@skepteis.bsky.social 🥲

Chiming in here: if you are using a library (e.g. Python's requests) to access Zenodo programmatically and get 429 errors, make sure to define a custom User-Agent header that identifies your client (e.g. <my tool>/<tool version> (<link to tool website>) to help distinguish from abusive traffic!

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!

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!

I was always wondering about the cost difference between classes of NPs (in microbes). NRPS/PKS are costly to set up but can crank out molecules quite efficiently. RiPPs piggyback-ride on existing infrastructure but the per-unit-cost is probably higher. Is there any existing literature on that

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 ...

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...

I am happy to have played a minor role in this study, which was funded by the @ec.europa.eu #Horizon2020 project #MARBLES (Grant Agreement no. 101000392).

However, the BGCs that were found appeared to be very dissimilar to characterized clusters and from BGCs found in other sponge microbiomes. This indicates that Inflatella pellicula has uniquely adapted to its "abyssal" lifestyle, and may yield novel natural products usable in medicine.

Sampled from 2,900 m depth, most of the microbiome of Inflatella pellicula could not be taxonomically classified (indicating that it is mostly unknown), and only a handful of biosynthetic gene clusters (BGCs) were detected - in stark contrast to the biosynthetic diversity harbored by other sponges.

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 ...

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...

If you happen to work with heterocycles and run into weird errors, make sure to check for the notations of your heteroatoms!

Turns out that the aromatic nitrogen in tryptophan can be written in two ways: Ketcher expresses it as ":[#7;h1]:", but you can also write it as ":[n&H1]:". The former is rejected by RDKit, while the latter is accepted. Only took me a few hours to figure that out :,)

Somehow, I could not make the reaction pass the validation check ("does the reaction SMARTS convert a substrate SMILES into the expected product SMILES"), with RDKit complaining that the resulting SMILES was not valid.

I am working on the nosiheptide pathway and one of the reactions it the installation of 3-methyl-2-indolic acid on the nascent precursor via the NosIJK complex. Because the substrate is quite large, I am drawing the reaction in Ketcher, exporting it as a reaction SMARTS, and validating it in RDKit.

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!

Cool stuff! I'm glad we don't have any mountain lions in Europe

Awesome work with implications for chemical ecology!

I am happy that the @w-u-r.bsky.social delegation @mmzdouc.bsky.social @marnixmedema.bsky.social @jorgenavarro-22.bsky.social could contribute to this publication and congratulations again to @garimasingh-gs.bsky.social who worked tirelessly to bring this paper over the finish line! (5/5)

Finally, we found that ~98% of the BGCs in LFF are putatively novel (uncharacterized to date) and that lichen metabolic profiles contain a plethora of unidentified metabolites! (4/5)

We also show that lichen are surprisingly diverse in putative ribosomally synthesized and post-translationally modified peptides #RiPPs, with roughly 1/5 of detected BGCs. They generally show low similarity with reported fungal RiPPs, representing a putative hotspot for discovery. (3/5)

We performed the first systematic comparison of the BGC diversity in
#lichen-forming fungi, analyzing 111 to detect 5,541 biosynthetic gene clusters. Using LC-MS, we were able to link five detected compouds to their BGCs - including alectoronic, alpha-collatolic, and evernic acid! (2/5)

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...

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)

Finally, a shout out to all contributors to #MIBiG and a special thanks to the co-authors of this Position article in #bib, especially to @catarinacarolina.bsky.social, @kblin.bsky.social, and @marnixmedema.bsky.social ! It was a great pleasure working with you on this piece! (8/8)

MIBiG 5.0 Annotathons Registration Form Planned for spring 2026

Speaking of MIBiG hackathons: iteration 5.0 it is planned for spring 2026 and registrations are open! Please sign up if you are interested and feel free to share with your colleagues! (7/8) forms.gle/JKsf3XL3d1XN...

In our Position article, we analyze the outcomes of our strategy and compare it with related biocuration frameworks. Our biocuration strategy can be used as inspiration for related community-driven efforts. We will also implement lessons learned in future MIBiG hackathons (6/8)!

Flow diagram of workflow used in the MIBiG biocuration framework.

This framework uses social and technical workflows to facilitate the creation of high-quality annotations, combining #Kanban boards for work coordination with controlled data input via a dedicated submission portal, using motivational strategies inspired by insights from social sciences (5/8).

To this end, we developed a new framework for community-driven biocuration, and successfully applied it during the MIBiG 4.0 annotation hackathons, mobilizing 267 researchers who collectively invested over 4,000 hours into biocuration (4/8).

One such initiative is #MIBiG. Founded in 2015, it has become the gold standard database for #biosynthetic gene clusters due to the tireless efforts of the #secmet #naturalproducts community. However, the biocuration efforts were mostly organized ad hoc, lacking a organizational framework (3/8).