Erik Bakkeren
@erikbakkeren.bsky.social
Assistant Professor at University of Calgary, Canada | Understanding and editing microbiomes using ecology | Mountain and trail runner🏃♂️⛰ | Postdoc in 🇬🇧, PhD in 🇨🇭 (he/him)
https://erikbakkeren.com/
https://erikbakkeren.com/
Pinned
Strain displacement in microbiomes via ecological competition - Nature Microbiology
Mathematical modelling and experimental tests reveal principles that govern displacement of a resident strain by an invader in microbial communities.
www.nature.com
Can we leverage bacterial competition for targeted replacement of harmful strains? Maybe! Our recent piece in @natmicrobiol.nature.com provides a theoretical framework and a set of experiments to show what it might take: www.nature.com/articles/s41...
Reposted by Erik Bakkeren
The latest paper by @erikbakkeren.bsky.social and the Foster group shows a potential way to engineer the microbiome by replacing problem strains with beneficial ones
Find out more @natmicrobiol.nature.com:
www.nature.com/articles/s41...
Find out more @natmicrobiol.nature.com:
www.nature.com/articles/s41...
Strain displacement in microbiomes via ecological competition - Nature Microbiology
Mathematical modelling and experimental tests reveal principles that govern displacement of a resident strain by an invader in microbial communities.
www.nature.com
November 10, 2025 at 10:40 AM
The latest paper by @erikbakkeren.bsky.social and the Foster group shows a potential way to engineer the microbiome by replacing problem strains with beneficial ones
Find out more @natmicrobiol.nature.com:
www.nature.com/articles/s41...
Find out more @natmicrobiol.nature.com:
www.nature.com/articles/s41...
Here's a behind the paper blog post our recent @natmicrobiol.nature.com paper:
communities.springernature.com/posts/learni...
communities.springernature.com/posts/learni...
Learning how to exploit bacterial competition to target harmful strains
Bacteria living in microbial communities naturally compete for resources. We show that by understanding how bacteria compete, we can repurpose natural competition and target harmful species from withi...
communities.springernature.com
November 7, 2025 at 10:47 PM
Here's a behind the paper blog post our recent @natmicrobiol.nature.com paper:
communities.springernature.com/posts/learni...
communities.springernature.com/posts/learni...
Can we leverage bacterial competition for targeted replacement of harmful strains? Maybe! Our recent piece in @natmicrobiol.nature.com provides a theoretical framework and a set of experiments to show what it might take: www.nature.com/articles/s41...
Strain displacement in microbiomes via ecological competition - Nature Microbiology
Mathematical modelling and experimental tests reveal principles that govern displacement of a resident strain by an invader in microbial communities.
www.nature.com
November 7, 2025 at 10:34 PM
Can we leverage bacterial competition for targeted replacement of harmful strains? Maybe! Our recent piece in @natmicrobiol.nature.com provides a theoretical framework and a set of experiments to show what it might take: www.nature.com/articles/s41...
Reposted by Erik Bakkeren
Strain displacement in microbiomes via ecological competition
Cool @natmicrobiol.nature.com publication by @erikbakkeren.bsky.social
@vit-pi.bsky.social @meganleeny.bsky.social @microscape.bsky.social & Kevin Foster
www.nature.com/articles/s41...
Cool @natmicrobiol.nature.com publication by @erikbakkeren.bsky.social
@vit-pi.bsky.social @meganleeny.bsky.social @microscape.bsky.social & Kevin Foster
www.nature.com/articles/s41...
Strain displacement in microbiomes via ecological competition - Nature Microbiology
Mathematical modelling and experimental tests reveal principles that govern displacement of a resident strain by an invader in microbial communities.
www.nature.com
November 7, 2025 at 2:19 PM
Strain displacement in microbiomes via ecological competition
Cool @natmicrobiol.nature.com publication by @erikbakkeren.bsky.social
@vit-pi.bsky.social @meganleeny.bsky.social @microscape.bsky.social & Kevin Foster
www.nature.com/articles/s41...
Cool @natmicrobiol.nature.com publication by @erikbakkeren.bsky.social
@vit-pi.bsky.social @meganleeny.bsky.social @microscape.bsky.social & Kevin Foster
www.nature.com/articles/s41...
Reposted by Erik Bakkeren
#NewResearch
Strain displacement in microbiomes via ecological competition
@erikbakkeren.bsky.social
#microsky
www.nature.com/articles/s41...
Strain displacement in microbiomes via ecological competition
@erikbakkeren.bsky.social
#microsky
www.nature.com/articles/s41...
Strain displacement in microbiomes via ecological competition - Nature Microbiology
Mathematical modelling and experimental tests reveal principles that govern displacement of a resident strain by an invader in microbial communities.
www.nature.com
November 7, 2025 at 11:09 AM
#NewResearch
Strain displacement in microbiomes via ecological competition
@erikbakkeren.bsky.social
#microsky
www.nature.com/articles/s41...
Strain displacement in microbiomes via ecological competition
@erikbakkeren.bsky.social
#microsky
www.nature.com/articles/s41...
Reposted by Erik Bakkeren
So happy to share this! Bacteriocins were first discovered over 100 years ago, but what do they actually do? We look at >1000 bacteriocin plasmids and find links to virulence and antimicrobial resistance, and frequent bacteriocin sharing in Enterobacteriaceae.
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Bacterial warfare is associated with virulence and antimicrobial resistance - Nature Communications
Bacteria employ a range of competition systems that deliver toxins to inhibit competing strains. This study shows that these systems are particularly important for the ecology of virulent and antibiot...
www.nature.com
November 5, 2025 at 7:32 AM
So happy to share this! Bacteriocins were first discovered over 100 years ago, but what do they actually do? We look at >1000 bacteriocin plasmids and find links to virulence and antimicrobial resistance, and frequent bacteriocin sharing in Enterobacteriaceae.
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Note it in your calendars! Aug 3-5, 2026. Excited to bring back MEEHubs to a hub near you (Switzerland, USA, Canada, Mexico, UK, Ukraine, or virtual only)‼️
We’re back! ✨ The next #MeeHubs26 is coming with 7 hubs across the globe and incredible lineups at each. Can’t wait to share more soon! meehubs.org
Home
meehubs.org
October 7, 2025 at 3:01 PM
Note it in your calendars! Aug 3-5, 2026. Excited to bring back MEEHubs to a hub near you (Switzerland, USA, Canada, Mexico, UK, Ukraine, or virtual only)‼️
Reposted by Erik Bakkeren
While you wait for the next MEEhubs conference: We've written up the participants' impressions, the organisers' thoughts, reflections on the expectations we scientists have on conferences, and much more in @femsjournals.bsky.social, led by Ariane Wenger. Check out doi.org/10.1093/fems....
September 16, 2025 at 4:26 PM
While you wait for the next MEEhubs conference: We've written up the participants' impressions, the organisers' thoughts, reflections on the expectations we scientists have on conferences, and much more in @femsjournals.bsky.social, led by Ariane Wenger. Check out doi.org/10.1093/fems....
Reposted by Erik Bakkeren
Thank you for the very well-written preview @romanagerner1.bsky.social !! Much appreciated.
In other good news, the paper is finally available open access:
pmc.ncbi.nlm.nih.gov/articles/PMC...
In other good news, the paper is finally available open access:
pmc.ncbi.nlm.nih.gov/articles/PMC...
June 15, 2025 at 8:29 PM
Thank you for the very well-written preview @romanagerner1.bsky.social !! Much appreciated.
In other good news, the paper is finally available open access:
pmc.ncbi.nlm.nih.gov/articles/PMC...
In other good news, the paper is finally available open access:
pmc.ncbi.nlm.nih.gov/articles/PMC...
Reposted by Erik Bakkeren
Our paper in @science.org 👉🏽 www.science.org/doi/10.1126/...
is accompanied by an especially thoughtful perspective by Carey Nadell and Chris Marx 👉🏽
www.science.org/doi/10.1126/...
is accompanied by an especially thoughtful perspective by Carey Nadell and Chris Marx 👉🏽
www.science.org/doi/10.1126/...
June 13, 2025 at 6:11 AM
Our paper in @science.org 👉🏽 www.science.org/doi/10.1126/...
is accompanied by an especially thoughtful perspective by Carey Nadell and Chris Marx 👉🏽
www.science.org/doi/10.1126/...
is accompanied by an especially thoughtful perspective by Carey Nadell and Chris Marx 👉🏽
www.science.org/doi/10.1126/...
Reposted by Erik Bakkeren
We are recruiting a tenure-track assistant professor in molecular microbiology in our department in Lausanne! Do consider appyling!!
Come join us in beautiful Lausanne! Deadline for applications: August 10th, 2025
wwwfbm.unil.ch/releve/appli...
wwwfbm.unil.ch/releve/appli...
June 12, 2025 at 12:45 PM
We are recruiting a tenure-track assistant professor in molecular microbiology in our department in Lausanne! Do consider appyling!!
Please read about how we think microbial metabolism might help us understand microbiomes a bit better!
Also, please appreciate the mountain goat in Fig 1 ⛰️🐐 and that it also represents my joy for trail running and the mountains 😁
Also, please appreciate the mountain goat in Fig 1 ⛰️🐐 and that it also represents my joy for trail running and the mountains 😁
Metabolic ecology of microbiomes: Nutrient competition, host benefits, and community engineering
Review by Erik Bakkeren, Vit Piskovsky, and Kevin R. Foster
www.cell.com/cell-host-mi...
Review by Erik Bakkeren, Vit Piskovsky, and Kevin R. Foster
www.cell.com/cell-host-mi...
June 11, 2025 at 5:08 PM
Please read about how we think microbial metabolism might help us understand microbiomes a bit better!
Also, please appreciate the mountain goat in Fig 1 ⛰️🐐 and that it also represents my joy for trail running and the mountains 😁
Also, please appreciate the mountain goat in Fig 1 ⛰️🐐 and that it also represents my joy for trail running and the mountains 😁
Out today, @cp-cellhostmicrobe.bsky.social! Microbiomes have many benefits, but they are also often incredibly diverse and variable. This makes them hard to understand and even harder to engineer. We argue that the key may lie in microbial metabolism!
www.sciencedirect.com/science/arti...
www.sciencedirect.com/science/arti...
Metabolic ecology of microbiomes: Nutrient competition, host benefits, and community engineering
Many plants and animals, including humans, host diverse communities of microbes that provide many benefits. A key challenge in understanding microbiom…
www.sciencedirect.com
June 11, 2025 at 4:54 PM
Out today, @cp-cellhostmicrobe.bsky.social! Microbiomes have many benefits, but they are also often incredibly diverse and variable. This makes them hard to understand and even harder to engineer. We argue that the key may lie in microbial metabolism!
www.sciencedirect.com/science/arti...
www.sciencedirect.com/science/arti...
My postdoc mentor Kevin Foster is hiring postdocs! Apply to join an exciting research group looking at ecology and evolution of the gut microbiome.
Kevin is a fantastic mentor and I can completely recommend: www.fosterlab.uk/vacancies
Kevin is a fantastic mentor and I can completely recommend: www.fosterlab.uk/vacancies
vacancies — Foster Lab
job vacancies in the Foster lab
www.fosterlab.uk
February 26, 2025 at 10:46 AM
My postdoc mentor Kevin Foster is hiring postdocs! Apply to join an exciting research group looking at ecology and evolution of the gut microbiome.
Kevin is a fantastic mentor and I can completely recommend: www.fosterlab.uk/vacancies
Kevin is a fantastic mentor and I can completely recommend: www.fosterlab.uk/vacancies
Reposted by Erik Bakkeren
Please circulate widely:
We are hiring two Ass Prof tt at the Institute of #ecology and #evolution at @unibern.bsky.social in conservation biology; mathematical & computational ecology
We are committed to diverse, inclusive and equitable leadership in research and education
tinyurl.com/IEEjobs
We are hiring two Ass Prof tt at the Institute of #ecology and #evolution at @unibern.bsky.social in conservation biology; mathematical & computational ecology
We are committed to diverse, inclusive and equitable leadership in research and education
tinyurl.com/IEEjobs
December 28, 2024 at 4:52 PM
Please circulate widely:
We are hiring two Ass Prof tt at the Institute of #ecology and #evolution at @unibern.bsky.social in conservation biology; mathematical & computational ecology
We are committed to diverse, inclusive and equitable leadership in research and education
tinyurl.com/IEEjobs
We are hiring two Ass Prof tt at the Institute of #ecology and #evolution at @unibern.bsky.social in conservation biology; mathematical & computational ecology
We are committed to diverse, inclusive and equitable leadership in research and education
tinyurl.com/IEEjobs
Reposted by Erik Bakkeren
Mentors play such an important role in the career and confidence of budding scientists...
Many congratulations to Rebecca and Erik, winners of the first Dunn School Marvellous Mentor Award. Another great initiative by our student association!
www.path.ox.ac.uk/news-article...
Many congratulations to Rebecca and Erik, winners of the first Dunn School Marvellous Mentor Award. Another great initiative by our student association!
www.path.ox.ac.uk/news-article...
January 31, 2025 at 2:24 PM
Mentors play such an important role in the career and confidence of budding scientists...
Many congratulations to Rebecca and Erik, winners of the first Dunn School Marvellous Mentor Award. Another great initiative by our student association!
www.path.ox.ac.uk/news-article...
Many congratulations to Rebecca and Erik, winners of the first Dunn School Marvellous Mentor Award. Another great initiative by our student association!
www.path.ox.ac.uk/news-article...
Reposted by Erik Bakkeren
Interested in microbial #metabolism, #mucosalbiology and #UTI? Then check out the open postdoctoral position in the Mucosal Immunology Group at ETH Zurich! NB: All applications must go via the ETH job portal:
www.jobs.ethz.ch/job/view/JOP...
Closing date: 24th Feburary
🧪🧫🔬
www.jobs.ethz.ch/job/view/JOP...
Closing date: 24th Feburary
🧪🧫🔬
Postdoctoral researcher –Understanding bacterial metabolism in the urinary tract
www.jobs.ethz.ch
January 26, 2025 at 1:25 PM
Interested in microbial #metabolism, #mucosalbiology and #UTI? Then check out the open postdoctoral position in the Mucosal Immunology Group at ETH Zurich! NB: All applications must go via the ETH job portal:
www.jobs.ethz.ch/job/view/JOP...
Closing date: 24th Feburary
🧪🧫🔬
www.jobs.ethz.ch/job/view/JOP...
Closing date: 24th Feburary
🧪🧫🔬
Reposted by Erik Bakkeren
We just can't stop recruiting!
Associate professor in cell and molecular biology @dunnschool, with a preference for immunology, inflammation and/or infection - all defined broadly
Come and be our colleague
Deadline 28 Feb, please spread the word
www.path.ox.ac.uk/vacancy/asso...
Associate professor in cell and molecular biology @dunnschool, with a preference for immunology, inflammation and/or infection - all defined broadly
Come and be our colleague
Deadline 28 Feb, please spread the word
www.path.ox.ac.uk/vacancy/asso...
January 14, 2025 at 4:52 PM
We just can't stop recruiting!
Associate professor in cell and molecular biology @dunnschool, with a preference for immunology, inflammation and/or infection - all defined broadly
Come and be our colleague
Deadline 28 Feb, please spread the word
www.path.ox.ac.uk/vacancy/asso...
Associate professor in cell and molecular biology @dunnschool, with a preference for immunology, inflammation and/or infection - all defined broadly
Come and be our colleague
Deadline 28 Feb, please spread the word
www.path.ox.ac.uk/vacancy/asso...
Reposted by Erik Bakkeren
Excited to share our opinion piece with the KC Huang Lab.
Check it out here:
Harnessing gut microbial communities to unravel microbiome functions
doi.org/10.1016/j.mi...
@typaslab.bsky.social
Check it out here:
Harnessing gut microbial communities to unravel microbiome functions
doi.org/10.1016/j.mi...
@typaslab.bsky.social
January 13, 2025 at 3:08 PM
Excited to share our opinion piece with the KC Huang Lab.
Check it out here:
Harnessing gut microbial communities to unravel microbiome functions
doi.org/10.1016/j.mi...
@typaslab.bsky.social
Check it out here:
Harnessing gut microbial communities to unravel microbiome functions
doi.org/10.1016/j.mi...
@typaslab.bsky.social
Reposted by Erik Bakkeren
Delighted to share the first peer-reviewed paper from our team @camvetschool.bsky.social where we investigate the ecological dynamics of Enterobacteriaceae in the human gut #microbiome: www.nature.com/articles/s41... @naturemicrobiol.bsky.social
Ecological dynamics of Enterobacteriaceae in the human gut microbiome across global populations - Nature Microbiology
Assessing more than 12,000 metagenomic samples from across the world using computational approaches, the authors determined interactions between species that co-colonize or co-exclude Enterobacteriace...
www.nature.com
January 10, 2025 at 10:06 AM
Delighted to share the first peer-reviewed paper from our team @camvetschool.bsky.social where we investigate the ecological dynamics of Enterobacteriaceae in the human gut #microbiome: www.nature.com/articles/s41... @naturemicrobiol.bsky.social
Reposted by Erik Bakkeren
Joy! Published today in PNAS: multi-toxin T6SS attacks limit resistance evolution in competitors!
Big thanks to our wonderful team of collaborators for all their help: @coytelab.bsky.social @knightjar.bsky.social @basler-lab.bsky.social @brockhurstlab.bsky.social 🎉
www.pnas.org/doi/10.1073/...
Big thanks to our wonderful team of collaborators for all their help: @coytelab.bsky.social @knightjar.bsky.social @basler-lab.bsky.social @brockhurstlab.bsky.social 🎉
www.pnas.org/doi/10.1073/...
January 9, 2025 at 5:02 PM
Joy! Published today in PNAS: multi-toxin T6SS attacks limit resistance evolution in competitors!
Big thanks to our wonderful team of collaborators for all their help: @coytelab.bsky.social @knightjar.bsky.social @basler-lab.bsky.social @brockhurstlab.bsky.social 🎉
www.pnas.org/doi/10.1073/...
Big thanks to our wonderful team of collaborators for all their help: @coytelab.bsky.social @knightjar.bsky.social @basler-lab.bsky.social @brockhurstlab.bsky.social 🎉
www.pnas.org/doi/10.1073/...
Just as the year ends, I wanted to share some news! I will be starting at the University of Calgary as an Assistant Professor in Sept. 2025 🇨🇦
Very excited to continue to work on understanding and editing microbiomes using ecology with new colleagues and coworkers! Stay tuned for recruitment updates
Very excited to continue to work on understanding and editing microbiomes using ecology with new colleagues and coworkers! Stay tuned for recruitment updates
December 30, 2024 at 1:19 AM
Just as the year ends, I wanted to share some news! I will be starting at the University of Calgary as an Assistant Professor in Sept. 2025 🇨🇦
Very excited to continue to work on understanding and editing microbiomes using ecology with new colleagues and coworkers! Stay tuned for recruitment updates
Very excited to continue to work on understanding and editing microbiomes using ecology with new colleagues and coworkers! Stay tuned for recruitment updates
Reposted by Erik Bakkeren
Register by 11:59pm MST on Jan. 3, 2025, to save $200 on our joint conference on Human Microbiome / Host-Microbe Co-Evolution. Enjoy 2 conferences for the price of one! keysym.us/KSHumanMicro25 / keysym.us/KSHostMicrob... #KSHumanMicro25 #KSHostMicrobe25 #microbiome #humanmicrobiome #microbiota
December 19, 2024 at 7:37 PM
Register by 11:59pm MST on Jan. 3, 2025, to save $200 on our joint conference on Human Microbiome / Host-Microbe Co-Evolution. Enjoy 2 conferences for the price of one! keysym.us/KSHumanMicro25 / keysym.us/KSHostMicrob... #KSHumanMicro25 #KSHostMicrobe25 #microbiome #humanmicrobiome #microbiota
Reposted by Erik Bakkeren
Are #pyoverdines effective antibacterials?🦠💊
Yes! We found strong competitive and antibacterial effects against #ESKAPE pathogens via iron depletion.
Out now in @elife.bsky.social: doi.org/10.7554/eLif... (1/4)
With @rkmicrobes.bsky.social and amazing collaborators from #UZH & @ethzurich.bsky.social
Yes! We found strong competitive and antibacterial effects against #ESKAPE pathogens via iron depletion.
Out now in @elife.bsky.social: doi.org/10.7554/eLif... (1/4)
With @rkmicrobes.bsky.social and amazing collaborators from #UZH & @ethzurich.bsky.social
Antimicrobial activity of iron-depriving pyoverdines against human opportunistic pathogens
Iron-chelating pyoverdines from environmental Pseudomonas spp. show promising antibacterial activity against key human pathogens through the induction of iron starvation, while associated toxicity for...
doi.org
December 20, 2024 at 11:19 AM
Are #pyoverdines effective antibacterials?🦠💊
Yes! We found strong competitive and antibacterial effects against #ESKAPE pathogens via iron depletion.
Out now in @elife.bsky.social: doi.org/10.7554/eLif... (1/4)
With @rkmicrobes.bsky.social and amazing collaborators from #UZH & @ethzurich.bsky.social
Yes! We found strong competitive and antibacterial effects against #ESKAPE pathogens via iron depletion.
Out now in @elife.bsky.social: doi.org/10.7554/eLif... (1/4)
With @rkmicrobes.bsky.social and amazing collaborators from #UZH & @ethzurich.bsky.social
Reposted by Erik Bakkeren
Nora finished her paper with a sentence I like a lot "Our results show that even under extremely restrictive, competitive conditions, the simplest biological entities on Earth can still find paths to coexistence." There is a curious dichotomy in her experiments... 1/3
www.science.org/doi/10.1126/...
www.science.org/doi/10.1126/...
Diverse phage communities are maintained stably on a clonal bacterial host
Bacteriophages are the most abundant and phylogenetically diverse biological entities on Earth, yet the ecological mechanisms that sustain this extraordinary diversity remain unclear. In this study, w...
www.science.org
December 16, 2024 at 11:38 AM
Nora finished her paper with a sentence I like a lot "Our results show that even under extremely restrictive, competitive conditions, the simplest biological entities on Earth can still find paths to coexistence." There is a curious dichotomy in her experiments... 1/3
www.science.org/doi/10.1126/...
www.science.org/doi/10.1126/...