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-...

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

academic.oup.com

Interested in engineering streptomycetes? Struggling with existing genome engineering tools? Then check out our newest paper on CASCADE-Cas3 based genome engineering in streptomycetes! Some highlights below:

CASCADE-Cas3 enables highly efficient genome engineering in Streptomyces species

Abstract. Type I clustered regularly interspaced short palindromic repeat (CRISPR) systems are widespread in bacteria and archaea. Compared to more widely

academic.oup.com

We are excited to see our review published! In it, we explore the diversity of enzymatic strategies for installing aromatic side chain cross-links in RiPPs. If you like interesting chemistry and new enzyme reactions, be sure to check it out!

Nature Chemical Biology@natchembio.nature.com · 2y ago

A Review from Sanath Kandy, Michael Pasquale, and Jonathan Chekan highlights newly discovered enzymes responsible for aromatic side-chain crosslinking in ribosomally synthesized and post-translationally modified peptides (RiPPs) www.nature.com/articles/s41...

~5y ago, Barbara, Serina, @marnixmedema.bsky.social & I teamed up to make a better NRPS A-domain specificity predictor. The Challis group & others joined along the way to add some very cool insights. Very proud of this work. Check it out now on biorxiv! doi.org/10.1101/2025...

PARAS: high-accuracy machine-learning of substrate specificities in nonribosomal peptide synthetases

Nonribosomal peptides are chemically and functionally diverse natural products with important applications in medicine and agriculture. Bacterial and fungal genomes contain thousands of nonribosomal p...

doi.org

Just in time for the holidays Convergent Evolution of the Antimycobacterial Lasso Peptide Triculamin www.biorxiv.org/content/10.1... @amerrild.bsky.social @tizianasvenningsen.bsky.social @thomastorring.bsky.social

Convergent Evolution of the Antimycobacterial Lasso Peptide Triculamin

Triculamin is a ribosomally synthesized and post-translationally modified peptide (RiPP) lasso peptide with potent antimycobacterial activity, produced by an unusual, non-canonical biosynthetic gene c...

biorxiv.org

Interesting tool alert. The thing that makes this look promising is a way to "plasmidify" biosynthetic gene clusters in their native producers. Could simplify refactoring and expression in chassis strains. #secmet www.science.org/doi/10.1126/...

Autologous DNA mobilization and multiplication expedite natural products discovery from bacteria

The transmission of antibiotic-resistance genes, comprising mobilization and relocation events, orchestrates the dissemination of antimicrobial resistance. Inspired by this evolutionarily successful p...

science.org

A Christmas present to all of the lasso peptide connoisseurs out there. The next chapter in our work is on triculamin is ready on bioRxiv. Great work by two incredibly talented graduate students @amerrild.bsky.social and @tizianasvenningsen.bsky.social. www.biorxiv.org/content/10.1...

Convergent Evolution of the Antimycobacterial Lasso Peptide Triculamin

Triculamin is a ribosomally synthesized and post-translationally modified peptide (RiPP) lasso peptide with potent antimycobacterial activity, produced by an unusual, non-canonical biosynthetic gene c...

biorxiv.org

Adam Rivers (USDA-ARS) and I are hiring a joint postdoc to on a microfluidics and sequencing based project to better understand synthetic and natural microbiome community dynamics and generate data to build AI/ML models to infer interspp. interactions. Hit me up if interested!

Are you working on natural products? We’ve just released version 4.0 of the MIBiG data standard and repository! It now includes 3059 biosynthetic gene clusters, thanks to the combined efforts of 288 expert contributors. A thread: (1/8) academic.oup.com/nar/advance-...

MIBiG 4.0: advancing biosynthetic gene cluster curation through global collaboration

Abstract. Specialized or secondary metabolites are small molecules of biological origin, often showing potent biological activities with applications in ag

academic.oup.com

Early morning and on my way to Copenhagen for the 2024 Congress in the Danish Microbiological Society #DMS2024. Looking forward to seeing friends - old and new.

Hey Natural Products folks! Do you have a favourite ontology covering natural product bioactivities? I'm trying to make MIBiG a bit more systematic for the next release and would like to avoid creating a separate ontology if at all possible. #secmet #microsky

For teaching purposes, I am looking for culture collection strains that consistently produce a known antibiotic like vancomycin , erythromycin, daptomycin or similar. Any suggestions? I’d prefer NRRL or DSMZ

#secmet folks : a teach-in in honor of Chris Walsh. All students and post-docs encouraged to attend. This is an outstanding speaker list inspired a great scientist & teacher.

Now releasing into your podcast feeds: JGI's Natural Prodcast talks to Alison Narayan (UMich) about biocatalysis and candy corn! Notes and transcripts (and in-browser audio) at naturalprodcast.com 🧪🧬🖥️ #chemsky

A good book, a cup of coffee, and PJ Harvey. This morning is off to a start

Looking forward to reading this one

Dr Katherine Duncan@kateduncan.bsky.social · 3y ago

Our review - Antibiotics from rare actinomycetes, beyond the genus Streptomyces - is now online Thanks to coauthors @jonathanparra.bsky.social @ainsleybeaton1 @ryanfseipke @barriewilksjic @matthutchings.bsky.social and editors Toni Gabaldón & Luiz Carvalho for the invitation

On the train to Copenhagen for the iimena symposium. Looking very much forward to two days of #naturalproducts

Come work with us!! Lecturer / Senior Lecturer in Antimicrobial Drug Discovery at Newcastle University @nubiosciences! Please RT #AMR #DrugDiscovery #NaturalProducts #Metabolomics #Microbiology www.jobs.ac.uk/job/DCX827/l...

Lecturer/ Senior Lecturer in Antimicrobial Drug Discovery at Newcastle University

Recruiting now: Lecturer/ Senior Lecturer in Antimicrobial Drug Discovery on jobs.ac.uk. Click for details and explore more academic job opportunities on the top job board

jobs.ac.uk