Patrick R. Secor

🚨Preprint! Happy to share the research from my PhD “Genome delivery of a contractile tailed phage and its superinfection exclusion mechanism”. We use cryoEM to study the genome ejection of the phage T4, revealing how the tape measure protein regulates the process.
www.biorxiv.org/content/10.6...

🖥️ 🧬 ⚛️ 🔬 Plz spread the word. 2-week computational biology workshop in Singapore. No registration fee or expenses for US citizens. Protein annotation, function, structural modeling, and simulation. ~35 attendees. Lectures and hands-on tutorials with intensive instructor interaction. compbioasia.net

Congrats!🍾

📣new preprint from the phagefoundry.org team 🎉 Jessica Trinh and Catherine Mageeney (Sandia National Laboratories)!!

Systematic analysis of prophages from ~1000 Acinetobacter baumannii isolates, induction & screening. We found this 😎 looking phage with bunch of 💍💍

🧵 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...

Diagram illustrating early genome erosion during the transition from a free-living Sodalis bacterium to two host-associated endosymbionts inside the long-tailed mealybug. Circular genomes show intact genes in blue and pseudogenes in red, highlighting increased pseudogene accumulation in symbiotic forms. Caption asks: “What are the downstream molecular consequences of early genome erosion?”

Happy to share a preprint—the last chapter of my dissertation with @mcsymbiont.bsky.social and Co—on what happens when bacterial endosymbionts accumulate huge numbers of pseudogenes during early genome reduction.

www.biorxiv.org/content/10.6...

It was definitely in there all night. When I came in I tapped it with my toe to see if Marilyn would pop out…

My office this morning

Cool, we saw cp32 dimers in our CA112a datasets, but we’re not sure if they were real

[Yelling] Hay!
[in a whisper]…is for horses.

That’s one of my go-to dad jokes

This Research Experiences for Undergraduates (REU) program is funded by the National Science Foundation to create "points of entry" for students interested in research. Students apply from across the country to spend 10 weeks in Bozeman, Montana this summer (May 26, 2026 - August 1, 2026). Admitted students are paired with a faculty mentor, who serves as an advisor for a student's summer project. Each student receives a stipend ($7000 for 10 wks). Travel compensation, room, and board are also provided. Our program leverages MSU’s unique microbiology expertise, focusing specifically on microbes living with little or no oxygen (like those in the hot springs of nearby Yellowstone). Low oxygen microbes are essential to human and ecosystem health. They influence (or control) such processes as the breakdown of food in the GI tract, removal of toxins from our bodies and the environment, and production of greenhouse gases. They are also models for understanding the origins of life on this planet, and the potential for life on other planets. A key goal of our program is to recruit students from schools with limited research infrastructure. Being in Montana, a state with a vibrant Native American community, we are particularly interested in applications from students at tribal colleges. However, ANYONE with an interest in microbiology - or biology/science in general - can and should apply. If willing and able, please share/tweet/spread the word far and wide. Applications are due February 14, 2026. Full details can be found through our website http://www.montana.edu/mbi/reu/

Friends, please help spread the word about our microbiology REU program at Montana State University.
www.montana.edu/mbi/reu/

Each student receives a stipend ($7000 for 10 wks). Travel compensation, room, and board are also provided.

Details in the attached pic--Feb 14 deadline
🧫🧪🦠#microsky

Welcome to MT!

Peptidoglycan architecture dictates protein interactions, tissue tropism, and arthritis in the Lyme disease spirochete Borrelia burgdorferi Author summary Many of the pathogenic mechanisms by which Borrelia burgdorferi causes disease involve cell envelope interactions with host components. To further elucidate the role of peptidoglycan in...

Check out our exciting new paper out now in @plos.org where Dr Ahmad manipulated #peptidoglycan chemistry to understand Lyme disease and arthritis 👇👏
#Microsky
#glycotime

journals.plos.org/plospathogen...

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...

Gulf Research Program Science Policy Fellowships The Gulf Research Program’s Science Policy Fellowship helps scientists hone their skills by putting them to practice for the benefit of Gulf Coast communities and ecosystems. Fellows gain first-hand e...

Are you a graduate student or postdoc who wants to apply your science to policy?

The Gulf Research Program’s Science Policy Fellowship provides experience for one year on the staff of federal, state, local, NGO in the Gulf region and impt networking.
www.nationalacademies.org/programs/GUL...

Here, we find that many Genomic islands have origins of transfer (oriT) mobilisable by conjugation, incl. known Pathogenicity & defense islands. iOriT use only an oriT for transfer by hitching on conjugative elements: they make abundant, diverse, ancient families of mobile genetic elements. See🧵

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

🚨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...

Now published in PLoS Pathogens! #microsky #phagesky
journals.plos.org/plospathogen...

A prophage-encoded sRNA limits phage infection of adherent-invasive E. coli Author summary Prophages—viral genomes integrated into bacterial chromosomes—are common in enteric bacteria and can profoundly influence bacterial physiology and ecological fitness. Here we show that ...

A prophage-encoded sRNA limits phage infection of adherent-invasive E. coli

#PLoSPathogen from @prsecor.bsky.social

journals.plos.org/plospathogen...

E. coli colonies as Christmas ornaments

Merry Christmas!
#microsky

A family of linear plasmid phages that detect a quorum-sensing autoinducer exists in multiple bacterial species | mBio The discovery of quorum-sensing responsive linear plasmid phages has transformed understanding of phage-bacterial interactions by demonstrating inter-domain chemical communication. To date, however, e...

The final form of my 2nd postdoc paper with the Bassler Lab! Turns out our favorite quorum-sensing phage isn’t a one-off, but rather a member of a globally dispersed family of phages that sense a universal autoinducer.

#phagesky #microsky

journals.asm.org/doi/10.1128/...

Looking for a paid summer research experience? Apply to MSU’s Extreme Biofilms REU and work on cutting-edge biofilm science in extreme environments. No prior research experience needed.

#MicroSky
#PhageSky

Environment and physiology shape antiphage system expression Bacteria and archaea encode on average ten antiphage systems. Quorum sensing, cellular, or transcription factors can regulate specific systems (CRISPR-Cas, CBASS). Yet, a systematic assessment of anti...

Bacterial genomes encode a rich repertoire of antiphage systems, but we still know surprisingly little about when these systems are actually expressed.

In this preprint, Lucas Paoli et al, ask what shapes antiphage systems expression in native contexts.
www.biorxiv.org/content/10.6...

The Gallatin Range, Montana

Congrats Nanami! It was a pleasure to be on your committee 🎉🥳🍾

Had our lab holiday party and this was one of the white elephant gifts 🤣🫡
@dominickfaith.bsky.social
#microsky
#phagesky

Phages are full of genes of unknown function that are likely adaptive in specific conditions.
New preprint: Phage TnSeq identifies essential genes rapidly and knocks all non-essentials. We would like to send a pool of phiKZ mutants to anyone wanting it! Reach out
tinyurl.com/bdcfrejh

I learned a ton from the Brewmaster 🍻

Beer!

Meta-virus resource (MetaVR): expanding the frontiers of viral diversity with 24 million uncultivated virus genomes Abstract. Viruses are ubiquitous in all environments and impact host metabolism, evolution, and ecology, although our knowledge of their biodiversity is st

🦠🧪🧬🚨 New paper and database alert: the new IMG/VR release is now MetaVR ! We have a new website - meta-virome.org - with quick search capabilities for the >24M viruses, >12M vOTUs, and >42M protein clusters (including >790k with predicted structures !). academic.oup.com/nar/advance-...