Enrico Orsi

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...

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...

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...

🔥🔥🔥 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...

Thanks! First challenge is to expand the substrate acceptance range in the cell factory

Please repost!

Postdoc in adaptive laboratory evolution and C1 synthetic metabolism!

Location: DTU Biosustain

🦠🧬🔬

Starting in 01/2026!

Fell free to reach out if you have questions!
efzu.fa.em2.oraclecloud.com/hcmUI/Candid...

🚨 We're hiring a #Postdoc in #Bioprocess #Engineering! | Enrico Orsi 🚨 We're hiring a #Postdoc in #Bioprocess #Engineering! 🌱 📍 Location: DTU Biosustain 📅 Start: January 2026 | 🕐 Duration: 1 year (with potential extension) Are you a recent PhD graduate excited b...

🔬 Start: Jan 2026 | 1-year funded
🏭 Work with AMBR + 10–30L reactors
📈 TRY optimization | in vivo polymerization | TEA & LCA
💼 Great stepping stone to fellowships (NNF, EU, etc.)

LinkedIn post with more info: www.linkedin.com/posts/enrico...

🧪 We're hiring a #Postdoc in Bioprocess Engineering!
Excited about scaling CO₂-based biomanufacturing from bench to pilot scale?
Join our group working on converting CO₂ + renewable electricity → polymers 💡🌱 👇

#ME16

This is quite subjective , but imo
@helenasm.bsky.social just gave the most impressive talk of the conference so far and she is "only" in the third year of her PhD.

If you are interested in synthetic pathway engineering or C1 fixation you should check out her research.

🎉 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...

Designed bacteria can detect specific molecules Researchers have developed a computer-guided method for designing and engineering bacteria that can detect the presence of specific molecules in the environment. This method will advance the use...

www.sciencenews.dk/en/designed-...

Piece from ScienceNews.dk on our glyoxylate and glycolate sensor strains

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... 🧵

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

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...

Streamlined and efficient genome editing in Cupriavidus necator H16 using an optimised SIBR-Cas system This study developed two simple, efficient, and rapid genome editing tools termed Self-splicing Intron-Based Riboswitch-Cas9 (SIBR-Cas9) and SIBR2.0-Cas12a, for editing the genome of the industrially relevant microbial strain Cupriavidus necator H16.…

Online now: Streamlined and efficient genome editing in Cupriavidus necator H16 using an optimised SIBR-Cas system

Excited to see our SIBR work out in Trends in Biotechnology :)
doi.org/10.1016/j.ti...

This is the first study I have coordinated from start to finish, and it brings me immense satisfaction to see it published.

For a brilliant description of the tech check this: www.linkedin.com/feed/update/...

We had great support from our labs in developing this toolkit. Thanks to @pabnik.bsky.social, @nicoc-micsynmet.bsky.social, Sjoerd, Luc, Angela, Chase, Harrison, Raymond, John, and Wei!

The plasmids will be available on Addgene. Feel free to reach out in case you want to try them!

These results demonstrates that a new state-of-the-art is available for making gene deletions in this promising bug.
With a turnaround time that is 50% shorter than the current systems available, we believe that SIBR-Cas9 and SIBR2.0-Cas12a will help using C. necator in new P2X applications! 8/n

SIBR2.0 was then functional and we moved testing it for Cas12a. The new architectures revealed to be tight, allowing precise and controllable induction of cas12a as well, with similar efficiencies to the ones observed for Cas9! 7/n

Here is where SIBR2.0 comes into place. Simona and Costas developed a script for strategically moving the intron position within the CDS to get rid of such hidden translation initiation starts. This was tested first in E. coli using GFP as readout. 6/n

Then, we moved at testing if SIBR would work also on Cas12a. To our surprise, induction during the targeting assay revealed a leaky cas12a expression despite the presence of the intron with the STOP codon. This was because of a hidden translation start site that required some adjustments. 5/n

We started by testing the SIBR setup on Cas9. This was because we already had evidence that it worked before, although poorly www.sciencedirect.com/science/arti...
Targeting worked fine & by combining SIBR w/ Cas9, we achieved high editing efficiencies of >80% in two loci! Great start! 4/n

Streamlined CRISPR genome engineering in wild-type bacteria using SIBR-Cas Abstract. CRISPR-Cas is a powerful tool for genome editing in bacteria. However, its efficacy is dependent on host factors (such as DNA repair pathways) an

Teaming up with Simona and Costas, we decided to apply the SIBR technology that Costas developed during his PhD to "pause" Cas counter-selection and allow endogenous homologous recombination (HR) to happen first. Our suspect was that C. necator is also poor at HR academic.oup.com/nar/article/... 3/n

C. necator holds potential for the conversion and valorization of CO2 for its ability to grow on this substrate using power-to-X feedstocks (like hydrogen or formate). However, making gene deletions in this organism has always been a pain due to its limited gene deletion toolkit 2/n

Streamlined and efficient genome editing in Cupriavidus necator H16 using an optimised SIBR-Cas system This study developed two simple, efficient, and rapid genome editing tools termed Self-splicing Intron-Based Riboswitch-Cas9 (SIBR-Cas9) and SIBR2.0-Cas12a, for editing the genome of the industrially ...

Our brand new CRISPR/Cas toolkit for genome editing of Cupriavidus necator is out🦠🧬
A joint effort w/ @dellavallesimo.bsky.social and Costas (and many more!)
Check 🧵 our long journey for developing a new state-of-the-art for the manipulation of this promising bug 1/n

www.cell.com/trends/biote...

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 ...

📑📑📑#synthetic_biology @eorsi.bsky.social @pabnik.bsky.social present a workflow for designing versatile auxotrophic metabolic sensors for glyoxylate and glycolate detection @naturecomms.bsky.social
www.nature.com/articles/s41...

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 ...

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...

Check out Sebastians crazy effort to engineer E. coli to grow on formate via the synthetic Serine-Threonine-Cycle. In contrast to the rGlyp the STC works even at ambient CO2!🔥

PhD aminosugar metabolism The Faculty of Science / the Institute for Biology is looking for a :PhD Candidate , Aminosugar metabolism and control of growth and development in bacteriaVacancy number: 15487 PhD project descriptio...

Only one week left to apply for this exciting PhD position, supervised by @gillesvanwezel.bsky.social and me!
Please apply if you are interested in microbial biochemistry and have a solid background in enzymes, metabolic pathways, and bacterial genetics.

www.universiteitleiden.nl/en/vacancies...

Interested in Sustainability, Metabolic Engineering and Evolution?
Check out how we convinced E. coli to grow on the CO2-derived substrate formic acid using the synthetic Serine Threonine Cycle! ♻️🌱🦠

OPEN ACCESS publication to be found here:
🚨 doi.org/10.1016/j.ym... 🚨

#MEvoSky #microsky

(1/🧵)

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 ...

🚀 The SEM Group (Lab Nikel) is officially on Bluesky!

We’re kicking things off with our latest paper: an end-to-end journey on designing, implementing & applying auxotrophic metabolic sensors for bioengineering! 🧬🔬

@naturecomms.bsky.social

Check it out: www.nature.com/articles/s41...

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)! 🧪