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Reed Stubbendieck

@bactereedia.bsky.social
1.4K followers 394 following 51 posts

Microbiologist 🧫 | Asst. Prof. OKState | specialized/secondary metabolism | bacterial interactions | respiratory microbiomes | he/him | posts are my own |

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Reposted by Reed Stubbendieck
Ákos T Kovács @evolvedbiofilm.bsky.social · 11/05/2026
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-...
academic.oup.com
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
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Reed Stubbendieck @bactereedia.bsky.social · 30/04/2026
Thanks! The toxins contain an N-terminal signal peptide. We can do heterologous expression in other Streptomyces and they will secrete the toxin without addition of any other genes.
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Reed Stubbendieck @bactereedia.bsky.social · 30/04/2026
Finally, we show that these toxigenic Streptomyces produce secondary metabolites when they consume insect carcassess. This work is the first demonstration of an exotoxin in Streptomyces and suggests they could be cryptic insect pathogens. If you're interested, please check out our paper!
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Reed Stubbendieck @bactereedia.bsky.social · 30/04/2026
We then show that SAIPs are insecticidal and used CRISPR-Cas9 screening to determine that their receptor is an insect membrane protein called Flower. This protein is localized to neurons, and we find that SAIP binding leads to insect paralysis, immunosuppression, and death.
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Reed Stubbendieck @bactereedia.bsky.social · 30/04/2026
We then demonstrate that SAIPs possess a conserved structure and identical mechanism of action as diphtheria toxin (DT). However, the receptor binding domain does not resemble the corresponding domain in DT.
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Reed Stubbendieck @bactereedia.bsky.social · 30/04/2026
We determined that these toxins evolved more than 100 million years ago in a lineage of Streptomyces and have been maintained through vertical transmission under strong stabilizing selection.
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Reed Stubbendieck @bactereedia.bsky.social · 30/04/2026
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...
nature.com
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...
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Reed Stubbendieck @bactereedia.bsky.social · 11/03/2026
We got power back as I was about to go on a dry ice run! Raised to -65 °C in 3 hours.
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Reed Stubbendieck @bactereedia.bsky.social · 05/03/2026
We have one in my laboratory. It's a recent acquisition, so we're still figuring it out, but happy to help.
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Reposted by Reed Stubbendieck
Matt Hutchings @matthutchings.bsky.social · 16/02/2026
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...
link.springer.com
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...
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Reed Stubbendieck @bactereedia.bsky.social · 12/02/2026
Agreed. Printing PP is a pain, but so worth it for lab stuff. There are also services you can upload an STL to and get a print that might be easier for one off pieces.
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Reposted by Reed Stubbendieck
Microbiology Society @microbiologysociety.org · 11/02/2026
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: 🔗 microb.io/4ax5M5I
Audience attentively listening to speaker at the Women Microbiologist Network from Annual Conference 2025.
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Reed Stubbendieck @bactereedia.bsky.social · 03/02/2026
Would you mind sharing a reference or sequence? Would love to look into this more.
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Reed Stubbendieck @bactereedia.bsky.social · 03/02/2026
Colleague I've talked to says they specifically have the problem using sacB in plasmids with R6K origins. Anyone else experience this?
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Reed Stubbendieck @bactereedia.bsky.social · 03/02/2026
Does anyone have experience with counter-selectable markers for Gram-negative bacteria besides sacB? It's been working poorly in our hands.
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Reed Stubbendieck @bactereedia.bsky.social · 19/01/2026
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...
microbiologyresearch.org
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...
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Reposted by Reed Stubbendieck
Dan May @dansmay.bsky.social · 30/09/2025
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...
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Reed Stubbendieck @bactereedia.bsky.social · 18/12/2025
Semester ended with two manuscripts accepted after over a year each in review! Happy Holidays all!
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Reposted by Reed Stubbendieck
Dan Udwary @danudwary.secondarymetabolism.com · 18/12/2025
#secmet
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Reposted by Reed Stubbendieck
Paul Hoskisson 🧫 🦠🐸 @paulhoskisson.bsky.social · 30/09/2025
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
gla.ac.uk
University of Glasgow - Postgraduate study - Centres for Doctoral Training - NorthWest Biosciences - Our Projects - Underpinning Bioscience - Paul A Hoskisson
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Reed Stubbendieck @bactereedia.bsky.social · 17/09/2025
Prabhakar Raghavan realized in 2019 if you make search less efficient, then you can serve customers more ads.
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Reed Stubbendieck @bactereedia.bsky.social · 24/06/2025
That's a gorgeous frog!
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Reed Stubbendieck @bactereedia.bsky.social · 23/04/2025
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...
journals.plos.org
Achromobacter spp.: Emerging pathogens in the cystic fibrosis lung
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Reposted by Reed Stubbendieck
Mark O. Martin @markowenmartin.bsky.social · 18/04/2025
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
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Reed Stubbendieck @bactereedia.bsky.social · 15/04/2025
We built this in my laboratory: www.frontiersin.org/journals/mic...
frontiersin.org
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...
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Reed Stubbendieck @bactereedia.bsky.social · 29/03/2025
Ooof. No thank you!
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Reed Stubbendieck @bactereedia.bsky.social · 29/03/2025
Yeah. Standard LB. This is looking possible likely based on some preliminary tests we've done.
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Reed Stubbendieck @bactereedia.bsky.social · 27/03/2025
Thanks! Yeah. Agreed. Both are worth testing. Might be time to dump the competent cells.
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Reed Stubbendieck @bactereedia.bsky.social · 26/03/2025
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?
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Reposted by Reed Stubbendieck
Morgan Carter @morgancarterphd.bsky.social · 21/03/2025
#NewPI life
A slack message from me saying "... is anyone waiting on something from me? I think I'm caught up again"
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Reposted by Reed Stubbendieck
K.T. Elliott @ktelliottmicro.bsky.social · 16/03/2025
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
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Reposted by Reed Stubbendieck
Kevin Forsberg @kvnforsberg.bsky.social · 03/03/2025
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
Functional Metagenomic Selections for Phage Defense
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Reposted by Reed Stubbendieck
Julia Willett @jlewillett.bsky.social · 01/03/2025
"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...
science.org
NSF downsizes summer research program for undergraduates
Many participants are from groups underrepresented in science
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Reposted by Reed Stubbendieck
Alex Chase 🧬🌋🌊 @microbomics.bsky.social · 28/02/2025
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??
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Reposted by Reed Stubbendieck
Marc Chevrette @wildtypemc.bsky.social · 28/02/2025
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...
doi.org
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...
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Reposted by Reed Stubbendieck
Rauf Salamzade @raufs.bsky.social · 24/02/2025
Our minireview on BGC evolution being shaped by genomic & ecological context is now live on mSystems: journals.asm.org/doi/10.1128/... #secmet #MEvoSky
journals.asm.org
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...
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Reposted by Reed Stubbendieck
Carolyn Ibberson @cbibberson.bsky.social · 22/02/2025
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...
docs.google.com
Graduate Reductions Across Biomedical Sciences (2025)
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Elinne Becket, PhD @bielleogy.bsky.social · 14/02/2025
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.
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Reposted by Reed Stubbendieck
Jo Handelsman, PhD @johandelsman.bsky.social · 13/02/2025
"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?"
wisconsintechnologycouncil.com
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...
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Reposted by Reed Stubbendieck
Dr Craig R McClain @drcraigmc.bsky.social · 29/01/2025
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.
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Reposted by Reed Stubbendieck
Jane Liebschutz, MD MPH (she/her) @liebschutz.bsky.social · 22/01/2025
All NIH study sections canceled indefinitely. This will halt science and devastate research budgets in universities.
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Reposted by Reed Stubbendieck
Marc Chevrette @wildtypemc.bsky.social · 12/01/2025
~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...
doi.org
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...
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Reposted by Reed Stubbendieck
Dan Udwary @danudwary.secondarymetabolism.com · 13/01/2025
www.biorxiv.org/content/10.1... #secmet 🧪🖥️🧬
biorxiv.org
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...
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Reed Stubbendieck @bactereedia.bsky.social · 15/01/2025
My current state is exemplifed by the duck of ennui.
A light up duck sitting on a desk looking over it.
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Reed Stubbendieck @bactereedia.bsky.social · 15/01/2025
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.
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Marc Chevrette @wildtypemc.bsky.social · 22/12/2024
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
biorxiv.org
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...
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Brian O. Bachmann @brianobachmann.bsky.social · 20/12/2024
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/...
science.org
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...
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Reposted by Reed Stubbendieck
Mitja M. Zdouc @mmzdouc.bsky.social · 10/12/2024
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-...
academic.oup.com
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
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Reed Stubbendieck @bactereedia.bsky.social · 04/12/2024
Thanks Drew!
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