@LinkLabs

We study and engineer microbial metabolism! Located at the University of Tübingen @uni_tue *The account is run by lab members

 Tübingen, Germany
linkmetabolism.com/
Joined November 2018
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🧬 PhD position open! We're looking for someone to engineer E. coli for bioplastic (cyanophycin) production using thermo-switches, CRISPR and metabolomics. If you're into synthetic biology and sustainable bioprocesses — get in touch! #PhDposition #SynBio linkmetabolism.com/join-us
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We are hiring! Our lab at the University of Tübingen is looking for a PhD student to work on host-pathogen interactions in ESKAPE bacteria. More info: linkmetabolism.com/join-us
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What happens if you knock down every metabolic gene in E. coli? We measured the metabolome of 1515 CRISPRi strains. Result: metabolism behaves like traffic. Block an enzyme and metabolites pile up upstream. 🚗🚗🚗 New paper 🧵
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Example: Knockdown of ispB increases farnesyl-PP. Add a carotenoid pathway and get more product. 🟠 Metabolite accumulation can reveal engineering targets.
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Technically this required metabolomics on ~3,000 samples from an arrayed CRISPRi library. The bottleneck wasn’t MS or sampling. It was sequencing the strains after arraying. Paper: cell.com/cell-systems/fullte…

The metabolome of an E. coli CRISPRi library identifies benefits of minimal metabolite levels and...

Rapp et al. combine genome-scale CRISPRi and metabolomics in E. coli. CRISPRi of enzymes enforces metabolite accumulation, which leads to regulatory crosstalk and side reactions. This suggests that...

cell.com
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New paper from our group: Metabolism Influences Fosfomycin Efficacy pubs.acs.org/doi/10.1021/acs…

The Metabolic State of E. coli Influences Fosfomycin Efficacy and Promotes Resistance Evolution

Abstract. The phosphonic antibiotic fosfomycin is a bacterial cell wall synthesis inhibitor that targets MurA, the first enzyme in the peptidoglycan pathwa

pubs.acs.org
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PhD and Postdoc positions opening in synthetic biology, CRISPR genome engineering of bacteria, and metabolomics. Details and contact here: linkmetabolism.com/join-us
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Preprint from our lab: In synthetic nasal communities a single Corynebacterium propinquum strain can exclude Staphylococcus aureus through nutrient competition. biorxiv.org/content/10.64898…

Community composition and strain identity drive metabolic competition and Staphylococcus aureus...

The human nasal microbiome is a low-diversity ecosystem whose assembly principles and mechanisms of colonization resistance remain poorly understood. In particular, Staphylococcus aureus colonization...

biorxiv.org
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We are searching PhD students in synthetic biology and metabolic engineering uni-tuebingen.de/universitae…
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Great collaboration with the @sourjik lab. Check out how isoprenoid biosynthesis, high oxygen and a membrane complex influence E. coli fitness 👇
SourjikLab@sourjik18 Apr 2025
Our paper describing importance of a highly evolutionary conserved membrane-organising protein complex in bacterial respiration is now published in PLoS Biology in its final version doi.org/10.1371/journal.pbio… Congratulations @MariaIsa_perezl !

The SPFH complex HflK-HflC regulates aerobic respiration in bacteria

The bacterial HflK-HflC membrane complex, part of the highly conserved SPFH protein family, plays a key role in cell membrane organization. This study shows that HflK-HflC is important for aerobic...

journals.plos.org
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Our CRISPR screen in E. coli shows that metabolic mutations influence antibiotic action. Pathway-specific bottlenecks cause resistance. Slow growth leads to tolerance. Read more 👉 doi.org/10.1038/s44320-024-0…

Metabolic mutations reduce antibiotic susceptibility of E. coli by pathway-specific bottlenecks

Molecular Systems Biology - Metabolic variation across pathogenic bacterial strains can impact their susceptibility to antibiotics and promote the evolution of antimicrobial resistance (AMR)....

link.springer.com
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New paper from our group: we developed intact protein barcoding, which uses small proteins as a barcode to identify CRISPRi strains with mass spectrometry. search.app/Tb7XiPbBoj1rnJbg9

Intact protein barcoding enables one-shot identification of CRISPRi strains and their metabolic...

Pahl et al. present a method called intact protein barcoding, which uses ubiquitin as a barcode to identify bacterial strains with mass spectrometry. The method can replace DNA sequencing of barcodes...

cell.com
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Congratulations Dr. Lubrano 🥳
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Our group was featured in the key to my research podcast. There is a short version and a deep dive about our research and episodes with other great scientists from @uni_tue, @Gh_Tabatabai, @EKemen. Check it out: keytomyresearch.podbean.com/
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Don't miss the #GCSB Conference⏰!  With less than a month to go, it's time to secure your spot and explore the latest advancements in synthetic biology📅. Check out the now published poster program and get your tickets right here👇 gcsb2024.de/
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Two-stage bioprocesses could overcome many limitations in bioengineering. Check out our review about this exciting topic👇 Led by @paulsimv. Thanks for the nice collaboration. nature.com/articles/s44222-0…
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Check out our new method to read library barcodes and measure metabolites of CRISPRi strains with #massspec. Works almost in real-time: biorxiv.org/cgi/content/shor…
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Thanks @VanessaPahl , @paul_lubrano92 and Daniel Petras @func_metabo_lab
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