Jonathan Parra
@jonathanparra.bsky.social
Scientist ⚗️🔬. Ocean lover 🌊. Assistant Professor at University of Costa Rica 🌻. Research Associate at CENIBiot 🧬. #NaturalProducts #ChemicalEcology #DrugDiscovery
https://parralab.netlify.app/
https://parralab.netlify.app/
Reposted by Jonathan Parra
By studying the process through which a soil bacterium naturally produces a well-known drug, scientists have discovered a powerful antibiotic that could help to fight drug-resistant infections
go.nature.com/4oyN3wc
go.nature.com/4oyN3wc
Powerful new antibiotic that can kill superbugs discovered in soil bacteria
Nature - Surprise discovery could pave the way for new treatments against drug-resistant infections.
go.nature.com
November 9, 2025 at 3:09 PM
By studying the process through which a soil bacterium naturally produces a well-known drug, scientists have discovered a powerful antibiotic that could help to fight drug-resistant infections
go.nature.com/4oyN3wc
go.nature.com/4oyN3wc
I had a great time at EMIC, sponsored by @asm.org, in Cali, Colombia. Meetings in Latin America have a vibe that's hard to describe. Amazing scientific chats with Cuauhtémoc Licona from UNAM and Pablo Cruz from DTU. Many thanks to Luz González for organizing the event.
November 8, 2025 at 12:53 PM
I had a great time at EMIC, sponsored by @asm.org, in Cali, Colombia. Meetings in Latin America have a vibe that's hard to describe. Amazing scientific chats with Cuauhtémoc Licona from UNAM and Pablo Cruz from DTU. Many thanks to Luz González for organizing the event.
Reposted by Jonathan Parra
Ozempic, MRI machines and flat screen televisions all emerged out of fundamental research decades earlier — the very types of study being slashed by the US government
go.nature.com/47hn0n5
go.nature.com/47hn0n5
7 basic science discoveries that changed the world
Ozempic, MRI machines and flat screen televisions all emerged out of fundamental research decades earlier — the very types of study being slashed by the US government.
go.nature.com
November 1, 2025 at 5:39 PM
Ozempic, MRI machines and flat screen televisions all emerged out of fundamental research decades earlier — the very types of study being slashed by the US government
go.nature.com/47hn0n5
go.nature.com/47hn0n5
Reposted by Jonathan Parra
Work with actinomycetes or mycobacteria? Dedicated symposia shine the spotlight on these remarkable bacteria at #Microbio26 in Belfast. Explore the full variety of sessions and submit your work today.
Abstract submissions close on 11 November: microb.io/AC26Abstracts
Abstract submissions close on 11 November: microb.io/AC26Abstracts
November 2, 2025 at 12:01 PM
Work with actinomycetes or mycobacteria? Dedicated symposia shine the spotlight on these remarkable bacteria at #Microbio26 in Belfast. Explore the full variety of sessions and submit your work today.
Abstract submissions close on 11 November: microb.io/AC26Abstracts
Abstract submissions close on 11 November: microb.io/AC26Abstracts
Reposted by Jonathan Parra
Antimicrobial resistance is projected to cause 39 million deaths worldwide over the next 25 years
go.nature.com/42x5KHD
go.nature.com/42x5KHD
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.
go.nature.com
October 7, 2025 at 4:26 PM
Antimicrobial resistance is projected to cause 39 million deaths worldwide over the next 25 years
go.nature.com/42x5KHD
go.nature.com/42x5KHD
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....
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), ...
pubs.acs.org
October 7, 2025 at 4:41 PM
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....
Reposted by Jonathan Parra
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
Origins of a tangled bank: Adaptation and evolution in antibiotic-producing Streptomyces
www.gla.ac.uk/postgraduate...
please repost
University of Glasgow - Postgraduate study - Centres for Doctoral Training - NorthWest Biosciences - Our Projects - Underpinning Bioscience - Paul A Hoskisson
www.gla.ac.uk
September 30, 2025 at 11:02 AM
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
Origins of a tangled bank: Adaptation and evolution in antibiotic-producing Streptomyces
www.gla.ac.uk/postgraduate...
please repost
Reposted by Jonathan Parra
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...
#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
September 27, 2025 at 9:32 AM
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...
#phylogeny #secmet #bioinformatics
www.biorxiv.org/content/10.1...
Reposted by Jonathan Parra
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👇
Find it in full below👇
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…
pubs.rsc.org
September 26, 2025 at 11:56 AM
Reposted by Jonathan Parra
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...
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.
doi.org
September 15, 2025 at 2:23 PM
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...
Reposted by Jonathan Parra
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
#naturalproducts #antibiotic #amr #drugdiscovery #drug
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 ...
pubs.rsc.org
September 10, 2025 at 3:01 PM
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
#naturalproducts #antibiotic #amr #drugdiscovery #drug
Reposted by Jonathan Parra
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)
Reposted by Jonathan Parra
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
September 1, 2025 at 10:35 PM
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...
Reposted by Jonathan Parra
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...
Read the article to learn how AI is revolutionizing antibiotic discovery: asm.org/articles/202...
September 2, 2025 at 11:36 AM
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...
Read the article to learn how AI is revolutionizing antibiotic discovery: asm.org/articles/202...
Reposted by Jonathan Parra
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.
What was antibiotic resistance like before we ever used antibiotics? How did we change what antibiotic resistance genes looked like over 100 years?
Our paper looking at resistance genes from a century of NCTC historical isolates now out in mGen:
www.microbiologyresearch.org/content/jour...
Our paper looking at resistance genes from a century of NCTC historical isolates now out in mGen:
www.microbiologyresearch.org/content/jour...
Genomic resistance in historical clinical isolates increased in frequency and mobility after the age of antibiotics
Antibiotic resistance is frequently observed shortly after the clinical introduction of an antibiotic. Whether and how frequently that resistance occurred before the introduction is harder to determin...
www.microbiologyresearch.org
September 2, 2025 at 9:28 AM
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.
Reposted by Jonathan Parra
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...
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...
www.microbiologyresearch.org
August 26, 2025 at 4:22 PM
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 | ACS Central Science pubs.acs.org/doi/full/10....
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...
pubs.acs.org
August 18, 2025 at 10:09 PM
An Assessment of Chemical Diversity in Microbial Natural Products | ACS Central Science pubs.acs.org/doi/full/10....
Reposted by Jonathan Parra
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
June 16, 2025 at 12:09 PM
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
Reposted by Jonathan Parra
Dracomicins, Hybrid Oligosaccharide–Nonribosomal Peptide Antibiotics from Amycolatopsis Species
pubs.acs.org/doi/10.1021/...
pubs.acs.org/doi/10.1021/...
June 13, 2025 at 9:40 PM
Dracomicins, Hybrid Oligosaccharide–Nonribosomal Peptide Antibiotics from Amycolatopsis Species
pubs.acs.org/doi/10.1021/...
pubs.acs.org/doi/10.1021/...
Reposted by Jonathan Parra
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...
www.nature.com/articles/s41...
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...
www.nature.com
June 13, 2025 at 7:38 PM
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...
www.nature.com/articles/s41...
Reposted by Jonathan Parra
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
→ 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
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...
www.biorxiv.org
May 30, 2025 at 1:47 PM
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
→ 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
Reposted by Jonathan Parra
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.
Self-supervised learning of molecular representations from millions of tandem mass spectra using DreaMS - @pluskal-lab.org @iocbprague.bsky.social go.nature.com/4k1n5iC
Self-supervised learning of molecular representations from millions of tandem mass spectra using DreaMS - Nature Biotechnology
A transformer model is used to construct the DreaMS Atlas—a molecular network of 201 million MS/MS spectra.
go.nature.com
May 24, 2025 at 8:21 AM
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.
Reposted by Jonathan Parra
#FERMO Prioritization of metabolite signals and metabolomics samples by streamlined data integration! 😎
#metabolomics #CompMetabolomics
www.linkedin.com/posts/jjjvan...
#metabolomics #CompMetabolomics
www.linkedin.com/posts/jjjvan...
#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...
www.linkedin.com
May 20, 2025 at 9:54 AM
#FERMO Prioritization of metabolite signals and metabolomics samples by streamlined data integration! 😎
#metabolomics #CompMetabolomics
www.linkedin.com/posts/jjjvan...
#metabolomics #CompMetabolomics
www.linkedin.com/posts/jjjvan...
Reposted by Jonathan Parra
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
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
May 20, 2025 at 10:40 AM
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
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