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Marnix Medema @marnixmedema.bsky.social · 9d

Very important initiative! This could really help facilitate increasing data sharing as well as appropriate attribution of data creation.

Alex Probst @alexjprobst.bsky.social · 11d

New article on equitable reuse of public sequencing data, published in @natmicrobiol.nature.com!
Led by the Data reuse core team @lhug.bsky.social @environmicrobio.bsky.social Cristina Moraru, @geomicrosoares.bsky.social, @folker.bsky.social and with Anke Heyer and The Data Reuse Consotrium!

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Reposted by Marnix Medema

Nadine Ziemert @nadineziemert.bsky.social · 11d

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...

PhyloNaP: a user-friendly database of Phylogeny for Natural Product-producing enzymes

Phylogenetic analysis is widely used to predict enzyme function, yet building annotated and reusable trees is labor-intensive and requires extensive knowledge about the specific enzymes. Existing reso...

www.biorxiv.org

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Marnix Medema @marnixmedema.bsky.social · 11d

Awesome work, @mmzdouc.bsky.social !

Mitja M. Zdouc @mmzdouc.bsky.social · 11d

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/...

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Reposted by Marnix Medema

Mitja M. Zdouc @mmzdouc.bsky.social · 11d

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/...

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Marnix Medema @marnixmedema.bsky.social · 13d

Thanks to Chunxu Song and the CAU for great partnership and collaboration, and Jos Raaijmakers (NIOO-KNAW) and Liesje Mommer (WUR) for their crucial roles in advising the work.

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Marnix Medema @marnixmedema.bsky.social · 13d

Also, catabolic gene cluster absence/presence profiles were shown to be strongly predictive of rhizosphere competence, even more so than a dataset of experimental assays of catabolic potential. 4/4

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Marnix Medema @marnixmedema.bsky.social · 13d

Running rhizoSMASH on a large collection of plant- and soil-associated genomes enabled charting the first map of root-associated catabolic functions across key plant-associated microbial taxa. 3/4

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Marnix Medema @marnixmedema.bsky.social · 13d

Similar as for antiSMASH and later gutSMASH, Yuze curated a set of profile HMMs and detection rules to reliably identify these gene clusters, guided by sequence similarity network analysis to distinguish true positives from false positives accurately. 2/4

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Marnix Medema @marnixmedema.bsky.social · 13d

Congratulations to #YuzeLi and all co-authors with the publication of rhizoSMASH: a new tool to identify catabolic gene clusters involved in the metabolism of plant root exudates, thus driving rhizosphere colonization. 1/4

rdcu.be/eH8tr

Predicting rhizosphere-competence-related catabolic gene clusters in plant-associated bacteria with rhizoSMASH

Nature Communications - Rhizosphere microbiomes are shaped by root exudation of diverse organic compounds. Here, the rhizoSMASH algorithm is introduced, which maps microbial genes involved in their...

rdcu.be

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Reposted by Marnix Medema

Elinne Becket, PhD @bielleogy.bsky.social · 16d

Giving a webinar on #BlueSoup this Friday, in case anyone wants to pop in during their lunch!

A promotional flyer for a webinar in the CSU Bioinformatics Webinar Series. On the left side, it shows the date and time: “26 Sep | 12 PM PST.” It includes instructions to join via Zoom with Meeting ID: 886 2442 3158 and a QR code above. On the right, there is a photo of Dr. Elinne Becket, Associate Professor in the Department of Biological Sciences at California State University San Marcos, sitting outdoors with plants and trees in the background. Below, the title of the talk is displayed: “The Soup that Blue up Twitter.” The description explains that Dr. Becket will discuss the shared curiosity of science, open science, and a story from February 2023 when leftover beef soup prepared by her mom turned bright blue. Scientists and people on Twitter collaborated to investigate, leading to a global effort among microbiologists and chemists. At the bottom, there are links to learn more about upcoming webinars at www.informatics.sdsu.edu and Dr. Becket’s website: https://elinneb.wixsite.com/becketlab

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Marnix Medema @marnixmedema.bsky.social · 16d

Thanks to @jjjvanderhooft.bsky.social for co-supervision and @wildtypemc.bsky.social @johandelsman.bsky.social @zachreitz.bsky.social #ClaraBelzer @YijunZhu for great contributions & collaborations!

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Marnix Medema @marnixmedema.bsky.social · 16d

We think this type of analysis can be used to predict/reveal functions of unknown biosynthetic gene clusters in the future, and understand interactions that mediate microbiome-associated phenotypes.

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Marnix Medema @marnixmedema.bsky.social · 16d

... and expression (anti-)correlations of biosynthetic gene clusters highlight positive and negative responses to antibiotic production (related to stress response, siderophores, redox balance).

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Marnix Medema @marnixmedema.bsky.social · 16d

Coexpression networks of primary metabolic modules highlight both competition and cross-feeding...

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Marnix Medema @marnixmedema.bsky.social · 16d

New preprint out by #RobertKoetsier, the first of his PhD project, on assessing the use of cross-species coexpression analysis to identify primary and secondary metabolic interactions in microbiomes: www.biorxiv.org/content/10.1...

Using cross-species co-expression to predict metabolic interactions in microbiomes

In microbial ecosystems, metabolic interactions are key determinants of species’ relative abundance and activity. Given the immense number of possible interactions in microbial communities, their expe...

www.biorxiv.org

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Reposted by Marnix Medema

Marnix Medema @marnixmedema.bsky.social · Aug 21

Check out the new MITE database! Kudos to @mmzdouc.bsky.social for his leadership in getting this community effort off the ground. Hopefully we can add many more data points with everyone's input!

Mitja M. Zdouc @mmzdouc.bsky.social · Aug 21

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)

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Marnix Medema @marnixmedema.bsky.social · Sep 8

@skepteis.bsky.social @jjjvanderhooft.bsky.social

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Marnix Medema @marnixmedema.bsky.social · Sep 8

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!

www.wur.nl

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Reposted by Marnix Medema

Marnix Medema @marnixmedema.bsky.social · Sep 1

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...

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...

www.biorxiv.org

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Marnix Medema @marnixmedema.bsky.social · Sep 1

All in all, thanks to the engineering efforts of Arjan Draisma, Catarina Loureiro, Nico Louwen, Satria Kautsar, Jorge Navarro and the rest of the author team, and shout-out to the @jgi.doe.gov and @nigelmouncey.bsky.social for a wonderful collaboration.

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Marnix Medema @marnixmedema.bsky.social · Sep 1

At the same time, for mid-size datasets (most frequent use case), BiG-SCAPE v2 approaches the speed of BiG-SLiCE. For larger datasets, BiG-SCAPE has become more resource-efficient, which now allowed us to analyse >250k BGCs (the antiSMASH database) with it in just a few days on a compute server.

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Marnix Medema @marnixmedema.bsky.social · Sep 1

Benchmarking on several different types of ground truth datasets shows the increases in accuracy, with BiG-SLiCE v2 often matching BiG-SCAPE v1 accuracy, and BiG-SCAPE v2 combining its speed increase with a small but notable accuracy gain as well.

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Marnix Medema @marnixmedema.bsky.social · Sep 1

BiG-SCAPE was completely rewritten from scratch over the past few years, and now features new alignment modes, a more prominent query mode (which allows you to search genomes from a single BGC query) and more scalable interactive visualizations and data selection/filtering.

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Marnix Medema @marnixmedema.bsky.social · Sep 1

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...

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...

www.biorxiv.org

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Reposted by Marnix Medema

Mitja M. Zdouc @mmzdouc.bsky.social · Aug 21

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)

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