Interfakultäres Institut für Mikrobiologie und Infektionsmedizin

Publikationen

2022

  • Gavriilidou, A., Kautsar, S.A., Zaburannyi, N. et al. Compendium of specialized metabolite biosynthetic diversity encoded in bacterial genomes. Nat Microbiol 7, 726–735 (2022). 
  • Negri T, Mantri S, Angelov A, Peter S, Muth G, Eustáquio AS, Ziemert N. A rapid and efficient strategy to identify and recover biosynthetic gene clusters from soil metagenomes. Appl Microbiol Biotechnol. 106(8):3293-3306 (2022). 

2021

  • Mungan, M. D., Blin, K. & Ziemert, N. ARTS-DB: a database for antibiotic resistant targets. Nucleic Acids Res. (2021).
  •  Mantri, S. S. et al. Metagenomic Sequencing of Multiple Soil Horizons and Sites in Close Vicinity Revealed Novel Secondary Metabolite Diversity. mSystems 6, e0101821 (2021).
  • Elfeki, M. et al. Evaluating the Distribution of Bacterial Natural Product Biosynthetic Genes across Lake Huron Sediment. ACS Chem. Biol. 16, 2623–2631 (2021).
  • Handayani, I. et al. Mining Indonesian Microbial Biodiversity for Novel Natural Compounds by a Combined Genome Mining and Molecular Networking Approach. Mar. Drugs 19, (2021).
  • Izoré, T. et al. Structures of a non-ribosomal peptide synthetase condensation domain suggest the basis of substrate selectivity. Nat. Commun. 12, 2511 (2021).
  • Schorn, M. A. et al. A community resource for paired genomic and metabolomic data mining. Nat. Chem. Biol. 17, 363–368 (2021).
  •  Cryle, M. et al. Understanding condensation domain selectivity in non-ribosomal peptide biosynthesis: structural characterization of the acceptor bound state. (2021).
  • Chevrette, M. G. et al. The confluence of big data and evolutionary genome mining for the discovery of natural products. Nat. Prod. Rep. 38, 2024–2040 (2021).
  • Spindler, S. et al. Modular Fragment Synthesis and Bioinformatic Analysis Propose a Revised Vancoresmycin Stereoconfiguration. Org. Lett. 23, 1175–1180 (2021).

2020

  • Stahlecker, J., Mingyar, E., Ziemert, N. & Mungan, M. D. SYN-View: A Phylogeny-Based Synteny Exploration Tool for the Identification of Gene Clusters Linked to Antibiotic Resistance. Molecules 26, (2020).
  • Chen, J., Frediansyah, A., Männle, D. & Straetener, J. New Nocobactin Derivatives with Antimuscarinic Activity, Terpenibactins A–C, Revealed by Genome Mining of Nocardia terpenica IFM 0406. (2020).
  • Hifnawy, M. S., Fouda, M. M., Sayed, A. M. & Mohammed, R. The genus Micromonospora as a model microorganism for bioactive natural product discovery. RSC Adv. (2020).
  • Ziemert, N., Weber, T. & Medema, M. H. Genome mining approaches to bacterial natural product discovery. Reference Module in Chemistry (2020).
  • Mungan, M. D. et al. ARTS 2.0: feature updates and expansion of the Antibiotic Resistant Target Seeker for comparative genome mining. Nucleic Acids Res. 48, W546–W552 (2020).
  • Männle, D. et al. Comparative Genomics and Metabolomics in the Genus Nocardia. mSystems 5, (2020).

2019

  • Adamek, M., Alanjary, M., Ziemert, N., 2019. Applied evolution: phylogeny-based approaches in natural products research. Nat. Prod. Rep. doi.org/10.1039/C9NP00027E
  • Greule, A., Izoré, T., Iftime, D., Tailhades, J., Schoppet, M., Zhao, Y., Peschke, M., Ahmed, I., Kulik, A., Adamek, M. and Goode, R.J.,Schittenhelm, R., Kaczmarski, J., Jackson, C., Ziemert, N., Krenske, E., Voss, J. De, Stegmann, E., Cryle, M., 2019. Kistamicin biosynthesis reveals the biosynthetic requirements for production of highly crosslinked glycopeptide antibiotics. Nature communications, 10(1), p.2613.
  • Ziemert, N., 2019. Bioinformatics strategies for new antibiotics. BIOspektrum , 25 (4), pp.461-462.
  • Alanjary, M., Steinke, K. and Ziemert, N., AutoMLST: an automated web server for generating multi-locus species trees highlighting natural product potential. Nucleic Acids Research,2019, gkz282, doi.org/10.1093/nar/gkz282.

2018

  • Kluj, R.M., Ebner, P., Adamek, M., Ziemert, N., Mayer, C. and Borisova, M., 2018. Recovery of the Peptidoglycan Turnover Product released by the Autolysin Atl in Staphylococcus aureus involves the Phosphotransferase System Transporter MurP and the Novel 6-phospho-N-acetylmuramidase MupG. Frontiers in microbiology, 9.
  • Moghaddam, J.A., Crüsemann, M., Alanjary, M., Harms, H., Dávila-Céspedes, A., Blom, J., Poehlein, A., Ziemert, N., König, G.M. and Schäberle, T.F., Analysis of the Genome and Metabolome of Marine Myxobacteria Reveals High Potential for Biosynthesis of Novel Specialized Metabolites. Scientific Reports, 2018, 8(1), p.16600.
  • Eustáquio, A.S. and Ziemert, N., Identification of Natural Product Biosynthetic Gene Clusters from Bacterial Genomic Data. Methods in Pharmacology and Toxicology, (2018): 1-21.
  • Elfeki M, Alanjary M, Green SJ, Ziemert N, Murphy BT: Assessing the efficiency of cultivation techniques to recover natural product biosynthetic gene populations from sediment. ACS Chem Biol, 2018
  • Adamek M, Alanjary M, Sales-Ortells H, Goodfellow M, Bull AT, Winkler A, Wibberg D, Kalinowski D, Ziemert N: Comparative genomics reveals phylogenetic distribution patterns of secondary metabolites in Amycolatopsis species. BMC genomics, 2018, 19 (1), 426
  • Spohn, M., S. Edenhart, M. Alanjary, N. Ziemert, D. Wibberg, J. Kalinowski, T. Niedermeyer, E. Stegmann, and W. Wohlleben. 2018. Identification of a unique aminoploycarboxylic acid siderophore gene cluster and its product by an in silico approach. Metallomics,

2017

  • Bruns,H., Crüsemann,M., Letzel,A.-C., Alanjary,M., McInerney,J.O., Jensen,P.R., Schulz,S., Moore,B.S. and Ziemert,N. (2017) Function-related replacement of bacterial siderophore pathways. ISME J., 10.1038/ismej.2017.137.
  • Adamek,M., Spohn,M., Stegmann,E. and Ziemert,N. (2017) Mining Bacterial Genomes for Secondary Metabolite Gene Clusters. Methods Mol. Biol., 1520, 23–47.
  • Alanjary,M., Kronmiller,B., Adamek,M., Blin,K., Weber,T., Huson,D., Philmus,B. and Ziemert,N. (2017) The Antibiotic Resistant Target Seeker (ARTS), an exploration engine for antibiotic cluster prioritization and novel drug target discovery. Nucleic Acids Res., 45, W42–W48.
  • Letzel,A.-C., Li,J., Amos,G.C.A., Millan-Aguinaga,N., Ginigini,J., Abdelmohsen,U.R., Gaudencio,S.P., Ziemert,N., Moore,B.S. and Jensen,P.R. (2017) Genomic insights into specialized metabolism in the marine actinomycete Salinispora. Environ. Microbiol., 10.1111/1462-2920.13867.

2016

  • Wohlleben W, Mast Y, Stegmann E, Ziemert N.: Antibiotic drug discovery. Microb Biotechnol. 2016 Sep;9(5):541-8. doi: 10.1111/1751-7915.12388.
  • Ziemert N*, Alanjary M, Weber T.*: The evolution of genome mining in microbes - a review. Nat Prod Rep 2016 33:988–1005.
  • Maansson M, Vynne NG, Klitgaard A, Nybo JL, Melchiorsen J, Nguyen DD, Sanchez LM, Ziemert N, Dorrestein PC, Andersen MR, Gram L. 2016. An Integrated Metabolomic and Genomic Mining Workflow To Uncover the Biosynthetic Potential of Bacteria. mSystems 1:e00028–15.
  • Schorn,M.A., Alanjary,M.M., Aguinaldo,K., Korobeynikov,A., Podell,S., Patin,N., Lincecum,T., Jensen,P.R., Ziemert,N. and Moore,B.S. (2016) Sequencing rare marine actinomycete genomes reveals high density of unique natural product biosynthetic gene clusters. Microbiol. (United Kingdom), 162.

2015

  • Medema MH, Kottmann R, …, Ziemert N, …Breitling R, Takano E, Glöckner FO: Minimum Information about a Biosynthetic Gene cluster. Nat Chem Biol. 2015 Sep;11(9):625-31. doi: 10.1038/nchembio.1890.
  • Awakawa T, Cruesemann M, Ziemert N, Munguia J, Nizet V, Fenical W, Moore BS: Salinipyrone and pacificanone are biosynthetic byproducts of the rosamicin polyketide synthase. ChemBioChem 2015
  • Duncan KR, Crüsemann M, Lechner A, Sarkar A, Li J, Ziemert N, Wang M, Bandeira N, Moore BS, Dorrestein P, Jensen PR: Molecular Networking and Pattern-Based Genome Mining Improves Discovery of Biosynthetic Gene Clusters and their Products from Salinispora Species. Chem Biol 2015, 460–471.

2014

  • Bonet B, Teufel R, Crüsemann M, Ziemert N*, Moore BS*: Direct Capture and Heterologous Expression of Salinispora Natural Product Genes for the Biosynthesis of Enterocin. J Nat Prod. 2014 Nov 10.
  • Ziemert N, Lechner A, Wietz M, Millán-Aguiñaga N, Chavarria KL, Jensen PR: Diversity and Evolution of Secondary Metabolism in the Marine Actinomycete Genus Salinispora. Proceedings of the National Academy of Sciences U S A 2014 Mar 25;111(12):E1130-9. doi: 10.1073/pnas.

2013

  • Kersten RD, Ziemert N, Gonzalez DJ, Duggan BM, Nizet V, Dorrestein PC, Moore BS: Glycogenomics as a mass spectrometry-guided genome-mining method for microbial glycosylated molecules. Proceedings of the National Academy of Sciences U S A 2013. 110(47): E4407-16.
  • Jensen PR, Chavarria KL, Fenical W, Moore BS, Ziemert N: Challenges and triumphs to genomics-based natural product discovery. Journal of industrial microbiology & biotechnology 2013. Epub.

2012

  • Ziemert N, Jensen PR: Phylogenetic approaches to natural product structure prediction. Methods in enzymology 2012, 517:161-182.
  • Ziemert N, Podell S, Penn K, Badger JH, Allen E, Jensen PR: The natural product domain seeker NaPDoS: a phylogeny based bioinformatic tool to classify secondary metabolite gene diversity. PloS one 2012, 7(3):e34064.

2011

  • Weiz AR, Ishida K, Makower K, Ziemert N, Hertweck C, Dittmann E: Leader peptide and a membrane protein scaffold guide the biosynthesis of the tricyclic peptide microviridin. Chemistry & biology 2011, 18(11):1413-1421.
  • Ziemert N, Ishida K, Weiz A, Hertweck C, Dittmann E: Exploiting the Natural Diversity of Microviridin Gene Clusters for the Discovery of Novel Tricyclic Depsipeptides. Applied and environmental microbiology 2010. 76(11):3568-74.

Before 2011

  • Ziemert N, Ishida K, Liaimer A, Hertweck C, Dittmann E: Ribosomal synthesis of tricyclic depsipeptides in bloom-forming cyanobacteria. Angew Chem Int Ed Engl 2008, 47(40):7756-7759.
  • Ziemert N, Ishida K, Quillardet P, Bouchier C, Hertweck C, de Marsac NT, Dittmann E: Microcyclamide biosynthesis in two strains of Microcystis aeruginosa: from structure to genes and vice versa. Applied and environmental microbiology 2008, 74(6):1791-1797.
  • Frangeul L, Quillardet P, Castets AM, Humbert JF, Matthijs HC, Cortez D, Tolonen A, Zhang CC, Gribaldo S, Kehr JC, Zilliges Y, Ziemert N, Becker S, Talla E, Latifi, A, Billault A, Lepelletier A, Dittmann E, Bouchier C and de Marsac NT: Highly plastic genome of Microcystis aeruginosa PCC 7806, a ubiquitous toxic freshwater cyanobacterium. BMC Genomics 2008, 9:274.