Vaughn Cooper
@vscooper.micropopbio.org
Evangelist for the study of evolution in action by everyone.
Pitt Prof | EvolvingSTEM | biofilms | EvMed | genomics entrepreneur (@SeqCoast.bsky.social, @midauthorbio.bsky.social) | ASM President-Elect | exercise addict ~ swim bike run
Pitt Prof | EvolvingSTEM | biofilms | EvMed | genomics entrepreneur (@SeqCoast.bsky.social, @midauthorbio.bsky.social) | ASM President-Elect | exercise addict ~ swim bike run
Pinned
Vaughn Cooper
@vscooper.micropopbio.org
· Jan 21
I'm incredibly honored by this opportunity to serve as President-Elect of @asm.org starting this summer. Looking forward to working with the Board, ASM leadership ,and staff to help advance the microbial sciences. I'm also glad to share my Vision statement, please join us!
asm.org/Press-Releas...
asm.org/Press-Releas...
Reposted by Vaughn Cooper
Neighborhood in Pittsburgh.
November 28, 2025 at 9:14 PM
Neighborhood in Pittsburgh.
Lots of pie for breakfast energy out there 👌.
I offer: pumpkin whoopie pie for brunch
I offer: pumpkin whoopie pie for brunch
November 28, 2025 at 4:30 PM
Lots of pie for breakfast energy out there 👌.
I offer: pumpkin whoopie pie for brunch
I offer: pumpkin whoopie pie for brunch
I just re-read The Big Short by listening to Michael Lewis’s new audio edition.
Here is what we all learned:
Absolutely nothing.
(Although I’m freshly angered by how much these crooks harmed my young family the first time)
Here is what we all learned:
Absolutely nothing.
(Although I’m freshly angered by how much these crooks harmed my young family the first time)
FT: Morgan Stanley "previously recommended investors buy credit-default swaps on Oracle, but hedging the exposure with long positions in its bonds.
".. They’re now recommending that investors ditch the bonds and simply go long Oracle CDS .."
@financialtimes.com $ORCL
www.ft.com/content/d2fd...
".. They’re now recommending that investors ditch the bonds and simply go long Oracle CDS .."
@financialtimes.com $ORCL
www.ft.com/content/d2fd...
Morgan Stanley thinks you should short Oracle
Single-name CDS are so hot right now
www.ft.com
November 28, 2025 at 1:03 PM
I just re-read The Big Short by listening to Michael Lewis’s new audio edition.
Here is what we all learned:
Absolutely nothing.
(Although I’m freshly angered by how much these crooks harmed my young family the first time)
Here is what we all learned:
Absolutely nothing.
(Although I’m freshly angered by how much these crooks harmed my young family the first time)
Reposted by Vaughn Cooper
1/ 🚀 Pathoplexus now supports Marburg virus (MARV) and Ravn virus (RAVN) (sister viruses in the same genus). MARV has two main clades and causes severe disease with reported fatality rates of 24–88%.
You can read more detail about adding Marburg here: pathoplexus.org/news/2025-11...
You can read more detail about adding Marburg here: pathoplexus.org/news/2025-11...
November 28, 2025 at 12:37 PM
1/ 🚀 Pathoplexus now supports Marburg virus (MARV) and Ravn virus (RAVN) (sister viruses in the same genus). MARV has two main clades and causes severe disease with reported fatality rates of 24–88%.
You can read more detail about adding Marburg here: pathoplexus.org/news/2025-11...
You can read more detail about adding Marburg here: pathoplexus.org/news/2025-11...
Reposted by Vaughn Cooper
![Comic. Panels up to the 10-year point are grayed out. New panels since the Ten Years comic, which chronicles the first ten years of PERSON 1's journey with cancer: (1) [two people in bed] PERSON 1 (woman): One more chapter? PERSON 2 (man): Don’t we both have to get up early? PERSON 1: Nnnnnggggh PERSON 2: Sure, good point. (2) [many people wearing masks, walking while looking at graphs on their phones] (3) [birds landing on people] PERSON 2 in beanie and scarf: Hah! They like *my* seeds best. PERSON 1 in scarf holding phone with a bird sitting on it: Wait, how do I take a picture of this one? (4) [two people rowing boats with tree landscape] (5) [Person 1 carries overflowing stack of things to Person 2 in bed] PERSON 1: I brought you honey lemon tea, more pillows, a cinnamon roll, Tylenol, another blanket, a– PERSON 2: It was just Appendicitis, I’m really– PERSON 1: *It is my turn to take care of you and I am going to do it right!* (6) [Two people in car] (7) [still in car) PERSON 1: Oh my god. PERSON 2: Oh my god. (8) [car driving] PERSON 1: Pull over! PERSON 2: I am! (9) [both people get out of car] (10) [Large colored panel of aurora borealis over water with both people looking on] (11) [Person 1 sits against tree while Person 2 lies on the ground] PERSON 1: Fifteen years. No sign of the cancer. (12) I *am* having some weird symptoms. Joint pain. Fatigue. I think I’m losing my close-up vision. PERSON 2: Yeah. Me too. (13) PERSON 2: I think we’re getting old. (14) PERSON 1: I guess that’s okay. PERSON 2: It’s all I wanted.](https://cdn.bsky.app/img/feed_thumbnail/plain/did:plc:cz73r7iyiqn26upot4jtjdhk/bafkreihwhjblp5lyiwp63ouar7ocfea7evmckytoeo7rkfuoo4gw5rnrra@jpeg)
November 26, 2025 at 10:32 PM
Proud of this work led by Rocio Espinosa and Henriette Lyng Roder. Fun collaboration & innovation!
*Used custom 3D-printed flow systems to study evolution in biofilms of two competing Pseudomonas species in communities of varying complexity, using microscopy + WGS
www.nature.com/articles/s41...
*Used custom 3D-printed flow systems to study evolution in biofilms of two competing Pseudomonas species in communities of varying complexity, using microscopy + WGS
www.nature.com/articles/s41...
Competition between Pseudomonas species constrains ecological diversification in polymicrobial biofilms - npj Biofilms and Microbiomes
npj Biofilms and Microbiomes - Competition between Pseudomonas species constrains ecological diversification in polymicrobial biofilms
www.nature.com
November 26, 2025 at 6:25 PM
Proud of this work led by Rocio Espinosa and Henriette Lyng Roder. Fun collaboration & innovation!
*Used custom 3D-printed flow systems to study evolution in biofilms of two competing Pseudomonas species in communities of varying complexity, using microscopy + WGS
www.nature.com/articles/s41...
*Used custom 3D-printed flow systems to study evolution in biofilms of two competing Pseudomonas species in communities of varying complexity, using microscopy + WGS
www.nature.com/articles/s41...
Reposted by Vaughn Cooper
Competition between Pseudomonas species constrains ecological diversification in polymicrobial biofilms
NPJ Biofilms and Microbiomes from Henriette Lyng Røder and @vscooper.micropopbio.org
www.nature.com/articles/s41...
NPJ Biofilms and Microbiomes from Henriette Lyng Røder and @vscooper.micropopbio.org
www.nature.com/articles/s41...
Competition between Pseudomonas species constrains ecological diversification in polymicrobial biofilms - npj Biofilms and Microbiomes
npj Biofilms and Microbiomes - Competition between Pseudomonas species constrains ecological diversification in polymicrobial biofilms
www.nature.com
November 26, 2025 at 7:07 AM
Competition between Pseudomonas species constrains ecological diversification in polymicrobial biofilms
NPJ Biofilms and Microbiomes from Henriette Lyng Røder and @vscooper.micropopbio.org
www.nature.com/articles/s41...
NPJ Biofilms and Microbiomes from Henriette Lyng Røder and @vscooper.micropopbio.org
www.nature.com/articles/s41...
Reposted by Vaughn Cooper
Introducing ** Incendiamoeba **, a eukaryote that can live at temperatures well beyond what we thought possible. 63C!!
Read @hbrappap.bsky.social thread to see what we’ve already started to learn from this amazing organism!
doi.org/10.1101/2025...
#MicroSky #protistsonsky 🧪 #evobio
Read @hbrappap.bsky.social thread to see what we’ve already started to learn from this amazing organism!
doi.org/10.1101/2025...
#MicroSky #protistsonsky 🧪 #evobio
So happy to announce our new preprint, “A geothermal amoeba sets a new upper temperature limit for eukaryotes.” We cultured a novel amoeba from Lassen Volcanic NP (CA, USA) that divides at 63°C (145°F) 🔥 - a new record for euk growth!
#protistsonsky 🧵
#protistsonsky 🧵
November 25, 2025 at 9:03 PM
Introducing ** Incendiamoeba **, a eukaryote that can live at temperatures well beyond what we thought possible. 63C!!
Read @hbrappap.bsky.social thread to see what we’ve already started to learn from this amazing organism!
doi.org/10.1101/2025...
#MicroSky #protistsonsky 🧪 #evobio
Read @hbrappap.bsky.social thread to see what we’ve already started to learn from this amazing organism!
doi.org/10.1101/2025...
#MicroSky #protistsonsky 🧪 #evobio
Reposted by Vaughn Cooper
I have eaten
the plums
that were on
the patio
and which
you were probably
saving
for breakfast
Forgive me
they were delicious
so sweet
and so cold
the plums
that were on
the patio
and which
you were probably
saving
for breakfast
Forgive me
they were delicious
so sweet
and so cold
Big news! The groundhog is back at my sister's and she gave him a plum
November 25, 2025 at 12:53 PM
I have eaten
the plums
that were on
the patio
and which
you were probably
saving
for breakfast
Forgive me
they were delicious
so sweet
and so cold
the plums
that were on
the patio
and which
you were probably
saving
for breakfast
Forgive me
they were delicious
so sweet
and so cold
Reposted by Vaughn Cooper
Really cool paper from @vincentdebakker.bsky.social @jonbakerlab.bsky.social now published @natcomms.nature.com #MicroSky www.nature.com/articles/s41...
Multi-omics profiling reveals atypical sugar utilization and a key membrane composition regulator in Streptococcus pneumoniae - Nature Communications
The pathogen Streptococcus pneumoniae can adapt to diverse microenvironments in the human body. Here, De Bakker et al. study these adaptation responses, showing unusual sugar utilization and identifyi...
www.nature.com
November 25, 2025 at 1:44 PM
Really cool paper from @vincentdebakker.bsky.social @jonbakerlab.bsky.social now published @natcomms.nature.com #MicroSky www.nature.com/articles/s41...
Reposted by Vaughn Cooper
Really pleased to share the first paper to come out of the lab.
We found that hospital patients were frequently colonised with P. aeruginosa and that the same clone was shared between the gut and the lung.
The phylogenies indicate that the clones moved from lung->gut
www.nature.com/articles/s41...
We found that hospital patients were frequently colonised with P. aeruginosa and that the same clone was shared between the gut and the lung.
The phylogenies indicate that the clones moved from lung->gut
www.nature.com/articles/s41...
High frequency body site translocation of nosocomial Pseudomonas aeruginosa - Nature Communications
Here, the authors report within-host diversity and body site translocation dynamics in hospital samples of Pseudomonas aeruginosa and reveal that body site sharing was likely due to within-patient tra...
www.nature.com
November 25, 2025 at 10:40 AM
Really pleased to share the first paper to come out of the lab.
We found that hospital patients were frequently colonised with P. aeruginosa and that the same clone was shared between the gut and the lung.
The phylogenies indicate that the clones moved from lung->gut
www.nature.com/articles/s41...
We found that hospital patients were frequently colonised with P. aeruginosa and that the same clone was shared between the gut and the lung.
The phylogenies indicate that the clones moved from lung->gut
www.nature.com/articles/s41...
Reposted by Vaughn Cooper
🚨NEW paper: Benchmarking Hi-C for virus–host inference
journals.plos.org/plosbiology/...
A clear baseline for anyone mapping virus–host interactions that establishes robust, benchmarked thresholds for Hi-C linkages.
Key results: 👇
journals.plos.org/plosbiology/...
A clear baseline for anyone mapping virus–host interactions that establishes robust, benchmarked thresholds for Hi-C linkages.
Key results: 👇
Benchmarking with synthetic communities provides a baseline for virus-host inferences from Hi-C proximity linking
Virus discovery has accelerated but linking viruses to hosts remains challenging. This study uses synthetic microbiomes to optimize and benchmark Hi-C for virus-host linkage inference, and applies thi...
journals.plos.org
November 21, 2025 at 7:31 PM
🚨NEW paper: Benchmarking Hi-C for virus–host inference
journals.plos.org/plosbiology/...
A clear baseline for anyone mapping virus–host interactions that establishes robust, benchmarked thresholds for Hi-C linkages.
Key results: 👇
journals.plos.org/plosbiology/...
A clear baseline for anyone mapping virus–host interactions that establishes robust, benchmarked thresholds for Hi-C linkages.
Key results: 👇
Reposted by Vaughn Cooper
Our new collaborative work led by @taliamycota.bsky.social
Jiajun Cui & Emma Caullireau between my lab @ucllifesciences.bsky.social @cloeucl.bsky.social & the Karasov Lab (tkarasovlab.org) @uofubiology.bsky.social
and collaborators: @plantricia.bsky.social et al.
tinyurl.com/5yx2wmz5
(1/n)
Jiajun Cui & Emma Caullireau between my lab @ucllifesciences.bsky.social @cloeucl.bsky.social & the Karasov Lab (tkarasovlab.org) @uofubiology.bsky.social
and collaborators: @plantricia.bsky.social et al.
tinyurl.com/5yx2wmz5
(1/n)
November 18, 2025 at 8:41 AM
Our new collaborative work led by @taliamycota.bsky.social
Jiajun Cui & Emma Caullireau between my lab @ucllifesciences.bsky.social @cloeucl.bsky.social & the Karasov Lab (tkarasovlab.org) @uofubiology.bsky.social
and collaborators: @plantricia.bsky.social et al.
tinyurl.com/5yx2wmz5
(1/n)
Jiajun Cui & Emma Caullireau between my lab @ucllifesciences.bsky.social @cloeucl.bsky.social & the Karasov Lab (tkarasovlab.org) @uofubiology.bsky.social
and collaborators: @plantricia.bsky.social et al.
tinyurl.com/5yx2wmz5
(1/n)
Reposted by Vaughn Cooper
We found that a bacterial trade-off between microbial competition and host colonization has persisted in nature for over ~10^5 generations (200 years), despite massive evolutionary opportunities to escape it.
(2/n)
(2/n)
November 18, 2025 at 8:41 AM
We found that a bacterial trade-off between microbial competition and host colonization has persisted in nature for over ~10^5 generations (200 years), despite massive evolutionary opportunities to escape it.
(2/n)
(2/n)
Reposted by Vaughn Cooper
One of my absolute favorite studies.
70 teaspoons placed in tearooms around the institute & observed weekly over 5 months. 80% of spoons disappeared; spoon halflife~81 days. Communal room halflife lower than in specific labs. 250 spoons annually required to maintain 70 spoon population.
pmc.ncbi.nlm.nih.gov/articles/PMC...
pmc.ncbi.nlm.nih.gov/articles/PMC...
The case of the disappearing teaspoons: longitudinal cohort study of the displacement of teaspoons in an Australian research institute
Objectives To determine the overall rate of loss of workplace teaspoons and whether attrition and displacement are correlated with the relative value of the teaspoons or type of tearoom. Design Longitudinal cohort study. Setting Research institute ...
pmc.ncbi.nlm.nih.gov
November 20, 2025 at 12:35 PM
One of my absolute favorite studies.
Reposted by Vaughn Cooper
The ecological roles of bacterial #immune systems are poorly understood. Rafael Custodio @ellinoralseth.bsky.social @brockhurstlab.bsky.social @brownlab.bsky.social & Edze Westra explore how mobile genetic elements and bacterial defenses shape #microbiome structure and function 🧪
Bacterial immune systems as causes and consequences of microbiome structure
Bacterial immune systems have evolved in response to diverse molecular "parasites", yet their ecological roles remain poorly understood. This Essay explores how interactions between mobile genetic…
plos.io
November 24, 2025 at 5:30 PM
The ecological roles of bacterial #immune systems are poorly understood. Rafael Custodio @ellinoralseth.bsky.social @brockhurstlab.bsky.social @brownlab.bsky.social & Edze Westra explore how mobile genetic elements and bacterial defenses shape #microbiome structure and function 🧪
Reposted by Vaughn Cooper
This...is exactly the kind of theory that has been needed for longer than a decade in microbiome-host evolution studies
Treating emergent traits of the microbiome like quantitative genetic traits of the host reveals how environmentally acquired symbionts can contribute to hosts' adaptation
Quantitative genetics of microbiome-mediated traits
Microbiomes, the complex communities of microorganisms associated with multicellular hosts, play a vital role in shaping host traits and fitness. But how d
buff.ly
November 24, 2025 at 3:33 PM
This...is exactly the kind of theory that has been needed for longer than a decade in microbiome-host evolution studies
Reposted by Vaughn Cooper
Great meeting in Shenzhen by @asm.org and SIAT! Really appreciated the microbiology insights — amazing how central microbes are to so many of today’s challenges. @vscooper.micropopbio.org @rebeleinlab.bsky.social @helgebode.bsky.social @friedrich-group.bsky.social
www.greeninger-chemistry.com/
www.greeninger-chemistry.com/
November 24, 2025 at 10:53 AM
Great meeting in Shenzhen by @asm.org and SIAT! Really appreciated the microbiology insights — amazing how central microbes are to so many of today’s challenges. @vscooper.micropopbio.org @rebeleinlab.bsky.social @helgebode.bsky.social @friedrich-group.bsky.social
www.greeninger-chemistry.com/
www.greeninger-chemistry.com/
Reposted by Vaughn Cooper
I wrote a little bit about the "missing heritability" question and several recent studies that have brought it to a close. A short 🧵
The missing heritability question is now (mostly) answered
Not with a bang but with a whimper
theinfinitesimal.substack.com
November 21, 2025 at 10:34 PM
I wrote a little bit about the "missing heritability" question and several recent studies that have brought it to a close. A short 🧵
Reposted by Vaughn Cooper
I fell through a Wikipedia rabbit hole this afternoon while waiting for basketball practice pickup, and I emerged knowing that the peak of Cayambe (in Ecuador) is the location where you rotate (along with the Earth) at the greatest velocity.
November 22, 2025 at 1:18 AM
I fell through a Wikipedia rabbit hole this afternoon while waiting for basketball practice pickup, and I emerged knowing that the peak of Cayambe (in Ecuador) is the location where you rotate (along with the Earth) at the greatest velocity.
🚨Announcing the NSF-NIST Bioeconomy Standards Scholar-in-Residence Initiative.
👉🏻Catalyze development of standards and metrics for the bioeconomy.
👉🏻Researchers spend time in a NIST laboratory to gain experience and help this initiative.
www.nsf.gov/funding/oppo...
👉🏻Catalyze development of standards and metrics for the bioeconomy.
👉🏻Researchers spend time in a NIST laboratory to gain experience and help this initiative.
www.nsf.gov/funding/oppo...
NSF-NIST Scholars in Residence
www.nsf.gov
November 22, 2025 at 1:08 AM
🚨Announcing the NSF-NIST Bioeconomy Standards Scholar-in-Residence Initiative.
👉🏻Catalyze development of standards and metrics for the bioeconomy.
👉🏻Researchers spend time in a NIST laboratory to gain experience and help this initiative.
www.nsf.gov/funding/oppo...
👉🏻Catalyze development of standards and metrics for the bioeconomy.
👉🏻Researchers spend time in a NIST laboratory to gain experience and help this initiative.
www.nsf.gov/funding/oppo...
Reposted by Vaughn Cooper
In which I fruitlessly beg NIH grant-seeking folks to focus on what is actually important. drugmonkey.wordpress.com/2025/11/21/i...
In which I fruitlessly beg NIH grant-seeking folks to focus on what is actually important.
A new webpage on the NIH site called “Implementing a Unified NIH Funding Strategy to Guide Consistent and Clearer Award Decisions” is causing a small kerfuffle on the socials. As per us…
drugmonkey.wordpress.com
November 22, 2025 at 12:26 AM
In which I fruitlessly beg NIH grant-seeking folks to focus on what is actually important. drugmonkey.wordpress.com/2025/11/21/i...
Reposted by Vaughn Cooper
Hot off the press! Our latest paper led by @fernpizza.bsky.social, understanding how plasmids evolve inside cells. These small, self-replicating DNA circles live inside bacteria and carry antibiotic resistance genes, but also compete with one another to replicate. 1/
www.science.org/doi/10.1126/...
www.science.org/doi/10.1126/...
Intracellular competition shapes plasmid population dynamics
From populations of multicellular organisms to selfish genetic elements, conflicts between levels of biological organization are central to evolution. Plasmids are extrachromosomal, self-replicating g...
www.science.org
November 20, 2025 at 9:42 PM
Hot off the press! Our latest paper led by @fernpizza.bsky.social, understanding how plasmids evolve inside cells. These small, self-replicating DNA circles live inside bacteria and carry antibiotic resistance genes, but also compete with one another to replicate. 1/
www.science.org/doi/10.1126/...
www.science.org/doi/10.1126/...
Reposted by Vaughn Cooper
Bacterial networks #BacNet26 in September 2026 will be chaired by @lalouxlab.bsky.social and co-chaired by @s-lab.bsky.social with @coralietesseur.bsky.social
Sneak peak on invited speakers and preliminary program:
meetings.embo.org/event/26-bac...
Sneak peak on invited speakers and preliminary program:
meetings.embo.org/event/26-bac...
November 20, 2025 at 8:47 AM
Bacterial networks #BacNet26 in September 2026 will be chaired by @lalouxlab.bsky.social and co-chaired by @s-lab.bsky.social with @coralietesseur.bsky.social
Sneak peak on invited speakers and preliminary program:
meetings.embo.org/event/26-bac...
Sneak peak on invited speakers and preliminary program:
meetings.embo.org/event/26-bac...