Great to see the antiSMASH family grow!

Nadine Ziemert@nadineziemert.bsky.social · last wk.

Looking for BGCs in large metagenomic datasets? Our new biorxiv preprint introduces metaSMASH, a scalable fork of antiSMASH designed specifically for metagenome-scale BGC detection and analysis : www.biorxiv.org/cgi/content/... Thanks @canerbagci.bsky.social and @kblin.bsky.social ❤️

Interested in natural products? We just published an article on hybrid peptide-polyketide-specialized lipids and describe the chitinimines, a new family of amphiphilic metabolites. Read it open access in JACS Au: doi.org/10.1021/jacs...

Charting the Biosynthetic Landscape of Hybrid Polyketide-Nonribosomal Peptide-Specialized Lipids

Polyunsaturated fatty acid (PUFA) synthase enzymes are best known for their role in membrane lipid biosynthesis in marine psychrophilic bacteria but have also evolved to assemble specialized lipid-con...

doi.org

Interested in tailoring enzymes? Meet MITE - the Minimum Information about a Tailoring Enzyme Database (mite.lisc.univie.ac.at), capturing the substrate- and reaction-specificity of enzymes in natural product biosynthesis. MITE has just passed a milestone: the 400th MITE entry has been added!

Are you correlating natural product #metabolomics and bioactivity data? Annoyed by the lack of tools that also integrate #antiSMASH results? Meet #FERMO, our metabolomics data analysis webtool (fermo.bioinformatics.nl), now finally published in ACS Meas Sci Au doi.org/10.1021/acsm...

FERMO: A Dashboard for Biochemometric Prioritization of Molecular Features from Mass Spectral Data

Many natural products can selectively modulate biological processes, making them prime candidates for drug discovery. However, the complexity of biological samples makes clear attribution of activity ...

doi.org

Are you correlating natural product #metabolomics and bioactivity data? Annoyed by the lack of tools that also integrate #antiSMASH results? Meet #FERMO, our metabolomics data analysis webtool (fermo.bioinformatics.nl), now finally published in ACS Meas Sci Au doi.org/10.1021/acsm...

FERMO: A Dashboard for Biochemometric Prioritization of Molecular Features from Mass Spectral Data

Many natural products can selectively modulate biological processes, making them prime candidates for drug discovery. However, the complexity of biological samples makes clear attribution of activity ...

doi.org

After a short hiatus from social media, I am back with some exciting news: I have recently been appointed assistant professor for Natural Product Research at the University of Vienna and have started my own research group: ZdoucLab.org!

Zdouc Lab

Microbial Natural Products Meet Data Science. The Zdouc research lab at the University of Vienna investigates naturally occurring, specialized molecules called natural products. These small molecules ...

zdouclab.org

@skepteis.bsky.social 🥲

Emily Hunt@emily.space · 5mo ago

The era of good Python tooling is over not long after it began 😂 Did anyone fork tools like uv & ruff yet? We need community-ran forks that remain FOSS and don't get bloatware added

Great to see it finally published! I've tried it during beta testing and it works great! Users of v1 will feel at home right away!

Marnix Medema@marnixmedema.bsky.social · 5mo ago

Now out in @natcomms.nature.com : versions 2.0 of both BiG-SCAPE and BiG-SLiCE! With significant speed and accuracy increases, as well as new interactive functionalities. Read the full paper here #openaccess: www.nature.com/articles/s41...

Now out in @natcomms.nature.com : versions 2.0 of both BiG-SCAPE and BiG-SLiCE! With significant speed and accuracy increases, as well as new interactive functionalities. Read the full paper here #openaccess: www.nature.com/articles/s41...

The MIBiG 5.0 Annotathon is coming soon, and registration is now open! 🧬 Does your research involve biosynthetic gene clusters? Do you love natural product biosynthesis? Do you have an interest in rare & exotic enzymes? We can use your help & expertise. Register here 👉 forms.gle/C1cWcLHtrjT2...

Make sure to join us in the MIBiG Annotathons! The MITE database (mite.bioinformatics.nl) will join the efforts! If you are interested in tailoring enzymes/maturases, make sure to join us!

@nicoleeavalon.bsky.social · 6mo ago

The MIBiG 5.0 Annotathon is coming soon, and registration is now open! 🧬 Does your research involve biosynthetic gene clusters? Do you love natural product biosynthesis? Do you have an interest in rare & exotic enzymes? We can use your help & expertise. Register here 👉 forms.gle/C1cWcLHtrjT2...

Marine #sponges are generally considered biosynthetic "hotspots" (e.g. Theonella) - but does this always hold true? In our newest study led by @stephenjackson.bsky.social we are looking at Inflatella pellicula's biosynthetic capacity - and our results are surprising doi.org/10.1099/mgen...

New insights into the microbiome of the deep-sea sponge Inflatella pellicula and the secondary metabolic potential of metagenome-assembled genomes and the wider microbiome

Marine sponges are found in all of the world’s oceans, from the surface waters to the deepest abyssal zones. The marine sponge holobiont is a rich source of microbial and chemical diversity. Up to 63 ...

doi.org

Marine #sponges are generally considered biosynthetic "hotspots" (e.g. Theonella) - but does this always hold true? In our newest study led by @stephenjackson.bsky.social we are looking at Inflatella pellicula's biosynthetic capacity - and our results are surprising doi.org/10.1099/mgen...

New insights into the microbiome of the deep-sea sponge Inflatella pellicula and the secondary metabolic potential of metagenome-assembled genomes and the wider microbiome

Marine sponges are found in all of the world’s oceans, from the surface waters to the deepest abyssal zones. The marine sponge holobiont is a rich source of microbial and chemical diversity. Up to 63 ...

doi.org

I am working with reaction SMARTS again and they can be really tricky in representing heterocycles! I just had a "fun" time debugging a reaction involving tryptophan - I will show you what I mean!

Awesome work with implications for chemical ecology!

Kaitlin Creamer@kaitlincreamer.bsky.social · 8mo ago

Our new paper on Salinispora is out in @asm.org #AppEnvMicro! @scrippsocean.bsky.social Ever wonder if an actinomycete living in 1m² ocean sediment is just one big clonal colony? We sequenced 99 Salinispora strains from a single Fiji reef plot to find out. 🧵1/8 doi.org/10.1128/aem....

Ever wondered about the funny moss growing on trees? Chances were good that you were looking at #lichen! These hybrid fungal-algae/cyanobacterial colonies are biosynthetically surprisingly diverse, as we show in our newest publication led by @garimasingh-gs.bsky.social doi.org/10.1099/mgen... (1/5)

Paired-omics-based exploration and characterization of biosynthetic diversity in lichenized fungi

The increasing demand for novel drug leads requires bioprospecting non-model taxa. Comparative genomics and correlative omics are a fast and efficient method for linking bioactive but genetically orph...

doi.org

Have you ever used a #bioinformatics #database and were frustrated by its lack of coverage? Did you ever think about starting your own resource? We just published a new strategy for community-driven #biocuration, based on our experiences with the #MIBiG database (1/8)! doi.org/10.1093/bib/...

Strategies for community-sourced biocuration in bioinformatics: a case study on MIBiG 4.0

Abstract. Biocuration is essential to transform molecular sequence data into standardized, machine-readable resources. Such curated datasets enable compara

doi.org

Congratulations to this great work, happy to have contributed a little bit :)

Masschelein Lab@masscheleinlab.bsky.social · 9mo ago

Polyunsaturated fatty acid (PUFA) synthase enzymes turn out to be far more versatile than we ever imagined! In our new preprint, we reveal a largely untapped biosynthetic space where they team up with PKSs and NRPSs to create new types of bioactive amphiphilic metabolites. 👉http://bit.ly/4hzUUak

Working on tailoring enzymes and want to learn more about the MITE database? We are organizing a hands-on training session on how use the DB and create new entries: October 30th and November 4th 10-11 am Amsterdam time. Sign up here: forms.gle/KHPqe9XV1RRg... See you there! #secmet #natprod

MITE training session registration form

Registration form for mailing list

forms.gle

Interested in Python programming and good software engineering practices? Check out my newest blog post where I introduce a "modern Python" GitHub repository template and talk about my motivation for its creation! mmzdouc.github.io/posts/2025/1...

Are you building applications using docker? In my recent blog post, I am investigating git's curious behavior when used as a subprocess inside a containerized Flask application. You can read more here: mmzdouc.github.io/posts/2025/1...

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

Nadine Ziemert@nadineziemert.bsky.social · 10mo ago

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/...

MITE: the Minimum Information about a Tailoring Enzyme database for capturing specialized metabolite biosynthesis

Abstract. Secondary or specialized metabolites show extraordinary structural diversity and potent biological activities relevant for clinical and industria

doi.org

Mitja M. Zdouc@mmzdouc.bsky.social · 12mo ago

Into natural product biosynthesis & tailoring enzymes? Frustrated by the lack of a dedicated resource to explore their functions? Tired of endless literature searches for reaction info? Meet the MITE database, freely available at mite.bioinformatics.nl. Preprint: doi.org/10.26434/che... (1/8)

Next at @vaam-microbes.bsky.social Workshop, Leo Dumjahn talks about the opportunistic pathogen Chromobacterium haemolyticum and the cyclic lipopeptides it uses as virulence factors.

Next at the @vaam-microbes.bsky.social Workshop, Valerie Rebhahn is talking about the cyanobacterial aetokthonotoxin and its mode of action in uncoupling the oxidative phosphorylation in mitochondria.

In today's third talk at @vaam-microbes.bsky.social Workshop at @freieuniversitaet.bsky.social, Nico Brüssow talks about the lanthipeptide II RiPP nostolanthin A which apparently oligomerizes - a very unusual property in RiPPs.

Next at VAAM Workshop at @freieuniversitaet.bsky.social , Alexandra Eckart from HIPS talking about her discoveries of tenacious bacteria isolated from Hydractinia echinata hydroids.

@mitjare.bsky.social kicking off the second day of the VAAM Workshop at @freieuniversitaet.bsky.social talking about the phyllosphere, its bacterial inhabitants and the natural products they produce - including surfactants!

If you are interested, make sure to apply! I have been working with Marnix, Justin, and Daniel over the last few years and they are awesome!

Marnix Medema@marnixmedema.bsky.social · 11mo ago

We are looking for a 3-year postdoc to work with Daniel Probst, Justin van der Hooft and myself on an exciting project involving federated learning and integrative omics for discovery of new antibiotics from natural products. Apply here: www.wur.nl/en/vacancy/p... Please share!

We are looking for a 3-year postdoc to work with Daniel Probst, Justin van der Hooft and myself on an exciting project involving federated learning and integrative omics for discovery of new antibiotics from natural products. Apply here: www.wur.nl/en/vacancy/p... Please share!