Tilmann Weber

Thanks a lot for the great conference!

Final chance to apply! Deadline 31.10!

Great conference coming up... Please share!
magic-molfun.dtu.dk/np21c-confer...
Application deadline 31.10.2024

Check out this new amazing preprint by David, @tuesparholt.bsky.social , @thombooth.bsky.social, and @tilmweber.bsky.social!

StreptoCAD: An Open-Source Software Toolbox Automating Genome Engineering Workflows in Streptomycetes Streptomycetes hold immense potential for discovering novel bioactive molecules for applications in medicine or sustainable agriculture. However, high-throughput exploration is hampered by the current Streptomyces genetic engineering methods that involve the manual design of complex experimental molecular biological engineering strategies for each targeted gene. Here, we introduce StreptoCAD, an open-source software toolbox that automates and streamlines the design of genome engineering strategies in Streptomyces, supporting various CRISPR-based and gene overexpression methods. Once initiated, StreptoCAD designs all necessary DNA primers and CRISPR guide sequences, simulates plasmid assemblies (cloning) and the resulting modification of the genomic target(s), and further summarizes the information needed for laboratory implementation and documentation. StreptoCAD currently offers six design workflows, including the construction of overexpression libraries, base-editing, including multiplexed CRISPR-BEST plasmid generation, and genome engineering using CRISPR-Cas9, CRISPR-Cas3, and CRISPRi systems. In addition to automating the design process, StreptoCAD further secures compliance with the FAIR principles, ensuring reproducibility and ease of data management via standardized output files. To experimentally demonstrate the design process and output of StreptoCAD, we designed and constructed a series of gene overexpression strains, and performed CRISPRi knockdowns in Streptomyces Gö40/10, underscoring the tool’s efficiency and user-friendliness.. This tool simplifies complex genetic engineering tasks and promotes collaboration through standardized workflows and design parameters. StreptoCAD is set to transform genome engineering in Streptomyces, making sophisticated genetic manipulations accessible for all and accelerating natural product discovery.

New paper alert!!

Led by Lucas, we automated all the design steps for genome engineering experiments in streptomycetes. If you are using our Streptomyces CRISPR toolbox, you can now design hundreds of experiments in a matter of minutes.

@tilmweber.bsky.social @kblin.bsky.social
....

𝘚𝘵𝘳𝘦𝘱𝘵𝘰𝘮𝘺𝘤𝘦𝘴 (and 𝘒𝘪𝘵𝘢𝘴𝘢𝘵𝘰𝘴𝘱𝘰𝘳𝘢🙂) aficionadas y aficionados take note 👇

...and no, the image doesn't show reconstituted 𝘒𝘪𝘵𝘢𝘴𝘢𝘵𝘰𝘴𝘱𝘰𝘳𝘢 telomeres (telomores) 😉
#MicroSky

Bacterial telomeres are common, just not so much in RefSeq 'complete' genomes. But they can be added by the new tool David Faurdal wrote. I am thrilled to see this out as a preprint here: www.biorxiv.org/content/10.1... @tilmweber.bsky.social @thombooth.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...

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👇

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

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/...

Happy to share this detective work by Rune Overlund Stannius now published in #mSystems

phenotype+genomes▶️GWAS▶️gene cluster for pigment production

Identification of widely conserved biosynthetic gene cluster involved in pigment production of Bacillus subtilis
journals.asm.org/doi/10.1128/...

After lunch at #ISBA2025: Keynote talk from Prof @lonegram.bsky.social (DTU) on ‘Tropodithietic acid - a multifunctional bacterial secondary metabolite’ #naturalproducts #specialisedmetabolites

A key aspect of my @erc.europa.eu Advanced project 'Community' was to predict biosynthetic gene cluster (BGC) function entirely on how BGCs are controlled, without looking at predicted gene function or natural product. We show proof of concept for this idea in this paper in @plosbiology.org (1/2)

Profs Gilles van Wezel and Eva Stegmann giving the Welcome Ceremony of the 20th International Symposium on the Biology of Actinomycetes in Edmond aan Zee (coastal Netherlands) #ISBA2025 #actinomycetes #streptomyces

Wonderful to have Prof Pieter Dorrestein @pieterdorrestein.bsky.social giving the opening keynote talk of #ISBA2025 on ‘Scaling the discovery of new microbial natural products through data science of unused metabolomics data’ #naturalproducts #specializedmetabolites #secmet

We’ve just released #antiSMASH 8.0.1, a bug-fix release. Find the tarball and containers in the usual places, it’s also live on our website now. Bioconda containers aren’t built by us, they might take a while to update. We recommend installing deps via bioconda and then running from our releases.

Bioprospectors mine microbial genomes for antibiotic gold But turning what they find into drugs isn’t so easy

Happy to contribute to a C&EN article on genome mining for antimicrobials cen.acs.org/pharmaceutic...
Great article by Max Barnhart, who’s not on BlueSky for all I can tell.

Great start of our MAGic-MOLFUN Industrial Training Event at NAICONS Srl in Milano!

EESMicrobiome

Join us at #EESMicrobiome!

Organisers Mani Arumugam (#uni_copenhagen), Ami Bhatt (@stanfordpress.bsky.social), Peer Bork (@borklab.bsky.social) and Nicola Segata (#CIBIO_UniTrento) look forward to welcoming #microbiome scientists in September at @embl.org!

@events.embl.org

I can highly recommend you to try out this tool developed by my PhD student @andersohd.bsky.social and other members of our research group in collaboration with @tilmweber.bsky.social team. It is still a beta version, but we hope to finish it soon.

I am thrilled to share after years of work/procrastination that the MassQL manuscript is finally published in @natmethods.nature.com - "A universal language for finding mass spectrometry data patterns". This was an team effort from all co-authors that helped shape MassQL and how it could be used.

Congratulations to Dr Lijie Song for defending her PhD today 🎉 exploring Bacillales genome sequences & encoded BGCs.

Project was jointly supervised by @tilmweber.bsky.social - my first PhD graduate where co-supervision truly meant equal supervision, for which I am thankfull to Tilmann!
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Time for our yearly #DTU microbes conference and we have a great program this year! 🦠🎤 #microbiology

Empowering natural product science with AI: leveraging multimodal data and knowledge graphs Artificial intelligence (AI) is accelerating how we conduct science, from folding proteins with AlphaFold and summarizing literature findings with large language models, to annotating genomes and…

🔓Don't miss this #OpenAccess Viewpoint by @jjjvanderhooft.bsky.social @marnixmedema.bsky.social Adam Skiredj & co at @w-u-r.bsky.social @univparissaclay.bsky.social @mit.edu on empowering natural product science with AI #natprod #chemsky

Check it out here🔽
pubs.rsc.org/en/content/a...

Many thanks to the funding agencies supporting the scientists contributing to #antiSMASH. At @dtu.dk, the #antiSMASH team would like to thank the Novo Nordisk Foundation, Danmarks Grundforskningsfond @dg.dk (@cemist.bsky.social), and the EU MSCA DN @magicmolfun.bsky.social. #dkforsk

antiSMASH 8.0: extended gene cluster detection capabilities and analyses of chemistry, enzymology, and regulation Abstract. Microorganisms synthesize small bioactive compounds through their secondary or specialized metabolism. Those compounds play an important role in

We're happy to announce that the #antiSMASH v8 paper is out in @narjournal.bsky.social: academic.oup.com/nar/advance-...
Many thanks to @kblin.bsky.social, @marnixmedema.bsky.social and many international collaborators!

Forskningens døgn/Science Fair - www.Forsk.dk
Come get inspired!
The Centers of Excellence at DTU invites everyone to come see our work on Thursday 24th of April at 10-13, Building 202, Anker Engelunds Vej 1

Contact @cemist.bsky.social for more info.
@dg.dk Danmarks Grundforskningsfond

Many thanks to Tenna A. Møller, @thombooth.bsky.social, Simon Shaw from DTU Biosustain and Vilhelm K. Møller and Rasmussen JN Frandsen from DTU Bioengineering

ActinoMation: A literate programming approach for medium-throughput robotic conjugation of Streptomyces spp The genus Streptomyces are valuable producers of antibiotics and other pharmaceutically important bioactive compounds. Advances in molecular engineeri…

Have a look at our latest tool: ActinoMation - a toolkit for automated E. coli – Streptomyces conjugation on Opentron laboratory automation systems: www.sciencedirect.com/science/arti...