Fire’s out…

Rapid evolution of Klebsiella pneumoniae biofilms in vitro delineates adaptive changes selected during infection - Nature Communications Biofilm formation on implanted medical devices facilitates infection by the pathogen Klebsiella pneumoniae. Here, Zaborskytė et al. use experimental evolution to show that the bacteria rapidly evolve ...

🆒 new pub!
Rapid evolution of Klebsiella pneumoniae biofilms in vitro -> adaptations selected during infection by @gretazabo.bsky.social & Linus Sandegren
*hypermucoidy evolves via 📈c-di-GMP, overlaps w/ mutations in UTI and wound isolates.
*pleasure to advise this!

www.nature.com/articles/s41...

No, lots of sirens and lights and firefighters are posted up at homes near the flames

Watching this wild fire burn during a rainstorm from my living room

Montana State Rodeo

Advancing “Science of Science” Research to Understand and Strengthen the Biomedical Research Ecosystem 🧪

"This topic encourages research projects focused on a better understanding of the biomedical research ecosystem and strengthening the study of the 'science of science' within biomedicine."

‼️Please share‼️

Nemudryi lab is looking for postdocs to join our team and study:

🦠 Bacterial phage defense mechanisms

🧬 RNA repair & CRISPR-based RNA editing

Excited about RNA, host-virus interactions & mechanistic biology?

Let's talk!

Apply: explore.jobs.ufl.edu/en-us/job/53...

Phage receptor prediction from genome sequencing alone. Bacterial receptor (blue) interacting with phage proteins (purple) is shown here

📣Huge preprint 🔔
Today we share something our group has been working toward for a long time, led by @lucasmoriniere.bsky.social We asked can we predict which receptor a phage targets from its genome sequence alone? For most phages, we couldn’t. So Lucas set out to do something I had only dreamed of.

Bacteriophage data on capsular Klebsiella bacteria barcoded library

New paper 🔔

Collaboration
@sullivan-lab.bsky.social
Marissa Gittrich led the work

Klebsiella phage biology has focused almost entirely on capsulated strains, but capsule loss is the #1 resistance mechanism under phage predation. We used a naturally acapsular host to reveal the receptor landscape

🚨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/...