Fresh out of the lab! Our new preprint is now up on BioRxiv, exploring how the beneficial bacterium Pseudomonas putida controls its T6SS nanoweapon. It turns out the Gac/Rsm pathway acts as a strict molecular brake on the system. 👇 (1/4) Read the full preprint here: doi.org/10.64898/202...

🧬 Even Earth's most abundant enzyme makes mistakes. Rubisco fixes CO₂ for nearly all life but wastes ~20% of potential crop yield on a 3-billion-year-old side reaction. We built a microbial sensor that finally makes it visible & tinkerable in living cells. www.biorxiv.org/content/10.6...

PntAB & SthA of #Pseudomonas are a flexible transhydrogenase system, supporting energy balance, acetate assimilation & formate tolerance, impacting redox-intensive & C1 metabolic engineering @michelepartipilo.bsky.social @labnikel.bsky.social @cp-cellsystems.bsky.social www.cell.com/cell-systems...

Our latest paper describes a single bacterial strain that can make different Phe derivatives from supplemented aromatic aldehydes or carboxylic acids and incorporate them into target proteins via genetic code expansion Congrats to Shelby Anderson and co-authors www.nature.com/articles/s41...

Cascading recombinase memory switch for programmable and stable gene expression in Pseudomonas putida by Javier Hernández @labnikel.bsky.social #SyntheticBiology #MetabolicEngineering #GeneticCircuit #OpenAccess academic.oup.com/nar/article/... @narjournal.bsky.social

Cascading recombinase memory switch for programmable and stable gene expression in Pseudomonas putida

Abstract. Genetic circuits for model bacteria often perform poorly in non-canonical hosts, limiting the deployment of regulatory programs in industrially r

academic.oup.com

#Pseudomonas vancouverensis as a platform for one-carbon (#C1) assimilation and #polyhydroxyalkanoate accumulation, led by Emil C. Ørsted @labnikel.bsky.social #Biotechnology #MetabolicEngineering #SynBio www.sciencedirect.com/science/arti...

Pseudomonas vancouverensis as a platform for one-carbon (C1) assimilation and polyhydroxyalkanoate accumulation

Metabolic engineering calls for new bacterial chassis that combine robust metabolic and physiological traits with genetic tractability. We developed P…

sciencedirect.com

🔓Check out the #OpenAccess review by @pabnik.bsky.social & co. @labnikel.bsky.social in our latest issue exploring emergent strategies and methods for isolating, creating & characterizing enzymes optimized for bioproduction #natprod Read in full on our website🔽

Accelerating enzyme discovery and engineering with high-throughput screening

Covering: up to August 2024 Enzymes play an essential role in synthesizing value-added chemicals with high specificity and selectivity. Since enzymes utilize substrates derived from renewable…

pubs.rsc.org

🧬 How do you read a gene that is thousands of years old? In our latest blog post, we explore how scientists use sequencing and metagenomics to reconstruct ancient microbial communities and identify genes linked to stress tolerance in the plant rhizosphere

Decoding Ancient DNA for Climate Resilience: Inside the TOLERATE Project - TOLERATE EU Project

The rhizobiome are the support systems of plants. These soil microbes living around plant roots help plants during stress like drought and heat periods. Learn how the TOLERATE project is using bioaugmentation and microbe engineering boost crop resilience

shorturl.at

🤝🌍 Last week, the #TOLERATE EU project consortium meeting took place in Groningen, The Netherlands. Partners came together for two intensive and productive days to share updates, reflect on progress, and align on next steps across all work packages.

For all PhD candidates interested in #syntheticbiology consider our #EMBOSynBio course! Applications open!

EMBL Events@events.embl.org · 9mo ago

Apply for #EMBOSynBio! 🥼🧪 The course offers hands-on experience with cutting-edge SynBio tools, supported by lectures covering the whole engineering cycle and its convergence toward a deeper understanding of biology. 30 Jun – 6 Jul 2026 EMBL Heidelberg s.embl.org/syn26-01-bl

How does Pseudomonas putida keep its redox balance steady across different metabolic states? Our new preprint shows that two transhydrogenases -membrane-bound PntAB and soluble SthA - act together as a flexible, reversible system to control NAD(H)/NADP(H) ratios. www.biorxiv.org/content/10.1...

Integrated control of redox and energy metabolism by the membrane-bound and soluble transhydrogenases of Pseudomonas putida across metabolic regimes

Redox homeostasis is central to microbial physiology and stress adaptation, yet the functional roles of transhydrogenases remain poorly understood beyond a few organisms. In this study, we systematica...

biorxiv.org

Growth-coupled microbial biosynthesis of the animal pigment xanthommatin — Led by Leah Bushin, featuring M. Gracia Alvan, @danielvolke.bsky.social @oscarpuiggene.bsky.social in a fantastic collaboration w/Brad Moore @labnikel.bsky.social @natbiotech.nature.com 🦑 www.nature.com/articles/s41...

🔥🔥🔥 Friday Evening, Paper Out, Feierabend 🔥🔥🔥 When evolution and enzyme engineering team up, they can convince microbes to assimilate sustainable carbon substrates preparing them for a life in a circular bioeconomy. doi.org/10.1016/j.ym...

🚀 Thrilled to share our new Nature Communications article: “A blueprint for designing the next-generation of synthetic C1 microbes” We propose a framework to unlock sustainable, carbon-efficient biomanufacturing using non-canonical hosts. 🔗 www.nature.com/articles/s41... A short 🧵1/4

A blueprint for designing the next-generation of synthetic C1 microbes - Nature Communications

Synthetic one-carbon assimilation could contribute to a more sustainable and circular carbon economy, but much work in this field has focused on model microorganisms. Here the authors provide their perspective on the potential value of non-model microbes, and how that potential could be realised.

nature.com

From the microbial networks behind kombucha fermentation to engineered strains powering sustainable fuels, #FEMSYeastRes brings you high-quality studies with major relevance across the field. 📊 Read the journal's most-read papers for the first half of 2025 buff.ly/NLKSc4N

🚨 New paper in mBio! We established strict formatotrophic & methylotrophic growth in engineered Pseudomonas putida via the reductive glycine pathway (rGlyP). journals.asm.org/doi/full/10.... Here’s a teaser of how we did it 🧵👇1/5

Synthetic C1 metabolism in Pseudomonas putida enables strict formatotrophy and methylotrophy via the reductive glycine pathway | mBio

Soluble C1 feedstocks, such as formate and methanol, have gained attention as sustainable substrates for biotechnology, with the potential to reduce greenhouse gas emissions and reliance on sugar-based resources. Despite their promise, the metabolic ...

journals.asm.org

#Synthetic C1 #metabolism in #Pseudomonas putida enables strict formatotrophy and methylotrophy via the reductive glycine pathway—led by J. Turlin, M. G. Alván, @oscarpuiggene.bsky.social w/@stefanodonati.bsky.social & @sebwenk.bsky.social @mbio.bsky.social #SynBio journals.asm.org/doi/10.1128/...

Synthetic C1 metabolism in Pseudomonas putida enables strict formatotrophy and methylotrophy via the reductive glycine pathway | mBio

Soluble C1 feedstocks, such as formate and methanol, have gained attention as sustainable substrates for biotechnology, with the potential to reduce greenhouse gas emissions and reliance on sugar-based resources. Despite their promise, the metabolic ...

journals.asm.org

🌱💧 Can #bioaugmentation help crops beat drought? Discover how the #TOLERATEproject is exploring microbial solutions to boost drought resilience in EU agriculture, sustainably and at scale. 👏 Great insights by Afnan Suleiman-Bioclear earth- 🔗 Read more: tolerate-eu-project.com/how-eu-toler...

How EU TOLERATE Project explores bioaugmentation to combat drought stress in agriculture - Cyprus Institute of Neurology & Genetics

Climate change is intensifying drought events, putting global food production under pressure. Within the EU-funded TOLERATE project, Work Package 3 (WP3), led by Bioclear earth, and in collaboration w...

tolerate-eu-project.com

After a long sleep, environmental remediation with live biologics is back to the mainstream R&D agenda at this side of the pond. Wanna join and EU-wide on line conversation with bioremediation stakeholders this Nov 10? Express interest and register here 👉 forms.cloud.microsoft/e/b7xVz7dJcu

🌍 At #FEMSMicrobiology 2025, the TOLERATE team had the great pleasure of sharing insights from the TOLERATE project! 🧬 Our session sparked great discussions around ancient DNA and how we can revive, through synthetic biology, lost functions beneficial for future agriculture.

📍 Milan | TODAY! Join Amedea Perfumo & @pabnik.bsky.social at #FEMS 2025 for a dynamic session🧬 "Something (very) old, something new: Innovative microbial solutions for sustainability challenges 🕦 15 July | 11:30–13:00 | Tower Lounge 🔗 femsmicro.org ▶️ youtu.be/0-bhcMpjJ_c #TolerateEUProject

Preprint finally published on @cp-trendsbiotech.bsky.social! Check out the word led by @oscarpuiggene.bsky.social on methanol assimilation in P. putida via enhanced serine–threonine cycle on www.cell.com/trends/biote... Below, the original thread🧵scratching the surface of a long yet satisfying work!

Systematic engineering of synthetic serine cycles in Pseudomonas putida uncovers emergent topologies for methanol assimilation

To advance sustainable bioproduction, we engineered Pseudomonas putida for methanol assimilation via modular synthetic serine cycle variants. By combining native and synthetic functions, we enabled me...

cell.com

@labnikel.bsky.social · last yr.

The utilization of #C1-feedstocks, such as methanol, by non-model bacteria demands an in-depth analysis of design alternatives, a modular strategy to identify bottlenecks and efficient solutions within the host #metabolism of the chosen host... www.biorxiv.org/content/10.1...

Online now @ Cell is the yeast multicellular engineering paper from Fankang Meng - the fruits of his productive PhD in our group. He developed modular synthetic biology tools to bring multicellular behaviours to yeast - specific adhesion, juxtacrine signalling and more. www.cell.com/cell/fulltex...

Engineering yeast multicellular behaviors via synthetic adhesion and contact signaling

By designing synthetic toolkits for contact-based signaling (MARS) and cell-cell adhesion (SATURN), we program yeast to form multicellular structures and perform complex tasks, like building logic cir...

cell.com

The 5th edition of the #Pseudomonas grass roots meeting will take place on the 27th/28th of October 2025 in Denmark. This year, our group at DTU Biosustain will host 2 exciting days of networking, exchanging ideas and learning for early career-stage scientists working with Pseudomonas. 👇

Check out our newest article led by @oscarpuiggene.bsky.social !

Pablo Ivan Nikel@pabnik.bsky.social · last yr.

Implementing synthetic serine cycles in #Pseudomonas putida unlock methanol assimilation in our favorite bug w/carbon conservation, led by ÒscarPuiggené @labnikel.bsky.social · #SynBio #MetabolicEngineering #Methanol published in @cp-trendsbiotech.bsky.social www.sciencedirect.com/science/arti...

🧫 @josephinegiard.bsky.social (HWU) presented #TOLERATE at the #MicrobiologySociety Early Career Conference 2025 in Newcastle 🇬🇧. Flash talk + poster led to great discussions on antifungal resistance with >10 peers & >50 attendees! 🌱 #TOLERATE #HorizonEurope #Microbiology

New phi15-based expression system in Pseudomonas putida uses #SEVA plasmids for high-yield gene expression. The work by @pabnik.bsky.social shows how single-copy vectors minimise toxicity, achieve 200×induction, and outperform T7 systems. 👉 www.nature.com/articles/s42...

Engineering a phi15-based expression system for stringent gene expression in Pseudomonas putida - Communications Biology

The development of a modular, phage-based expression system optimized for Pseudomonas putida enables stringent, tunable and high yield expressions with minimal cytotoxicity.

nature.com

Today, the #TOLERATEProject held its 1st Review Meeting (M1–M18) with PO & PM highlighting our progress, innovation & first results. A key step to shape the road ahead! 🔬🌱💦 Learn more: https://tolerate-eu-project.com/  #HorizonEurope #EUProjects #Biotechnology #SustainableAgriculture

Ethylene glycol is widely used as monomer of the plastic PET. It is therefore highly relevant as sustainable feedstock for microbial biotechnology. In our new paper in @natcomms.nature.com, we characterize efficient enzymes for ethylene glycol oxidation: www.nature.com/articles/s41...

Back from an inspiring week at #ME16 in our home #Copenhagen! 🌍 Engaging talks, exciting science, and amazing connections — we’re full of new ideas! 🎉 Big congrats to @giusifav.bsky.social for winning a poster award 🏆 🙌 And proud to have our PI @pabnik.bsky.social as co-chair of the event!