Synthetic bacterial community colonizes wheat roots grown in soil and mimics the assembly pattern of a field community in a cultivar dependent manner Abstract. The root microbiome is important for plant development. The impact of the root microbiome is the result of multiple complex interactions among mi

We love a SynCom when they reliably mimic natural microbiomes. New work from @fredebak.bsky.social shows that our SynCom mimics the temporal dynamics of field-grown wheat - but only for the cultivar from which the SynCom was built. Check out the details!
academic.oup.com/ismecommun/a...

Automated genome mining predicts structural diversity and taxonomic distribution of peptide metallophores across bacteria Automated detection of metallophore biosynthesis reveals that metal-chelating non-ribosomal peptides are widespread, chemically diverse, and deeply rooted in bacterial evolution.

Are you interested in how to predict functions of natural product biosynthetic gene clusters (BGCs) and their products? And/or do you love metallophores and would love to identify their producers in microbiomes? Check out @zachreitz.bsky.social 's new paper!
elifesciences.org/articles/109... 1/n

Automated genome mining predicts structural diversity and taxonomic distribution of peptide metallophores across bacteria Automated detection of metallophore biosynthesis reveals that metal-chelating non-ribosomal peptides are widespread, chemically diverse, and deeply rooted in bacterial evolution.

Automated genome mining predicts structural diversity and taxonomic distribution of peptide metallophores across bacteria

@elife.bsky.social by Zachary Reitz and Bita Pourmohsenin et al from @marnixmedema.bsky.social and @nadineziemert.bsky.social

elifesciences.org/articles/109...

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...

Thank you to everyone who attended and participated at day 1 of the PhD Symposium!

Roll on day 2….

#phd #agtech #Agriculture #agriscience

Rothamsted PhD Symposium is officially underway! 🎓
Across the next two days, we’ll be hearing from PhD students sharing their work, ideas, and the research questions they’re tackling across the institute.
It’s a great chance to celebrate students, learn, collaborate 🥼

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!

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...

MSMM26

‼️Call for abstracts is now open — deadline: March 1st‼️

Join us 7–9 June 2026 for the 4th International Conference on Microbial Secondary Metabolites in Microbiomes

Check out the program and the confirmed speakers on the conference website:

www.conferencemanager.dk/microbialsec...

Congratulations to Katerina Velchova for successfully defending her PhD thesis today, with no corrections! 👏 Thank you to examiners Jim Harris (Cranfield Uni) and Ute Voß (University of Nottingham) for the great discussions.

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

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/...

Now out in @asm.org #mSystems! journals.asm.org/doi/10.1128/...
Congratulations to Robert and thanks to all collaborators. See thread below for a summary of the work, exploring the use of cross-species coexpression analyses to predict primary and secondary metabolic interactions in microbiomes.

The pre print of my PhD research is out! 📣 Check it out for some cool results on high-throuhput microbial isolation, #SynComs and #Tree #Microbiome 🌳🧫
doi.org/10.1101/2025...
#PhDone 💯

Large-scale culturing of the tree microbiome enables targeted disease suppression The tree microbiome is essential for host health and pathogen suppression. Synthetic microbial communities (SynComs) are emerging as important tools to understand microbiome dynamics and engineer micr...

🧵 1/ New preprint alert! From the FUTURE OAK project, led by the super talented @alejandra1909.bsky.social

Large-scale culturing of the tree microbiome enables targeted disease suppression

Here's what we found... 👇

www.biorxiv.org/content/10.1...

Figure 2 in Waclawiková and others (2025): "Serotonin metabolism protects P. fluorescens from oxidative stress possibly via upregulation of phenylalanine and tyrosine catabolic pathways. A RNA-seq experimental design. B Heat map of the genes that are significantly regulated (at 10 and 12 h) in the presence of serotonin as compared to the untreated control. Data represent log2(fold change). FDR ≤ 0.05, fold change ≥ 2. GSEA analysis of upregulated genes from stimulation with serotonin (FDR ≤ 0.05, fold change ≥ 2) after 10 h and 12 h. Data show -log2(p value) for specific GO biological pathways (bar graphs on the left); number of genes involved in the regulated pathways (bar graphs in the middle); and, expression patterns of individual genes involved in the regulated pathways (graphs on the right). C Volcano plots of differentially abundant proteins after 12 h (left panel) and 24 h (right panel) of stimulation with serotonin in P. fluorescens. D Overview of phenylalanine, tyrosine and arginine catabolic pathway and its regulation by serotonin on the RNA and protein level"

New publication: #Serotonin modulation of #metabolism and #stress response in Pseudomonas fluorescens, by @gillesvanwezel.bsky.social and others.
doi.org/10.1186/s129...

Home - SEVA plasmids - Standard European Vector Architecture Standard European Vector Architecture 4.0 Welcome to the CNB-hosted database and material repository of standard and modular plasmid vectors for (de/re) constructing complex bacterial phenotypes WHAT…

👩🔬 Want to team up with us to expand the #SEVA collection?
Contribute your own constructs to our open plasmid repository and help make #SynBio more reproducible for everyone.
✨ Check out our contribution guidelines and join the mission!👇👇
seva-plasmids.com

High-resolution profiling of bacterial and fungal communities using pangenome-informed taxon-specific long-read amplicons - Microbiome Background High-throughput sequencing technologies have greatly advanced our understanding of microbiomes, but resolving microbial communities at species and strain levels remains challenging. Results...

Still using 16S/ITS profiling? You might want to reconsider👀

Our new paper presents pangenome-informed amplicons that provide up to 10× higher phylogenetic resolution than full-length ribosomal markers- while remaining cost effective and scalable!
microbiomejournal.biomedcentral.com/articles/10....

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...

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

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...

📣 I’m excited to share two open positions in my lab @leibniz-hki.de. For this interdisciplinary project with @luziagyr.bsky.social, I’m seeking (1) an enthusiastic PhD student interested in fungal natural product research and genetic engineering, as well as (2) a technical assistant 👇🏻

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!

BiG-SCAPE 2.0 and BiG-SLiCE 2.0: scalable, accurate and interactive sequence clustering of metabolic gene clusters Microbial metabolic gene clusters encode the biosynthesis or catabolism of metabolites that facilitate ecological specialization, mediate microbiome interactions and constitute a major source of medic...

Now out as preprint: versions 2.0 of both BiG-SCAPE and BiG-SLiCE have been released! With significant speed and accuracy increases, as well as new interactive functionalities. www.biorxiv.org/content/10.1...

Discovery of a widespread chemical signalling pathway in the Bacteroidota - Nature The N-acyl-cyclolysine system regulates the expression of co-localized operons encoding diverse secreted molecules in Bacteroidota.

www.nature.com/articles/s41...

#microsky

Are you a theoretical biologist that is intererested in the ecology and evolution of metabolic interactions among microorganisms?

Do you like to cooperate with experimentalists?

Do you have a PhD and experience in modelling and statistics?

Then this position might be for you👇:

shorturl.at/iiiOv

Learning from fungicide resistance: Evolutionary insights to guide RNAi-based control of fungal crop pathogens Crop protection against fungal pathogens is essential to prevent crop losses and maintain food security. Current crop protection relies heavily on che…

New paper out now in @britmycolsoc.org.uk Fungal Biology Reviews. Learning from fungicide resistance: Evolutionary insights to guide RNAi-based control of fungal crop pathogens. www.sciencedirect.com/science/arti...

skDER and CiDDER: two scalable approaches for microbial genome dereplication An abundance of microbial genomes have been sequenced in the past two decades. For fundamental comparative genomic investigations, where the goal is to determine the major gain and loss events shaping...

Great to see our manuscript on skDER & CiDDER - programs for selection of representative microbial genomes - now published.

Please give them a try and if you have any feature requests or issues, just let us know.

www.microbiologyresearch.org/content/jour...

github.com/raufs/skDER

Targeting de novo purine biosynthesis for tuberculosis treatment - Nature The validation of inhibitors targeting PurF, a novel drug target for tuberculosis drug discovery, is described.

🎯 New antibiotic target in TB!
👉 Small-molecule inhibitor targeting PurF, the first enzyme in the mycobacterial de novo purine biosynthesis pathway.
👉 Effective vs drug-resistant Mycobacterium tuberculosis in vivo (in mice)
#TBSky #IDSky #MedSky 🧪
@nature.com
www.nature.com/articles/s41...

Proud to share our latest pre-print manuscript entitled 'Downy mildew disease-suppressive soils transmit a protective core microbiome to the phyllosphere' (lnkd.in/dBk28gnT). Super cool to see the final chapter of my PhD at the Plant-Microbe Interactions group of Universiteit Utrecht now online!

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

In the past decade or so, new techniques have enabled a resurgence of antimicrobial discovery. A new golden age of antibiotics may be upon us, though getting a drug candidate into the clinic isn’t so easy: cen.acs.org/pharmaceutic... #chemsky 🧪

Big thanks to the team @Rothamsted, collaborators, and funders @BBSRC as part of the Growing Health Institute Strategic Programme.
Feedback welcome!
#preprint #microbiology #secondarymetabolites #genomemining #plantpathology