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...

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.

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!

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! [1/n]

Time for our yearly #DTU microbes conference and we have a great program this year! 🦠🎤 #microbiology

🔓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...

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

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...

8/8 Finally, a big thank you to all co-authors - Peter, David, Renata, Tetiana, and @tilmweber.bsky.social ! This has been a fun collaboration!

7/8 We further further sequenced hosts after BAC integration and verified multicopy integrations, and showed that the genomes remain stable, even in non-selective medium. If your are engineering streptomycetes, please give it a try and let us know how it goes! All plasmids are on Addgene!

6/8We then demonstrated how the high efficiencies of CASCADE-Cas3 can be used for streamlined host construction by substitution of large genomic regions with PhiC31 integration sites - allowing multicopy expression of BGCs. Reintroduction of the act BGC resulted in significantly higher production.

5/8 In all three strains, CASCADE-Cas3 installed the desired deletions with very high efficiencies (up to 100%)! This did not require modifications to the plasmids or modified methods, showcasing that CASCADE-Cas3 can be used "out of the box" across different species.

4/8 Furthermore, efficiencies appeared to be less dependant on which spacer was used, indicating less background/off-target activity. What about other streptomycetes? We picked S. albidoflavus, S. venezuelae, as well as NBC1270, an isolate from our collection, for further experiments.

3/8 So we were wondering - is CASCADE-Cas3 much better suited for genome engineering of streptomycetes? Targeting the act BGC of S. coelicolor, we got some very strong initial data supporting this hypothesis. We obtained very precise deletions with robustly high efficiencies.

2/8 The minimal type I-C CASCADE-Cas3 is fascinating. A complex consisting of Cas5, Cas7, and Cas8 binds the target site and recruits the processive nuclease Cas3, which generates recombinogenic overhangs! Sounds great for homologous recombination!

1/8 We found that type I CRISPR systems (like CASCADE-Cas3) are much more widespread in streptomycetes than type II CRISPR systems (e.g. Cas9). CASCADE-Cas3 also has a TA rich PAM, which translates to way fewer potential off-target sites.

Interested in engineering streptomycetes? Struggling with existing genome engineering tools? Then check out our newest paper on CASCADE-Cas3 based genome engineering in streptomycetes! Some highlights below:

Are you struggling in engineering streptomycetes? Have a look on our new Cas3-based toolkit just out in @narjournal.bsky.social academic.oup.com/nar/article/... Many thanks to @chriiswh.bsky.social, Peter Gockel, David Faurdal, Tetiana Gren and Renata Sigrist @dtu.dk #DTUBiosustain #CRISPR

Echoing @marnixmedema.bsky.social, excited and looking forward to the symposium this afternoon!! 😎🎉🎊😊

Looking forward to keynotes from our international guest speakers @pieterdorrestein.bsky.social @tilmweber.bsky.social & #MargheritaSosio, and pitches from our NPlinker workshop participants @echarria21.bsky.social #KristiinaVind & #NicoleAvalon!

The #NPLinker eScience #workshop 2025 started today with a round of introductions & theory and hands-on of #genome #mining and #gene cluster grouping led by @tilmweber.bsky.social & Arjan Draisma! 😎 The first NPLinker data type covered! #antiSMASH #MIBiG #BiGSCAPE Wageningen University & Research

Nice perspective on the discovery of novel small molecule antibiotics www.nature.com/articles/s44...

Congrats to Garret for officially becoming Dr. O'Connell! Garret had his Ph.D. viva on synthetic #fluorochemical #metabolism in #Pseudomonas today. Thanks to @tilmweber.bsky.social r.bsky.social, @pavelcito.bsky.social & Esteban Martinez for their insights🧪🦠 #SynBio @labnikel.bsky.social

Many thanks for having me on board. I’m looking forward to working with the Editorial Board!

Ten days left to apply!!

Streptomyces are not even in the top 50 most studied and yet they provide so many important molecules including >50% of clinically used antibiotics. Same for TB, the most deadly human pathogen. Do most scientists take the easy route?

New deadline for abstract submission and Early Bird Registration for the #ISBA20 conference in the Netherlands from 15.-19.June 2025! Participation highly recommended! Deadline is 21. March 2025. Information, registration and abstract submission at www.universiteitleiden.nl/isba2025

We will be hosting the first @mzmine.bsky.social Community Meeting at @iocbprague.bsky.social. Please register if you wish to learn about the latest developments in mzmine. More info: docs.google.com/document/d/1...

Gaining insights into the complexity of specialized metabolites and their possible ecological roles These metabolites not only function as antimicrobials, but also as cue molecules among other peculiar functions -see our paper in microLIFE of @femsjournals.bsky.social on surfactin and subtilosin A

One of the kindest and most interesting scientists I have known, Julian Davies, passed away. I had some remarkable conversations with him. Watch this seminar, and you will see what I mean. RIP, Julian. www.youtube.com/watch?v=Cjdb...

You'd be amazed how often dot plots are the best visualisation of genome comparisons. Good one, Thom.

Hello Everyone! 👋 Nucleic Acids Research is excited to be on Bluesky! Please follow us for the latest #Research, #Breakthrough articles, journal issues and more. Also, please consider adding us to your starter packs!

Congratulations Lijie!

A recent study by the Institut Pasteur highlights the emergence of a cholera strain resistant to 10 antibiotics, including key treatments azithromycin and ciprofloxacin. This study demonstrates the need to strengthen global surveillance of the cholera agent. 🌍🔬 #cholera #AntibioticResistance

See the numerous positions at Novonesis on bacterial and fungal strain development - in 🇩🇰 www.novonesis.com/en/careers/j...

New bioRxiv from the group by Lijie Song combined with the bioinformatics expertise of @matinnu.bsky.social in @tilmweber.bsky.social group, we report a biosynthetic potential of Paenibacilli through a genus-wide exploration of BGCs www.biorxiv.org/content/10.1...

I'd like to thank again everyone who contributed to this project, especially everyone who submitted GitHub issues! Also of course, @tilmweber.bsky.social, @wemakemolecules.bsky.social and the elusive but essential Simon Shaw! 5/5