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Erik Bakkeren

@erikbakkeren.bsky.social
834 followers 710 following 44 posts

Canada Research Chair II and Assistant Professor at University of Calgary 🇨🇦 | Understanding and editing microbiomes using ecology | Mountain and trail runner🏃‍♂️⛰ | Postdoc in 🇬🇧, PhD in 🇨🇭 (he/him) erikbakkeren.com

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Reposted by Erik Bakkeren
Corrie Moreau @corriemoreau.bsky.social · 23/08/2026
📣 📣 📣 UPDATE: The 2026-2027 list of faculty and postdoc positions in ecology and evolutionary biology is out! Be sure to check out this active and helpful community run resource! docs.google.com/spreadsheets...
docs.google.com
ecoevojobs.net 2026-27
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IMPACTT Microbiome @impactt-microbiome.bsky.social · 29/09/2026
This morning was full of inspiring talks and great research @HavingIMPACTT2026! We heard from Plenary Speakers - Drs. @erikbakkeren.bsky.social, Thierry Mallevaey, Maziar Divangahi and Aline Ignacio.
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David Sünderhauf @davvi36.bsky.social · 10/09/2026
Please share! We are looking for a PhD student excited about gene transfer, and tackling Antimicrobial Resistance in Klebsiella pneumoniae. 🧬 More details & applications on funder website by 21st Oct 👇🏻 gw4biomed.ac.uk/developing-c...
gw4biomed.ac.uk
Developing CRISPR-Cas antimicrobials to tackle antibiotic resistance spread in Klebsiella pneumoniae - GW4 BioMed MRC DTP
Project Code IIAR27Ex van Houte Project Type Wet lab Research Theme Infection, Immunity, and Antimicrobial Resistance Project Summary Download Summary Antimicrobial resistance (AMR) poses a major thre...
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Noah Whiteman @nkwhiteman.bsky.social · 06/08/2026
I’m thrilled to share that our search for a tenure-track colleague in my *truly wonderful and collegial* Genetics, Genomics, Evolution and Development Division in the MCB Department at Berkeley @berkeleymcb.bsky.social is live! Please share this broad search widely: aprecruit.berkeley.edu/JPF05481
aprecruit.berkeley.edu
Assistant Professor -Genetics, Genomics, Evolution, and Development - Molecular and Cell Biology
University of California, Berkeley is hiring. Apply now!
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IMPACTT Microbiome @impactt-microbiome.bsky.social · 06/08/2026
Meet Plenary Speaker Dr. Erik Bakkeren (@erikbakkeren.bsky.social), Assistant Professor @ucalgarymed.bsky.social, who will speak about ecology within the human gut: using bacterial competition to understand and engineer the gut microbiome at #HavingIMPACTT2026
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MEEhubs @meehubs.bsky.social · 06/08/2026
Missing MEEhubs already? Well don't worry! If you have registered, you can still access the talks for a year from now! Catch up on the talks and posters you may have missed! #MEEHubs2026 #MEEhubs26 meehubs.org
meehubs.org
Home
Abstract submission now closed but we now invite all poster presenters to upload their posters to our platform using the above link by July 31, 2026.
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Reposted by Erik Bakkeren
MEEhubs @meehubs.bsky.social · 06/08/2026
Congrats to our poster and talk winners at the various hubs! #MEEHubs26 #MEEHubs2026 Bhaskar Kumawat James Riddell Ariel Favier Kurt Castro Brenna Fox Pascale Lemieux Nicolás Rodríguez-Romero Yael Sorokin Rose Evard Greg McCallum Louise Flanagan
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Erik Bakkeren @erikbakkeren.bsky.social · 06/08/2026
Excellent talk by Myles at #MEEHubs2026, our lab's first grad student. If you ever wonder what a gut microbiome and the different pieces of a burger have in common, ask him.
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Erik Bakkeren @erikbakkeren.bsky.social · 05/08/2026
Please consider helping out next time!! It's a great time to organize! Have your say where the hubs are in 2028.
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MEEhubs @meehubs.bsky.social · 05/08/2026
What, is it over already? MEEHubs2026 concluded just minutes ago. It's been a blast, and here are some stats for you: 711 registrations, 241 posters, 71 talks, 3 days, participants from 32 countries. Bye from all the hubs 🩵🩵🩵 #MEEHubs2026 #MEEHubs26
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MEEhubs @meehubs.bsky.social · 05/08/2026
MEEHubs doesn't stop when the talks stop: from a mouth-watering spread in Morelia to a bonfire in Irvine to an Apero in Zurich, we've got your social calendar covered during the conference #MEEHubs2026 #MEEHubs26
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MEEhubs @meehubs.bsky.social · 04/08/2026
MEEHubs has both in-person posters at the hubs and virtual posters online! We're so excited to be able to bring great research together through this platform #meehubs26 #meehubs2026
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Reposted by Erik Bakkeren
MEEhubs @meehubs.bsky.social · 04/08/2026
MEEHubs or MEEPubs? Our cross-hub pub quiz pitted hubs against each other in a thrilling battle. Congrats to "alan", "Tom" and "swayam" for winning free registration to a local hub at the next MEEHubs! #MEEHubs26 #MEEHubs2026
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MEEhubs @meehubs.bsky.social · 04/08/2026
Great atmospheres at social events at each hub! Not only a great place to listen to MEE talks, but an opportunity to eat a massive spread in Chernihiv, play bocce in Ann Arbor, or stand in the rain in Manchester. Don't worry Montreal, you're not the only hub with downpour! #MEEHubs26 #MEEHubs2026
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MEEhubs @meehubs.bsky.social · 04/08/2026
Day 1 wrapped up with the Irvine and Ann Arbor hubs hosting. Thanks all for an amazing first day and see you tomorrow! Grab a beer, a coffee, or finish off your z's to prep for a fully packed Day 2. #MEEHubs26 #MEEHubs2026
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MEEhubs @meehubs.bsky.social · 03/08/2026
The next few sessions were hosted by Chernihiv, Morelia, and Montreal. That's excellent science spanning 9h of time difference! #MEEHubs2026 Sad you missed out on one of these talks? Don't worry! They're all recorded so you can view whenever you want!
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Reposted by Erik Bakkeren
Anna S. Weiss @annasophieweiss.bsky.social · 03/08/2026
You know it’s @meehubs.bsky.social if one hub has beer while another has breakfast. The Zürich hub is concluding a fantastic first day of #MEEHubs26 - can’t wait to rewatch what we’ll be missing out on tonight and excited for two more days of science and fun across hubs 🙌🏼🚀
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MEEhubs @meehubs.bsky.social · 03/08/2026
MEEHubs2026 is underway! We had a great start in the first two sessions with Zurich and Manchester hosting some excellent talks! It's not too late to join us virtually via last-minute registration: meehubs.org #MEEHubs2026
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Reposted by Erik Bakkeren
MEEhubs @meehubs.bsky.social · 29/07/2026
Registration for MEEHubs2026 taking place Aug 3-5 is closing this Friday (July 31, 2026)!! There's still time to join us in Montreal, Ann Arbor, Irvine, Morelia, Zurich, Manchester, Chernihiv, or online. Register here: meehubs.org
meehubs.org
Home
Abstract submission now closed but we now invite all poster presenters to upload their posters to our platform using the above link by July 31, 2026.
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MEEhubs @meehubs.bsky.social · 23/07/2026
One week left to register for MEEHubs2026 taking place Aug 3-5!! Please join us in Montreal, Ann Arbor, Irvine, Morelia, Zurich, Manchester, Chernihiv, or online. Register here: meehubs.org
meehubs.org
Home
Abstract submission now closed but we now invite all poster presenters to upload their posters to our platform using the above link by July 31, 2026.
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Reposted by Erik Bakkeren
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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Ricardo León-Sampedro @rleonsampedro.bsky.social · 22/06/2026
New Perspective out co-led with Lisa Pagani! We look at how microbiome ecology and evolution shape AMR across scales, from within-host communities to hospitals and environments, and how mathematical models can help us understand them. @natmicrobiol.nature.com www.nature.com/articles/s41...
nature.com
Modelling the role of the microbiome in antimicrobial resistance across scales - Nature Microbiology
The microbiome plays a significant yet underexplored role in antimicrobial resistance by influencing ecological and evolutionary processes. This Perspective proposes a framework to integrate microbiom...
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MEEhubs @meehubs.bsky.social · 20/04/2026
We didn't want anyone to miss out, so we've extended the deadline for abstract submission to MEEHubs2026 until this Sunday (April 26). ✨ Please submit and please re-share! meehubs.org
meehubs.org
Home
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MEEhubs @meehubs.bsky.social · 17/04/2026
2 days left ‼️ Don't forget to submit your abstract to MEEHubs2026: Aug 3-5, 2026 meehubs.org
meehubs.org
Home
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Will Smith @willpjsmith.bsky.social · 17/04/2026
🚨 Calling all microbiologists! 🚨 The MEEHubs abstract submission deadline (19/04) is fast approaching. Come showcase your science!! Submission portal is here: app.oxfordabstracts.com/auth?redirec...
app.oxfordabstracts.com
Oxford Abstracts
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MEEhubs @meehubs.bsky.social · 15/04/2026
Just a few days left‼️ Abstract submission deadline for MEEHubs2026 is April 19! Come present at one of the hubs August 3-5, 2026✨ Links and more info here: meehubs.org
meehubs.org
Home
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MEEhubs @meehubs.bsky.social · 08/04/2026
REMINDER - Abstract submission deadline for MEEHubs2026 is April 19! Get you abstract in and present at one of the hubs August 3-5, 2026✨You'll be in great company! We have a fantastic lineup of speakers‼️ Links and more info here: meehubs.org
meehubs.org
Home
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Erik Bakkeren @erikbakkeren.bsky.social · 18/03/2026
Please register and submit an abstract to MEEHubs2026!
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Reposted by Erik Bakkeren
MEEhubs @meehubs.bsky.social · 18/03/2026
MEEHubs2026 registration and abstract submission is now online! 🚨🦠✨ Join us Aug 3 - 5, 2026 at one of the 7 hubs or online. We are incredibly excited about our lineup of speakers, and hope that you submit an abstract to contribute too! More information and registration links at: meehubs.org
meehubs.org
Home
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Nature Microbiology @natmicrobiol.nature.com · 19/12/2025
As the year ends, we decided to select our favorite papers of 2025 Turns out, it is impossible as we love them all! So, we picked 'some' that exhibit the range of microbiology highlighted through the columns of Nature Microbiology. Here is a glimpse into #EditorPicks of 2025 #MicroSky 🦠
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Atin Sharma @atinsharma.bsky.social · 12/12/2025
Two interesting papers, two different contexts, but both reminded me of the super cool recent article in @natmicrobiol.nature.com by @erikbakkeren.bsky.social that goes about setting general rules for ecological success in microbial communities. #MicroSky #MicrobiomeSky Links in the reply
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The Dunn School, Oxford @dunnschool.bsky.social · 10/11/2025
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...
nature.com
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.
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Erik Bakkeren @erikbakkeren.bsky.social · 07/11/2025
Here's a behind the paper blog post our recent @natmicrobiol.nature.com paper: communities.springernature.com/posts/learni...
communities.springernature.com
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...
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Erik Bakkeren @erikbakkeren.bsky.social · 07/11/2025
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...
nature.com
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.
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Ákos T Kovács @evolvedbiofilm.bsky.social · 07/11/2025
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...
nature.com
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.
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Nature Microbiology @natmicrobiol.nature.com · 07/11/2025
#NewResearch Strain displacement in microbiomes via ecological competition @erikbakkeren.bsky.social #microsky www.nature.com/articles/s41...
nature.com
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.
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Connor Sharp @magicmicrobe.bsky.social · 05/11/2025
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...
nature.com
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...
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Erik Bakkeren @erikbakkeren.bsky.social · 07/10/2025
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)‼️
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MEEhubs @meehubs.bsky.social · 16/09/2025
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....
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Emma Slack @mucosalimmunology.bsky.social · 15/06/2025
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...
pmc.ncbi.nlm.nih.gov
Vaccine-enhanced competition permits rational bacterial strain replacement in the gut
Colonization of the intestinal lumen precedes invasive infection for a wide range of enteropathogenic and opportunistic pathogenic bacteria. Here we show that combining oral vaccination with engineere...
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Reposted by Erik Bakkeren
Glen Dsouza @nonresidentdesi.bsky.social · 13/06/2025
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/...
science.org
Antagonism as a foraging strategy in microbial communities
In natural habitats, nutrient availability limits bacterial growth. We discovered that bacteria can overcome this limitation by acquiring nutrients by lysing neighboring cells through contact-dependen...
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Sara Mitri @saramitri.bsky.social · 12/06/2025
We are recruiting a tenure-track assistant professor in molecular microbiology in our department in Lausanne! Do consider appyling!!
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Erik Bakkeren @erikbakkeren.bsky.social · 11/06/2025
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 😁
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Erik Bakkeren @erikbakkeren.bsky.social · 11/06/2025
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...
sciencedirect.com
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…
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Erik Bakkeren @erikbakkeren.bsky.social · 26/02/2025
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
fosterlab.uk
vacancies — Foster Lab
job vacancies in the Foster lab
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Ole Seehausen @oleseehausen.bsky.social · 28/12/2024
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
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The Dunn School, Oxford @dunnschool.bsky.social · 31/01/2025
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...
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Emma Slack @mucosalimmunology.bsky.social · 26/01/2025
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 🧪🧫🔬
jobs.ethz.ch
Postdoctoral researcher –Understanding bacterial metabolism in the urinary tract
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The Dunn School, Oxford @dunnschool.bsky.social · 14/01/2025
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...
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Samir Giri @isamirgiri.bsky.social · 13/01/2025
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
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