Publications

2025

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Lubrano P, Smollich F, Schramm T, Lorenz E, Alvarado A, Eigenmann SC, Stadelmann A, Thavapalan S, Waffenschmidt N, Glatter T, Hoffmann N, Peter S, Drescher K, Link H (2025) Metabolic mutations reduce antibiotic susceptibility of E. coli by pathway-specific bottlenecks. Molecular Systems Biology, https://doi.org/10.1038/s44320-024-00084-z

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Doello S , Sauerwein J , von Manteuffel N, Burkhardt M, Neumann, Appel J, Rapp J,  Just P, Link H, Gutekunst K, Forchhammer K (2025) Metabolite-level regulation of enzymatic activity controls awakening of cyanobacteria from metabolic dormancy. Current Biology DOI: 10.1016/j.cub.2024.11.011

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2024

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Pahl V, Lubrano P, Troßmann F,  Petras D, Link H. Intact protein barcoding enables one-shot identification of CRISPRi strains and their metabolic state. Cell Reports Methods, online first, DOI: 10.1016/j.crmeth.2024.100908

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Shabestary K, Klamt S, Link H, Mahadevan R, Steuer R, Hudson EP (2024). Design of microbial catalysts for two-stage processes. Nature Reviews Bioengineering, 1-17 DOI: 10.1038/s44222-024-00225-x

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Pakkir et al. (2024) Statistical analysis of feature-based molecular networking results from non-targeted metabolomics data. Nature Protocols, 1-71 DOI: 10.1038/s41596-024-01046-3

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Nissan RB, Milshtein E, Pahl V, Pins B, Jona G, Levi D, Yung H, Nir N, Ezra D, Gleizer S, Link H, Noor E, Milo R (2024). Autotrophic growth of Escherichia coli is achieved by a small number of genetic changes.eLife DOI: 10.7554/eLife.88793

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Warneke R, Herzberg C, Weiß M, Schramm T, Hertel D, Link H, Stülke J (2024). DarA—the central processing unit for the integration of osmotic with potassium and amino acid homeostasis in Bacillus subtilis. Journal of Bacteriology DOI: 10.1128/jb.00190-24

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Maier L, Stein-Thoeringer C, Ley RE, Brötz-Oesterhelt H, Link H, Ziemert N, Wagner S, Peschel A (2024). Integrating research on bacterial pathogens and commensals to fight infections—an ecological perspective. The Lancet Microbe DOI: 10.1016/S2666-5247(24)00049-1

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Mardoukhi MSY, Rapp J, Irisarri I, Gunka K, Link H, Marienhagen J, de Vries J, Stülke J, Commichau FM (2024). Metabolic rewiring enables ammonium assimilation via a non-canonical fumarate-based pathway. Microbial Biotechnology DOI: 10.1111/1751-7915.14429

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Lo Presti L, Link H (2024). Mobile CRISPRi moves through the complexity of bacterial genetics. Cell Reports Methods DOI: 10.1016/j.crmeth.2024.100697

 

2023

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Schramm T, Lubrano P, Pahl V, Stadelmann A, Verhülsdonk A, Link H (2023). Mapping temperature-sensitive mutations at a genome scale to engineer growth switches in Escherichia coli. Molecular Systems Biology DOI: 10.15252/msb.202311596

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Bi S, Kargeti M, Colin R, Farke N, Link H, Sourjik V (2023). Dynamic fluctuations in a bacterial metabolic network. Nature Communications DOI: 10.1038/s41467-023-37957-0

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Schwedt I, Collignon M, Mittelstädt C, Giudici F, Rapp J, Meißner J, Link H, Hertel R, Commichau FM (2023). Genomic adaptation of Burkholderia anthina to glyphosate uncovers a novel herbicide resistance mechanism. Environmental Microbiology Reports DOI: 10.1111/1758-2229.13184

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Hauke M, Metz F, Rapp J, Faass L, Bats SH, Radziej S, Link H, Eisenreich W, Josenhans C (2023). Helicobacter pylori modulates heptose metabolite biosynthesis and heptose-dependent innate immune host cell activation by multiple mechanisms. Microbiology Spectrum DOI: 10.1128/spectrum.03132-22

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Krauss S, Harbig TA, Rapp J, Schaefle T, Franz-Wachtel M, Reetz L, Elsherbini AMA, MacEk B, Grond S, Link H, et al. (2023) Horizontal transfer of bacteriocin biosynthesis genes requires metabolic adaptation to improve compound production and cellular fitness. Microbiology Spectrum DOI: 10.1128/spectrum.03176-22

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Goldfinger V, Spohn M, Rodler JP, Sigle M, Kulik A, Cryle MJ, Rapp J, Link H, Wohlleben W, Stegmann E (2023). Metabolic engineering of the shikimate pathway in Amycolatopsis strains for optimized glycopeptide antibiotic production. Metabolic Engineering DOI: 10.1016/j.ymben.2023.05.005

 

Farke N, Schramm T, Verhülsdonk A, Rapp J, Link H (2023). Systematic analysis of in-source modifications of primary metabolites during flow-injection time-of-flight mass spectrometry. Analytical Biochemistry DOI: 10.1016/j.ab.2023.115036

 

2022

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Radoš D, Donati S, Lempp M, Rapp J, Link H (2022). Homeostasis of the biosynthetic E. coli metabolome. iScience DOI: 10.1016/j.isci.2022.104503

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Meißner J, Schramm T, Hoßbach B, Stark K, Link H, Stülke J (2022). How to deal with toxic amino acids: the bipartite AzlCD complex exports histidine in Bacillus subtilis. Journal of Bacteriology DOI: 10.1101/2022.07.07.499250

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Stecker D, Hoffmann T, Link H, Commichau FM, Bremer E (2022). L-Proline synthesis mutants of Bacillus subtilis overcome osmotic sensitivity by genetically adapting L-arginine metabolism. Frontiers in Microbiology DOI: 10.3389/fmicb.2022.908304

 

2021

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Díaz-Pascual F, Lempp M, Nosho K, Jeckel H, Jo JK, Neuhaus K, Hartmann R, Jelli E, Hansen MF, Price-Whelan A, et al. (2021) Spatial alanine metabolism determines local growth dynamics of Escherichia coli colonies. eLife DOI: 10.7554/eLife.70794

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Boecker S, Slaviero G, Schramm T, Szymanski W, Steuer R, Link H, Klamt S (2021) Deciphering the physiological response of Escherichia coli under high ATP demand. Molecular Systems Biology DOI: 10.15252/msb.202110504

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Schubert C, Winter M, Ebert-Jung A, Kierszniowska S, Nagel-Wolfrum K, Schramm T, Link H, Winter S, Unden G (2021). C4-dicarboxylates and L-aspartate utilization by Escherichia coli K-12 in the mouse intestine: L-aspartate as a major substrate for fumarate respiration and as a nitrogen source. Environmental Microbiology DOI: 10.1111/1462-2920.15478

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Schramm T, Link H (2021). From stoichiometry to the control of metabolic networks. BioSpektrum DOI: 10.1007/s12268-021-1538-0

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Wang CY, Lempp M, Farke N, Donati S, Glatter T, Link H (2021). Metabolome and proteome analyses reveal transcriptional misregulation in glycolysis of engineered Escherichia coli. Nature Communications DOI: 10.1038/s41467-021-25142-0

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Donati S, Kuntz M, Pahl V, Farke N, Beuter D, Glatter T, Gomes-Filho JV, Randau L, Wang CY, Link H (2021). Multi-omics analysis of CRISPRi-knockdowns identifies mechanisms that buffer decreases of enzymes in Escherichia coli metabolism. Cell Systems DOI: 10.1016/j.cels.2020.10.011

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Alseekh S, Aharoni A, Brotman Y, Contrepois K, D’Auria J, Ewald JC, Fraser PD, Giavalisco P, Hall RD, Link H, et al. (2021). Mass spectrometry-based metabolomics: a guide for annotation, quantification, and best reporting practices. Nature Methods DOI: 10.1038/s41592-021-01197-1

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Gauttam R, Desiderato CK, Radoš D, Link H, Seibold GM, Eikmanns BJ (2021). Metabolic engineering of Corynebacterium glutamicum for production of UDP-N-acetylglucosamine. Frontiers in Bioengineering and Biotechnology DOI: 10.3389/fbioe.2021.748510

 

Kochanowski K, Sander T, Link H, Chang J, Altschuler SJ, Wu LF (2021). Systematic alteration of in vitro metabolic environments reveals empirical growth relationships in cancer cell phenotypes. Cell Reports DOI: 10.1016/j.celrep.2020.108647

 

2020

 

Ni B, Colin R, Link H, Endres RG, Sourjik V (2020). Growth-rate dependent resource investment in bacterial motile behavior quantitatively follows the potential benefit of chemotaxis. Proceedings of the National Academy of Sciences of the United States of America DOI: 10.1073/pnas.1910849117

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Schramm T, Lempp M, Beuter D, Sierra SG, Glatter T, Link H (2020) High-throughput enrichment of temperature-sensitive argininosuccinate synthetase for two-stage citrulline production in Escherichia coli. Metabolic Engineering DOI: 10.1016/j.ymben.2020.03.004

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Lempp M, Lubrano P, Bange G, Link H (2020) Metabolism of non-growing bacteria. Biological Chemistry DOI: 10.1515/hsz-2020-0201

 

2019​

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Sander T, Farke N, Diehl C, Kuntz M, Glatter T, Link H (2019) Allosteric feedback inhibition enables robust amino acid biosynthesis in Escherichia coli by enforcing enzyme overabundance. Cell Systems DOI: 10.1016/j.cels.2018.12.005

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Lempp M, Farke N, Kuntz M, Freibert SA, Lill R, Link H (2019) Systematic identification of metabolites controlling gene expression in E. coli. Nature communications 10 (1), 4463

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Díaz-Pascual F, Hartmann R, Lempp M, Vidakovic L, Song B, Jeckel H, Thormann KM, Yildiz FH, Dunkel J, Link H, et al. (2019). Breakdown of Vibrio cholerae biofilm architecture induced by antibiotics disrupts community barrier function. Nature Microbiology DOI: 10.1038/s41564-019-0579-2

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Boecker S, Zahoor A, Schramm T, Link H, Klamt S (2019) Broadening the scope of enforced ATP wasting as a tool for metabolic engineering in Escherichia coli. Biotechnology Journal DOI: 10.1002/biot.201800438

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Sander T, Wang CY, Glatter T, Link H (2019) CRISPRi-based downregulation of transcriptional feedback improves growth and metabolism of arginine overproducing Escherichia coli. ACS Synthetic Biology DOI: 10.1021/acssynbio.9b00183

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Laganenka L, Sander T, Lagonenko A, Chen Y, Link H, Sourjik V (2019) Quorum sensing and metabolic state of the host control lysogeny-lysis switch of bacteriophage T1. mBio DOI: 10.1128/mBio.01884-19

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2018

 

Buffing MF, Link H, Christodoulou D, Sauer U (2018) Capacity for instantaneous catabolism of preferred and non-preferred carbon sources in Escherichia coli and Bacillus subtilis. Scientific Reports DOI: 10.1038/s41598-018-30266-3

 

Donati S, Sander T, Link H (2018) Crosstalk between transcription and metabolism: how much enzyme is enough for a cell?

Wiley Interdisciplinary Reviews: Systems Biology and Medicine DOI: 10.1002/wsbm.1396

 

Krink-Koutsoubelis N, Loechner AC, Lechner A, Link H, Denby CM, Vögeli B, Erb TJ, Yuzawa S, Jakociunas T, Katz L, et al. (2018) Engineered production of short-chain acyl-coenzyme A esters in Saccharomyces cerevisiae. ACS Synthetic Biology DOI: 10.1021/acssynbio.7b00466

 

Christodoulou D, Link H, Fuhrer T, Kochanowski K, Gerosa L, Sauer U (2018) Reserve flux capacity in the pentose phosphate pathway enables Escherichia coli's rapid response to oxidative stress. Cell Systems DOI: 10.1016/j.cels.2018.04.009

 

Beuter D, Gomes-Filho JV, Randau L, Díaz-Pascual F, Drescher K, Link H (2018) Selective enrichment of slow-growing bacteria in a metabolism-wide CRISPRi library with a TIMER protein. ACS Synthetic Biology DOI: 10.1021/acssynbio.8b00379