Jonathan Parra

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...

Bacterial enzymes help reveal natural product stereochemistry The peptidases can break bonds between specific <small>D</small>- and <small>L</small>-amino acids, filling a gap in the toolbox for natural products characterization

Newly discovered enzymes that are vital for bacterial defenses can also help chemists characterize the stereochemistry in natural products. cen.acs.org/biological-c... #chemsky 🧪

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...

Revitalizing actinobacteria research: an urgent response to the antimicrobial resistance crisis - Natural Products and Bioprospecting Abstract The crisis of antimicrobial resistance (AMR) is escalating while the antibiotic pipeline remains stagnant. Our bibliometric analysis of eight decades of literature reveals a critical imbalanc...

Research into filamentous actinomycetes, the antibiotic producers, is in steep decline. Loads of natural products chemistry research worldwide but not much aimed at understanding their biology and ecology. The latter is key to unlocking their specialised metabolism

link.springer.com/article/10.1...

I am super excited that our paper on inter-laboratory comparability of non-targeted LC–MS/MS analysis of dissolved organic matter was just published in ES&T.

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

Biosynthetic gene clusters everywhere, but the environment selects https://www.biorxiv.org/content/10.64898/2026.01.28.702283v1

Fermentation conditions outweigh phylogeny in shaping the metabolome of novel Micromonospora strains: an integrated genomics-metabolomics analysis | Applied and Environmental Microbiology Our study provides a comprehensive genomic and metabolomic elucidation of the significant biosynthetic potential within the genus Micromonospora. It reveals a core biosynthetic capacity for terpenes a...

Fermentation conditions outweigh phylogeny in shaping the metabolome of novel Micromonospora strains: an integrated genomics-metabolomics analysis | Applied and Environmental Microbiology journals.asm.org/doi/10.1128/...

Good to see this out - new CRISPRi work from the
@ryanfseipke.bsky.social lab/ #microsky #streptomyces

A platform for CRISPRi-seq in Streptomyces albidoflavus

journals.asm.org/doi/pdf/10.1...

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 ...

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...

The Pseudonocardia ecology never disappoints. Wonderful work.

Salinirifamycins A–E: Rifamycin S Derivatives from the Brazilian Marine Actinomycete Salinispora arenicola Five new rifamycin derivatives, named salinirifamycins A–E (1–5), were isolated from a Brazilian marine Salinispora arenicola (BRA-213) strain extract. The structures of the new rifamycins were elucid...

Salinirifamycins A–E: Rifamycin S Derivatives from the Brazilian Marine Actinomycete Salinispora arenicola | Journal of Natural Products pubs.acs.org/doi/full/10....

Big congratulations to my former PhD student, Max Chavarría, on his amazing career trajectory after returning to Costa Rica—now fittingly recognized with the country’s most prestigious National Science Award. A well-deserved honor & a real pleasure to see his work acknowledged by his own compatriots

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....

MtrAB activates ectoine production and triggers sporulation in response to osmotic stress in Streptomyces venezuelae The MtrAB two-component system is a master regulator of antibiotic biosynthesis in Streptomyces species. MtrA is also required for sporulation under certain growth conditions, which means that on some...

New preprint. Work led by @ainsley-beaton.bsky.social & Rebecca Devine.

They show the highly conserved Streptomyces MtrAB two component system activates ectoine production and triggers sporulation in response to osmotic stress in Streptomyces venezuelae

www.biorxiv.org/content/10.6...

Very happy to see this remarkable work published. Led by @tommclean.bsky.social and @ainsley-beaton.bsky.social. We show how Streptomyces bacteria sense & respond to misfolded secreted proteins. A great collaboration with @barriewilks.bsky.social

#microsky

1/2

journals.asm.org/doi/epub/10....

Taxonomic and biosynthetic diversity of the marine actinomycete Salinispora across spatial scales | Applied and Environmental Microbiology The marine actinomycete genus Salinispora has become a model organism for natural product discovery and to address actinomycete diversity and distributions in marine systems. While biogeographic patterns have been reported at global scales, contrasts have yet to be made with the species diversity that can be recovered from a single location. Here we sequenced the genomes of 96 S. arenicola strains cultured from marine sediments collected within a 1 m2 plot and compared the diversity detected to public genomes obtained from global collection sites. The results provide evidence of geographic isolation among S. arenicola populations and biosynthetic genes that are mobilized across population boundaries. Multi-omic analyses linked compounds to their respective biosynthetic genes and revealed compounds not previously reported from the genus. This study adds to our growing understanding of Salinispora diversity and biosynthetic potential.

Taxonomic and biosynthetic diversity of the marine actinomycete Salinispora across spatial scales | Applied and Environmental Microbiology journals.asm.org/doi/full/10....

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/...

The undiscovered natural product potential of Actinomycetes The Journal of Antibiotics - The undiscovered natural product potential of Actinomycetes

Recommended reading for those of us who study actinomycetes using untargeted metabolomics. Incredible work by @amcaraballor.bsky.social, @pieterdorrestein.bsky.social, and collaborators. rdcu.be/eSRxT

Can A Microbe Conservation Movement Take Off? Microbes make up about 99% of all species, but they’re not part of any global conservation plans. One group is trying to change that.

Deeply care about #conservation?

Then listen to @gilbertjacka.bsky.social from @scrippsocean.bsky.social discuss the importance of microbial conservation as the foundation for all other conservation (including us macrobes).

www.sciencefriday.com/segments/mic...

Top: (Top row) Sensitivity of S. coelicolor mutants to GlcNAc. Spores (5 × 105 CFU) of S. coelicolor M145 and its mutant derivatives ∆nagB, SMA11, ∆nagB∆nagS, ∆nagB∆nagSC (∆nagB∆nagS expressing nagS) and ∆nagB∆nagSE (∆nagB∆nagS with empty plasmid pSET152) were streaked on MM agar plates with 1% mannitol (Mann) and 1% mannitol plus 10 mM GlcNAc (GlcNAc). (Bottom row) NagS and its role in GlcNAc sensing. Spores of M145 and ∆nagS were plated on MM and R5 with 0, 0.001, 0.01, 0.1, 1, 5, 10, 20, 50, 100, 150, and 200 mM GlcNAc. Note that nagS mutants hardly respond to GlcNAc. Bottom: Model for the metabolic control of development by GlcNAc and NagS. During late vegetative growth of streptomycetes, the old vegetative or substrate hyphae are degraded in a process of programmed cell death (PCD), to produce the nutrients required to build the aerial mycelium (see mycelial drawings on the right). Mycelial lysis results in breakdown of the cell-wall, leading to the accumulation of GlcNAc-6P, which is a major nutritional signal for the onset of development and antibiotic production. NagS converts GlcNAc-6P into 6P-chromogen I (denoted as X-Ac-6P), which in turn is deacetylated by NagA into a toxic metabolite (denoted as X-6P) that resembles ribose. The toxic metabolite promotes cell lysis, thus releasing more GlcNAc-6P that serves as substrate for NagS and NagA. A salvage pathway then switches off the toxic pathway again. For this, GlcNAc-6P is converted by NagA and NagB into Fructose-6P (Fru-6P), which enters the pentose phosphate pathway (PPP), thereby producing 6-phosphogluconate (6-PG), a metabolic inhibitor of NagS. Thus, production of toxic metabolites ceases and the transition to aerial growth can be initiated. Arrows with round ends represent inhibition, dashed arrow shows proposed activity.

GlcNAc build-up acts as a key metabolic signal in #Streptomyces, but how does it triggers developmental responses? @gillesvanwezel.bsky.social &co show that the enzyme NagS dehydrates GlcNAc-6P into a reactive intermediate, triggering a toxicity-based checkpoint @plosbiology.org 🧪 plos.io/44pE08I

Streptomyces formicae was isolated from Tetraponera penzigi plant-ants and has bioactivity against Gram-positive pathogens due to the production of formicamycins.

Read the latest Microbe Profile on Streptomyces formicae KY5: an ANT-ibiotic factory. Published Open Access and fee-free in Microbiology using a Publish and Read agreement: doi.org/10.1099/mic.... #MicrobioJ #PublishAndRead

Discovery of Spiroketal Acids and Antarmycin Analogues from Deep-Sea Derived Pseudonocardia antarctica and Its ΔantB3 Mutant Strain This study reports the discovery of eight new polyketide natural products from the deep-sea actinomycete Pseudonocardia antarctica SCSIO 07407 and its ΔantB3 mutant strain. Through OSMAC (One Strain M...

Discovery of Spiroketal Acids and Antarmycin Analogues from Deep-Sea Derived Pseudonocardia antarctica and Its ΔantB3 Mutant Strain | Journal of Natural Products pubs.acs.org/doi/full/10....

Molecules to medicine: advances in metabolomics for natural product drug discovery Recent advances in metabolomics are accelerating natural product (NP) drug discovery. NPs possess diverse biological relevance and comprise a signific…

Molecules to medicine: advances in metabolomics for natural product drug discovery by Victoria Deleray,
Pieter C Dorrestein & Nicole E Avalon
#naturalproducts #secmet #metabolomics
www.sciencedirect.com/science/arti...

Applied Molecular Microbiology | John Innes Centre John Innes/Rudjer Bošković – Summer Schools in Applied Molecular Microbiology Applications are invited for a summer school on Microbial Specialised Metabolites: Discovery…

EVENT - Apply today for the John Innes/Rudjer Bošković: Applied #Molecular #Microbiology Summer School (Microbial Specialised Metabolites: Discovery, Biosynthesis and Function)

🗓️ 12 - 20 Sept 2026

📍Inter-University Centre, Dubrovnik, Croatia

Deadline: 23 Jan 2026

www.jic.ac.uk/training-car...

Genome-Mining Based Discovery of Pyrrolomycin K and L from the Termite-Associated Micromonospora sp. RB23 Natural products derived from symbiotic microbes remain a rich source of structurally diverse and bioactive molecules. In this study, we report de novo genome sequencing of the termite-associated iso...

Genome-Mining Based Discovery of Pyrrolomycin K and L from the Termite-Associated Micromonospora sp. RB23 | Journal of Natural Products pubs.acs.org/doi/full/10....

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.

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

The proper way to close a scientific event in Colombia

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.

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.

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

Night view of Belfast City Hall illuminated with colourful lights, promoting abstract submission closing for Annual Conference 2026 at ICC Belfast from April 13-16.

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