COMMBAT: a web platform for exploring expression control of biosynthetic gene clusters @narjournal.bsky.social from @sebarigali.bsky.social With @gillesvanwezel.bsky.social @marnixmedema.bsky.social academic.oup.com/nar/advance-...

COMMBAT: a web platform for exploring expression control of biosynthetic gene clusters

Abstract. Bacterial genomes contain thousands of biosynthetic gene clusters (BGCs) responsible for the production of structurally diverse natural products

academic.oup.com

Excited to announce our new paper in Nature Microbiology describing diphtheria toxin homologues in Streptomyces called Streptomyces antiquus insecticidal proteins (SAIP), stemming from a long term collaboration with Ying Xu, Min Dong, Cameron Currie, and many others. www.nature.com/articles/s41...

Streptomyces produce a diphtheria toxin-like exotoxin that targets insects - Nature Microbiology

Bioinformatic, structural and functional analyses characterize Streptomyces antiquus insecticidal protein (SAIP) as a diphtheria toxin homologue that is lethal to insect cells and targets the Flower p...

nature.com

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...

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...

link.springer.com

On International Day of Women and Girls in Science 🔬👩‍🔬 We’re launching the Women Microbiologists Network: a member-led networking and discussions event for women in microbiology by Dr. Enas Newire. Read the news story and join: 🔗 https://microb.io/4ax5M5I

Does anyone have experience with counter-selectable markers for Gram-negative bacteria besides sacB? It's been working poorly in our hands.

My lab has published our first paper! We previously showed that Rothia are associated with healthy nasal microbiomes and inhibit the pathobiont Moraxella catarrhalis. We now describe the novel species Rothia similimucilaginosa. Check it out here: www.microbiologyresearch.org/content/jour...

Rothia similimucilaginosa sp. nov., isolated from the human nasal cavity

Four strains of a Gram-stain-positive, coccoid, catalase-positive, non-motile bacterium were recovered from nasal lavage samples collected from children in Wisconsin during the Spring of 2008. These s...

microbiologyresearch.org

I’m excited to share the first paper from my lab that was led largely by undergraduate students at University of Wisconsin and Washington College! #secmet #natprod www.frontiersin.org/journals/mic...

Semester ended with two manuscripts accepted after over a year each in review! Happy Holidays all!

#secmet

Fusion Conferences@fusionconf.bsky.social · 8mo ago

🚨SAVE THE DATE! 5th Synthetic Biology of Natural Products Conference 📅Date: 01 - 04 November 2026 🌏Location: Playa del Carmen, Mexico 📢Early Bird & Talk Submission: 04 May 2026 Don't miss out, Register now ➡️https://bit.ly/4s4F3VU #SBNP #FusionGenomics #FusionMolBio #FusionBioChem

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

The first paper from PhD student Niladri Bhowmik is out today as a PLOS Pathogens Pearl: Achromobacter spp.: Emerging pathogens in the cystic fibrosis lung. Congrats Niladri! journals.plos.org/plospathogen...

Achromobacter spp.: Emerging pathogens in the cystic fibrosis lung

journals.plos.org

Recorded #MattersMicrobial Episode 88 with Dr. Reed Stubbendieck from Oklahoma State today. Great conversation about how microbes converse with one another during sickness and health. Fascinating! @bactereedia.bsky.social

We have been dealing with high background using erythromycin selection for multiple E. coli strains in my lab. We've tried multiple vendors and lots, but the problem persists. Has anyone else had this problem before? Any ideas?

#NewPI life

In biology, I keep thinking of the bacterial strains, yeast strains, plasmids, mouse lines, worm mutants etc etc etc that will be lost to science FOREVER because the freezers and animal facilities won't be maintained Generations of work will be lost in essentially an instant

David Ho@davidho.bsky.social · last yr.

People might think that whatever destruction is done to science in the US, we can undo in 4 years with a Democratic president and Congress. The problem is that many areas require specialized knowledge and skills built up over years, and once that's lost, it's hard to get back.

My lab’s first preprint! We used functional metagenomics to identify phage defenses in human and soil microbiomes. We scaled these selections while maintaining accuracy, enabling us to examine 9 habitats for defense elements against 7 phages. www.biorxiv.org/content/10.1... 1/10

"downsizes" is a weak way of saying "forced to cancel dozens of programs, which jeopardizes future STEM careers of talented undergrads" @science.org www.science.org/content/arti...

NSF downsizes summer research program for undergraduates

Many participants are from groups underrepresented in science

science.org

Some of my first year grad students in my class are asking for books to read that will get them thinking about what questions to ask and how to know what they should ask. I have a couple of recs but wondering if anyone can help. What inspired you??

GATOR-GC preprint is live! If you haven't already, check out our new tool for targeted gene cluster mining. @jcedielbecerra.bsky.social doi.org/10.1101/2025...

Targeted genome mining with GATOR-GC maps the evolutionary landscape of biosynthetic diversity

Gene clusters, groups of physically adjacent genes that work collectively, are pivotal to bacterial fitness and valuable in biotechnology and medicine. While various genome mining tools can identify a...

doi.org

bioRxivpreprint@biorxivpreprint.bsky.social · last yr.

Targeted genome mining with GATOR-GC maps the evolutionary landscape of biosynthetic diversity https://www.biorxiv.org/content/10.1101/2025.02.24.639861v1

Our minireview on BGC evolution being shaped by genomic & ecological context is now live on mSystems: journals.asm.org/doi/10.1128/... #secmet #MEvoSky

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...

journals.asm.org

We are crowd sourcing reductions in graduate admissions and hiring freezes across biomedical research and higher ed in response to pauses in NIH funding and EO’s. If you have information if you could add to this spreadsheet, it would be greatly appreciated!: docs.google.com/spreadsheets...

Graduate Reductions Across Biomedical Sciences (2025)

docs.google.com

Just sitting here, trying to write a grant, crying for so many thousands who dedicated their lives to making the world better and safer, just thrown out like trash today.

"Make America Great Again. Make America Healthy Again. These were promises made by candidate Trump in his campaign to be president of the United States of America. What in this campaign platform should have prepared us for a war on discovery?"

Guest column: “The war on discovery” is antithesis of campaign pledge to make America great again - Wisconsin Technology Council

By Jo Handelsman MADISON, Wis. – Make America Great Again. Make America Healthy Again. These were promises made by candidate Trump in his campaign to be president of the United States of America. What...

wisconsintechnologycouncil.com

Somewhere in the U.S., there’s a scientist staring at their NSF/NIH grant application wondering why they bother. This post is for you. Science and society both need you. Hang in there and know there is a whole community supporting you.

All NIH study sections canceled indefinitely. This will halt science and devastate research budgets in universities.

~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

www.biorxiv.org/content/10.1... #secmet 🧪🖥️🧬

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...

biorxiv.org

My current state is exemplifed by the duck of ennui.

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