Erik Bakkeren

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 🦠

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

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.

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...

Here's a behind the paper blog post our recent @natmicrobiol.nature.com paper:

communities.springernature.com/posts/learni...

This demonstrates that if we learn about the natural ecology of bacterial competition, we might be able to manipulate microbiomes rationally. We wrote about this more broadly in a recent review.
doi.org/10.1016/j.ch...

When we then supplemented that private nutrient for the invading strain, boom, the resident strain was displaced by the invading strain!

Then, we took a community of gut microbes that included a resident antimicrobial E. coli clinical isolate and identified a nutrient that was not consumed by any species in the community. We then added an invading strain of E. coli that could use that private nutrient, and gave it a bacterial weapon.

Bacterial weapons only start to take effect once a strain has invaded. If the invading strain carries a weapon and can grow to a sufficient density based on its metabolism and available nutrients, it can now displace a resident strain!

We confirmed this first with theory and then with experiments.

Microbiome diversity protects against pathogens by nutrient blocking Diverse communities of commensal gut bacteria collectively limit pathogen colonization by blocking nutrient access.

It turns out that invasion of a strain into a community is not facilitated by bacterial weapons, but rather by differences in nutrient utilization. This fit really well with our recent work on nutrient blocking in colonization resistance: www.science.org/doi/10.1126/...

We began by thinking about how microbes naturally compete in communities. It happens in two main ways: bacteria use metabolic capacity to access nutrients better than competitors via resource competition, or they invest in bacterial weapons to kill competitors called interference competition.

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.

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.

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...

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.

#NewResearch

Strain displacement in microbiomes via ecological competition

@erikbakkeren.bsky.social

#microsky

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...

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...

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)‼️

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....

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...

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/...

We are recruiting a tenure-track assistant professor in molecular microbiology in our department in Lausanne! Do consider appyling!!

Replaced by my favourite, the mountain goat, this time 😁

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 😁

Very fun collaborative piece with @vit-pi.bsky.social and Kevin Foster

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…

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...

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

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

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...

Postdoctoral researcher –Understanding bacterial metabolism in the urinary tract

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
🧪🧫🔬

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...

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

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...

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