Reed Stubbendieck
@bactereedia.bsky.social
Microbiologist 🧫 | #newPI OKState | specialized/secondary metabolism | bacterial interactions | respiratory microbiomes | he/him | posts are my own |
Reposted by 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
Origins of a tangled bank: Adaptation and evolution in antibiotic-producing Streptomyces
www.gla.ac.uk/postgraduate...
please repost
University of Glasgow - Postgraduate study - Centres for Doctoral Training - NorthWest Biosciences - Our Projects - Underpinning Bioscience - Paul A Hoskisson
www.gla.ac.uk
September 30, 2025 at 11:02 AM
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
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...
journals.plos.org/plospathogen...
Achromobacter spp.: Emerging pathogens in the cystic fibrosis lung
journals.plos.org
April 23, 2025 at 2:53 PM
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/plospathogen...
Reposted by Reed Stubbendieck
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
April 18, 2025 at 1:03 AM
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?
March 26, 2025 at 11:40 PM
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?
Reposted by Reed Stubbendieck
Reposted by Reed Stubbendieck
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
Generations of work will be lost in essentially an instant
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.
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.
The damage will be far worse than just a 4-yr gap. Both I and the individual who has managed this site for most of the past 50 yrs are retiring within the next 2 years. With this closure, we will not be able to plan a transition.
March 16, 2025 at 11:48 PM
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
Generations of work will be lost in essentially an instant
Reposted by Reed Stubbendieck
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
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
March 3, 2025 at 12:12 PM
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
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
Reposted by Reed Stubbendieck
"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
www.science.org
March 1, 2025 at 12:13 PM
"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...
Reposted by Reed Stubbendieck
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??
February 28, 2025 at 9:27 PM
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??
Reposted by Reed Stubbendieck
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/10.1101/2025...
February 28, 2025 at 3:16 PM
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/10.1101/2025...
Reposted by Reed Stubbendieck
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/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
February 24, 2025 at 5:00 PM
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/doi/10.1128/...
#secmet #MEvoSky
Reposted by Reed Stubbendieck
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
February 22, 2025 at 6:09 PM
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...
Reposted by Reed Stubbendieck
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.
February 14, 2025 at 10:46 PM
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.
Reposted by Reed Stubbendieck
"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
February 13, 2025 at 7:55 PM
"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?"
Reposted by Reed Stubbendieck
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.
January 29, 2025 at 4:52 PM
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.
Reposted by Reed Stubbendieck
All NIH study sections canceled indefinitely. This will halt science and devastate research budgets in universities.
January 22, 2025 at 8:46 PM
All NIH study sections canceled indefinitely. This will halt science and devastate research budgets in universities.
Reposted by Reed Stubbendieck
~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...
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
January 12, 2025 at 6:31 PM
~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...
Very proud of this work. Check it out now on biorxiv!
doi.org/10.1101/2025...
Reposted by Reed Stubbendieck
My current state is exemplifed by the duck of ennui.
January 15, 2025 at 1:37 AM
My current state is exemplifed by the duck of ennui.
Reposted by Reed Stubbendieck
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
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...
www.biorxiv.org
December 22, 2024 at 1:47 PM
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
www.biorxiv.org/content/10.1...
@amerrild.bsky.social @tizianasvenningsen.bsky.social @thomastorring.bsky.social
Reposted by Reed Stubbendieck
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/...
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...
www.science.org
December 20, 2024 at 2:24 PM
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/...
www.science.org/doi/10.1126/...
Reposted by Reed Stubbendieck
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
December 10, 2024 at 8:05 AM
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-...
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!
December 3, 2024 at 7:44 PM
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!
Just submitted the first manuscript from our lab! Wish us luck!
November 27, 2024 at 4:46 PM
Just submitted the first manuscript from our lab! Wish us luck!