatever else happens on a grain of sand | 🏳️🌈 | he / they | thevirtuallaboratory.com
Please check out our review on the impact of spatial structure in microbial ecosystems! In it, we discuss how spatial patterns impact microbial ecology and evolution, eventually impacting everything we see around us!
See @marcelbaecker.bsky.social's amazing summary below :)
🦠 𝚂𝙿𝙰𝙲𝙴 𝙼𝙰𝚃𝚃𝙴𝚁𝚂 ! 🦠
See @marcelbaecker.bsky.social's amazing summary below :)
🦠 𝚂𝙿𝙰𝙲𝙴 𝙼𝙰𝚃𝚃𝙴𝚁𝚂 ! 🦠
Most microbes don't live in shaking flasks; spatial structure shapes how microbes interact and evolve at every scale, as we discuss in our recent review @jeroenmeijer.bsky.social @simonvanvliet.bsky.social @bedutilh.bsky.social @bramvandijk.bsky.social and others
academic.oup.com/femsre/artic... 🧵👇
academic.oup.com/femsre/artic... 🧵👇
Spatial structure: shaping the ecology and evolution of microbial communities
Spatial structure naturally emerges in microbial communities, shaping growth, interactions, and evolution, and revealing how microscale processes scale up
academic.oup.com
February 13, 2026 at 12:11 PM
Please check out our review on the impact of spatial structure in microbial ecosystems! In it, we discuss how spatial patterns impact microbial ecology and evolution, eventually impacting everything we see around us!
See @marcelbaecker.bsky.social's amazing summary below :)
🦠 𝚂𝙿𝙰𝙲𝙴 𝙼𝙰𝚃𝚃𝙴𝚁𝚂 ! 🦠
See @marcelbaecker.bsky.social's amazing summary below :)
🦠 𝚂𝙿𝙰𝙲𝙴 𝙼𝙰𝚃𝚃𝙴𝚁𝚂 ! 🦠
Reposted by Bram van Dijk 🏳️🌈
Everyone knows that space and spatial structure is super important in shaping the Microverse 🌎🌍🌏 Check out this amazing review where @marcelbaecker.bsky.social and @bramvandijk.bsky.social et al bring together a huge body of knowledge @microverse.bsky.social @binfutrecht.bsky.social
Most microbes don't live in shaking flasks; spatial structure shapes how microbes interact and evolve at every scale, as we discuss in our recent review @jeroenmeijer.bsky.social @simonvanvliet.bsky.social @bedutilh.bsky.social @bramvandijk.bsky.social and others
academic.oup.com/femsre/artic... 🧵👇
academic.oup.com/femsre/artic... 🧵👇
Spatial structure: shaping the ecology and evolution of microbial communities
Spatial structure naturally emerges in microbial communities, shaping growth, interactions, and evolution, and revealing how microscale processes scale up
academic.oup.com
February 12, 2026 at 8:26 PM
Everyone knows that space and spatial structure is super important in shaping the Microverse 🌎🌍🌏 Check out this amazing review where @marcelbaecker.bsky.social and @bramvandijk.bsky.social et al bring together a huge body of knowledge @microverse.bsky.social @binfutrecht.bsky.social
Reposted by Bram van Dijk 🏳️🌈
...not in shaking flasks, not in microtiter plates either 😉
February 12, 2026 at 3:57 PM
...not in shaking flasks, not in microtiter plates either 😉
Reposted by Bram van Dijk 🏳️🌈
Most microbes don't live in shaking flasks; spatial structure shapes how microbes interact and evolve at every scale, as we discuss in our recent review @jeroenmeijer.bsky.social @simonvanvliet.bsky.social @bedutilh.bsky.social @bramvandijk.bsky.social and others
academic.oup.com/femsre/artic... 🧵👇
academic.oup.com/femsre/artic... 🧵👇
Spatial structure: shaping the ecology and evolution of microbial communities
Spatial structure naturally emerges in microbial communities, shaping growth, interactions, and evolution, and revealing how microscale processes scale up
academic.oup.com
February 12, 2026 at 3:46 PM
Most microbes don't live in shaking flasks; spatial structure shapes how microbes interact and evolve at every scale, as we discuss in our recent review @jeroenmeijer.bsky.social @simonvanvliet.bsky.social @bedutilh.bsky.social @bramvandijk.bsky.social and others
academic.oup.com/femsre/artic... 🧵👇
academic.oup.com/femsre/artic... 🧵👇
Reposted by Bram van Dijk 🏳️🌈
@bramvandijk.bsky.social (and many other)'s new paper covered insights in microbial ecology, evolution and theoretical biology.
Wrapping up a productive week: very glad to have contributed to this review on how spatial structure shapes microbial ecology and evolution, led by @marcelbaecker.bsky.social, @bedutilh.bsky.social, @bramvandijk.bsky.social and many others. doi.org/10.1093/fems...
Spatial structure: shaping the ecology and evolution of microbial communities
Spatial structure naturally emerges in microbial communities, shaping growth, interactions, and evolution, and revealing how microscale processes scale up
doi.org
February 12, 2026 at 1:58 PM
@bramvandijk.bsky.social (and many other)'s new paper covered insights in microbial ecology, evolution and theoretical biology.
Reposted by Bram van Dijk 🏳️🌈
Wrapping up a productive week: very glad to have contributed to this review on how spatial structure shapes microbial ecology and evolution, led by @marcelbaecker.bsky.social, @bedutilh.bsky.social, @bramvandijk.bsky.social and many others. doi.org/10.1093/fems...
Spatial structure: shaping the ecology and evolution of microbial communities
Spatial structure naturally emerges in microbial communities, shaping growth, interactions, and evolution, and revealing how microscale processes scale up
doi.org
February 11, 2026 at 3:46 PM
Wrapping up a productive week: very glad to have contributed to this review on how spatial structure shapes microbial ecology and evolution, led by @marcelbaecker.bsky.social, @bedutilh.bsky.social, @bramvandijk.bsky.social and many others. doi.org/10.1093/fems...
Reposted by Bram van Dijk 🏳️🌈
Spatial structure: Shaping the ecology and evolution of microbial communities
@femsjournals.bsky.social Microbiology Review by @marcelbaecker.bsky.social et al
from @bedutilh.bsky.social @bramvandijk.bsky.social
academic.oup.com/femsre/advan...
@femsjournals.bsky.social Microbiology Review by @marcelbaecker.bsky.social et al
from @bedutilh.bsky.social @bramvandijk.bsky.social
academic.oup.com/femsre/advan...
Spatial structure: Shaping the ecology and evolution of microbial communities
Abstract. Most microbes grow in spatially structured communities, and this profoundly shapes their ecology and evolution. At the microscale, short interact
academic.oup.com
February 10, 2026 at 12:39 PM
Spatial structure: Shaping the ecology and evolution of microbial communities
@femsjournals.bsky.social Microbiology Review by @marcelbaecker.bsky.social et al
from @bedutilh.bsky.social @bramvandijk.bsky.social
academic.oup.com/femsre/advan...
@femsjournals.bsky.social Microbiology Review by @marcelbaecker.bsky.social et al
from @bedutilh.bsky.social @bramvandijk.bsky.social
academic.oup.com/femsre/advan...
Reposted by Bram van Dijk 🏳️🌈
Reposted by Bram van Dijk 🏳️🌈
Less than two 2 weeks to apply for this PhD position in my group.
Please do not miss the opportunity to apply if the topic is of interest to you 👇
Please do not miss the opportunity to apply if the topic is of interest to you 👇
I am very excited to announce that a fully funded PhD position is available in my group.
Topic: Synergistic coevolution in mono-specific and multi-species microbial consortia
Please RT or forward this information to interested candidates.
Deadline: 11.01.26
More info:
shorturl.at/f1TuF
Topic: Synergistic coevolution in mono-specific and multi-species microbial consortia
Please RT or forward this information to interested candidates.
Deadline: 11.01.26
More info:
shorturl.at/f1TuF
December 30, 2025 at 10:36 AM
Less than two 2 weeks to apply for this PhD position in my group.
Please do not miss the opportunity to apply if the topic is of interest to you 👇
Please do not miss the opportunity to apply if the topic is of interest to you 👇
Reposted by Bram van Dijk 🏳️🌈
Very happy to see this piece out in @plosbiology.org, on the bacterial immune systems and microbial communities. It was a great team effort with Rafael Custodio, @brockhurstlab.bsky.social , @brownlab.bsky.social, and Edze Westra! 🦠🧫 #phagesky #mevosky
journals.plos.org/plosbiology/...
journals.plos.org/plosbiology/...
Bacterial immune systems as causes and consequences of microbiome structure
Bacterial immune systems have evolved in response to diverse molecular "parasites", yet their ecological roles remain poorly understood. This Essay explores how interactions between mobile genetic ele...
journals.plos.org
November 19, 2025 at 6:35 PM
Very happy to see this piece out in @plosbiology.org, on the bacterial immune systems and microbial communities. It was a great team effort with Rafael Custodio, @brockhurstlab.bsky.social , @brownlab.bsky.social, and Edze Westra! 🦠🧫 #phagesky #mevosky
journals.plos.org/plosbiology/...
journals.plos.org/plosbiology/...
Great work by @prczhaoyansong.bsky.social, once again elucidating how much flow of information there is in complex microbial ecosystems.
@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/...
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 29, 2025 at 7:19 AM
Great work by @prczhaoyansong.bsky.social, once again elucidating how much flow of information there is in complex microbial ecosystems.
Getting old means going to your own Google Scholar and seeing "if you wrote a paper about something"
October 4, 2025 at 12:30 PM
Getting old means going to your own Google Scholar and seeing "if you wrote a paper about something"
I must admit, PerplexityAI is really blowing my mind when it comes to literature searching. I've been avoiding it but I got stuck and decided to take a swing at it. It gave great papers, got my out of my bubble, and really gave me a fresh perspective. :)
September 15, 2025 at 10:34 AM
I must admit, PerplexityAI is really blowing my mind when it comes to literature searching. I've been avoiding it but I got stuck and decided to take a swing at it. It gave great papers, got my out of my bubble, and really gave me a fresh perspective. :)
Does anyone know a gene in E. coli that duplicated "fairly recently", as to compare and contrast it's sequence divergence with that found in mobile elements?
#sciencesky #microsky
#sciencesky #microsky
September 15, 2025 at 8:26 AM
Does anyone know a gene in E. coli that duplicated "fairly recently", as to compare and contrast it's sequence divergence with that found in mobile elements?
#sciencesky #microsky
#sciencesky #microsky
This picture is too low-res to include in a presentation in 2025, so I went full CSI 😂
I wonder though: even though it copies the copyright statement... this does count as a copyright violation? Thoughts?
I wonder though: even though it copies the copyright statement... this does count as a copyright violation? Thoughts?
September 8, 2025 at 9:50 AM
This picture is too low-res to include in a presentation in 2025, so I went full CSI 😂
I wonder though: even though it copies the copyright statement... this does count as a copyright violation? Thoughts?
I wonder though: even though it copies the copyright statement... this does count as a copyright violation? Thoughts?
Reposted by Bram van Dijk 🏳️🌈
Willing to join us @pasteur.fr for a PhD for a project on how interactions between mobile genetic elements shape bacterial adaptation? Subject to be tailored to candidates with keen interest in evolution, genomics, computational biology, microbiology. Check www.pasteur.fr/en/education...
September 8, 2025 at 8:56 AM
Willing to join us @pasteur.fr for a PhD for a project on how interactions between mobile genetic elements shape bacterial adaptation? Subject to be tailored to candidates with keen interest in evolution, genomics, computational biology, microbiology. Check www.pasteur.fr/en/education...
A bachelor student gifted me this beautiful artwork she made based on my first year course, and I am sp excited I wanna share it with “the internet” ❤️
September 3, 2025 at 2:38 PM
A bachelor student gifted me this beautiful artwork she made based on my first year course, and I am sp excited I wanna share it with “the internet” ❤️
Reposted by Bram van Dijk 🏳️🌈
We are also hiring a 4-year postdoc to study the dynamics and evolution of mobile genetic elements in the C-fixing Icelandic host-spring microbiomes
Join our exciting multidisciplinary team funded by @ukri.org BBSRC sLoLa
www.jobs.manchester.ac.uk/Job/JobDetai...
Join our exciting multidisciplinary team funded by @ukri.org BBSRC sLoLa
www.jobs.manchester.ac.uk/Job/JobDetai...
August 13, 2025 at 10:41 AM
We are also hiring a 4-year postdoc to study the dynamics and evolution of mobile genetic elements in the C-fixing Icelandic host-spring microbiomes
Join our exciting multidisciplinary team funded by @ukri.org BBSRC sLoLa
www.jobs.manchester.ac.uk/Job/JobDetai...
Join our exciting multidisciplinary team funded by @ukri.org BBSRC sLoLa
www.jobs.manchester.ac.uk/Job/JobDetai...
Reposted by Bram van Dijk 🏳️🌈
A new 4 year PostDoc position in our lab! Modeling + experiments to explore dynamics of carbon fixing hot-spring microbiomes. Part of an exciting multidisciplinary team with Sophie Nixon, @brockhurstlab.bsky.social & others
Please share & get in touch if interested!
tinyurl.com/e7j7bha3
Please share & get in touch if interested!
tinyurl.com/e7j7bha3
Research Associate in Microbiome Ecology:Oxford Road
www.jobs.manchester.ac.uk
August 12, 2025 at 2:59 PM
A new 4 year PostDoc position in our lab! Modeling + experiments to explore dynamics of carbon fixing hot-spring microbiomes. Part of an exciting multidisciplinary team with Sophie Nixon, @brockhurstlab.bsky.social & others
Please share & get in touch if interested!
tinyurl.com/e7j7bha3
Please share & get in touch if interested!
tinyurl.com/e7j7bha3
This is very cool. @sanmillan.bsky.social I wonder to what extend these non-random IS-dynamics are naturally selected for. Could it be the result of a long co-evolutionary history of ISs and bacteria? Are there differences in natural/non-natural antimicrobials?
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Plasmids promote antimicrobial resistance through Insertion Sequence-mediated gene inactivation
Antimicrobial Resistance (AMR) is a major threat to public health. Plasmids are mobile genetic elements that can rapidly spread across bacterial populations, promoting the dissemination of AMR genes i...
www.biorxiv.org
August 18, 2025 at 8:15 AM
This is very cool. @sanmillan.bsky.social I wonder to what extend these non-random IS-dynamics are naturally selected for. Could it be the result of a long co-evolutionary history of ISs and bacteria? Are there differences in natural/non-natural antimicrobials?
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Reposted by Bram van Dijk 🏳️🌈
New paper out! 🔈🔈📣📣
Plasmids promote antimicrobial resistance through Insertion Sequence-mediated gene inactivation.
Combining experimental and computational approaches, we unveil how two of the most prevalent bacterial MGE accelerate the evolution of AMR. 🧵👇🏻
www.biorxiv.org/content/10.1...
Plasmids promote antimicrobial resistance through Insertion Sequence-mediated gene inactivation.
Combining experimental and computational approaches, we unveil how two of the most prevalent bacterial MGE accelerate the evolution of AMR. 🧵👇🏻
www.biorxiv.org/content/10.1...
Plasmids promote antimicrobial resistance through Insertion Sequence-mediated gene inactivation
Antimicrobial Resistance (AMR) is a major threat to public health. Plasmids are mobile genetic elements that can rapidly spread across bacterial populations, promoting the dissemination of AMR genes i...
www.biorxiv.org
August 13, 2025 at 6:26 AM
New paper out! 🔈🔈📣📣
Plasmids promote antimicrobial resistance through Insertion Sequence-mediated gene inactivation.
Combining experimental and computational approaches, we unveil how two of the most prevalent bacterial MGE accelerate the evolution of AMR. 🧵👇🏻
www.biorxiv.org/content/10.1...
Plasmids promote antimicrobial resistance through Insertion Sequence-mediated gene inactivation.
Combining experimental and computational approaches, we unveil how two of the most prevalent bacterial MGE accelerate the evolution of AMR. 🧵👇🏻
www.biorxiv.org/content/10.1...
If I were me a few years ago, I would immediately apply. Wonderful environment to work in and Osnabrück is a (suprisingly 😝) fun city.
I am excited to announce that the position of a senior postdoc (3 +3 years) in the field of theoretical biology is available in my group.
The position provides the opportunity to closely interact with experimentalists and develop own research projects.
Please RT.
Details 👇:
shorturl.at/iiiOv
The position provides the opportunity to closely interact with experimentalists and develop own research projects.
Please RT.
Details 👇:
shorturl.at/iiiOv
116 FB 5 Research Assistant (m/f/d) field of Theoretical Ecology and Evolution or Computational Biology: Uni Osnabrück
shorturl.at
August 11, 2025 at 7:09 AM
If I were me a few years ago, I would immediately apply. Wonderful environment to work in and Osnabrück is a (suprisingly 😝) fun city.
Reposted by Bram van Dijk 🏳️🌈
Highly recommend this great opportunity to develop #theory together with @kostchristian.bsky.social and group who are simply a wonderful bunch!!
I am excited to announce that the position of a senior postdoc (3 +3 years) in the field of theoretical biology is available in my group.
The position provides the opportunity to closely interact with experimentalists and develop own research projects.
Please RT.
Details 👇:
shorturl.at/iiiOv
The position provides the opportunity to closely interact with experimentalists and develop own research projects.
Please RT.
Details 👇:
shorturl.at/iiiOv
116 FB 5 Research Assistant (m/f/d) field of Theoretical Ecology and Evolution or Computational Biology: Uni Osnabrück
shorturl.at
August 10, 2025 at 6:35 PM
Highly recommend this great opportunity to develop #theory together with @kostchristian.bsky.social and group who are simply a wonderful bunch!!