A Grammar of Graphics for Comparative Genomics An extension of ggplot2 for creating complex genomic maps. It builds on the power of ggplot2 and tidyverse adding new ggplot2-style geoms & positions and dplyr-style verbs to manipulate the…

gggenomes: A Grammar of Graphics for Comparative Genomics thackl.github.io/gggenomes/ #Rstats

Long contractile tailed bacteriophage in a yellow-gold environment.

I made a phage… I think it’s in LB

Started / going

Here's a view of Jupiter from NASA's Juno spacecraft, now in orbit there. science.nasa.gov/mission/juno

Image processed from raw data by @kevinmgill.bsky.social

Happy to see this paper finally out in @pnas.org!

#phage #microbiology #MicroSky #VirEvol 🦠 🧫 🔬

Gift link: www.pnas.org/eprint/YYDZ9...

Black and white ink illustration of a myovirus in a steampunk style

Happy World Phage Day! Tiny viruses have mighty roles, shaping our environment and life on Earth. Phages maintain microbial community stability, impact primary production, nutrient cycle and pathogen virulence. We can also use phages in phage therapy to combat bacterial infections. #PhageSky

Research position in Microbial Pharmacology and Population Biology (282139) | UiT The Arctic University of Norway Job title: Research position in Microbial Pharmacology and Population Biology (282139), Employer: UiT The Arctic University of Norway, Deadline: Wednesday, August 27, 2025

Feels surreal to say but: I'm hiring! If you are or know anyone interested in looking at the evolution of phage resistance using A. baumannii and natural transformation, then this might be for you
www.jobbnorge.no/en/available...

Phages with a broad host range are common across ecosystems - Nature Microbiology Proximity-ligation-based sequencing from 111 samples and 5 environments reveals that a substantial proportion of phages infect multiple species.

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

#phagesky #phage

Phold is a fantastic tool and my go to for detailed annotation and visualization of phage genomes. Congrats!

Protein Structure Informed Bacteriophage Genome Annotation with Phold Bacteriophage (phage) genome annotation is essential for understanding their functional potential and suitability for use as therapeutic agents. Here we introduce Phold, an annotation framework utilis...

Stoked to finally have a preprint out for Phold, our tool that uses protein structural information to enhance phage genome annotation #phagesky 1/n

www.biorxiv.org/content/10.1...

a canva graphic that says "How it works Step 1: Go to SkypeAScientist.com Step 2: Click “Sign Up” then “Scientist Sign Up Form” Step 3: Tell us about yourself Step 4: Get matched with a classroom Step 5: Connect with the teacher Step 6: Make a kid’s day isn't that great? @SkypeAScientist"

Scientists!

@skypeascientist.bsky.social matches scientists with classrooms, libraries, & more for virtual Q&As! It's easy and fun!

We are looking for 750 more volunteers by 8/15

If you're down to chat with 1-5 classrooms this semester, sign up here
www.skypeascientist.com/sign-up.html

New lab logo

Incredible conversations at #ASMicrobe2025! Thank you to everyone who stopped by to talk phages, evolution, and the potential of phage steering in complex infections! @asm.org #PhageSky #PhageSteering

Phage tRNAs: decoding the enigma The presence of tRNAs in bacteriophage genomes has intrigued scientists since their discovery in the early 1960s, as phages were believed to rely on the host tRNAs for their translation. Over the years, a multitude of hypotheses have been explored, providing evidence that phages with different lifestyles utilize tRNAs in distinct ways. In recent years, several studies have provided evidence that phage tRNAs play a crucial role in evading phage defense systems. In this review we summarize the current state of the field of phage tRNAs, highlighting their diverse roles in phage infection. We also discuss the host response to phage tRNAs and the application of this knowledge to improve phage-based therapeutics to combat bacterial infections.

Phage tRNAs: decoding the enigma

Going to ASM Microbe 2025?

Check out the in-depth symposium "Phage Ecology: From Prophage Decision Making to Ecosystem Modulation" hosted by Dr. Hernandez (@cathyhernandez.bsky.social) and I!

We have some really cool talks lined up.
Hope to see you there!

🧪🦠🔬
#Phagesky
#Microsky

Hello everyone! I am pleased to share information on the first ever Computational Structural Virology Symposium, conducted August 4th on zoom and highlighting work in this emerging field. You can register for this event here: forms.gle/CNiqskMwQEuV.... Please re-post!

I’d love to chat more about this work and the potential of phage steering in complex, drug-resistant infections. Come find me at my poster at ASM Microbe 2025 - Sunday, June 22nd!

Mutations in key regulatory factors of T4P biogenesis confer phage resistance. (A) PilR serves as the response regulator of pilA transcription. The sensor kinase, PilS, phosphorylates PilR, activating it, which, in turn, activates transcription of pilA, which encodes for the major pilin subunit, PilA. (B) PilZ regulates T4P biogenesis. By binding to the extension ATPase, PilB activates shaft polymerization. PilZ and FimX are necessary for PilB activation. (C) Without PilZ binding, PilB remains inactive, and energy is not generated for shaft assembly. (D) Defective PilR does not activate transcription of pilA, no PilA subunits are synthesized, and thus, the shaft is not assembled.

We found SNPs in pilR and pilZ, key regulators of T4P biogenesis. One line had a SNP in pqsR, a transcriptional regulator of quorum sensing in PA, because is it ever not quorum sensing? These mutations conferred resistance to the phage and attenuated T4P function!

Chromosomal single-nucleotide polymorphisms (SNPs) defined for all co-evolution condition replicates and the ancestral PAO1. SNPs were determined using breseq (version 0.31). SNPs of two variations in 5 out of 5 (5/5) +Luz19 co-evo replicates and 3/5 +SA+Luz19 co-evo replicates. In all but one of these replicate sequences, the SNP in pilR is C192Y (TGC → TAC). Replicate B of the +Luz19 condition had a different SNP in pilR, P189Q (CCG → CAG). Of the replicates in the two conditions that were subject to co-evolution with Luz19, two lacked an SNP in pilR, both in the +SA+Luz19 condition. Replicate B instead had a 197 bp deletion in pilZ. Replicate A of +SA+Luz19 was the only replicate co-evolved alongside Luz19 that sequencing did not reveal a pil gene mutation; instead, a PQS system mutation was identified in pqsR.

Curiously, lines evolved in the presence of S. aureus showed greater SNP diversity conferring resistance to the phage. See the bold SNPs...

It's out! We used the T4P-dependent phage Luz19 to select against the type IV pilus virulence factor in P. aeruginosa, despite the presence of competing S. aureus.

Thanks very much!

Really exciting preprint, congrats! I’ve been working on identifying novel phages from P. aeruginosa CF isolates, but suspect some (or many) may be missed by my pipeline. I’d love to try Phager. I saw phager.py mentioned and assume the SI is pending, but any chance early access might be possible?

Colossal Squid, 1st Live Observation | Searching for New Species in the South Sandwich Islands YouTube video by Schmidt Ocean

🦑 This baby is COLOSSAL! 🦑
First confirmed live observation of the colossal squid, Mesonychoteuthis hamiltoni, in its natural habitat. Filmed at about 600m near the South Sandwich Islands during the #SouthSandwichIslands expedition. youtu.be/lzPoG9H8Hlo

#NASA's #Chandra X-ray Observatory

Vela Pulsar

chandra.harvard.edu/photo/2013/v...

NASA/CXC/Univ of Toronto/M.Durant/j. Roger

Cytoplasmic contractile injection systems mediate cell death in Streptomyces - Nature Microbiology Characterization of a contractile injection system (CIS) in the Gram-positive multicellular model organism Streptomyces coelicolor finds that CIS mediate cell death in response to stress that impacts ...

Susan today explains contractile injection systems of Streptomyces
- see their cool paper in @naturemicrobiol.bsky.social
www.nature.com/articles/s41...

#KNVM2025

Filamentous cheater phages drive bacterial and phage populations to lower fitness Many bacteria carry phage genome(s) in their chromosome (i.e., prophage), and this intertwines the fitness of the bacterium and the phage. Most Pseudomonas aeruginosa strains carry filamentous phages ...

Fantastic new preprint of Vaughn Cooper's lab @vscooper.micropopbio.org - filamentous phages can get cancer and it's contagious. 🔥👇🏼

www.biorxiv.org/content/10.1...

Bacteriocin production facilitates nosocomial emergence of vancomycin-resistant Enterococcus faecium - Nature Microbiology Genomic and functional analyses of healthcare-associated vancomycin-resistant Enterococcus faecium reveal that bacteriocin T8 is enriched in emergent lineages and provides a competitive advantage in v...

Excited to share our latest, out today in @naturemicrobiol.bsky.social Bacteriocin production facilitates nosocomial emergence of vancomycin-resistant Enterococcus faecium www.nature.com/articles/s41... @idpittstop.bsky.social

Beautiful video of inter-cellular signaling in a swarming response that I pulled from the other place, produced by @strickland-evelyn.bsky.social in collaboration with D. Irimia lab.

The dye detects calcium flux that indicates a signal being received by each cell: you're seeing the 'alarm' go out.

Just because its fun~ This is one of my favorite videos I've taken in my PhD! Here is 60x imaging of neutrophils swarming to attack yeast targets in blue :)

Bright green spots are phages (viruses), bacteria are the faint rods in light blue.

We developed a microscopy-based technique🔬 to measure attachment of viruses #phages to host cells. 🦠

The paper was posted online today:
www.pnas.org/doi/10.1073/...

#phagesky #microsky

I had images in my head of what I wanted to capture on my recent adventure to the southern USA. I wanted storms and sprites with Bayou foregrounds. Man, it is a tough place to chase- dark skies are hard to find as are accessible, treeless areas to get a view.