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labnikel.bsky.social

@labnikel.bsky.social
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Patricia Bernal @pbernalt6ss.eurosky.social · 11/07/2026
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...
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Enrico Orsi @eorsi.bsky.social · 12/07/2026
🧬 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...
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Pablo Ivan Nikel @pabnik.bsky.social · 23/06/2026
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...
cell.com
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Aditya Kunjapur @kunjapur.bsky.social · 12/06/2026
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...
nature.com
Combined biosynthesis and site-specific incorporation of phenylalanine derivatives from aryl aldehydes or carboxylic acids - Nature Communications
Genetic code expansion can be limited by the need to supply non-standard amino acids. The authors design bacteria that perform integrated steps of converting supplemented aldehydes to L-phenylalanine ...
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Pablo Ivan Nikel @pabnik.bsky.social · 11/06/2026
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
academic.oup.com
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
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Pablo Ivan Nikel @pabnik.bsky.social · 30/03/2026
#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...
sciencedirect.com
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…
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Natural Product Reports @natprodreports.rsc.org · 13/03/2026
🔓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🔽
pubs.rsc.org
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…
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TOLERATE EU Project @tolerateeu.bsky.social · 04/03/2026
🧬 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
shorturl.at
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
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TOLERATE EU Project @tolerateeu.bsky.social · 15/12/2025
🤝🌍 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.
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Nico Claassens @nicoc-micsynmet.bsky.social · 06/12/2025
For all PhD candidates interested in #syntheticbiology consider our #EMBOSynBio course! Applications open!
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labnikel.bsky.social @labnikel.bsky.social · 09/11/2025
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...
biorxiv.org
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...
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Pablo Ivan Nikel @pabnik.bsky.social · 03/11/2025
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...
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Sebastian Wenk @sebwenk.bsky.social · 24/10/2025
🔥🔥🔥 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...
doi.org
Redirecting
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labnikel.bsky.social @labnikel.bsky.social · 08/10/2025
🚀 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
nature.com
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.
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FEMS Journals @femsjournals.bsky.social · 19/08/2025
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
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labnikel.bsky.social @labnikel.bsky.social · 22/08/2025
🚨 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
journals.asm.org
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 ...
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Pablo Ivan Nikel @pabnik.bsky.social · 21/08/2025
#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/...
journals.asm.org
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 ...
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TOLERATE EU Project @tolerateeu.bsky.social · 05/08/2025
🌱💧 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...
tolerate-eu-project.com
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...
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Victor de Lorenzo (CNB, Madrid) @vdlorenzo.bsky.social · 22/07/2025
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
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TOLERATE EU Project @tolerateeu.bsky.social · 22/07/2025
🌍 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.
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TOLERATE EU Project @tolerateeu.bsky.social · 15/07/2025
📍 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
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labnikel.bsky.social @labnikel.bsky.social · 13/07/2025
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!
cell.com
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...
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Tom Ellis @proftomellis.bsky.social · 11/07/2025
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...
cell.com
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...
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labnikel.bsky.social @labnikel.bsky.social · 09/07/2025
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. 👇
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labnikel.bsky.social @labnikel.bsky.social · 09/07/2025
Check out our newest article led by @oscarpuiggene.bsky.social !
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TOLERATE EU Project @tolerateeu.bsky.social · 03/07/2025
🧫 @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
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SEVA Plasmids @sevaplasmids.bsky.social · 03/07/2025
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...
nature.com
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.
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TOLERATE EU Project @tolerateeu.bsky.social · 30/06/2025
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: tolerate-eu-project.com  #HorizonEurope #EUProjects #Biotechnology #SustainableAgriculture
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Lennart Schada von Borzyskowski @lennartschada.bsky.social · 01/07/2025
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...
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labnikel.bsky.social @labnikel.bsky.social · 23/06/2025
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!
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Pablo Ivan Nikel @pabnik.bsky.social · 09/06/2025
Happy to host @kunjapur.bsky.social as a sabbatical #professor at DTU Biosustain, supported by Otto Mønsteds Fond! We share a passion for using #SynBio to engineer #microbes with non-natural building blocks for advanced #biotechology. He’s in #Europe — drop a line to connect & discuss cool #Science!
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Enrico Orsi @eorsi.bsky.social · 03/06/2025
🎉 Excited to share that I’ve received an Emerging Investigator Grant from the Novo Nordisk Foundation! I’ll start my research group in Jan 2026 to develop universal cell factories for P2X & CO₂-based biomanufacturing 🌱🔬 👉 researchleaderprogramme.com/recipients/e...
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TOLERATE EU Project @tolerateeu.bsky.social · 02/06/2025
The TOLERATE team met at DTU (Denmark) for a productive General Assembly. New coordinator Pablo Ivan Nikel opened the meeting, presenting the transition and confirming that the project continues full speed ahead. More info 👉 tolerate-eu-project.com Subscribe 👉 eepurl.com/i6uufM #EUProjects
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fillouxlab.bsky.social @fillouxlab.bsky.social · 13/05/2025
What a very cool work from the @fillouxlab.bsky.social alumni Sophie Howard and @ronanmccarthy.bsky.social . Plastic degrading #Pseudomonas aeruginosa and the threat it poses in nosocomial infections and to medical devices in healthcare system. See at rb.gy/c8s6mh @cp-cellreports.bsky.social
rb.gy
Pseudomonas aeruginosa clinical isolates can encode plastic-degrading enzymes that allow survival on plastic and augment biofilm formation
Howard et al. demonstrate that clinical isolates of the opportunistic pathogen Pseudomonas aeruginosa can encode functional plastic-degrading enzymes and that these enzymes can influence bacterial bio...
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Membrane Enzymology @membraneenzymology.bsky.social · 13/05/2025
Solène’s 4.5 years of postdoctoral work in our lab (she started just before the corona pandemic) has now been published. A heroic effort that revealed -at the single molecule level- that ATP drives the dissociation of an ECF transporter complex under turnover conditions. See rdcu.be/elTKc
rdcu.be
Single-molecule visualization of ATP-induced dynamics of the subunit composition of an ECF transporter complex under turnover conditions
Nature Communications - The association and dissociation dynamics of the ECF transporter complex for vitamin B12 are visualized by single-molecule FRET, highlighting the original transport...
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Mike Jetten @msmjetten.bsky.social · 06/05/2025
Pathways to sustainability: a quantitative comparison of #aerobic and #anaerobic C1 bioconversion routes #methane #methanol www.sciencedirect.com/science/arti...
sciencedirect.com
Pathways to sustainability: a quantitative comparison of aerobic and anaerobic C1 bioconversion routes
One-carbon (C1) substrates are attractive feedstocks for biological upgrading as part of a circular, carbon-negative bioeconomy. Nature has evolved a …
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Ari Satanowski @ari-satanowski.bsky.social · 04/04/2025
Excited to share a main project from my PhD, out now in @naturecomms.bsky.social! 📝 We've designed and brought to life the “CORE cycle” – a new-to-nature pathway that provides a novel route for biological CO2 capture 🦠🌱 nature.com/articles/s41... Take a look! Thread below... 🧵
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labnikel.bsky.social @labnikel.bsky.social · 04/04/2025
Interested in engineering bacteria to turn #C1feedstocks into high-value chemicals for #bioproduction? Here is a thread summarizing our latest review on the roadblocks and how we might bio-hack our way past them 🧵 1/n academic.oup.com/femsre/advan...
academic.oup.com
Seven Critical Challenges in Synthetic One-Carbon Assimilation and Their Potential Solutions
Abstract. Synthetic C1 assimilation holds the promise of facilitating carbon capture while mitigating greenhouse gas emissions, yet practical implementatio
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Pablo Ivan Nikel @pabnik.bsky.social · 02/04/2025
Genetic dissection of cyclic di-GMP signalling in #Pseudomonas aeruginosa via systematic diguanylate cyclase disruption—led by Roman di Martino & Daniel Volke @labnikel.bsky.social @microbiotech.bsky.social #OpenAccess enviromicro-journals.onlinelibrary.wiley.com/doi/full/10....
enviromicro-journals.onlinelibrary.wiley.com
Genetic Dissection of Cyclic di‐GMP Signalling in Pseudomonas aeruginosa via Systematic Diguanylate Cyclase Disruption
All 32 diguanylate cyclase (DGC)-encoding genes of P. aeruginosa PA14 were interrupted by premature STOP codons, introduced through a multiplexed cytosine base-editor. The synthesis of c-di-GMP was i...
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Victor de Lorenzo (CNB, Madrid) @vdlorenzo.bsky.social · 25/03/2025
Pseudomonas putida joins the Olympus of effective Cell Factories www.nature.com/articles/s41... Not any longer *a promising platform* for metabolic engineering, but a phenomenal, consolidated chassis for programming degradation and synthesis of amazing molecules 😃!
nature.com
Comprehensive evaluation of the capacities of microbial cell factories - Nature Communications
Constructing an efficient microbial cell factory still requires exploring and selecting various host strains, as well as identifying the best-suited metabolic engineering strategies, which demand sign...
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Pablo Ivan Nikel @pabnik.bsky.social · 17/03/2025
Congrats to Garret for officially becoming Dr. O'Connell! Garret had his Ph.D. viva on synthetic #fluorochemical #metabolism in #Pseudomonas today. Thanks to @tilmweber.bsky.social r.bsky.social, @pavelcito.bsky.social & Esteban Martinez for their insights🧪🦠 #SynBio @labnikel.bsky.social
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labnikel.bsky.social @labnikel.bsky.social · 16/03/2025
Microbes like Cupriavidus necator naturally grow on #renewable feedstocks ♻️🧫 (CO₂, formate, hydrogen), yet their potential remains untapped due to the lack of efficient genetic tools... 1/2 www.cell.com/trends/biote...
cell.com
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Pablo Ivan Nikel @pabnik.bsky.social · 13/03/2025
Glad to see Julia Vorholt as winner of the @novonesis.com #Biotechnology Prize 2025 for her research on the plant #microbiome — among other achievements (e.g. synthetic C1 assimilation). Amazing and inspiring colleague #WomenInScience @eth-dbiol.bsky.social novonordiskfonden.dk/en/news/pion...
novonordiskfonden.dk
Pioneering plant microbiome research: Julia Vorholt receives 2025 Novonesis Biotechnology Prize - Novo Nordisk Fonden
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Nico Claassens @nicoc-micsynmet.bsky.social · 27/02/2025
Very happy and proud of this work led by @beaubd.bsky.social with many others involved, in which we show that synthetic C1 metabolism can do better than nature for biotech!
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labnikel.bsky.social @labnikel.bsky.social · 09/03/2025
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...
biorxiv.org
Systematic engineering of synthetic serine cycles in Pseudomonas putida uncovers emergent topologies for methanol assimilation
The urgent need for a circular carbon economy has driven research into sustainable substrates, including one-carbon (C1) compounds. The non-pathogenic soil bacterium Pseudomonas putida is a promising ...
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Michele Partipilo @michelepartipilo.bsky.social · 05/03/2025
With great collaborations come great outcomes! A fine example from @eorsi.bsky.social from @pabnik.bsky.social's lab et collaborators of how to design, build and develop cell biosensors for value-added chemicals (related to synthetic C1 assimilation, of course)! 🧪
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Pablo Ivan Nikel @pabnik.bsky.social · 21/02/2025
Preprint alert🚨Systematic #engineering of synthetic serine cycles in #Pseudomonas putida uncovers emergent topologies for #methanol assimilation · @biorxivpreprint.bsky.social led by Òscar Puiggené #SynBio #Methylotrophy #CircularEconomy www.biorxiv.org/content/10.1...
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Pablo Ivan Nikel @pabnik.bsky.social · 04/03/2025
Computation-aided designs enable developing auxotrophic #metabolic #sensors for wide-range glyoxylate and glycolate detection—spearheaded by Enrico Orsi w/a choral assembly of cool collaborators @naturecomms.bsky.social #SynBio #OpenAccess www.nature.com/articles/s41...
nature.com
Computation-aided designs enable developing auxotrophic metabolic sensors for wide-range glyoxylate and glycolate detection - Nature Communications
Auxotrophic metabolic sensors (AMS) are vital for bioengineering but are often time-consuming to develop. Here, the authors present a workflow for designing versatile AMS, demonstrating their use for ...
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Enrico Orsi @eorsi.bsky.social · 04/03/2025
We just #published an end-to-end work for the computer-aided design💻, construction🛠️, validation✅, characterization🔬 & application💪 of #auxotroph metabolic sensors, the work-horses of in vivo growth-coupled selection screening systems-using glycolate as test case. 🧵👇1/ www.nature.com/articles/s41...
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Helena Schulz-Mirbach @helenasm.bsky.social · 04/03/2025
Really happy to share that our work on constructing six glyoxylate / glycolate sensors covering a three order of magnitude concentration range is out now in Nature Communications ! 🔥 Read below to see how we developed the sensors and what they are good for 🥳. www.nature.com/articles/s41...
nature.com
Computation-aided designs enable developing auxotrophic metabolic sensors for wide-range glyoxylate and glycolate detection - Nature Communications
Auxotrophic metabolic sensors (AMS) are vital for bioengineering but are often time-consuming to develop. Here, the authors present a workflow for designing versatile AMS, demonstrating their use for ...
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