Joe Zackular

So good catching up, Arnaldo! Had an amazing visit and was so honored to be hosted by the students at UTSW. What a wonderful community!

It’s always great to catch up with colleagues and friends. Thank you, @joeyzacks.bsky.social, for visiting us, sharing your science, and spending time with our community. We truly enjoyed having you.

Vaccine Makers Curtail Research and Cut Jobs

New from the New York Times:

"There will be less invention, investment and innovation in vaccines across all companies."
- Stephen Hoge, Moderna

What needs to change? "The Health Secretary."
- Albert Bourla, Pfizer

#vaccines #HHS #FDA #RFKJr

🎁 article

www.nytimes.com/2026/02/16/h...

🧵 New preprint! Our 4-lab team evolved Streptococcus pneumoniae in antibiotic-treated mice of varying immune states and discovered something surprising: bacteria rarely evolved resistance. Instead, they found a different way to survive — by rewiring RNA turnover.
🔗 www.biorxiv.org/content/10.6...

A valentine from Public Health of Seattle and King County. A man shivers in bed while a smiling lady in a red mask shows off her bandage on her arm. Text: Noses are red Ice packs are blue I'm vaxed so miss me with severe symptoms of flu.

A valentine from Public Health of Seattle and King County. Two lady scientists shrug lackadaisically. Text reads: My love for you can't be explained by science. Just like the new federal vaccine guidelines.

A valentine from Public Health of Seattle and King County. Protesters in Minneapolis wear thick clothes and hold signs of support for immigrant neighbors. Text reads: To the health departments in the Twin Cities: Love unites us. Our hearts are with you.

Oh my GOD King County Public Health is just wilding out for Valentines Day (and a lovely one).

Thrilled to share this study tracking Staph aureus carriage and transmission across the NICU using genomics! Work done w @pjplanet.bsky.social & @ahmedmicrobes.bsky.social and made possible by @centermicrobialmed.bsky.social.

Study co-led by the amazing @qianxuan.bsky.social & Lakshmi Srinivasan!

GitHub - microbialARC/THRESHER: THRESHER is a bacterial phylogenomics toolkit for strain and/or transmission clusters identification, genome profiling of substitution rates and MGEs, and bacterial evo... THRESHER is a bacterial phylogenomics toolkit for strain and/or transmission clusters identification, genome profiling of substitution rates and MGEs, and bacterial evolution simulation. - microbia...

We’ve made our analytical pipeline THRESHER publicly available! Just provide your genomes and it handles strain and/or cluster composition, and generates quality visualizations for you. Easy to install,thoroughly documented,and validated on published datasets and simulations. Manuscript coming soon!

It’s a great honor to be part of these efforts. Check out our new paper co-led by our talented co-mentored PhD student @qianxuan.bsky.social & our colleague from the CHOP NICU Lakshmi Srinivasan! This would not happen without amazing collaborations across multiple departments & divisions at CHOP.

F.D.A. Refuses to Review Moderna Flu Vaccine

NEW: The F.D.A. refused to accept an application from Moderna for its mRNA flu vaccine.

Its reason: The agency did not think Moderna compared the new vaccine to one of the best flu shots available. The company spent $750M+ on a 41,000 person study.

www.nytimes.com/2026/02/10/h...

Congratulations on leading this beautiful study, Sean! Incredible work!

Researchers from @centermicrobialmed.bsky.social @chopresearch.bsky.social identify strategies for preventing the most infectious strains of Staph aureus.

@pjplanet.bsky.social @ahmedmicrobes.bsky.social @qianxuan.bsky.social @joeyzacks.bsky.social

Over 3 years we performed WGS-based surveillance of S. aureus in the NICU at @childrensphila.bsky.social, sequencing both surveillance and bloodstream infection isolates, to understand how colonization, transmission, and persistence are associated with invasive infection in high-risk neonates.

This work was made possible through an amazing collaboration across @chopresearch.bsky.social including CHOP NICU, CHOP Infectious Disease Diagnostics Lab (IDDL), CHOP Infection Prevention & Control, the MicrobialARC at CHOP, the CHOP MIcrobiome Center, and
@centermicrobialmed.bsky.social!!

We tracked S. aureus using whole genome sequencing over 3 years in the NICU and identify spatial and temporal links for transmission between babies. We also demonstrate a strong association between colonization, transmission, persistence, and the development of invasive infections.

Thrilled to share this study tracking Staph aureus carriage and transmission across the NICU using genomics! Work done w @pjplanet.bsky.social & @ahmedmicrobes.bsky.social and made possible by @centermicrobialmed.bsky.social.

Study co-led by the amazing @qianxuan.bsky.social & Lakshmi Srinivasan!

Looking forward to the visit and reconnecting, Arnaldo!!

NSF GRFP applicants (and mentors): Was your application Returned Without Review and deemed ineligible despite fitting in the allowed topics?
1) Write NSF
2) Write your Congressperson
3) CC us at grfp@grant-witness.us so we can compile + follow up

Details and template at grant-witness.us/grfp-letter

Commensal-myeloid crosstalk in neonatal skin regulates IL-1 signaling and cutaneous type 17 inflammation @cp-immunity.bsky.social
www.cell.com/immunity/ful... @scharschmidtlab.bsky.social

Parents Navigate a Fracturing Vaccine Landscape

As the CDC removes vaccines from its childhood schedule, vaccination rates decline and measles spreads, parents are trying to figure out how to keep their children safe — including, in some cases, by limiting their activities or seeking vaccinations early. I talked to a number of them. Gift link:

I'm hearing from multiple people that students who submitted ecology GRFP proposals are having those proposals rejected without review, despite ecology being listed as an eligible field. If this is a programmatic change, this is devastating. Ecology is the study of Earth's life support systems.

Enterococcus faecalis-derived lactic acid suppresses macrophage activation to facilitate persistent and polymicrobial wound infections Macrophage activation is essential for innate immunity and antimicrobial defense. We show that Enterococcus faecalis suppresses macrophage activation …

Lactic acid lover? Check out @ronni.bsky.social 's new work in
@cp-cellhostmicrobe.bsky.social showing how Enterococcus faecalis-derived LA suppresses macrophage activation, in turn promoting bacterial persistence and polymicrobial wound infection in vivo.
www.sciencedirect.com/science/arti...

Excited to announce the upcoming 2026 Microbial Toxins and Pathogenicity GRC and GRS meeting taking place July 12 - 17, 2026 at Waterville Valley in New Hampshire. This meeting will be chaired by yours truly and co-chaired by
@sunnyshinlab.bsky.social www.grc.org/microbial-to...

Screenshot from STAT article that says "What we're going to have is a real-world experience of when unvaccinated people get measles," he said. "What is the new incidence of hospitalization? What's the incidence of death?"

RFK Jr. appointee Kirk Milhoan has just clearly stated, out loud, that he wants to experiment on the people of the United States by seeing what happens as vaccination coverage plummets and infectious diseases spread.

US science after a year of Trump: what has been lost and what remains A series of graphics reveals how the Trump administration has sought historic cuts to science and the research workforce.

Trump has been in office for one year. We at @nature.com did a deep dive looking at the administration's disruption of science in numbers.

Take a look—the numbers are staggering. By me, @dangaristo.bsky.social, Jeff Tollefson, @kimay.bsky.social, & help from @noamross.net @scott-delaney.bsky.social

Baby-to-baby strain transmission shapes the developing gut microbiome - Nature A metagenomic survey of babies attending the first year of nursery detected extensive baby-to-baby microbial strain transmission, pointing to social interactions in infancy as crucial drivers of infan...

🥁 NEW

Our study on infant gut microbiome and #straintransmission is now published in @nature.com:

doi.org/10.1038/s415...

1/10

I’m stoked to share my postdoc work with @sunnyshinlab.bsky.social, a collaborative effort with @metabailism.bsky.social & Brian Goldspiel, aided by many valued collaborators: Environmental Amino Acid Sensing Regulates the Rate of ASC Translation and NLRP3 Inflammasome Assembly. Some big takeaways:

This line graph illustrates the percentage change in agency staff levels from the previous year for nine major U.S. federal scientific and health organizations between the fiscal years 2016 and 2025. The agencies tracked include the CDC, Department of Energy, EPA, FDA, NASA, NIH, NIST, NOAA, and NSF. For the majority of the timeline between 2016 and 2023, the agencies show relatively stable fluctuations, generally staying within a range of +5% to -5% change per year. However, there is a dramatic and uniform plummet starting in the 2024–25 period. Every agency depicted shows a sharp downward trajectory, with staffing losses ranging from approximately -15% to over -25%. The Environmental Protection Agency (EPA) shows the most significant decline, dropping to roughly -26%, while the National Institute of Standards and Technology (NIST) shows the least severe but still substantial drop at approximately -15%.

This is the most astonishing graph of what the Trump regime has done to US science. They have destroyed the federal science workforce across the board. The negative impacts on Americans will be felt for generations, and the US might never be the same again.

www.nature.com/immersive/d4...

A phage protein screen identifies triggers of the bacterial innate immune system - Nature Microbiology A library of 400 phage protein-coding genes is used to find a trove of antiphage systems, revealing systems that target tail fibre and major capsid proteins.

I’m thrilled to share our work on phage triggers of the bacterial immune system in its final form @natmicrobiol.nature.com www.nature.com/articles/s41...

Getting asked about how academics can continue to do science & inspire trainees even in the midst of a continued (escalated) assault on science, reason, truth, & human rights. I don’t have great answers.

I would love to hear from mentors about advice they’re giving to trainees/ colleagues.

Enterococcus fans: Check out our latest on E. faecalis EET, advancing our understanding of both the fundamental physiology of this bug and new mechanisms of its virulence. This is the product of a thrilling collaboration with friends in Singapore @gthibault.bsky.social led by @aarontan.bsky.social.