Francesco De Batté

A new review paper from our lab courtesy of @jazzsynbio.bsky.social is published in Trends in Biotechnology
In this review, we look at the many opportunities for synthetic biology to be used in the research and applications of Holobionts.

Early morning today in the Anza Borrego desert

Moments like this, a sunrise in the desert, remind me that science begins with wonder.
Discovery starts when we pause long enough to notice. Isn't it amazing how life always finds a way to adapt and persist? And how are Plants so good at this?
#Science #Discovery #Nature #AnzaBorrego #PlantScience

I’m excited to announce the launch of my lab at EPFL in Jan 2026 🎉. We’ll combine evolution & synthetic biology to study and (re)engineer bacterial communication.
I’m recruiting PhD students to start in the first semester of 2026.
Apply via EPFL PhD programs by Nov 1
drive.google.com/file/d/1cm-t...

Emergence of population-level feedback control by transposon-plasmid coevolution
doi.org/10.1101/2025...

1 week left to apply for a postdoctoral position in my group to lead the experimental component of a 5 year BBSRC project on synthetic microbial communities

www.ucl.ac.uk/work-at-ucl/...

Highly recommended👇

🛠️New tool from the lab! #SHARK🦈: a new strain to support complex cloning of transient R6K expression plasmids – perfect for genome engineering. Work led by the talented Shivang Joshi and all strains and strain assembly tools enroute to Addgene. #synbio doi.org/10.1101/2025...

Microbial stem cells support productivity in dedicated factory cells in an asymmetrically dividing E. coli system
doi.org/10.1101/2025...

**Please Repost**

Pallavi Singh Lab is looking for two Postdocs to join our team studying how plants balance carbon, water, and resilience in a changing climate.

PlantPlug PDRA: vacancies.essex.ac.uk/tlive_webrec...

REVOLUTION PDRA: vacancies.essex.ac.uk/tlive_webrec...

Deadline: October 15.

Genetic controllers for enhancing the evolutionary longevity of synthetic gene circuits in bacteria - Nature Communications Engineered gene circuits often degrade over time due to mutation and selection. Here the authors use a host-aware modelling framework to develop genetic controllers to sustain synthetic gene expression. They identify a range of design trade-offs in production, robustness and long-term performance.

Genetic controllers for enhancing the evolutionary longevity of synthetic gene circuits in bacteria
doi.org/10.1038/s414...

Loved having a chance this weekend to showcase the science behind bioluminescence & talk about the bioluminescent bays of Puerto Rico at the Harvard Museum's Celebremos Puerto Rico 🕺🇵🇷!

London SynBio Network 10 London SynBio afterwork talks and networking event on Thursday 25th of September

🎉 London SynBio Network is back! Join us on 25th of September.

🧬 Surpassing Nature – Metabolic engineering for novel biological CO2 fixation routes
Ari Satanowski

💐 Open Flower: designer flowers for art and education
Nick Desnoyer

➡️ Register at: events.humanitix.com/london-synbi...

Marchantia berteroana at 3000 meters above the sea level. Vallecitos, Mendoza.

Synthetic promoters has relied on naturally occurring TFs or Cas9. With de novo designed DNA binding proteins, there are so much potential for synbio, whether it's targeting natural promoters or designing synthetic ones.

Deciphering microbial spatial organization: insights from synthetic and engineered communities Abstract. Microbial communities are frequently organized into complex spatial structures, shaped by intrinsic cellular traits, interactions between communi

Deciphering microbial spatial organization: insights from synthetic and engineered communities url: academic.oup.com/ismecommun/a...

We are looking for a PDRA for the PlantPlug project, turning parasitic plants into programmable bio-modules! Using mistletoe as a novel chassis, we are exploring the frontiers of inter-species communication.
Apply online by 15/10/2025.
*RP*
#PlantSciencesJobs

vacancies.essex.ac.uk/tlive_webrec...

Fluctuating DNA methylation tracks cancer evolution at clinical scale Nature - Cancer evolutionary dynamics are quantitatively inferred using a method, EVOFLUx, applied to fluctuating DNA methylation.

Cancer is an evolutionary disease, but does knowing a cancer’s evolutionary past help predict its future? Out today in @nature, we learnt the evolution of 2000 lymphoid cancers and found it was highly correlated with clinical outcomes! (1/7)
rdcu.be/eFrrc

SynBio UK London 2025. Submit your abstract and register before 12 September for earlybird discount.

🚨I have a fully funded 4-year #PhD opportunity in my lab on 'Tuneable multi-input genetic logic circuits for designer probiotics'.🦠 We'll be throwing all the tech we have at this one to make reliable engineering of diverse microbes a reality. Applicants must be UK national...

Educational and entertaining video demonstrating a system for building interactive multi-neighbourhood cellular automata. Well worth a watch

Can a virus help uncover Turing patterns in nature? In this @commsbio.nature.com paper, researchers show how the tulip breaking virus triggers the expression of a pigment that can display a broad range of (observable) stripe patterns @philipcball.bsky.social
biorxiv.org/content/10.1...

YouTube video by 3Blue1Brown Simulating Phase Change | Guest video by Vilas Winstein

Guest video 3/5 while I'm on leave is now up! It's by a former SoME winner, covering key ideas in statistical mechanics to create a simple and discrete model mirroring the behavior of a fluid transitioning between a liquid and gaseous state. Enjoy!

youtu.be/itRV2jEtV8Q

1 month of liverwort growth in 12 seconds.

The thallus of Marchantia polymorpha grows slow and steady, creeping over its substrate.

Engineering non-exponential proliferation in Escherichia coli using functionalized protein aggregates https://www.biorxiv.org/content/10.1101/2025.08.23.671898v1

Friday Flower 001: Mimulus lewisii 🌸✨

Monkeyflowers are masterpieces of design with nectar-guide spots formed by an activator–inhibitor system of MYB transcription factors. These generate reaction–diffusion patterns across the ventral petal.

a man in a suit standing in a greenhouse ALT: a man in a suit standing in a greenhouse

So I am absolutely going to host a Flower Design symposium in 2030. This is a formal call for designers. We have @nickdesnoyer.bsky.social with his beautiful Arabidopsis roses, and I'm likely giving my life to my Alice Petunia...but we need more people. Where you at?!

SHOW US YOUR BLOOM PLANS

Are you a theoretical biologist that is intererested in the ecology and evolution of metabolic interactions among microorganisms?

Do you like to cooperate with experimentalists?

Do you have a PhD and experience in modelling and statistics?

Then this position might be for you👇:

shorturl.at/iiiOv

Have you signed up to speak at our seminar series the upcoming academic year? Sign up is open till end of the month. Share among your networks for this amazing opportunity to showcase your research 📝📩

Frequency-dependent fitness effects are ubiquitous In simple microbial populations, the fitness effects of most selected mutations are generally taken to be constant, independent of genotype frequency. This assumption underpins predictions about evolutionary dynamics, epistatic interactions, and the maintenance of genetic diversity in populations. Here, we systematically test this assumption using beneficial mutations from early generations of the Escherichia coli Long-Term Evolution Experiment (LTEE). Using flow cytometry-based competition assays, we find that frequency-dependent fitness effects are the norm rather than the exception, occurring in approximately 80\% of strain pairs tested. Most competitions exhibit negative frequency-dependence, where fitness advantages decline as mutant frequency increases. Furthermore, we demonstrate that the strength of frequency-dependence is predictable from invasion fitness measurements, with invasion fitness explaining approximately half of the biological variation in frequency-dependent slopes. Additionally, we observe violations of fitness transitivity in several strain combinations, indicating that competitive relationships cannot always be predicted from fitness relative to a single reference strain alone. Through high-resolution measurements of within-growth cycle dynamics, we show that simple resource competition explains a substantial portion of the frequency-dependence: when faster-growing genotypes dominate populations, they deplete shared resources more rapidly, reducing the time available for fitness differences to accumulate. Our results demonstrate that even in a simple model system designed to minimize ecological complexity, subtle ecological interactions between closely related genotypes create frequency-dependent selection that can fundamentally alter evolutionary dynamics. ### Competing Interest Statement The authors have declared no competing interest.

How common are frequency dependent fitness effects?

New preprint out today 👇
doi.org/10.1101/2025...

STEPS To It Announcing a new program, called STEPS, to simulate the dynamics of evolving microbial populations.

Excited to share new #program, STEPS, which can simulate #dynamics of the E. coli Long-Term Evolution Experiment (#LTEE) or other microbes in serial transfer regime.

telliamedrevisited.wordpress.com/2025/08/12/s...

STEPS developed by @devinmlake.bsky.social, Zachary Matson, Minako Izutsu, and me.