Nadine Ziemert

Automated genome mining predicts structural diversity and taxonomic distribution of peptide metallophores across bacteria Automated detection of metallophore biosynthesis reveals that metal-chelating non-ribosomal peptides are widespread, chemically diverse, and deeply rooted in bacterial evolution.

Automated genome mining predicts structural diversity and taxonomic distribution of peptide metallophores across bacteria

@elife.bsky.social by Zachary Reitz and Bita Pourmohsenin et al from @marnixmedema.bsky.social and @nadineziemert.bsky.social

elifesciences.org/articles/109...

Join this super initiative to support our understanding of secondary metabolites biosynthesis!

Looking forward to contributing 😃

📅 Save the Date – CMFI Conference 2027
Feb 17–19, 2027

📍 Tuebingen, Germany

Confirmed speakers:
Benoit Chassaing · Eran Elinav · Neha Garg · Kiran Patil · Bertrand Routy · Nina van Sorge

Subscribe to stay updated and join us in Tuebingen:

www.cmfi.uni-tuebingen.de/en/cmfi2027

PanBGC: A pangenome-inspired framework for comparative analysis of biosynthetic gene clusters Abstract. Bacterial secondary metabolites are a major source of therapeutics and play key roles in microbial ecology. These compounds are encoded by biosyn

PanBGC: A pangenome-inspired framework for comparative analysis of biosynthetic gene clusters

#ISMEComms from @nadineziemert.bsky.social

academic.oup.com/ismecommun/a...

Ultra-deep long-read metagenomics captures diverse taxonomic and biosynthetic potential of soil microbes AbstractBackground. Soil ecosystems have long been recognised as hotspots of microbial diversity, but most estimates of their microbial and functional comp

Want to know how diverse soil really is?
Our ultra deep sequencing is now published in GigaScience: academic.oup.com/gigascience/...
Soil is wild! Thanks for leading the study @canerbagci.bsky.social
#secmet #soil #metagenomics #bacterialdiversity

Discovery and Heterologous Expression of the Soil Metagenome-Derived Lasso Peptide Metanodin with an Unprecedented Ring Structure Culture-independent metagenomic approaches have proven to be effective tools for identifying previously hidden biosynthetic gene clusters (BGCs) encoding novel natural products with potential medical relevance. However, producing these compounds remains challenging as metagenomic BGCs often originate from organisms phylogenetically distant from available heterologous hosts. Lasso peptides, a subclass of ribosomally synthesized and post-translationally modified peptide (RiPP) natural products, exhibit diverse bioactivities, yet no lasso peptide has previously been discovered directly from a metagenome. Here, we report the discovery and heterologous expression of the first soil metagenome-derived lasso peptide. Expression of its biosynthetic gene cluster in Escherichia coli, followed by mass spectrometry analysis, strongly supported the predicted amino acid sequence and lasso structure of the peptide. Notably, this lasso peptide is the first to feature asparagine as the ring-forming residue at position one. Taxonomic analysis of the corresponding BGC identified an uncultivated member of the Steroidobacterales family (Gammaproteobacteria) as the closest known relative of the potential native host. These findings underscore the potential of metagenomic genome mining to reveal structurally novel RiPPs and to expand our understanding of the natural diversity of lasso peptides.

Happy to share our newest manuscript about the discovery and hererologous expression of metanodin, a new lassopeptide with unprecedented structural features directly from soil metagenomes. pubs.acs.org/doi/full/10....
#secmet #lassopeptides #syntheticbiology

🧬 Share your science at Natural Products in the 21st Century (NP21C) — 9–11 Feb 2026, Leuven
Join researchers exploring genomics, metabolomics & microbial natural products!
www.conferencemanager.dk/naturalprodu...
#NP21C #secmet
@tilmweber.bsky.social @marnixmedema.bsky.social @kblin.bsky.social

Great to see PhyloNaP out! Great tool, and it also connects to mite.bioinformatic.nl! #openscience #collaboration

Working with natural products? With PhyloNaP you can place proteins from BGCs into annotated phylogenetic trees—making functional inference easier! #phylogeny #bioinformatics #naturalproducts #magicmolfun #ziemertlab

PhyloNaP: a user-friendly database of Phylogeny for Natural Product-producing enzymes https://www.biorxiv.org/content/10.1101/2025.09.23.677986v1

PhyloNaP: a user-friendly database of Phylogeny for Natural Product-producing enzymes Phylogenetic analysis is widely used to predict enzyme function, yet building annotated and reusable trees is labor-intensive and requires extensive knowledge about the specific enzymes. Existing reso...

PhyloNaP: a user-friendly database of Phylogeny for Natural Product-producing enzymes
doi.org/10.1101/2025...

Trends in metabolite discovery from Actinomycetes Covering: 2013 to 2023 In this review, we analyzed the scientific literature of the period 2013–2023 that reported novel specialized metabolites from the Actinomycetes, one of the most prolific…

Be sure to read this review, part of our Industrial Perspective themed collection, by Stefano Donadio & co. from NAICONS Srl discussing the trends in metabolite discovery from Actinomycetes #secmet #natprod

Find it in full below👇

Led by @sashakorenskaia.bsky.social, thanks for the collaboration @tilmweber.bsky.social, @kblin.bsky.social and @magicmolfun.bsky.social

PhyloNaP: a user-friendly database of Phylogeny for Natural Product-producing enzymes Phylogenetic analysis is widely used to predict enzyme function, yet building annotated and reusable trees is labor-intensive and requires extensive knowledge about the specific enzymes. Existing reso...

Happy to share our newest preprint. PhyloNaP as a user friendly database of phylogeny for enzymes involved in natural product production and as public repository for well curated phylogenetic trees. Happy Tree Building!!!
#phylogeny #secmet #bioinformatics

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

Aaand it's out! Meet MITE - the natural product tailoring enzyme database, just published in @narjournal.bsky.social! MITE DB captures the substrate- and reaction-specificity of tailoring enzymes, allowing to capture this information in a human- and machine-readable way! doi.org/10.1093/nar/...

Naming Challenge: Help Redefine the Glycopeptide Family! We are excited to launch a naming competition inspired by the recent preprint "Phylogenetic distance and structural diversity directing a reclassification of glycopeptide antibiotics" (https://www.bio...

⏰ Just 7 days left for our Glycopeptide Renaming Challenge!
💡 Share your best name idea and win 500€

👉 More info and submission here: docs.google.com/forms/d/1ym9...

#secmet #NaturalProducts #Antibiotics #NamingChallenge #Glycopeptides @gdwantibiotics.bsky.social @marghesosio.bsky.social

Plug-and-Play System Boosts Streptomyces Metabolite Production In the relentless quest to harness nature’s biochemical arsenal, researchers have pushed the boundaries of microbial engineering, uncovering novel strategies for scalable production of valuable secondary metabolites. These compounds—ranging from antibiotics to anticancer agents—are vital to medicine, agriculture, and biotechnology. Among the microbial workhorses, species of the genus Streptomyces stand out as prolific producers of these bioactive molecules. However, translating the rich secondary metabolite profiles of…

Plug-and-Play System Boosts Streptomyces Metabolite Production

In the relentless quest to harness nature’s biochemical arsenal, researchers have pushed the boundaries of microbial engineering, uncovering novel strategies for scalable production of valuable secondary metabolites. These…

Conferencing with my favorite natural product chemist this week at the #ASP2025 in Grands Rapids, Michigan. Great science, inspiring talks, and reconnecting with friends and colleagues! @claesengroup.bsky.social @eustaquiolab.bsky.social @balunaslab.bsky.social #SecMet #NaturalProducts

We are delighted to be sponsoring the 32nd International Symposium on the Chemistry of Natural Products! #ISCNP32 #ICOB12 #IUPAC #RACI #natprod

🚨Registration closes in two weeks! Don't miss your final chance to attend▶https://bit.ly/4mfyZHd

Find more info here👉https://www.iscnp32-icob12.org/about

ZiemertLab The Ziemert lab is interested in the evolution and distribution of bacterial secondary metabolites. These bioactive compounds are especially important in human medicine as the chemical scaffolds are t...

Check out the Ziemert Lab’s new YouTube channel
m.youtube.com/@ZiemertLab
We’ve uploaded short tutorial videos on how to use our tools for genome mining and natural product discovery.
Thanks Semih, @martinaadamek.bsky.social @turgutmesut.bsky.social ! #GenomeMining #SecMet #naturalproducts

Nice new building on our campus @unituebingen.bsky.social but the designer monoculture lawn in the front is clearly not climate change-resistant. New strategy please!

🚨 Naming Challenge:
Help redefine the #glycopeptide family!

🏆Submit your idea & win 500 € + authorship credit

Let’s rethink antibiotic classification—together!

🧬 Deadline: Sept 15, 2025

👉 docs.google.com/forms/d/e/1F...

@nadineziemert.bsky.social #NameChallenge #NaturalProducts #Antibiotics

Anytime @matthutchings.bsky.social 😁

The last day at #ISBA2025 Hanna Augustijn from @marnixmedema.bsky.social and @gillesvanwezel.bsky.social labs giving a brilliant talk about her PhD project mapping the transcription factors and regulation networks in Actinomycetes. Very cool work! #naturalproducts #secmet #bacterialregulation

New Session at #ISBA2025 Paul Jensen and @matthutchings.bsky.social talking about the fascinating interactions of actinomycetes with predators and plants… #secmet #bacterialinteractions #naturalproducts

A broad-spectrum lasso peptide antibiotic targeting the bacterial ribosome - Nature A new lasso peptide antibiotic exhibits broad-spectrum activity against Gram-negative and Gram-positive bacteria by interfering with bacterial protein synthesis, is unaffected by common resistanc...

Next up at #ISBA2025 Manoj Jangra from @gdwantibiotics.bsky.social lab talking about the discovery of the new lassopeptide #antibiotic lariocidine targeting the bacterial ribosome. Very cool story and great talk! www.nature.com/articles/s41... #secmet #amr

@kateduncan.bsky.social Talking about the diversity and biosynthesis potential in the rare actinomycete genus Rhodococcus at #ISBA2025

Thankful that I had the opportunity to chair the #Genomics and #NaturalProductsBiosynthesis Session at #ISBA2025
Thanks to the awesome speakers and their inspiring talks! Lei Dong, Jaclyn Winter, @kblin.bsky.social, Lisa Vader, Eric Helfrich!

Lisa highlights the upcoming “Natural Products in the 21st Century” conference, hosted by the MAGic-MOLFUN @magicmolfun.bsky.social doctoral network!
📅 February 9–11, 2026
📍 Leuven, Belgium (Provinciehuis Conference Center) - more info soon! #ISBA2025

At #ISBA2025, Jaclyn Winter (University of Utah) on ‘bioprospecting hypersaline microorganisms from Great Salt Lake for Natural Product Discovery and Environmental Adaption’ in the genomics & natural products biosynthesis session chaired by @nadineziemert.bsky.social & @marnixmedema.bsky.social