Reed Stubbendieck

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

Prabhakar Raghavan realized in 2019 if you make search less efficient, then you can serve customers more ads.

That's a gorgeous frog!

Achromobacter spp.: Emerging pathogens in the cystic fibrosis lung

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...

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

Frontiers | Inexpensive Apparatus for High-Quality Imaging of Microbial Growth on Agar Plates The ability to capture images of results or processes is an important tool in the biologist’s tool kit. In microbiology, capturing high-quality images of mic...

We built this in my laboratory: www.frontiersin.org/journals/mic...

Ooof. No thank you!

Yeah. Standard LB. This is looking possible likely based on some preliminary tests we've done.

Thanks! Yeah. Agreed. Both are worth testing. Might be time to dump the competent cells.

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?

A slack message from me saying "... is anyone waiting on something from me? I think I'm caught up again"

#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

Functional Metagenomic Selections for Phage Defense

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

NSF downsizes summer research program for undergraduates Many participants are from groups underrepresented in science

"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...

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...

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

Graduate Reductions Across Biomedical Sciences (2025)

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...

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.

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...

"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?"

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.

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...

~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...

www.biorxiv.org/content/10.1...

#secmet 🧪🖥️🧬

A light up duck sitting on a desk looking over it.

My current state is exemplifed by the duck of ennui.

Congratulations! Protect your time and make others work to be put on your calendar. Make small progress every day on something you enjoy. When juggling multiple things, learn which balls are plastic and which are glass. Make friends with your grants office.

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...

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

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...

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/...

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

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-...