iiinova — where your digital self keeps evolving

Reposted by Sonja Lehtinen

Alan Pacheco @pachecolab.bsky.social · 12/10/2026

Our group is recruiting a PhD student! Interested in microbial interactions, metabolic ecology, and community dynamics? Join us to combine experiments, data, and quantitative thinking, within the context of soil- and plant-associated microbial communities. 📅 Apply by Oct 30 🔗 tinyurl.com/u9bvjphb

career5.successfactors.eu

Opportunités de carrière : Doctoral Student SNSF in Quantitative Microbial Ecology and Metabolic Interactions (23002)

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Reposted by Sonja Lehtinen

Janani Durairaj (Jay) @ninjani.bsky.social · 16/09/2026

The PhD and Postdoc application links are now live! Come join me at UNIL to work on deep learning for protein structure, interactions & design. pickybinders.org#open-positions

career5.successfactors.eu

Career Opportunities: PhD student position in deep learning for enzyme structure & catalysis (22980)

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Charles Mullon @charlesmullon.bsky.social · 03/08/2026

Looking for an Associate Prof position? Interested in behavioural ecology & cultural evolution? Come join us at the Dpt of Ecology and Evolution in Lausanne🇨🇭 @dee-unil.bsky.social @unil.bsky.social! Great department & great place to live. Pls RP. Apply here: wwwfbm.unil.ch/releve/appli...

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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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Charles Mullon @charlesmullon.bsky.social · 09/05/2026

1 week left to apply for scholarships ! If you are based at an institution in an ODA recipient country (e.g. Brazil, South Africa, India, Mexico; full list: tinyurl.com/5dv7vvs8), you can get all expenses covered to attend the summer school in Lausanne for a week.

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Mathilde Boumasmoud @mboum.bsky.social · 29/04/2026

New paper out in @pnas.org 🎆! Across healthy humans, the same bacterium encounters markedly different gut microbiomes. How does this shape the ecological interactions it experiences? We explored this focusing on commensal E. coli.  www.pnas.org/doi/10.1073/... Image: @illuzation.bsky.social

Artistic representation of variation in the human gut microbiome. Four silhouettes contain colorful bubbles and abstract shapes, representing individualized community compositions.

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Charles Mullon @charlesmullon.bsky.social · 22/04/2026

Applications now open for the UNIL Summer School on Modelling for Evolutionary Biology (31 Aug–5 Sep 2026, Lausanne)! For PhD & postdocs interested in formal approaches to evolutionary ecology (incl. social evo, life-history, species interactions). Scholarships available, Pls RP! shorturl.at/fo1GA

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IDDjobs @iddjobs.org · 21/04/2026

Early career faculty (Coventry, United Kingdom) 6 Assistant Professor positions are available in the School of Life Sciences with research areas including infectious disease at University of Warwick More details: iddjobs.org/jobs/2524

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Sonja Lehtinen @sonjalehtinen.bsky.social · 14/04/2026

Interested in predicting the dynamics of antibiotic resistance? Come work with us! We're looking for two postdocs to develop predictive models of resistance. We're interested in a range of approaches (mathematical & statistical modelling, causal inference, machine learning). tinyurl.com/6c4y3jke

tinyurl.com

Career Opportunities: Postdoctoral positions in predictive modelling of antibiotic resistance spread (22755)

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Benjamin Towbin @betowbin.bsky.social · 08/04/2026

Join us at the LS2 #Theory #across #Biology chalk talk symposium! 12 June 2026 in Bern, CH. @lifesciswitzerland.bsky.social No movies that fail, no Mac to PC issues. Only the best ideas and exchange across biology from evolution and ecology to physics of life. meetings.ls2.ch/theory-acros...

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Marie Vasse @marievasse.bsky.social · 09/04/2026

Registration is open for the Microbial Predation Conference 2026! Abstract submission deadline is May 29th microbialpredation.ethz.ch/registration...

microbialpredation.ethz.ch

Registration instructions

Registration for the Microbial Predation Conference 2026

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Simon Cauchemez @scauchemez.bsky.social · 09/04/2026

Just a few days left to apply to one of these postdoc positions in my Unit at @pasteur.fr!

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Sonja Lehtinen @sonjalehtinen.bsky.social · 09/04/2026

A real pleasure working with Martin Guillemet and many thanks to the reviewers’ whose comments considerably improved the paper.

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Sonja Lehtinen @sonjalehtinen.bsky.social · 09/04/2026

Our work generalises these ideas to any mechanism giving rise to NFDS.

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Sonja Lehtinen @sonjalehtinen.bsky.social · 09/04/2026

Similar ideas about strain structure have previously been developed in the context of NFDS arising from allele-specific acquired immunity, most recently in this lovely paper: www.pnas.org/doi/abs/10.1...

pnas.org

A multilocus perspective on the evolutionary dynamics of multistrain pathogens | PNAS

Many human pathogens, including malaria, dengue, influenza, Streptococcuspneumoniae, and cytomegalovirus, coexist as multiple genetically distinct ...

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Sonja Lehtinen @sonjalehtinen.bsky.social · 09/04/2026

By comparing allele combinations observed in different pneumococcal populations, we indeed see a signal consistent with selection acting to reinforce existing structure.

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Sonja Lehtinen @sonjalehtinen.bsky.social · 09/04/2026

Multi-locus NFDS combining to reinforce existing strain structure is interesting. Unlike classical epistasis, this predicts that favoured allele combinations depend on initial conditions - i.e. historical contingency rather than inherent fitness advantage.

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Sonja Lehtinen @sonjalehtinen.bsky.social · 09/04/2026

The key point is that there is no particular reason to assume NFDS would be neutral (i.e. have no effect) on strain structure.

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Sonja Lehtinen @sonjalehtinen.bsky.social · 09/04/2026

Here, we develop theory to show that NFDS acting across multiple loci, which maintains diversity, also acts to structure it. Depending on how NFDS is assumed to combine across loci, it can either act to abolish or reinforce existing strain structure.

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Sonja Lehtinen @sonjalehtinen.bsky.social · 09/04/2026

Recombination acts to destroy these associations, so how is strain structure maintained?

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Sonja Lehtinen @sonjalehtinen.bsky.social · 09/04/2026

Second, strain structure. Intermediate frequency genes are not randomly distributed across genomes: certain allele combinations are seen together more often than expected, giving rise to strain structure.

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Sonja Lehtinen @sonjalehtinen.bsky.social · 09/04/2026

New paper: mechanisms that maintain diversity in bacterial genomes also play a role in organising it. This paper combines two of my favourite topics in bacterial evolution: NFDS and strain structure. journals.plos.org/ploscompbiol...

journals.plos.org

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Yonatan Grad @yhgrad.bsky.social · 30/01/2026

Now published: our work using phylodynamics from surveillance data to quantify and experimentally validate the fitness impact of antibiotic resistance determinants & how this changes with patterns of antibiotic use: www.nature.com/articles/s41...

nature.com

Quantifying the real-world impact of antibiotic use and genetic determinants of resistance on gonococcal dynamics

Nature Microbiology - Phylodynamic modelling shows how the changing antibiotic landscape and genetic determinants of resistance shape real-world gonococcal dynamics. Experiments validated that...

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Reposted by Sonja Lehtinen

Jordan S. Martin @jsmartin.bsky.social · 02/02/2026

I am looking for a PhD student to join my new Socio-Eco-Evo group, hosted in Katie Peichel's Evolutionary Ecology Division @ University of Bern. We're offering a fully funded 4-year position, studying social plasticity and behavioral adaptation among stickleback in Greenland. Please share around!

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PLOS Biology @plosbiology.org · 12/12/2025

Conjugative plasmids help spread AMR genes. @andrewmatthews.bsky.social @sonjalehtinen.bsky.social & @tatianadimitriu.bsky.social show that #AMR loss in evolving populations involves streamlined #plasmids that gain a transmission advantage by deleting AMR genes @plosbiology.org 🧪 plos.io/48NM0BL

Evolved plasmid-carrying clones with high copy number contain a mix of full-length and streamlined plasmids. Left: summary of the initial experimental evolution design and nomenclature used for the evolved plasmid-carrying clones. Host strains had either wildtype (w) or increased (m) mutation rate. Treatment indicates the % of plasmid-free hosts added at each passage during evolution. Right: coverage map of evolved clones. Relative coverage of sequencing reads is shown for all clones across R1 sequence length (only the first 50 kb are shown). The AMR region and copies of IS1 are shown against the ancestral R1 (“anc” treatment) coverage map.

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Reposted by Sonja Lehtinen

Ricardo León-Sampedro @rleonsampedro.bsky.social · 07/11/2025

🚨 Excited to share our new paper is out! 🎉 We show how interactions within gut microbiomes allow certain antibiotic-resistant E. coli strains to persist even without antibiotics, helping explain how resistance is maintained in the human gut. Now published in @natcomms.nature.com rdcu.be/eOf63

rdcu.be

Multi-layered ecological interactions determine growth of clinical antibiotic-resistant strains within human microbiomes

Nature Communications - The role of ecological factors in modulating the spread of antibiotic-resistance bacteria in the gut remains unclear. Here, the authors use anaerobic microcosms to study the...

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Reposted by Sonja Lehtinen

Faculté de biologie et de médecine @fbm-unil.bsky.social · 06/11/2025

Save the date! 𝗦𝘄𝗶𝘀𝘀 𝗠𝗶𝗰𝗿𝗼𝗯𝗶𝗼𝗺𝗲𝘀 𝗙𝗼𝗿𝘂𝗺 𝟮𝟬𝟮𝟲 The NCCR Microbiomes presents the third edition of the #Swiss #Microbiomes #Forum 🗓️ Thursday, Feb 5th 2026 🕑 14h00 📍 EPFL Rolex Learning Center, Lausanne 🎟️ Free to attend, but registration is required. 🔗 nccr-microbiomes.ch/tech-transfe...

nccr-microbiomes.ch

Third edition - 2026 - NCCR

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Reposted by Sonja Lehtinen

EvolDir @evoldir.bsky.social · 04/11/2025

The University of Bern seeks a Professor in Plant Population Ecology (Tenure-Track or Open Rank) to develop a research program and teach. Applications due by 23.01.2026. Details: www.ips.unibe.ch/questionnaire #job

ips.unibe.ch

Professor in Plant Population Ecology (80-100%), Tenure-Track Assistant Professor or Open Rank

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Sonja Lehtinen @sonjalehtinen.bsky.social · 31/10/2025

Love this! I'm so upset this is not available in Switzerland. I'm following it vicariously by listening to Marina Hyde and Richard Osman talk about it on this is entertainment - and now also statistics blogging.

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Sonja Lehtinen @sonjalehtinen.bsky.social · 31/10/2025

Very proud of @krishnaaswin77.bsky.social first PhD paper and grateful to all the excellent collaborators!

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Sonja Lehtinen @sonjalehtinen.bsky.social · 31/10/2025

A key motivation for this study was to estimate resistance fitness costs in natura. It’s interesting they remain so elusive. In these data, we can only quantify effects associated with clearance and establishment, not transmission - so one possibility is that we’d see clearer effects there.

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Sonja Lehtinen @sonjalehtinen.bsky.social · 31/10/2025

We did find some evidence that resistant strains are worse within-host competitors than sensitive strains, particularly for macrolide resistance. The direction of the overall effect across all analysed antibiotics is consistent with a fitness cost, but with CIs overlapping zero.

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Sonja Lehtinen @sonjalehtinen.bsky.social · 31/10/2025

We were also interested in quantifying the fitness cost of resistance. We checked whether there's a cost on clearance rate, but resistant strains are associated with lower clearance. We think this is because resistance is more beneficial on longer carried strains. www.pnas.org/doi/abs/10.1...

pnas.org

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Sonja Lehtinen @sonjalehtinen.bsky.social · 31/10/2025

We also quantified the fitness effects of antibiotics and antibiotic resistance. Antibiotic exposure is associated with a 71% increase in clearance rate of sensitive strains and, interestingly, a 40% increase in the clearance rate of resistant strains.

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Sonja Lehtinen @sonjalehtinen.bsky.social · 31/10/2025

We find that the presence of another pneumococcal strain (i.e. competitor) in the host is associated with a 33% increase in clearance rate and a 54% reduction in the probability of establishment.

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Sonja Lehtinen @sonjalehtinen.bsky.social · 31/10/2025

We used survival analysis to quantify how the presence of a within-host competitor affects the establishment and clearance of serotypes in the Maela pneumococcal carriage study (~1000 infants, sampled monthly over a 2 year period).

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Reposted by Sonja Lehtinen

Ben Engel @cellarchlab.com · 30/09/2025

EXCITING NEWS!! We're searching for a new professor colleague at the Biozentrum🇨🇭. Ideal candidates are exploring novel biological questions with structure, biophysics, or high-resolution imaging. 🧪 🧶🧬 🔬 The call closes Nov 3. Please get in touch if you would like more information. Come join us! 👩‍🔬🤓

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Sonja Lehtinen @sonjalehtinen.bsky.social · 25/09/2025

This sounds like a super cool project!

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John Lees @johnlees.bacpop.org · 17/09/2025

The EMBL PhD programme is open until 13th October (entry ~Sep 2026): www.embl.org/about/info/e... We have three positions in microbial genomics at EMBL-EBI, including one in my group. Please do apply, or if you know anyone that would be interested pass on to them

embl.org

EMBL International PhD Programme – Unique in the world and waiting for you!

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Andries van Tonder @handle.invalid · 08/09/2025

The next online version of our "Working with Bacterial Genomes" course is now open for registration. We aim to provide you with comprehensive training in analysing bacterial genomes covering everything from QC to clustering plasmids. Sign up here: www.training.cam.ac.uk/bioinformati...

training.cam.ac.uk

Research Informatics - Working with Bacterial Genomes (ONLINE LIVE TRAINING) - Mon 27 Oct 2025

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Kat Coyte @coytelab.bsky.social · 12/08/2025

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

jobs.manchester.ac.uk

Research Associate in Microbiome Ecology:Oxford Road

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Zoltán Kutalik @zkutalik.bsky.social · 27/06/2025

Lausanne Comp Bio Symposium 2025 (cbiosymposium.unil.ch) 🗓 Abstract deadline 30 June (𝟑 𝐝𝐚𝐲𝐬 𝐭𝐨 𝐠𝐨!!!) 🎤 Oral presentation notifications: 7 July ✅ Early Bird registration deadline: 11 July 💰 Registration fee for non-PI: 150 CHF

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Christian Fankhauser @chfankhauser.bsky.social · 16/06/2025

Great job opportunity at The Center for Integrative Genomics, Lausanne University, Switzerland unil.ch/cig/en/home.... For a tenure-track Assistant Professor position. More details for how to apply are here nature.com/naturecareer...

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