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Reed Stubbendieck

@bactereedia.bsky.social
1.4K followers 393 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
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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Matt Hutchings @handle.invalid · 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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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
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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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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Dan Udwary @danudwary.secondarymetabolism.com · 18/12/2025
#secmet
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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 · 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 · 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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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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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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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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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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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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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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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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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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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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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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Reposted by Reed Stubbendieck
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 · 03/12/2024
Completed my reappointment talk yesterday! It was nice to reflect on two years of progress in the laboratory. I am so fortunate to get to work with this excellent team of scientists!
Photograph of the Stubbendieck Lab standing together in front of the Life Science East building on the Oklahoma State campus.
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Reed Stubbendieck @bactereedia.bsky.social · 27/11/2024
Just submitted the first manuscript from our lab! Wish us luck!
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Reed Stubbendieck @bactereedia.bsky.social · 29/10/2024
Does anyone know of any opportunities for funding #natprod postdocs that non-US citizens are eligible for?
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Reed Stubbendieck @bactereedia.bsky.social · 23/10/2024
This is my revolutionary new idea to obtain funding for the laboratory.
Picture depicting a jar on the left labeled "Swear Jar" with a few coins. On the right is a jar labeled "Sent my PI an unlabeled gel picture" on the right that is nearly full.
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Reed Stubbendieck @bactereedia.bsky.social · 22/10/2024
Is anyone else having problems logging into NCBI right now? Trying to update a bibliography for a submission.
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Dan Udwary @danudwary.secondarymetabolism.com · 20/10/2024
Looks like there was another Twitter exodus, and I'm seeing new followers. If you're interested, I have a Starter Pack of Bluesky secondary metabolism and chemistry-related folks. Let me know if you belong in there! Please share widely! go.bsky.app/Q9svkYf
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Reed Stubbendieck @bactereedia.bsky.social · 23/09/2024
Working on an analysis using published data in the SRA, but missing metadata is an issue. About half of the authors I've contacted shared it upon request, the rest haven’t responded despite follow-ups. Debating whether to keep asking, contact journals, or move on. Any advice?
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Reed Stubbendieck @bactereedia.bsky.social · 19/08/2024
.@paulhoskisson.bsky.social opening #LatAmGenomeMining24 at the CITMAT!
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Reed Stubbendieck @bactereedia.bsky.social · 17/08/2024
En route to Guanajuato for the Latin American Natural Product Genome Mining Workshop. See you soon @wildtypemc.bsky.social @lore-fermar.bsky.social @paulhoskisson.bsky.social et al. You better have the S. venezuelae cultures ready!
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Reed Stubbendieck @bactereedia.bsky.social · 18/04/2024
When life gives you an orange bacterial strain...
An orange bacterial strain used to depict the Oklahoma State University logo.
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Paul Hoskisson 🧫 🦠🐸 @paulhoskisson.bsky.social · 11/03/2024
Está abierta la convocatoria para que investigadores jóvenes nos acompañen en la 2nd Minería genómica de productos naturales de Latinoamérica - Applications are now open for #ECRs to join us at the 2nd Genome mining of natural products, Latin America 2024 -please use QR code #Microsky
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Reed Stubbendieck @bactereedia.bsky.social · 20/02/2024
Please share: The Stubbendieck Lab is hiring a postdoc to study microbial competition & secondary metabolism in human microbiomes. Experience in natural product chemistry or BGCs preferred. For more info and to apply: apply.interfolio.com/141377
apply.interfolio.com
Apply - Interfolio {{$ctrl.$state.data.pageTitle}} - Apply - Interfolio
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Reed Stubbendieck @bactereedia.bsky.social · 03/02/2024
Our Pearl "Dolosigranulum pigrum: A promising nasal probiotic candidate" with @hjillianh.bsky.social and Matthew Kelly is out in PLOS Pathogens! Take a look if you're interested in this beneficial microbe! dx.plos.org/10.1371/jour...
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Reed Stubbendieck @bactereedia.bsky.social · 29/01/2024
Incredibly excited to be a founding research project leader for the Oklahoma Center for Microbiome Research! news.okstate.edu/articles/com...
news.okstate.edu
$10.7M NIH grant to fund Oklahoma Center for Microbiome Research
The National Institutes of Health awarded Oklahoma State University researchers a $10.7 million grant to fund the Oklahoma Center for Microbiome Research, which will add a critical mass of new investi...
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Duncan Ng @duncan-ng.bsky.social · 18/12/2023
Another exciting antimicrobial peptide found in the nose! www.nature.com/articles/s41...
nature.com
Commensal production of a broad-spectrum and short-lived antimicrobial peptide polyene eliminates na...
Staphylococcus epidermidis IVK83, a nasal commensal, produces an extremely short-lived, broad-spectrum antimicrobial peptide–polyene called epifadin, which eliminates Staphylococcus aureus in vitro ...
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Reed Stubbendieck @bactereedia.bsky.social · 21/12/2023
Celebrating the End of the Semester and our new lab members Mercedes and Niladri! www.stubbendiecklab.com/post/20231215/
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Reed Stubbendieck @bactereedia.bsky.social · 21/12/2023
We are excited to announce the Stubbendieck lab's manager Mercedes Perez! Mercedes comes to us from Kyler Miller's lab at The University of Texas-Austin. Mercedes will work on various projects and help us to keep the lab running smoothly! www.stubbendiecklab.com/authors/merc...
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Reed Stubbendieck @bactereedia.bsky.social · 06/12/2023
We are excited to announce the Stubbendieck lab's first Ph.D. student Niladri Bhowmik! Niladri comes to us from Dmitri Mavrodi's lab at The University of Southern Mississippi. Niladri is going to work on microbial interactions within the CF lung microbiome! www.stubbendiecklab.com/authors/nila...
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