Mitja M. Zdouc
@mmzdouc.bsky.social
Pharmacist turned Bioinformatician. PhD in Natural Product Chemistry. PostDoc at Wageningen University. Biosynthesis is my passion, software my daily bread.
Reposted by Mitja M. Zdouc
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
January 13, 2026 at 6:54 AM
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...
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
January 13, 2026 at 6:54 AM
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 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!
December 30, 2025 at 6:09 PM
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!
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 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....
December 25, 2025 at 7:50 PM
Awesome work with implications for chemical ecology!
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
December 18, 2025 at 8:58 AM
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)
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
December 11, 2025 at 7:19 PM
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/...
Congratulations to this great work, happy to have contributed a little bit :)
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
👉http://bit.ly/4hzUUak
Charting the biosynthetic landscape of hybrid polyketide-nonribosomal peptide-specialized lipids
Polyunsaturated fatty acid (PUFA) synthase-like enzymes are best known for their role in membrane lipid biosynthesis in marine bacteria, but have also been repurposed for the assembly of specialized l...
bit.ly
October 27, 2025 at 10:55 AM
Congratulations to this great work, happy to have contributed a little bit :)
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
October 24, 2025 at 1:37 PM
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
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...
Modern Python Project GitHub Template
TL;DR: I created a freely available template to facilitate setting up “modern” Python projects.
mmzdouc.github.io
October 22, 2025 at 2:06 PM
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...
Fixing Persistence Issues with Git Inside Docker Containers
TL;DR: Cloned Git directories inside Docker containers can persist across builds or runs, causing branching and committing issues. Explicitly removing the directory before cloning prevents these error...
mmzdouc.github.io
October 21, 2025 at 1:51 PM
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
September 27, 2025 at 11:21 AM
Great to see PhyloNaP out! Great tool, and it also connects to mite.bioinformatic.nl! #openscience #collaboration
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/...
September 27, 2025 at 9:11 AM
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/...
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.
September 25, 2025 at 8:11 AM
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.
September 25, 2025 at 8:04 AM
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.
September 25, 2025 at 7:46 AM
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.
September 25, 2025 at 7:33 AM
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!
September 25, 2025 at 6:42 AM
@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!
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!
Apply here: www.wur.nl/en/vacancy/p...
Please share!
www.wur.nl
September 8, 2025 at 10:09 AM
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!
Reposted by Mitja M. Zdouc
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!
Apply here: www.wur.nl/en/vacancy/p...
Please share!
www.wur.nl
September 8, 2025 at 9:07 AM
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!
Apply here: www.wur.nl/en/vacancy/p...
Please share!
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)
August 21, 2025 at 10:52 AM
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)
Great to see it out @georgelund.bsky.social! Congrats!
🚨 New preprint!
We've developed a bioassay-guided genome mining approach to identify bacterial secondary metabolites that inhibit Zymoseptoria tritici — a major fungal pathogen of wheat.
Available now on bioRxiv: doi.org/10.1101/2025...
We've developed a bioassay-guided genome mining approach to identify bacterial secondary metabolites that inhibit Zymoseptoria tritici — a major fungal pathogen of wheat.
Available now on bioRxiv: doi.org/10.1101/2025...
Development of a bioassay guided genome mining approach for antifungal natural product discovery from pseudomonads
Zymoseptoria tritici causes Septoria Leaf Blotch disease of wheat and has evolved to overcome most chemical and genetic control methods. As such, new tools are required for future disease control.
We...
doi.org
June 4, 2025 at 4:46 AM
Great to see it out @georgelund.bsky.social! Congrats!
Reposted by Mitja M. Zdouc
We have an opening for a 4-year postdoc position to study the #rhizosphere #microbiome in @utrechtuniversity.bsky.social @w-u-r.bsky.social, joint project with @marnixmedema.bsky.social in the context of MiCRop. Please tag/forward this to potential candidates and/or repost: www.uu.nl/en/organisat...
Bioinformatics Postdoc at UU/WUR: Map Metabolic Interactions in the Rhizosphere
Contribute to plant health and our understanding of the metabolic interactions between microbes and plants in the rhizosphere by computational modelling!
www.uu.nl
December 4, 2024 at 4:09 PM
We have an opening for a 4-year postdoc position to study the #rhizosphere #microbiome in @utrechtuniversity.bsky.social @w-u-r.bsky.social, joint project with @marnixmedema.bsky.social in the context of MiCRop. Please tag/forward this to potential candidates and/or repost: www.uu.nl/en/organisat...
Are you working on natural products? We’ve just released version 4.0 of the MIBiG data standard and repository! It now includes 3059 biosynthetic gene clusters, thanks to the combined efforts of 288 expert contributors. A thread: (1/8) academic.oup.com/nar/advance-...
MIBiG 4.0: advancing biosynthetic gene cluster curation through global collaboration
Abstract. Specialized or secondary metabolites are small molecules of biological origin, often showing potent biological activities with applications in ag
academic.oup.com
December 10, 2024 at 8:05 AM
Are you working on natural products? We’ve just released version 4.0 of the MIBiG data standard and repository! It now includes 3059 biosynthetic gene clusters, thanks to the combined efforts of 288 expert contributors. A thread: (1/8) academic.oup.com/nar/advance-...