iiinova — where your digital self keeps evolving

Vaughn Cooper @vscooper.micropopbio.org · 27/09/2026

As various bacterial phenotypes changed in concert, due to common regulatory mutations, so too did the pattern of diversification AND the decline of lung function. Drivers of chronicity spawned several enduring lineages and the patient's health suffered.

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Vaughn Cooper @vscooper.micropopbio.org · 27/09/2026

We were stunned by the convergent evolution by different strains in each patient. In total, 108 genes acquired parallel mutations indicating common host selection. 55 genes had ≥4 independent mutations! Each infection gained a combination of 5 of the most frequent, like a winning hand of cards.

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Vaughn Cooper @vscooper.micropopbio.org · 27/09/2026

Led by Leonilde Moreira with 🤩 work by Mirela Ferreira, who visited us a few years go, we combine sequencing, lots of phenotyping, and host lung function data over 7-17 years per patient. @jameszlosnik.bsky.social Importantly, phylogenetic reconstructions show which mutations drive later success

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Vaughn Cooper @vscooper.micropopbio.org · 06/08/2026

Northern flicker: “Oh yes, the bugs in your lawn are so tasty 😋” “But if you come 1 inch closer I’m outta here…⚠️ …told ya!”

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Vaughn Cooper @vscooper.micropopbio.org · 29/07/2026

At ISEMPH meeting @evmed.bsky.social in beautiful Kiel. Enjoyed the tour de force presentation by @trevorgraham.bsky.social showing power of fluctuating methylation for inferring evolutionary history and speed in various cancers. See www.nature.com/articles/s41...

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Vaughn Cooper @vscooper.micropopbio.org · 26/07/2026

The *rny* mutants dodge that crash in two ways: most cells enter a quiescent, low-RNA state while a resilient minority idles near baseline. When the drug wave passes, the quiescent majority reboots its ribosomal transcripts first and the population recovers hours faster than wild type.

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Vaughn Cooper @vscooper.micropopbio.org · 26/07/2026

That convergent evolution indicated that the bacteria hadn't found a drug-specific solution but rather more general stress tolerance.

rny SNPs increase drug tolerance across drug classes

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Vaughn Cooper @vscooper.micropopbio.org · 24/07/2026

🤯 Pogacar might be the best athlete on the planet. So unfathomably dominant, his career win rate is >30%. The Alpe record is an all time benchmark. He sliced more than a minute off Pantani’s standard

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Vaughn Cooper @vscooper.micropopbio.org · 08/07/2026

And the Cooper and Van Tyne labs watched this in person! A 10 RBI game 🤯

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Vaughn Cooper @vscooper.micropopbio.org · 07/06/2026

Ideal timing of this announcement at this Science and Society panel @asm.org Microbe

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Vaughn Cooper @vscooper.micropopbio.org · 07/06/2026

Delighted to be a part of this Phage Therapy P01 network, as the CAPT program at the University of Pittsburgh led by @dariavantyne.bsky.social @ including WRAIR, Intralytics and many Pittsburgh colleagues. We are part of Project 1 “Find the Phage” which will include evolving better phages.

CAPT-CEP
Centers for Accelerating
Phage Therapy to
Combat ESKAPE Pathogens
GLADSTONE INSTITUTES
Center for
PhAlge Therapy
Stanford University
Center for
Phage Pharmaceuticals
University of
Pittsburgh.
Center for Accelerating
Phage Therapy
A nationwide research network uniting expertise to advance phage therapy against antibiotic-resistant infections.
GLADSTONE INSTITUTES
WRAIR

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Vaughn Cooper @vscooper.micropopbio.org · 06/06/2026

My favorite science featured at ASM Microbe, experimental evolution. Chaired by @luiszaman.bsky.social and kicked off by @benwolfe.bsky.social

Experimental evolution: theory in action from food to the clinic

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Vaughn Cooper @vscooper.micropopbio.org · 05/06/2026

So proud and exhilarated by son Soren’s Denison U baseball team, who won its first D3 National Championship yesterday! Dramatically, they won in extra innings of Game 3, capping an incredible 51-3 season. Soren was a key contributor in the bullpen of the playoff roster, which kept our ❤️ racing!

The freshman pitchers and roommates with the championship trophy

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Vaughn Cooper @vscooper.micropopbio.org · 21/05/2026

We must start now to build a better future for science @joshuasweitz.bsky.social

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Vaughn Cooper @vscooper.micropopbio.org · 21/05/2026

Last week Joshua Weitz @joshuasweitz.bsky.social gave an excellent talk at Princeton as prelude to a panel on the future of science. Highly recommend, watch and share! Screenshot of the central message. Video 🔗 bit.ly/4dAapx9

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Vaughn Cooper @vscooper.micropopbio.org · 18/05/2026

Office view: catching smallmouth

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Vaughn Cooper @vscooper.micropopbio.org · 12/05/2026

Amazing COVID-19 memorial in Chillicothe Ohio, under Gov Mike DeWine. Seems like another time in many ways

Sculpture of a flock of birds flying away in negative and positive relief

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Vaughn Cooper @vscooper.micropopbio.org · 29/04/2026

Ok this is hilarious 😂 Be the C diff Watch out Cavs! It’s not gonna be pretty!

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Vaughn Cooper @vscooper.micropopbio.org · 28/04/2026

How are you feeling this morning?

Screech owl in a tree who was just woken up

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Vaughn Cooper @vscooper.micropopbio.org · 26/04/2026

The truly stunning part of this marathon WR is his final full 5K split from 35-40K. 13:42 🤯 That wins most major 5K races

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Vaughn Cooper @vscooper.micropopbio.org · 04/04/2026

Zen during a local ride 🚲 Near Freeport on the Butler Freeport trail

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Vaughn Cooper @vscooper.micropopbio.org · 03/04/2026

Today’s moment of zen Silver Falls State Park, Oregon, 2 weeks ago

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Vaughn Cooper @vscooper.micropopbio.org · 25/03/2026

I asked Claude "What expertise is represented by these individuals named to PCAST" See this table: Martinis is the only member with a traditional academic research background. Only 3 PhD's (physics or EE). No biology or social science. Four college dropouts. Only 1 woman.

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Vaughn Cooper @vscooper.micropopbio.org · 15/03/2026

Sharing a proud moment from our athletic life. Married the best coach I’ve ever met.

Shady Side Academy girls swimming won the Pennsylvania 2A State Championships, led by Coach Erika Cooper

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Vaughn Cooper @vscooper.micropopbio.org · 11/03/2026

Interactive XKCD 🔗 editor.p5js.org/isohedral/fu...

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Vaughn Cooper @vscooper.micropopbio.org · 09/03/2026

Seen on the Hill last week, no notes

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Vaughn Cooper @vscooper.micropopbio.org · 01/03/2026

Like the newer study, Pseudomonas defluvii evolved new traits in simple communities but became constrained in complex ones. The coexisting P. brenneri barely changed at all! Adaptations were linked to similar mutations including a YfiR homolog just like 👆🏻 & regulators of c-di-GMP and aerotaxis.

etagenomics analysis of samples of P. defluvii-derived variants obtained from different combinations after the 18-day experiment and analysis of genomes of selected evolved P. defluvii variants. Color gradient represents mutation frequencies across combinations in metagenomic samples (gray: 100%; light brown: 0%); gray boxes represent 100% frequency in isolated variants. DGC diguanylate cyclase.

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Vaughn Cooper @vscooper.micropopbio.org · 01/03/2026

WGS of populations ID'd mutations in csrD in K. pneumoniae, yfiBNR in P. protegens, and cheA in P. aeruginosa that arose early, persisted, and were enriched in mixed-species isolates. These single mutations recapitulated most compositional shifts in community structure and function!

Relative abundance of mixed isolates of K. pneumoniae, P. protegens and P. aeruginosa with and without mutations in csrD, yfiBNR and cheA, respectively. (B) Differences in cell counts during competition assays between mixed isolates of the three species.

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Vaughn Cooper @vscooper.micropopbio.org · 01/03/2026

Biofilm adaptations were relatively constrained in mixed species communities. This PCA summarizes phenotypic data clearly.

plots display Principal Component 1 (PC1) on the x-axis and Principal Component 2
(PC2) on the y-axis and the variance are indicated in the brackets. (A) The data points are colored according to their group (mono vs. mixed). Ellipses represent the 95% confidence interval for each group. The mean point for each of the group are represented with bigger circle.

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Vaughn Cooper @vscooper.micropopbio.org · 01/03/2026

Mono-species populations adapted and diversified as expected from our prior work. Mixed-species communities underwent compositional shifts, w/ P. protegens becoming dominant in biofilm and K. pneumoniae dominating the supernatant.

Dynamics of mono and mixed species biofilm communities during LTEE.
261 (A, B) Temporal changes in cell counts (Log₁₀ CFU/mL) of K. pneumoniae, P. protegens and
262 P. aeruginosa recovered from biofilm beads and planktonic supernatants in mono and mixed
263 species communities. Individual points represent absolute CFU counts, while solid lines and
264 shaded regions depict the smoothed trajectory (loess function with 95% confidence interval).
265 (C) Relative abundance of the three species in mixed species communities across six replicate
266 lines (M1–M6). The first facet (top left) shows the average relative abundance across all
267 replicates, while subsequent facets display individual community replicates.

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Vaughn Cooper @vscooper.micropopbio.org · 26/02/2026

The view above, from inside the Union Trust building in dahntahn Pittsburgh. One more beautiful example of gilded age architecture and design here.

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Vaughn Cooper @vscooper.micropopbio.org · 16/02/2026

Check out the preprint for this main story and for many other convergent mutations that mostly defy the bug-drug predictions and rather show how S. pneumo maximizes fitness when balancing drug x immune interactions. Thanks for reading!

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Vaughn Cooper @vscooper.micropopbio.org · 16/02/2026

The result? Dramatically shortened lag phase after antibiotic exposure — a major advantage in fluctuating host environments. RNA turnover isn't just housekeeping — it's a tunable switch for stress survival, and a potential target for combating tolerance. Preprint 🔗 www.biorxiv.org/content/10.6...

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Vaughn Cooper @vscooper.micropopbio.org · 16/02/2026

The mutants appear to hedge their bets: most cells enter a quiescent, low-RNA state while a resilient minority maintains baseline transcription. Upon stress removal, both populations execute a prioritized "ribosomal reboot" — rebuilding translational machinery first to accelerate recovery.

WT S pneumoniae cells undergo progressive loss of RNA quality in cefepime (top) but rny mutant cells lose maintain their RNA quality (Bottom).

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Vaughn Cooper @vscooper.micropopbio.org · 16/02/2026

The Congressionally Directed Medical Research Program (CDMRP) has long supported translational research benefiting military service members. cdmrp.health.mil/prmrp/default Like all US science funding, CDMRP has also dwindled. Insane funding rate of only 2% for the PRMRP program in 2025:

Of 227 clinical trial proposals to the PRMRP program, only 5 were funded. Of 753 technology or therapeutic development proposals, only 14 were funded. Success rates of roughly 2%

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Vaughn Cooper @vscooper.micropopbio.org · 07/02/2026

One more @washingtonpost.com casualty: the podcast Post Reports. This was a good program 😮‍💨

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Vaughn Cooper @vscooper.micropopbio.org · 09/01/2026

🚨Call for papers🚨 Microbial Evolution: Impacts on Human Health in the society journal Evolution, Medicine, and Public Health Guest Editors: Bob Woods, Silvie Huijben & Camilo Barbosa EIC: me This will be great, please submit and share! academic.oup.com/emph/pages/m...

Microbial Evolution: Impacts on Human Health

Call for Papers

A defining characteristic of infectious diseases is that they evolve. The consequences of this evolution are among the most pressing medical issues facing humanity, including emerging pandemics, antibiotic resistance, and the success or failure of vaccines. Pathogen evolution profoundly influences virulence, transmission, and responses to a broad array of human interventions. While the evolutionary dynamics of pathogens have historically been challenging to study, large-scale genomic sequencing, novel computational tools, and experimental methods are rapidly changing the field. We encourage submissions on the broad topic of the evolution of infectious diseases.

This Special Issue aims to feature research that blends evolutionary approaches to understanding pathogen heterogeneity and ongoing genetic change in clinical samples and models of human infection. It also seeks to highlight opportunities to design treatment and prevention strategies that remain effective in the face of ongoing pathogen evolution.

Submission – open until January 31, 2027

Guest editors
Robert Woods, MD PhD, University of Michigan
Camilo Barbosa, PhD, University of Michigan
Silvie Huijben, PhD, Arizona State University

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Vaughn Cooper @vscooper.micropopbio.org · 08/01/2026

sharing a useful collaboration between me and Claude to pick the best heatmap colorscheme

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Vaughn Cooper @vscooper.micropopbio.org · 06/01/2026

The @asm.org statement in response to the changes in the childhood immunization schedule: asm.org/press-releas...

Jan. 5, 2026

The rationale for the recent updates to the U.S. childhood immunization schedule is, at best, uncertain and sets a potentially dangerous precedent for public health. Whatever improvements may be needed to the process the U.S. Centers for Disease Control and Prevention (CDC) has followed in the past to update vaccine recommendations, it is unclear what scientific evidence led to these new guidelines.

Protecting a country’s public health presents unique challenges that are specific to that country’s population. The prevalence of diseases in the U.S. is not the same as it is in other countries, and public health recommendations should be made based on the public health challenges faced by the American people.

The changes by the CDC will reduce the number of recommended childhood vaccines from 17 to 11. This includes narrowing the recommendation for the flu, which has already contributed to the deaths of at least 9 children this season and a near record number of pediatric flu deaths last season.

Vaccines are a safe and effective tool to prevent the spread of infectious disease and infection-related deaths, and they have saved and continue to save lives. While we concur with National Institutes of Health Director Jay Bhattacharya that “science demands continuous evaluation,” that must occur with full transparency and input from the scientific community. The schedule changes weaken vaccine recommendations at a particularly critical time. It is crucial that expert consultation and a review of scientific evidence be included in the decisions that impact the health and safety of the country.

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Vaughn Cooper @vscooper.micropopbio.org · 29/12/2025

Finally made the trip to DC from Pittsburgh the best possible way, the GAP-CO, in 3 days with an old friend. Planning another big ride this summer

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Vaughn Cooper @vscooper.micropopbio.org · 14/12/2025

The 🐐 Katie Ledecky just became the first woman in history to break 15 minutes in the 1650yd freestyle. She did it all alone at the hometown Maryland meet that bears her name. What a legend, what a leader!

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Vaughn Cooper @vscooper.micropopbio.org · 07/12/2025

Highlights •Vaccine-switching benefits of 9-21% •Bivalent vaccine superiority: •Vaccination-first pathways consistently outperformed infection-first pathways. •Evidence against natural immunity strategies: Robust evidence supports early vaccination policies for future pandemic preparedness.

Highlights
•
Platform-switching benefits: Switching from CoronaVac to BNT162b2 reduced infection risk by 9–21 % compared to homologous boosting.
•
Bivalent vaccine superiority: The Bivalent Omicron BA.4/BA.5 BNT162b2 vaccine provided 30–58 % lower hazard compared to standard mRNA boosters.
•
Vaccination sequence matters: Vaccination-first pathways consistently outperformed infection-first pathways.
•
Evidence against natural immunity strategies: Robust evidence supports early vaccination policies for future pandemic preparedness.

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Vaughn Cooper @vscooper.micropopbio.org · 02/12/2025

GREAT blog about scientific publishing including this provocative figure: danielroelfs.com/posts/the-mo...

Figure correlating Journal Impact Factor and Open Access Article Processing Fees

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Vaughn Cooper @vscooper.micropopbio.org · 01/12/2025

Bald eagle 🦅 fishing the Mon river. Shot from office window just now

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Vaughn Cooper @vscooper.micropopbio.org · 28/11/2025

Lots of pie for breakfast energy out there 👌. I offer: pumpkin whoopie pie for brunch

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Vaughn Cooper @vscooper.micropopbio.org · 05/11/2025

Love the idea of the "deletion test" posed by @needhibhalla.bsky.social & coauthors in their commentary about costs of cutting DEI efforts in science. What if that student were "deleted?" What will the costs be? Screenshots attached to enhance access. www.nature.com/articles/s41...

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