Jonathan Parra

The rise of ‘nightmare bacteria’: antimicrobial resistance in six charts Data reveal how the global challenge to reduce deaths and infections from drug-resistant bacteria is not going according to plan.

Antimicrobial resistance is projected to cause 39 million deaths worldwide over the next 25 years

go.nature.com/42x5KHD

Discovery and Biosynthesis of Cinnamoyl-Containing Pepticinnamins Q–V Produced by the Marine-Derived Streptomyces sp. SCSIO 68065 Guided by comprehensive bioinformatic analysis and global molecular networking, four previously undescribed peptidic natural products, pepticinnamins Q–T (1–4), along with two known analogues (5, 6), ...

Discovery and Biosynthesis of Cinnamoyl-Containing Pepticinnamins Q–V Produced by the Marine-Derived Streptomyces sp. SCSIO 68065 | Journal of Natural Products pubs.acs.org/doi/full/10....

Come and work with me and @ariannebabina.bsky.social on #Streptomyces evolution and antibiotic production

Origins of a tangled bank: Adaptation and evolution in antibiotic-producing Streptomyces

www.gla.ac.uk/postgraduate...

please repost

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...

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...

Trends in metabolite discovery from Actinomycetes Covering: 2013 to 2023 In this review, we analyzed the scientific literature of the period 2013–2023 that reported novel specialized metabolites from the Actinomycetes, one of the most prolific…

Be sure to read this review, part of our Industrial Perspective themed collection, by Stefano Donadio & co. from NAICONS Srl discussing the trends in metabolite discovery from Actinomycetes #secmet #natprod

Find it in full below👇

Multi-omics analysis reveals important role for microbial-derived metabolites from Botryllus schlosseri in metal interactions | mSystems Given the importance of marine invertebrates and their microbial communities in marine ecosystems, we sought to characterize the largely unknown microbial associates, metal sequestration, and metabolite production of the marine colonial tunicate, Botryllus schlosseri, a model organism for cellular and developmental studies. Using an integrated multidisciplinary approach, we identified significant correlations between metals, metabolites, and bacterial taxa. B. schlosseri tissue was highly enriched in metals compared to seawater, and B. schlosseri microbiome beta-diversity was significantly different from seawater. We also introduced the concept of the pan-metabolome to classify metabolites based on their presence or absence across complex samples and found microbial metabolites in both the core and flexible metabolome. These findings offer insights into B. schlosseri’s biological and chemical interactions with microorganisms and their environment, bridging the knowledge gap of host-microbiome-environment interactions and establishing a foundation for continuing research on the ecological effects of trace metals in these biological systems.

Congrats to Dulce Guillén Matus for her newest manuscript out today! A collaborative manuscript on the microbes, metals, and metabolites of Botryllus schlosseri, a marine tunicate! doi.org/10.1128/msys...

Natural product-derived compounds in clinical trials and drug approvals Covering: January 2014–June 2025. Previous review: Natural Product Reports, 2014, 31, 1612Natural products (NPs) have long been foundational in medicine, from ancient herbal remedies to the discovery ...

Want to know what natural products are in clinical trials? Read this review! Great job from Mark Butler, Rob Capon, Mark Blaskovich! pubs.rsc.org/en/content/a...

#naturalproducts #antibiotic #amr #drugdiscovery #drug

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)

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...

woolly mammoths

The world desperately needs new antibiotics. Scientists are using AI to accelerate the search, transforming how—and where—we look for compounds to defeat drug-resistant bacteria.

Read the article to learn how AI is revolutionizing antibiotic discovery: asm.org/articles/202...

functional antibiotic resistance genes were circulating in clinically relevant isolates before the age of antibiotics, but human usage is associated with increasing both their overall prevalence and mobility.

Assessing the effect of temperature on Rhodococcus metabolite production Rare actinomycetes are increasingly recognised as a valuable yet underexplored source of bioactive compounds with significant biomedical potential. While it is well established that bacteria have evol...

New paper alert. Insight into metabolic shifts in response to temperature in marine strains of Rhodococcus. Implications for mining the biochemistry of rare Actinomycetes. @microbiologysociety.org @kateduncan.bsky.social www.microbiologyresearch.org/content/jour...

An Assessment of Chemical Diversity in Microbial Natural Products Natural products continue to play important roles in biomedical, agricultural and ecological science. Yet despite ongoing advances in “omics” technologies, including genomics, transcriptomics, phenomi...

An Assessment of Chemical Diversity in Microbial Natural Products | ACS Central Science pubs.acs.org/doi/full/10....

Thanks Pieter, I'm glad you found it interesting. Nothing would have been possible without GNPS. Thank you for helping make science more accessible for everyone.

Awesome to see Duncan lab alumni Dr Jonathan Parra @jonathanparra.bsky.social present the work from his group at #ISBA2035 in the Netherlands ‘A beach microbiome: on the possible ecological role of actinomycetes in a turtle nesting area’ 🐢 🇨🇷 #puravida #acinomycetes #specialisedmetabolites

On the left, a picture of a Petri dish showing an amycalotopsis from which comes in the center, a cartoon dragon and under the dragon the molecules called Dracomycins, which are drawn in the shape of the dragon. On the right a petri dish showing a cartoon of zones of inhibition.

Dracomicins, Hybrid Oligosaccharide–Nonribosomal Peptide Antibiotics from Amycolatopsis Species

pubs.acs.org/doi/10.1021/...

A widespread metabolic gene cluster family in metazoans - Nature Chemical Biology Grayson et al. report the genomic discovery and biochemical characterization of a widely distributed gene cluster family for briarane diterpenoid biosynthesis in metazoans. This study expands our unde...

A new paper reports the genomic discovery and biochemical characterization of a widely distributed gene cluster family for briarane diterpenoid biosynthesis in metazoans

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

Ultra-deep long-read metagenomics captures diverse taxonomic and biosynthetic potential of soil microbes Background Soil ecosystems have long been recognized as hotspots of microbial diversity, but most estimates of their complexity remain speculative, relying on limited data and extrapolation from shall...

New preprint: we sequenced one soil sample with ultra-deep hybrid metagenomics and found…
→ 800+ MAGs
→ 11,000+ BGCs
→ and still nowhere near saturation.
Soil is wild.
Preprint here: www.biorxiv.org/content/10.1...
#microbiome #metagenomics #BGCs #naturalproducts #secmet

enviromicro-journals.onlinelibrary.wiley.com/share/G3MHSV...

This paper represents a great effort by @roman-bushuiev.bsky.social and his brother @anton-bushuiev.bsky.social. The DreaMS foundation model for mass spectra of small molecules now opens lots of avenues for possible downstream applications. It might be a game changer for computational metabolomics.

#ms2query #antismash #metabolomics #compmetabolomics #prioritization… | Justin J.J. van der Hooft 🚨 Preprint (update) alert 🚨 --> Prioritizing Metabolite Features with FERMO Very proud of Mitja Zdouc, PhD, Hannah Augustijn 😊👏, and all colleagues and collaborators involved: the FERMO preprint...

#FERMO Prioritization of metabolite signals and metabolomics samples by streamlined data integration! 😎
#metabolomics #CompMetabolomics
www.linkedin.com/posts/jjjvan...

Super happy to see our work on lydiamycin biosynthesis, structure and function published in @pnas.org 😀
www.pnas.org/doi/10.1073/...

The work is described in the thread below, where we use BGC info to guide the discovery of multiple key features of this antibiotic.
@johninnescentre.bsky.social

AutoMLST2: a web server for phylogeny and microbial taxonomy Abstract. Accurate and accessible phylogenetic analysis is essential for understanding microbial taxonomy and evolution, which are integral to microbiology

Happy to announce that our „newest old tool“ autoMLST2.0 is out and published. You need an accurate and easy to use tool to build #phylogenetictrees from #bacterialgenomes: academic.oup.com/nar/advance-...

I am thrilled to share after years of work/procrastination that the MassQL manuscript is finally published in @natmethods.nature.com - "A universal language for finding mass spectrometry data patterns". This was an team effort from all co-authors that helped shape MassQL and how it could be used.

Peptide surfactants with post-translational C-methylations that promote bacterial development - Nature Chemical Biology Soil-dwelling Actinomyces bacteria have been found to employ an iterative B12-dependent radical S-adenosylmethionine metalloenzyme to synthesize hypermethylated ribosomal peptides. These amphiphilic p...

Soil-dwelling Actinomyces bacteria have been found to synthesize hypermethylated ribosomal peptides, which serve as surface-active agents and promote the growth of aerial, reproductive structures

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

A broad-spectrum lasso peptide antibiotic targeting the bacterial ribosome Nature - A new lasso peptide antibiotic exhibits broad-spectrum activity against Gram-negative and Gram-positive bacteria by interfering with bacterial protein synthesis, is unaffected by common...

The latest discovery from the lab and great colleagues at McMaster and U Illinois, Chicago. Lariocidin, a new lasso peptide antibiotic that inhibits the ribosome. rdcu.be/efdha

Yesterday we celebrated the 1st Costa Rican Symposium on Metabolomics. Happy to have been part of the event and see the growth of this field in my country.

Canumycins A–E, Macrocyclic Napyradiomycins from a Marine-Derived Streptomyces canus Five new macrocyclic napyradiomycins with different types of scaffolds were isolated from marine-derived Streptomyces canus SJ-019. Compounds 1 and 2 are uniquely typified by a spirocyclic core, while 1, 2 and 4 also contain a unique macrolide structure not known in any other napyradiomycins. Compound 3 is composed of a dearomatized napyradiomycin core and an intramolecular double-arch bridge system. Compound 4 displays potent inhibition of Staphylococcus aureus, while C-type napyradiomycin 5 shows notable anti-inflammatory effect.

Canumycins A–E, Macrocyclic Napyradiomycins from a Marine-Derived Streptomyces canus | Organic Letters pubs.acs.org/doi/full/10....

La próxima semana celebraremos el I Simposio Costarricense en Metabolómica. Super emocionado de ser parte de este evento.
Aún quedan algunos espacios disponibles!

Context matters: assessing the impacts of genomic background and ecology on microbial biosynthetic gene cluster evolution | mSystems Microbial secondary metabolites are compounds produced by bacteria and fungi that are not required for their replication and unconditional survival (1, 2). While they are thus not expected to be unive...

Our minireview on BGC evolution being shaped by genomic & ecological context is now live on mSystems:

journals.asm.org/doi/10.1128/...

#secmet #MEvoSky