We mapped out a fundamental temporal trade-off: growing cells long enough to dilute out pre-existing target proteins, without waiting so long that escaper mutants take over the population. By doing so, we could pinpoint the time at which the physiological response to the knockdown is strongest

In this work, spearheaded by Mariana, we
✅ Constructed and validated a robust CRISPRi system in the bacterium Pseudomonas putida
✅ Tested this system by targeting essential genes in continuous-growth experiments, backed by a thorough time-course multi-omics characterization

New preprint from our group! When we first started working with affordable, continuous-culture mini-bioreactors a few years ago, we realized they offered a unique solution for CRISPRi experiments, which rely on cell growth to dilute targeted proteins.

www.biorxiv.org/content/10.6...

4/ 🙌 Big thanks to lead author Catarina Rocha and to the rest of the team Sergi Pujol Pinto, Sheila Ingemann Jensen, Lars Keld Nielsen

3/ Biological insight:
• A comparative analysis of E. coli, P. putida, C. necator, B. subtilis, P. thermoglucosidasius
• PCA reveals strain- and condition-specific metabolic fingerprints
• P. thermoglucosidasius shows a lower adenylate energy charge than mesophiles

2/ Highlights:
• Cost-effective 13C-labeled internal standard production
• 96 metabolites quantified in <16 minutes
• Applicable across Gram-positive and Gram-negative species
• Captures inter- and intra-species metabolic phenotypes

A Robust Isotope Ratio LC-MS/MS Workflow for High-Throughput Metabolic Profiling of Bacteria Stable isotope dilution mass spectrometry (IDMS) has become a cornerstone of quantitative metabolomics, enabling accurate intracellular metabolite quantification across a range of biological systems. ...

1/ 🚨 New preprint!
We've developed a robust IDMS-based LC-MS/MS workflow for high-throughput intracellular metabolomics in diverse bacteria. www.biorxiv.org/content/10.1...
#Metabolomics #MassSpec #SystemsBiology

Now published in Microbial Biotechnology! enviromicro-journals.onlinelibrary.wiley.com/doi/epdf/10....

Heading over to #ME16, excited to catch up with many old friends and collaborators! If you are there, make sure to check out posters from our group: @magnusgj.bsky.social poster nr 203 sunday/monday; Mariana Arango Saavedra and Catarina Rocha posters 52 and 53 on monday/tuesday

Optimizing Cupriavidus necator H16 as a host for aerobic C1 conversion Biological systems capable of converting CO2 or CO2-derived, single-carbon (C1) compounds can be used to reduce or reverse carbon emissions while esta…

Hot off the press! 📰 Excited to share our latest opinion piece, co-authored with Christopher Johnson, where we explore why Cupriavidus necator stands out as a top microbial host for converting C1 substrates into valuable products

www.sciencedirect.com/science/arti...

Comparative genomic assessment of the Cupriavidus necator species for one-carbon based biomanufacturing The transition from a petroleum-based manufacturing to biomanufacturing is an important step towards a sustainable bio-economy. In particular biotechnological processes which use one carbon (C1) compo...

📢 Preprint alert! In this study we provide new genomic insights into #CupriavidusNecator for #C1Biomanufacturing:
- Genome assemblies for more strains
- Species definition refined
- Traits & methylation systems explored
Great job by @magnusgj.bsky.social and team

www.biorxiv.org/content/10.1...

Advances in engineering substrate scope of Pseudomonas cell factories Most current industrial bioprocesses use well-established model microorganisms and simple sugar substrates from edible starch or molasses. To broaden …

Good news everyone! (I'd need more good news these days) I'm happy to share here our latest contribution in COBIOT on advances in engineering substrate scope in Pseudomonas cell factories. Great collaboration with @stefanodonati.bsky.social and Miguel Silva! www.sciencedirect.com/science/arti...

New initiative aims to strengthen the bio-based economy - Novo Nordisk Fonden

📣 Exciting news!

The Novo Nordisk Foundation will continue to support an excellence center for #biotechnology at #DTU, building on the legacy of DTU Biosustain over the past 14 years. Grateful to have been part of this!

Now an even BRIGHTer future ahead 🌟

novonordiskfonden.dk/en/news/new-...

Proud of the efforts of our team to deeply think about how to improve practices our laboratory, now certified LEAF bronze (hopefully soon silver and gold!). Thank you especially to Baris Kara who led the effort as well as Mariana Arango Saavedra and Catarina Rocha

CRISPRi-mediated metabolic switch enables concurrent aerobic and synthetic anaerobic fermentations in engineered consortium - Nature Communications An important parameter for synthetic multi-strain bioprocess development is population control and stability. Here, the authors developed a synthetic consortium platform consisting of two engineered E...

We recently published an article, where we through genetic engineering and CRISPRi enable synthetic anaerobic and aerobic physiology in one bioreactor. Two fermentations in one go. Give it a read.
www.nature.com/articles/s41...

P.S.: @angelgm.bsky.social you were right!

About me, I work at DTU Biosustain applying systems and synthetic biology approaches to microbial metabolism, focusing on assimilation of C1 compounds

www.biosustain.dtu.dk/research/res...

Judging on the number of followers I got without posting almost anything 😅 I assume a large part of the scientific community is actually moving here! Genuinely curious whether this science-twitter 2.0 will work out

A nice collaborative effort with @enricoorsi (first of many!) born after many long conversations. I am also grateful to @pabnik.bsky.social and Lars Nielsen for their feedback and mentorship.

Synergistic investigation of natural and synthetic C1-trophic microorganisms to foster a circular ca... Using one carbon (C1) molecules as primary feedstock for bioproduction holds great potential for a circular and carbon neutral economy. Here, the authors discuss the potential of merging knowledge gai...

In our most recent perspective, we argue that we need to bridge more effectively knowledge on C1-trophy obtained in synthetic and natural organisms, and that this approach will enable the engineering of efficient microbes for C1-based biomanufacturing www.nature.com/articles/s41...

We are recruiting a Postdoc and a Research Assistant to work with us on systems biology C1-trophic microorganisms @DTUBiosustain. Last week to apply!

For more info and to apply:
- Postdoc shorturl.at/wFNR8
- RA shorturl.at/dJKU1

Finally made it to the "new place".. really curious to see whether the scientific community will actually move here